Sequence deletion. Medical search

Deletion of sequences of nucleic acids from the genetic material of an individual.

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.

Actual loss of portion of a chromosome.

Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.

The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

Any method used for determining the location of and relative distances between genes on a chromosome.

Biochemical identification of mutational changes in a nucleotide sequence.

Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.

In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.

Removal, via CELL DEATH, of immature lymphocytes that interact with antigens during maturation. For T-lymphocytes this occurs in the thymus and ensures that mature T-lymphocytes are self tolerant. B-lymphocytes may also undergo clonal deletion.

The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.

The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.

Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.

Transformation mediated by RhoA requires activity of ROCK kinases. (1/14225)

BACKGROUND: The Ras-related GTPase RhoA controls signalling processes required for cytoskeletal reorganisation, transcriptional regulation, and transformation. The ability of RhoA mutants to transform cells correlates not with transcription but with their ability to bind ROCK-I, an effector kinase involved in cytoskeletal reorganisation. We used a recently developed specific ROCK inhibitor, Y-27632, and ROCK truncation mutants to investigate the role of ROCK kinases in transcriptional activation and transformation. RESULTS: In NIH3T3 cells, Y-27632 did not prevent the activation of serum response factor, transcription of c-fos or cell cycle re-entry following serum stimulation. Repeated treatment of NIH3T3 cells with Y-27632, however, substantially disrupted their actin fibre network but did not affect their growth rate. Y-27632 blocked focus formation by RhoA and its guanine-nucleotide exchange factors Dbl and mNET1. It did not affect the growth rate of cells transformed by Dbl and mNET1, but restored normal growth control at confluence and prevented their growth in soft agar. Y-27632 also significantly inhibited focus formation by Ras, but had no effect on the establishment or maintenance of transformation by Src. Furthermore, it significantly inhibited anchorage-independent growth of two out of four colorectal tumour cell lines. Consistent with these data, a truncated ROCK derivative exhibited weak ability to cooperate with activated Raf in focus formation assays. CONCLUSIONS: ROCK signalling is required for both the establishment and maintenance of transformation by constitutive activation of RhoA, and contributes to the Ras-transformed phenotype. These observations provide a potential explanation for the requirement for Rho in Ras-mediated transformation. Moreover, the inhibition of ROCK kinases may be of therapeutic use. (+info)

Deletion analysis of the Drosophila Inscuteable protein reveals domains for cortical localization and asymmetric localization. (2/14225)

The Drosophila Inscuteable protein acts as a key regulator of asymmetric cell division during the development of the nervous system [1] [2]. In neuroblasts, Inscuteable localizes into an apical cortical crescent during late interphase and most of mitosis. During mitosis, Inscuteable is required for the correct apical-basal orientation of the mitotic spindle and for the asymmetric segregation of the proteins Numb [3] [4] [5], Prospero [5] [6] [7] and Miranda [8] [9] into the basal daughter cell. When Inscuteable is ectopically expressed in epidermal cells, which normally orient their mitotic spindle parallel to the embryo surface, these cells reorient their mitotic spindle and divide perpendicularly to the surface [1]. Like the Inscuteable protein, the inscuteable RNA is asymmetrically localized [10]. We show here that inscuteable RNA localization is not required for Inscuteable protein localization. We found that a central 364 amino acid domain - the Inscuteable asymmetry domain - was necessary and sufficient for Inscuteable localization and function. Within this domain, a separate 100 amino acid region was required for asymmetric localization along the cortex, whereas a 158 amino acid region directed localization to the cell cortex. The same 158 amino acid fragment could localize asymmetrically when coexpressed with the full-length protein, however, and could bind to Inscuteable in vitro, suggesting that this domain may be involved in the self-association of Inscuteable in vivo. (+info)

Superimposed histologic and genetic mapping of chromosome 9 in progression of human urinary bladder neoplasia: implications for a genetic model of multistep urothelial carcinogenesis and early detection of urinary bladder cancer. (3/14225)

The evolution of alterations on chromosome 9, including the putative tumor suppressor genes mapped to the 9p21-22 region (the MTS genes), was studied in relation to the progression of human urinary bladder neoplasia by using whole organ superimposed histologic and genetic mapping in cystectomy specimens and was verified in urinary bladder tumors of various pathogenetic subsets with longterm follow-up. The applicability of chromosome 9 allelic losses as non-invasive markers of urothelial neoplasia was tested on voided urine and/or bladder washings of patients with urinary bladder cancer. Although sequential multiple hits in the MTS locus were documented in the development of intraurothelial precursor lesions, the MTS genes do not seem to represent a major target for p21-23 deletions in bladder cancer. Two additional tumor suppressor genes involved in bladder neoplasia located distally and proximally to the MTS locus within p22-23 and p11-13 regions respectively were identified. Several distinct putative tumor suppressor gene loci within the q12-13, q21-22, and q34 regions were identified on the q arm. In particular, the pericentromeric q12-13 area may contain the critical tumor suppressor gene or genes for the development of early urothelial neoplasia. Allelic losses of chromosome 9 were associated with expansion of the abnormal urothelial clone which frequently involved large areas of urinary bladder mucosa. These losses could be found in a high proportion of urothelial tumors and in voided urine or bladder washing samples of nearly all patients with urinary bladder carcinoma. (+info)

Level of retinoblastoma protein expression correlates with p16 (MTS-1/INK4A/CDKN2) status in bladder cancer. (4/14225)

Recent studies have shown that patients whose bladder cancer exhibit overexpression of RB protein as measured by immunohistochemical analysis do equally poorly as those with loss of RB function. We hypothesized that loss of p16 protein function could be related to RB overexpression, since p16 can induce transcriptional downregulation of RB and its loss may lead to aberrant RB regulation. Conversely, loss of RB function has been associated with high p16 protein expression in several other tumor types. In the present study RB negative bladder tumors also exhibited strong nuclear p16 staining while each tumor with strong, homogeneous RB nuclear staining were p16 negative, supporting our hypothesis. To expand on these immunohistochemical studies additional cases were selected in which the status of the p16 encoding gene had been determined at the molecular level. Absent p16 and high RB protein expression was found in the tumors having loss of heterozygosity within 9p21 and a structural change (mutation or deletion) of the remaining p16 encoding gene allele, confirming the staining results. These results strongly support the hypothesis that the RB nuclear overexpression recently associated with poor prognosis in bladder cancer is also associated with loss of p16 function and implies that loss of p16 function could be equally deleterious as RB loss in bladder and likely other cancers. (+info)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (5/14225)

We have investigated the effects of the truncated trkB receptor isoform T1 (trkB.T1) by transient transfection into mouse N2a neuroblastoma cells. We observed that expression of trkB.T1 leads to a striking change in cell morphology characterized by outgrowth of filopodia and processes. A similar morphological response was also observed in SH-SY5Y human neuroblastoma cells and NIH3T3 fibroblasts transfected with trkB.T1. N2a cells lack endogenous expression of trkB isoforms, but express barely detectable amounts of its ligands, brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4). The morphological change was ligand-independent, since addition of exogenous BDNF or NT-4 or blockade of endogenous trkB ligands did not influence this response. Filopodia and process outgrowth was significantly suppressed when full-length trkB.TK+ was cotransfected together with trkB.T1 and this inhibitory effect was blocked by tyrosine kinase inhibitor K252a. Transfection of trkB.T1 deletion mutants showed that the morphological response is dependent on the extracellular, but not the intracellular domain of the receptor. Our results suggest a novel ligand-independent role for truncated trkB in the regulation of cellular morphology. (+info)

Over-representation of a germline RET sequence variant in patients with sporadic medullary thyroid carcinoma and somatic RET codon 918 mutation. (6/14225)

The aetiology of sporadic medullary thyroid carcinoma is unknown. About 50% harbour a somatic mutation at codon 918 of RET (M918T). To investigate whether other RET sequence variants may be associated with or predispose to the development of sporadic medullary thyroid carcinoma, we analysed genomic DNA from the germline and corresponding tumour from 50 patients to identify RET sequence variants. In one patient, tumour DNA showed a novel somatic 12 bp in-frame deletion in exon 15. More interestingly, we found that the rare polymorphism at codon 836 (c.2439C > T; S836S) occurred at a significantly higher frequency than that in control individuals without sporadic medullary thyroid carcinoma (Fisher's exact test, P = 0.03). Further, among the nine evaluable cases with germline c.2439C/T, eight also had the somatic M918T mutation in MTC DNA which was more frequent than in patients with the more common c.2439C/C (89% vs 40%, respectively; Fisher's exact test, P = 0.01). These findings suggest that the rare sequence variant at codon 836 may somehow play a role in the genesis of sporadic medullary thyroid carcinoma. (+info)

Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. (7/14225)

The rice homeobox gene OSH15 (Oryza sativa homeobox) is a member of the knotted1-type homeobox gene family. We report here on the identification and characterization of a loss-of-function mutation in OSH15 from a library of retrotransposon-tagged lines of rice. Based on the phenotype and map position, we have identified three independent deletion alleles of the locus among conventional morphological mutants. All of these recessive mutations, which are considered to be null alleles, exhibit defects in internode elongation. Introduction of a 14 kbp genomic DNA fragment that includes all exons, introns and 5'- and 3'- flanking sequences of OSH15 complemented the defects in internode elongation, confirming that they were caused by the loss-of-function of OSH15. Internodes of the mutants had abnormal-shaped epidermal and hypodermal cells and showed an unusual arrangement of small vascular bundles. These mutations demonstrate a role for OSH15 in the development of rice internodes. This is the first evidence that the knotted1-type homeobox genes have roles other than shoot apical meristem formation and/or maintenance in plant development. (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (8/14225)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed. (+info)

... www-sequence.stanford.edu/group/yeast_deletion_project/project_desc.html http://www-sequence.stanford.edu/group/yeast_deletion_ ... Gene deletion, or gene knockout, is one of the main ways in which the function of genes are discovered. Many of the deletion ... The yeast deletion project, formally the Saccharomyces Genome Deletion Project, is a project to create data for a near-complete ... www-sequence.stanford.edu. Retrieved 2020-04-21. Giaever, Guri; Nislow, Corey (June 2014). "The Yeast Deletion Collection: A ...

https://en.wikipedia.org/wiki/Yeast_deletion_project

There are several gaps in the sequence. There is no further information available about the DNA-sequence in those areas up ... A common deletion is restricted to the distal area. This is a Class I-deletion.[citation needed] In some cases the deletion is ... Mefford states that the standard for a deletion is 1.35Mb. The largest deletion seen on a living human is over 5 Mb.[citation ... DECIPHER database entry for 1q21.1 deletion syndrome 1q21.1 deletion, GeneReviews NCBI Bookshelf Orpha.net (Articles with short ...

https://en.wikipedia.org/wiki/1q21.1_deletion_syndrome

... aligns two sequences by matches/mismatches (also known as substitutions), insertions, and deletions. ... The size of the matrix is the length of one sequence plus 1 by the length of the other sequence plus 1. The additional first ... Sankoff D. (1972). "Matching Sequences under Deletion/Insertion Constraints". Proceedings of the National Academy of Sciences ... Bioinformatics Sequence alignment Sequence mining Needleman-Wunsch algorithm Levenshtein distance BLAST FASTA Smith, Temple F ...

https://en.wikipedia.org/wiki/Smith–Waterman_algorithm

doi:10.1016/0022-0000(80)90002-1. Sankoff D (1972). "Matching sequences under deletion/insertion constraints". Proceedings of ... NW-align: A protein sequence-to-sequence alignment program by Needleman-Wunsch algorithm (online server and source code) A live ... There is one row for each character in sequence A, and one column for each character in sequence B. Thus, if aligning sequences ... Wagner-Fischer algorithm Smith-Waterman algorithm Sequence mining Levenshtein distance Dynamic time warping Sequence alignment ...

https://en.wikipedia.org/wiki/Needleman–Wunsch_algorithm

Sankoff, D. (1972). "Matching sequences under deletion-insertion constraints". Proceedings of the National Academy of Sciences ... In particular, he had a key role in introducing dynamic programming for sequence alignment and other problems in computational ... In 1973, Sankoff and Robert Cedergren developed a joint estimation method for phylogeny and multiple sequence alignment of 5S ... In 1971, Sankoff became interested in molecular sequence comparison and devised the first quadratic-time variant of the ...

https://en.wikipedia.org/wiki/David_Sankoff

Bandwidth optimization based on NULL packet deletion. Support for high bit-rate streams by extending the RTP sequence number. ...

https://en.wikipedia.org/wiki/Reliable_Internet_Stream_Transport

Morphemic vowel deletion is the most common. Some suffixes never co-occur with the preceding vowel in the root, whereas others ... iii) If the sequence is composed of two identical vowels, one will delete. Vowel elision can be syntactically conditioned. For ... The high vowels /i u/ occur as mid-high /e o/ when near uvular consonants /q qʰ qʼ χ/. Vowel deletion is frequent in Aymara. ... Phonotactic vowel deletion takes the shape of hiatus reduction when two vowels co-occur through word construction or through ...

https://en.wikipedia.org/wiki/Aymara_language

Freund, A. M.; Bichara, M.; Fuchs, R. P. (1989). "Z-DNA-forming sequences are spontaneous deletion hot spots". Proceedings of ... In mammalian cells, the presence of such sequences was found to produce large genomic fragment deletions due to chromosomal ... Wang, G.; Christensen, L. A.; Vasquez, K. M. (2006). "Z-DNA-forming sequences generate large-scale deletions in mammalian cells ... A study on Escherichia coli found that gene deletions spontaneously occur in plasmid regions containing Z-DNA-forming sequences ...

https://en.wikipedia.org/wiki/Z-DNA

Kam W, Clauser E, Kim YS, Kan YW, Rutter WJ (Feb 1986). "Cloning, sequencing, and chromosomal localization of human term ... Evolution of the 5' flanking region by deletion/substitution". J. Biol. Chem. 263 (24): 12020-7. doi:10.1016/S0021-9258(18) ... Millán JL (1986). "Molecular cloning and sequence analysis of human placental alkaline phosphatase". J. Biol. Chem. 261 (7): ... Ezra E, Blacher R, Udenfriend S (1984). "Purification and partial sequencing of human placental alkaline phosphatase". Biochem ...

https://en.wikipedia.org/wiki/Placental_alkaline_phosphatase

"Conserved Inserts and Deletions in Protein Sequences". Bacterial Phylogeny. Gupta RS. Retrieved 2 April 2012. Gupta, Radhey S ... A 4 aa deletion in RNA polymerase b-subunit and a 1 aa deletion in ribosomal protein L16 were found uniquely in various species ... Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for ... Archaea), it can be inferred whether the indel is an insert or a deletion, and which of these two groups A, B, C or X, Y, Z is ...

https://en.wikipedia.org/wiki/Conserved_signature_indels

Correct schwa deletion is also critical because the same letter sequence is pronounced two different ways in Hindi depending on ... a) Schwa deletion:... VCəCV → VC0CV.... Schwa deletion in Maithili occurs.... Manindra K. Verma; Karavannur Puthanvettil ... The rule is reported to result in correct predictions on schwa deletion 89% of the time. Schwa deletion is computationally ... is pronounced həmrā rather than həmərā from the deletion of a medial schwa. Marathi exhibits extensive schwa deletion.: 95-111 ...

https://en.wikipedia.org/wiki/Schwa_deletion_in_Indian_languages

Simons R, Alon N, Riordan JR (1987). "Human myelin DM-20 proteolipid protein deletion defined by cDNA sequence". Biochem. ... cloning and sequencing of human proteolipid protein cDNA". J. Neurosci. Res. 18 (3): 395-401. doi:10.1002/jnr.490180303. PMID ...

https://en.wikipedia.org/wiki/Proteolipid_protein_1

... deletions and duplications, greater than 100 kilobases in the human genome. However, by 2015 whole genome sequencing studies ... Other classes of complex structural variant include deletion-inversion-deletions, duplication-inversion-duplications, and ... De novo sequence assembly may be applied with reads that are accurate enough. While in practice use of this method is limited ... There are also deletions related to resistance against malaria and AIDS. Also, some highly variable segments are thought to be ...

https://en.wikipedia.org/wiki/Structural_variation

Theses test are; Sequence analysis of the entire coding region and Deletion/duplication analysis. Pyle disease may be confused ... Sequencing of coding regions of SFRP4 gene from an 11-year-old female with PYL was performed. A novel homozygous nonsense ... Galada C, Shah H, Shukla A, Girisha KM (April 2017). "A novel sequence variant in SFRP4 causing Pyle disease". Journal of Human ...

https://en.wikipedia.org/wiki/Metaphyseal_dysplasia

An update contains 4 types of blocks: a transaction header block, a sequence of data blocks, a corresponding sequence of ... A deletion does not remove any data from the archive, but rather indicates that the file is not to be extracted unless the ... An edit is either a file update or a file deletion. An update includes a file name, last modified date, attributes, and a list ... The data blocks contain a sequence of file fragments compressed together. The fragment tables give the size and SHA-1 hash of ...

https://en.wikipedia.org/wiki/ZPAQ

A deletion of the hfq gene causes loss of secondary metabolite production. It is a source for bioluminescence imaging. ... P. luminescens' genome has been sequenced. It contains a MACPF protein, however, this molecule appears non-lytic. It also ...

https://en.wikipedia.org/wiki/Photorhabdus_luminescens

Homologous sequence in insert to sequence in plasmid DNA resulting in deletion. A number of commercially available DNA cloning ... A major advantage of blunt-end cloning is that the desired insert does not require any restriction sites in its sequence as ...

https://en.wikipedia.org/wiki/Ligation_(molecular_biology)

In fact, many official gene symbol-gene name pairs do not even share their initial-letter sequences (although some do). ... "an 11-bp deletion at nucleotide 188." This corollary rule (which forms an adjunct to the spell-everything-out rule) often also ... deletion with replacement (ΔleuA::nptII(KanR) indicates that the leuA gene has been deleted and replaced with the gene for ... deletion (ΔleuA) - = fusion (leuA-lacZ) : = fusion (leuA:lacZ) :: = insertion (leuA::Tn10) Ω = a genetic construct introduced ...

https://en.wikipedia.org/wiki/Gene_nomenclature

Most multiple sequence alignment methods try to minimize the number of insertions/deletions (gaps) and, as a consequence, ... Point mutations and insertion or deletion events (called indels) can be detected. Multiple sequence alignments can also be used ... Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological ... This similarity in sequences can then go on to help find common ancestry. Alignment-free sequence analysis Cladistics ...

https://en.wikipedia.org/wiki/Multiple_sequence_alignment

Levenshtein, V. (1966). "Binary codes capable of correcting deletions, insertions, and reversals". Soviet Physics Doklady. 10: ... of exponential-distance models Sequence networks Representing a single sequence as a network Meta network of sequences Sequence ... and sequence-network. Given an alignment rule, a set of sequences can be represented in tabular form with sequences in rows and ... while sequence length rarely exceeds 100. We may distinguish between state sequences and event sequences, where states last ...

https://en.wikipedia.org/wiki/Sequence_analysis_in_social_sciences

Kondrashov AS, Rogozin IB (February 2004). "Context of deletions and insertions in human coding sequences". Human Mutation. 23 ... the sequence change event is referred to as an "indel".[citation needed] Insertion (genetics) Deletion (genetics) Mills RE, ... "Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a ... If the mode of selection is unknown, one can not tell if species A lost one G (a "deletion" event") or species B gained one G ( ...

https://en.wikipedia.org/wiki/Indel

Insertions and deletions between sequences give rise to disruptions in this diagonal. Regions of local similarity or repetitive ... Note, that the sequences can be written backwards or forwards, however the sequences on both axes must be written in the same ... Dot plots compare two sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When the ... a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16 (1): 1-11. doi:10.1111 ...

https://en.wikipedia.org/wiki/Dot_plot_(bioinformatics)

FISH or EHMT1 sequencing. The forty patients were divided into two groups: 1 group of 16 patients with the 9q34 deletion, and 1 ... The greater the deletions, the greater the severity of the condition. However, in recent studies, 9q34 deletion syndrome occurs ... 9q34 deletion syndrome is a rare genetic disorder. Terminal deletions of chromosome 9q34 have been associated with childhood ... tracks chromosome deletions and or amplifications using fluorescent dyes on genomic sequences of DNA samples. The DNA samples ( ...

https://en.wikipedia.org/wiki/9q34.3_deletion_syndrome

"Sequence Homology at the Breakpoint and Clinical Phenotype of Mitochondrial DNA Deletion Syndromes". PLOS ONE. 5 (12): e15687. ... A common mtDNA deletion associated with Pearson syndrome is the deletion of 4977 bp. This deletion has been labeled as m.8470_ ... It is caused by a deletion in mitochondrial DNA. Pearson syndrome is very rare, less than a hundred cases have been reported in ... With the use of molecular genetic testing, the deletions of mitochondrial DNA with Pearson syndrome ranges in size from 1.1 to ...

https://en.wikipedia.org/wiki/Pearson_syndrome

... cDNA sequence supports partial gene deletion model". Proc Natl Acad Sci U S A. 79 (10): 3260-4. Bibcode:1982PNAS...79.3260A. ... 1986). "Sequence of a human immunoglobulin gamma 3 heavy chain constant region gene: comparison with the other human C gamma ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Wolfenstein-Todel C, Frangione B, Prelli F, Franklin EC (1976). "The amino acid sequence of "heavy chain disease" protein ZUC. ...

https://en.wikipedia.org/wiki/IGHG3

A 5885T deletion and 5877G-A substitution have been associated with the disease. Anderson S, Bankier AT, Barrell BG, de Bruijn ... "Sequence and organization of the human mitochondrial genome". Nature. 290 (5806): 457-65. Bibcode:1981Natur.290..457A. doi: ... "CPEO associated with a single nucleotide deletion in the mitochondrial tRNA(Tyr) gene". Neurology. 57 (12): 2298-301. doi: ...

https://en.wikipedia.org/wiki/MT-TY

"Activation of a mcf.2 oncogene by deletion of amino-terminal coding sequences". Oncogene. 3 (6): 709-15. PMID 2577874. Galland ... "Entrez Gene: MCF2 MCF.2 cell line derived transforming sequence". Eva A, Aaronson SA (1985-07-18). "Isolation of a new human ... April 1991). "A region of proto-dbl essential for its transforming activity shows sequence similarity to a yeast cell cycle ... May 1987). "Localization of the mcf.2 transforming sequence to the X chromosome". The EMBO Journal. 6 (5): 1301-7. doi:10.1002/ ...

https://en.wikipedia.org/wiki/MCF2

Parallel sequencing follows the hybridization, which results in about 3.5 Gb of sequence data. These sequence data are then ... When researching HCS in mice, the homozygous deletion of NOTCH2 leads to death. This observation is important because it ... The result is a mature NOTCH2 gene with a partially completed PEST sequence. In some cases, no PEST sequence at all is seen. ... Through sequence analysis and symptom presentation in HCS patients, this proves to be the most definitive method of diagnosis.[ ...

https://en.wikipedia.org/wiki/Hajdu–Cheney_syndrome

Similar to other GTPases, RhoA presents a Rho insert in its primary sequence in the GTPase domain. RhoA contains also four ... insertion or deletion sites with an extra helical subdomain; these sites are characteristic of many GTPases in the Rho family. ... The primary protein sequences of members of the Rho family are mostly identical, with the N-terminal containing most of the ...

https://en.wikipedia.org/wiki/Transforming_protein_RhoA

... of all sequence variants. Other sequence variations are single base exchanges, deletions and insertions. SNPs occur on average ... This added to the two haploid sequences which were amalgamations of sequences from many individuals, published by the Human ... either single nucleotide polymorphisms or brief insertions or deletions (indels) in the genetic sequence, but structural ... This was concluded in 2007 from analysis of the diploid full sequences of the genomes of two humans: Craig Venter and James D. ...

https://en.wikipedia.org/wiki/Human_genetic_variation

This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

https://en.wikipedia.org/wiki/HOXD8

An observation sequence is given by Y = ( Y 1 = y 1 , Y 2 = y 2 , … , Y T = y T ) {\displaystyle Y=(Y_{1}=y_{1},Y_{2}=y_{2},\ ... deletions, duplications and four transition states. Solving this model using Baum-Welch demonstrated the ability to predict the ... This is equivalent to the number of times state i is observed in the sequence from t = 1 to t = T − 1. b i ∗ ( v k ) = ∑ t = 1 ... For example, the probability of the sequence NN and the state being S 1 {\displaystyle S_{1}} then S 2 {\displaystyle S_{2}} is ...

https://en.wikipedia.org/wiki/Baum–Welch_algorithm

Norman PJ, Carey BS, Stephens HA, Vaughan RW (June 2003). "DNA sequence variation and molecular genotyping of natural killer ... deletion in psoriatic patients and healthy controls". Human Immunology. 64 (4): 458-61. doi:10.1016/S0198-8859(03)00025-9. PMID ... a common null allele of the ILT6 gene results from a 6.7-kbp deletion". European Journal of Immunology. 30 (12): 3655-62. doi: ... "HLA class I allelic sequence and conformation regulate leukocyte Ig-like receptor binding". Journal of Immunology. 186 (5): ...

https://en.wikipedia.org/wiki/LILRA3

It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. These ... Paternal inheritance of a deletion of this region is associated with Prader-Willi syndrome (characterised by hypotonia, obesity ... by RNA-sequencing from F1 hybrids resulting from reciprocal crosses. The result however has been challenged by others who ... transcriptome sequencing, and in silico prediction pipelines. Imprinting is a dynamic process. It must be possible to erase and ...

https://en.wikipedia.org/wiki/Genomic_imprinting

... explanation of the genome shrinking is the chromosomal rearrangement because insertion/deletion of larger portion of sequence ... Evidence of the deletion of the function of repair and recombination is the loss of the gene recA, gene involved in the ... The random deletion will be then mainly deleterious and not selected due to the reduction of the gained fitness but ... An example for this is the deletion of recF, gene required for the function of recA, and its flanking genes. One of the ...

https://en.wikipedia.org/wiki/Genome_size

2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... "Deletion of fatty acid transport protein 2 (FATP2) in the mouse liver changes the metabolic landscape by increasing the ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

https://en.wikipedia.org/wiki/Very_long-chain_acyl-CoA_synthetase

2012). "Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma". PLOS ONE. 7 (5): e37029. ... December 2018). "Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma". Nature ...

https://en.wikipedia.org/wiki/Esthesioneuroblastoma

"High-throughput sequencing of a 4.1 Mb linkage interval reveals FLVCR2 deletions and mutations in lethal cerebral vasculopathy ...

https://en.wikipedia.org/wiki/FLVCR2

Activity of ABL1 protein is negatively regulated by its SH3 domain, and deletion of the SH3 domain turns ABL1 into an oncogene ... Pendergast AM, Muller AJ, Havlik MH, Maru Y, Witte ON (July 1991). "BCR sequences essential for transformation by the BCR-ABL ...

https://en.wikipedia.org/wiki/ABL_(gene)

In contrast to STR analysis, mtDNA sequencing uses Sanger sequencing. The known sequence and questioned sequence are both ... Deletion breakpoints frequently occur within or near regions showing non-canonical (non-B) conformations, namely hairpins, ... Human mitochondrial DNA was the first significant part of the human genome to be sequenced. This sequencing revealed that the ... If the known sample sequence and questioned sequence originated from the same matriline, one would expect to see identical ...

https://en.wikipedia.org/wiki/Mitochondrial_DNA

1994). "Sequence of a variant thyroxine-binding globulin (TBG) in a family with partial TBG deficiency in Japanese (TBG-PDJ)". ... 1991). "Nucleotide deletion resulting in frameshift as a possible cause of complete thyroxine-binding globulin deficiency in ... 1989). "Sequence of the variant thyroxine-binding globulin of Australian aborigines. Only one of two amino acid replacements is ... 1992). "Sequencing of the variant thyroxine-binding globulin (TBG)-San Diego reveals two nucleotide substitutions". Biochim. ...

https://en.wikipedia.org/wiki/Thyroxine-binding_globulin

Other mutations observed include a nonsense mutation, an in-frame deletion of amino acids and an entire gene deletion. De novo ... Sanger sequencing or the use of WES of parental samples confirmed the de novo status of the truncating and missense mutations ... Whole exome sequencing (WES) can be used as a non-biased tool in the diagnostic evaluation of individuals with suspected ... SON is a large protein consisting of 2426 amino acids and repeat sequences. SON is located within the human chromosomal region ...

https://en.wikipedia.org/wiki/ZTTK_syndrome

These findings are corroborated by evidence from mice models, Kanga mice with a deletion of DCC, whose CST has been shown not ... have been found in many CMM disorder patients through genome-wide linkage analysis and exome sequencing. In a mouse model, ...

https://en.wikipedia.org/wiki/Congenital_mirror_movement_disorder

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens ... sequence and characterization of a glycosylated RNA-binding protein". Nucleic Acids Research. 21 (18): 4210-7. doi:10.1093/nar/ ... "Generation and analysis of 280,000 human expressed sequence tags". Genome Research. 6 (9): 807-28. doi:10.1101/gr.6.9.807. PMID ...

https://en.wikipedia.org/wiki/RBMX

Of the 510 identified hCONDELs, only one of these deletions has been shown to remove a 92 bp sequence that is part of a protein ... hCONDELs refer to regions of deletions within the human genome containing sequences that are highly conserved among closely ... locus suggest a role in deletions that affect regulatory sequences in humans. An hCONDEL located near the locus of the androgen ... The deletion that affects the protein coding region in humans results in a frameshift mutation in the CMAH gene which codes for ...

https://en.wikipedia.org/wiki/HCONDELs

Deletion of the Lect2 gene in mice improves peripheral glucose entry into tissues. These studies suggest that mouse Lect2 ... 2004). "The DNA sequence and comparative analysis of human chromosome 5". Nature. 431 (7006): 268-74. doi:10.1038/nature02919. ... Yamagoe S, Yamakawa Y, Matsuo Y, Minowada J, Mizuno S, Suzuki K (1996). "Purification and primary amino acid sequence of a ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...

https://en.wikipedia.org/wiki/LECT2

Eddy, S. R.; Gold, L. (1991). "The phage T4 nrdB intron: A deletion mutant of a version found in the wild". Genes & Development ... Feb 2001). "Initial sequencing and analysis of the human genome" (PDF). Nature. 409 (6822): 860-921. Bibcode:2001Natur.409.. ... Finn, R. D.; Clements, J.; Eddy, S. R. (2011). "HMMER web server: Interactive sequence similarity searching". Nucleic Acids ... His research interests are in bioinformatics, computational biology and biological sequence analysis. As of 2016[update] ...

https://en.wikipedia.org/wiki/Sean_Eddy

Udey JA, Blomberg B (1987). "Human lambda light chain locus: organization and DNA sequences of three genomic J regions". ... lambda gene segments of the human immunoglobulin lambda light chain locus are separated by 14 kb and rearrange by a deletion ...

https://en.wikipedia.org/wiki/IGLJ3

Interstitial deletions of chromosome 3 are rare, and only a few patients with a microdeletion of 3p21.31 have been reported to ... No ortholog sequences of C3orf62 were found for the following life forms: Bacteria, archaea, protist, plant, fungus, trichoplax ... The groupings of nearly all Mammalia ortholog sequences of C3orf62 are as follows: E-value: 2e-94 to 1e-169; similarity 56-84 ... Lovrecic L, Bertok S, Žerjav Tanšek M (May 2016). "A New Case of an Extremely Rare 3p21.31 Interstitial Deletion". Molecular ...

https://en.wikipedia.org/wiki/C3orf62

"Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain ... Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens ... Evidence to date shows that of the 110,000 gene enhancer sequences identified in the human genome, HACNS1 has undergone the ...

https://en.wikipedia.org/wiki/CENTG2

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty-one tests were ... Lord KA, Hoffman-Liebermann B, Liebermann DA (July 1990). "Nucleotide sequence and expression of a cDNA encoding MyD88, a novel ...

https://en.wikipedia.org/wiki/MYD88

January 2006). "Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in ... "Early-onset autoimmune hepatitis is associated with a C4A gene deletion". Gastroenterology. 104 (5): 1478-84. doi:10.1016/0016- ...

https://en.wikipedia.org/wiki/HLA_A1-B8-DR3-DQ2

Based on a sequence homology search for genes relate to the folate receptor, the gene for folate receptor 4 was first ... Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Additional screens ...

https://en.wikipedia.org/wiki/Juno_(protein)

It is now believed[by whom?] that the theory of 1% divergence only applies when looking at sequences that are aligned. After ... This includes insertions and deletions as well as rearrangements and inversions of the genome. These genomic features help ... Britten, Roy J. (2002). "Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels". Proceedings ... using resources not available in 1975, such as sequence data that is now available for multiple species, found multiple other ...

https://en.wikipedia.org/wiki/The_Myth_of_the_One_Percent

... beta-thalassemia alleles can be created by many different mutations including both deletion and non-deletion forms.[citation ... Diagnostic tests include DNA sequencing, hemoglobin electrophoresis, and high-performance liquid chromatography. Treatment is ...

https://en.wikipedia.org/wiki/Sickle_cell-beta_thalassemia

"Somatic allelic deletion of nm23 in human cancer". Cancer Res. 51 (9): 2490-3. PMID 2015608. Hailat N, Keim DR, Melhem RF, Zhu ... which encodes a fusion protein consisting of sequence sharing identity with each individual gene product. NME1 has been shown ...

https://en.wikipedia.org/wiki/NME1

"The interleukin 3 gene is located on human chromosome 5 and is deleted in myeloid leukemias with a deletion of 5q". Proc. Natl ... "Characterization of a human multilineage-colony-stimulating factor cDNA clone identified by a conserved noncoding sequence in ...

https://en.wikipedia.org/wiki/Interleukin_3

This conserved sequence has been exploited to learn more about SMS and PTLS. Through genetic studies on both laboratory mice ... 16q deletion and 17p duplication) in a child with MR/MCA". Clinical Case Reports. 2 (6): 303-309. doi:10.1002/ccr3.117. PMC ... The Reciprocal of the Smith-Magenis Syndrome Deletion?". American Journal of Medical Genetics. 63 (2): 373-377. doi:10.1002/( ...

https://en.wikipedia.org/wiki/Potocki–Lupski_syndrome

Brazel D, Pollner R, Oberbäumer I, Kühn K (1988). "Human basement membrane collagen (type IV). The amino acid sequence of the ... alpha 2(IV) chain and its comparison with the alpha 1(IV) chain reveals deletions in the alpha 1(IV) chain". Eur. J. Biochem. ... 1992). "Short amino acid sequences derived from C1q receptor (C1q-R) show homology with the alpha chains of fibronectin and ... Hostikka SL, Kurkinen M, Tryggvason K (1987). "Nucleotide sequence coding for the human type IV collagen alpha 2 chain cDNA ...

https://en.wikipedia.org/wiki/Collagen,_type_IV,_alpha_2

seqfan] Sequence data deletion. William Rex Marshall w.r.marshall at actrix.co.nz Sat Dec 4 23:36:59 CET 2010 *Previous message ... There has now been a deletion from sequence data on the grounds of a term having 118 digits. If necessary, couldnt the extra ...

http://list.seqfan.eu/pipermail/seqfan/2010-December/006593.html

Recommended test to confirm a clinical diagnosis or family history of Birt-Hogg-Dubé syndrome (BHDS). ||Transport 3 mL whole blood. (Min: 3 mL) Lavender or pink (EDTA) or yellow (ACD solution A or B).

https://ltd.aruplab.com/Tests/Pub/3005703

We add the ability to delete elements from our CRDT sequence and test the behavior for correctness. ...

http://talk.objc.io/episodes/S01E300-crdts-deletion-in-sequences

Specific RNA sequences of rous sarcoma virus (RSV) recovered from tumors induced by transformation-defective RSV deletion ... Specific RNA sequences of rous sarcoma virus (RSV) recovered from tumors induced by transformation-defective RSV deletion ... Occurrence of partial deletion and substitution of the src gene in the RNA genome of avian sarcoma virus ... Restitution of fibroblast-transforming ability in src deletion mutants of avian sarcoma virus during animal passage. ...

https://m.wikidata.org/wiki/Q40234689

Lin, H., Miller, M. L., Granas, D. M., & Dutcher, S. K. (2013). Whole Genome Sequencing Identifies a Deletion in Protein ... T1 - Whole Genome Sequencing Identifies a Deletion in Protein Phosphatase 2A That Affects Its Stability and Localization in ... title = "Whole Genome Sequencing Identifies a Deletion in Protein Phosphatase 2A That Affects Its Stability and Localization in ... Whole Genome Sequencing Identifies a Deletion in Protein Phosphatase 2A That Affects Its Stability and Localization in ...

https://profiles.wustl.edu/en/publications/whole-genome-sequencing-identifies-a-deletion-in-protein-phosphat

... bioinformatics library for nucleotide sequence manipulation and analysis. - ... deletion( [Nt.Seq offset], [Integer length] ) Nt.Seq#repeat( [Integer count] ) Nt.Seq#mask( [Nt.Seq sequence] ) Nt.Seq#cover( [ ... sequence(); // === CCC- // this is the optimistic sequence that could match both map.best().alignmentCover().sequence(); ... var seqA = (new Nt.Seq()).read(ATGC); var seqB = (new Nt.Seq()).read(AWTS) var seqC = seqA.mask(seqB); seqC.sequence(); ...

https://github.com/keithwhor/NtSeq

Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), ... share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in ... Arrufatina in inverted orientation flanking the 5′ end of the deletion. The Arrufatina Mule displayed ... Sequencing coverage and copy number variation (CNV). The sequence coverage and the CNVs along chromosome 3 (A) and chromosome 8 ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1280-3

... is a disorder caused by the deletion of a small piece of chromosome 22. Explore symptoms, inheritance, genetics of this ... 22q11.2 deletion syndrome (which is also known by several other names, listed below) ... Most people with 22q11.2 deletion syndrome are missing a sequence. of about 3 million DNA building blocks (base pairs. ) on one ... 22q11.2 deletion syndrome (which is also known by several other names, listed below) is a disorder caused by the deletion. of a ...

https://medlineplus.gov/genetics/condition/22q112-deletion-syndrome

Test ID CASRG CASR Full Gene Sequencing with Deletion/Duplication, Varies Ordering Guidance. Targeted testing for familial ... 3. Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus ... For more information, see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies. ...

https://pediatric.testcatalog.org/show/CASRG

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands The analysis in the European Journal of Human Genetics finds ... "And well basically ask, now that we have these robust phenotypes for the full deletions, whether these sub-deletion models ... Using an engineered mouse model, Alea Mills and her colleagues show in a paper published in PNAS last month that the deletion ... MGI Sequencing Platform and Sentieon Machine Learning Model Enable Improved Small Variant Calling Accuracy for Whole-Genome ...

https://www.genomeweb.com/archive/researchers-use-mouse-model-chromosomal-deletion-study-autism

The aim of this study was to evaluate the efficiency of each of these main approaches in detecting germline deletions.WGS data ... This analysis has validated the utility of WGS based CNV detection software to reliably identify deletions, and these findings ... Concordance across software packages was poor, with only 27 of the total 612 benchmark deletions identified by all five ... and Pindel was assessed by comparing the accuracy and sensitivity of each software package in detecting deletions exceeding 1? ...

https://www.pacb.com/publications/evaluation-of-the-performance-of-copy-number-variant-prediction-tools-for-the-detection-of-deletions-from-whole-genome-sequencing-data/

Sequence Deletion / genetics* * Trans-Activators / genetics* Substances * Intracellular Signaling Peptides and Proteins ... Small intragenic deletions of the 3 region of the gene have also been reported in patients with BOR syndrome. We have ... One patient with OFC syndrome carried a large deletion of the EYA1 gene region, confirming that OFC syndrome is allelic with ... This dosage assay, combined with microsatellite marker analysis, has identified de novo deletions of the EYA1 gene and ...

https://pubmed.ncbi.nlm.nih.gov/11409867/

A high-throughput method to produce deletions of non-coding DNA is needed. We report a high-throughput genomic deletion ... We validated 9 of 51 lncRNA hits using CRISPR-Cas9-mediated genomic deletion, functional rescue, CRISPR activation or ... Our high-throughput pgRNA genome deletion method will enable rapid identification of functional mammalian non-coding elements. ... Long non-coding RNAs are identified using a high-throughput paired-guide RNA genomic deletion screen. CRISPR-Cas9 screens have ...

https://www.nature.com/articles/nbt.3715?error=cookies_not_supported&code=4462f3e3-97e0-4b91-be80-affa74873ffe

The approach used is based on dHPLC mutation screening of the BRCA1 gene, followed by sequencing of fragments suspected to ... Finally, MLPA revealed deletion of exon 20 of the BRCA1 gene in one family, a deletion that encompasses 3.2 kb of the gene ... We conclude that a combination of techniques capable of detecting both single base mutations and small insertions / deletions ... Single base putative pathogenic mutations were identified by dHPLC and confirmed by sequence analysis in 4 families: 5382insC ( ...

https://bmccancer.biomedcentral.com/articles/10.1186/1471-2407-4-61

Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags.. Randhawa, H S; Dilbirligi, M; Sidhu, D; ... arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints ... About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ...

https://pesquisa.bvsalud.org/perinatal/resource/es/mdl-15514044

Other computation methods were selected to discover DNA sequencing deletion errors such as end-sequence profiling.[15][16] ... In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: Δ) is a mutation (a genetic ... Monosomies/deletions. *(1q21.1 copy number variations/1q21.1 deletion syndrome/1q21.1 duplication syndrome/TAR syndrome/1p36 ... In contrast, a deletion that is evenly divisible by three is called an in-frame deletion.[8] ...

https://en.wikipedia.org/wiki/Gene_deletion

Draft genome sequences of 50 methicillin-resistant Staphylococcus aureus sequence type 5 isolates obtained from a U.S. hospital ... Large scale parallel pyrosequencing technology: PRRSV strain VR-2332 nsp2 deletion mutant stability in swine - (Peer Reviewed ... Draft genome sequences of 63 swine-associated methicillin-resistant Staphylococcus aureus sequence type 5 isolates from the ... Complete genome sequences of two Staphylococcus aureus sequence type 5 isolates from California, USA. Genome Announcements. 5: ...

https://www.ars.usda.gov/people-locations/person/?person-id=40343

Deletion of the MBD5 gene has been identified in all individuals affected by a microdeletion syndrome characterized by ... The team also identified novel changes in the MBD5 DNA sequence in 0.8% of autism cases. ... In contrast, they found no deletions of the 2q23.1 segment, the full MBD5 locus, or any MBD5 coding exons in 7878 control ... Regardless of the size of the deletion, the MBD5 gene is the primary contributor to the core features of the syndrome, she ...

https://www.medscape.com/viewarticle/754462

Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. ...

https://ir.sinica.edu.tw/handle/201000000A/7616

Objective(s) : Sequence analysis: entire coding region, Deletion / Duplication analysis. Technique(s) : NGS sequencing (except ... Objective(s) : Sequence analysis: entire coding region, Deletion / Duplication analysis. Technique(s) : NGS sequencing (except ... Objective(s) : Sequence analysis: entire coding region, Deletion / Duplication analysis. Technique(s) : NGS sequencing (except ... Objective(s) : Sequence analysis: entire coding region, Deletion / Duplication analysis. Technique(s) : NGS sequencing (except ...

https://www.orpha.net/consor/cgi-bin/ClinicalLabs_Search_Simple.php?lng=EN&LnkId=19302&Typ=Pat

... sequence diagrams, class diagrams, and state-transition diagrams); b) describe the UML notation used for these diagrams; and c ... Deletion. An X is used to indicate the termination (deletion) of an object. ... We want to make certain that we can trace from the use cases to the sequence diagrams and from the sequence diagrams back to ... Sequence Diagram. A sequence diagram describes how groups of objects collaborate in accomplishing some system behavior. This ...

https://www.stickyminds.com/article/sequence-diagrams

We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to ... Importantly, a 24 nt in-frame deletion was detected in over half of the subgenomic mRNAs encoding the spike (S) glycoprotein ... Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows ... Our data emphasises that the viral genome sequence should be carefully monitored during the growth of viral stocks for research ...

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-00763-0

Plasmodium falciparum parasites with deletion of the pfhrp2 gene encoding this antigen have now been identified in dozens of ... but confirmation of a deletion (or mutation) of pfhrp2 requires more intensive laboratory molecular assays, and new tools and ... countries across Asia, Africa, and South America, with new reports revealing a high prevalence of deletions in some selected ... Plasmodium falciparum WGS involves sequencing individual DNA molecules in a sample using one of several sequencing platforms, ...

https://malariajournal.biomedcentral.com/articles/10.1186/s12936-022-04226-2

Deletion/Duplication Analysis. ENO3 Deletion/Duplication Analysis. Test Code: 2528 Sequence & Deletion/Duplication Analysis. ... ENO3 Comprehensive - Sequence & Deletion/Duplication Analysis. Test Code: 2529 Sequence Analysis. ENO3 Sequence Analysis. Test ... ENO3 Sequence Analysis. Test Code: 2526. This test can only be performed if there is a previously identified familial mutation. ... ENO3 Sequence Analysis. Test Code: 2527. We require that the referring center consult with our laboratory genetic counselors ...

https://www.bcm.edu/research/medical-genetics-labs/test_detail.cfm?testcode=2525

... insertion/deletion cost = 3; mismatch cost = 2. Contigs were screened for SSR regions using the search function described above ... Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. American ... Next-generation sequencing (NGS) platforms are now routinely used for isolation of microsatellite, or simple sequence repeat ( ... and adapter sequences. For the purpose of primer design, reads containing SSR motifs were identified as follows. Raw sequence ...

https://bioone.org/journals/applications-in-plant-sciences/volume-2/issue-4/apps.1300089/Whole-Genome-Shotgun-Sequences-for-Microsatellite-Discovery-and-Application-in/10.3732/apps.1300089.full

KEY-WORDS : Oligonucleotide Array Sequence Analysis. Chromosomes. Chromosome Deletion. Didier LACOMBE*, Caroline ROORYCK-THAMBO ... Most of these deletions or duplications are not recognized on standard karyotype. The most common terminal deletions are 1p36 ...

https://www.academie-medecine.fr/apport-des-puces-a-adn-et-nouveaux-syndromes-microdeletionnels/?lang=en

DNA sequence effects on single base deletions arising during DNA polymerization in vitro by Escherichia coli Klenow fragment ... DNA sequence effects on single base deletions arising during DNA polymerization in vitro by Escherichia coli Klenow fragment ... Most single base deletions detected after DNA polymerization in vitro ... Most single base deletions detected after DNA ... Previous studies had shown that deletions opposite the G were frequent but that deletions opposite its neighboring A were never ...

https://polbase.neb.com/references/338

Normal sequence. Various mutations. Heterogeneous sequence changes. Bi-allelic deletion. Protein null. ... coding sequences in exons 1α, 2, and 3 and ARF. coding sequences in exons 1β and 2 are indicated by different shading patterns ... deletion show negative p16 IHC staining and cells with mono-allelic INK4A. deletion show mutations with loss of heterozygosity ... Sanger sequencing. [86, 87]. INK4A. promoter methylation Pyrosequencing (PyroMark Q24 CpG p16 Kit, Qiagen, Valencia, CA). [82, ...

https://www.intechopen.com/chapters/42240

Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. (biomedcentral.com)

Using chromosome engineering technology and the Mutagenic Insertion and Chromosome Engineering Resource of vector sequences and targets specifically developed to make high-throughput manipulation of mouse genomes easier for researchers, Mills' team created mice with deletions in 16p11.2, and duplications of the same region. (genomeweb.com)
We would like to subdivide the interval, so we can disrupt specific genes that we're interested in, and we can make sub-deletions or sub-duplications within the interval," Mills adds. (genomeweb.com)
Most of these deletions or duplications are not recognized on standard karyotype. (academie-medecine.fr)
Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. (blueprintgenetics.com)
For deletions/duplications extending beyond the reference transcript resp. (lovd.nl)
Accumulations of TEs (TE islands) comprising 7.18% of the genome evolve faster than other regions with regard to single-nucleotide variants, gene/exon duplications and deletions and gene homology. (wurmlab.com)

From 5 representative F. F. tularensis is included among the top 6 "category A" po- tularensis genome sequences, 38 indel markers with ca- tential bioterrorism agents believed to have the greatest po- nonical properties, i.e., capable of sorting strains into ma- jor genetic groups, were selected. (cdc.gov)
About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. (bvsalud.org)
Draft genome sequences of two Bison-type and two Sheep-type strains of Mycobacterium avium subspecies paratuberculosis. (usda.gov)
Here, two species of Machilus (Lauraceae) were selected to determine the entire chloroplast genome sequences. (frontiersin.org)
Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. (cam.ac.uk)
Although entire genome sequences are available for numerous species, lack of reverse genetic tools has hindered cross-species comparisons of gene function. (bioseek.eu)
We characterize variant diversity, amino acid mutation frequency, functionality and associations with COVID-19 infections in one of the largest datasets of SARS-CoV-2 genome sequences collected from wastewater in the New York metropolitan area. (bvsalud.org)

The vast majority of mutations described to date are point mutations and small insertions and deletions http://research.nhgri.nih.gov/bic/ . (biomedcentral.com)
If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). (unix.com)
The main innovation of GLAM2 is that it allows insertions and deletions in motifs. (unix.com)
ZFNs and TALENs induce double-strand breaks at desired loci that can be repaired by error-prone non-homologous end-joining to yield small insertions and deletions (indels) at the break sites. (bioseek.eu)
Recent efforts in coding theory have focused on building codes for insertions and deletions, called insdel codes, with optimal trade-offs between their redundancy and their error-correction capabilities, as well as {\em efficient} encoding and decoding algorithms. (nsf.gov)
Inspired by these notions, Ostrovsky and Paskin-Cherniavsky (Information Theoretic Security, 2015) generalized Hamming LDCs to insertions and deletions. (nsf.gov)
To the best of our knowledge, these are the only known results that study the analogues of Hamming LDCs in channels performing insertions and deletions. (nsf.gov)

In the work presented in here we took advantage of the availability of the citrus clementine genome (GenBank: AMZM00000000.1) to show that both mutants certainly share a similar 2 Mb deletion of chromosome 3 and that the ARR deletion is associated with the activation of a Mutator-like element (MULE). (biomedcentral.com)
Using an engineered mouse model, Alea Mills and her colleagues show in a paper published in PNAS last month that the deletion of a 27-gene cluster on chromosome 16 can cause autism-like features, and that copy-number variations in this region can affect the architecture of the brain and the behavioral phenotype. (genomeweb.com)
The deletion occurs near the middle of the chromosome at a location designated q11.2. (medlineplus.gov)
To localize wheat ( Triticum aestivum L.) ESTs on chromosomes , 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome , arm , and sub- arm aneuploid and deletion stocks. (bvsalud.org)
Δ ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is left out during DNA replication. (wikipedia.org)
[1] Some chromosomes have fragile spots where breaks occur which result in the deletion of a part of chromosome. (wikipedia.org)
When a chromosome breaks, a part of it is deleted or lost, the missing piece of chromosome is referred to as deletion or a deficiency. (wikipedia.org)
For synapsis to occur between a chromosome with a large intercalary deficiency and a normal complete homolog, the unpaired region of the normal homolog must loop out of the linear structure into a deletion or compensation loop . (wikipedia.org)
Terminal deletion - a deletion that occurs towards the end of a chromosome. (wikipedia.org)
Intercalary/interstitial deletion - a deletion that occurs from the interior of a chromosome. (wikipedia.org)
(A) A tumour karyotype in a male with loss of the Y chromosome, (B) Prader-Willi Syndrome i.e. deletion in the 15q11-q12 region and (C) an arbitrary karyotype that involves a variety of autosomal and allosomal abnormalities. (wikipedia.org)
Abbreviations include a minus sign (-) for chromosome deletions, and del for deletions of parts of a chromosome. (wikipedia.org)
[9] Deletion of part of the short arm of chromosome 5 results in Cri du chat syndrome. (wikipedia.org)
November 30, 2011 (Montreal, Quebec) - Partial or complete deletion of a specific gene, the MBD5 gene, on a specific region of chromosome 2 has been identified in every single individual affected by a microdeletion syndrome characterized by intellectual disability, epilepsy, and autism spectrum disorder (ASD). (medscape.com)
The structural chromosome alterations may arise at the chromosome level (e.g., translocations and gains or losses of large portions of chromosomes) or at the nucleotide level, which influence gene structure or expression such as mutations, insertions, deletions, gene amplifications, and gene silencing by epigenetic effects ( Jefford and Irminger-Finger, 2006 ). (frontiersin.org)
We report on a 12-year-old female with both a partial duplication and deletion involving chromosome 6. (hindawi.com)
Homozygous sterile deletion chromosome balanced by GFP-marked translocation. (umn.edu)
This protein has the identical amino acid coding (sequence) found in Human DNA-Chromosome 8. (ethealing.com)
Human DNA gene sequencing has long been known for Chromosome 8, commonly known as the God Gene for its specific effect on Human Behaviors (see definition in next section). (ethealing.com)
All "Vaccine" Injections contain the spiked protein which has the same sequencing (coding) as Chromosome 8, VMAT2. (ethealing.com)
The PCR test template (gene sequence) for the "lab test" also is the same as that found on Chromosome 8, and it has also been found in Swabs used to collect nasal cell samples. (ethealing.com)

The approach used is based on dHPLC mutation screening of the BRCA1 gene, followed by sequencing of fragments suspected to carry a mutation including intron - exon boundaries. (biomedcentral.com)
Finally, MLPA revealed deletion of exon 20 of the BRCA1 gene in one family, a deletion that encompasses 3.2 kb of the gene starting 21 bases into exon 20 and extending 3.2 kb into intron 20 and leads to skipping of the entire exon 20. (biomedcentral.com)
Sequence analysis of a normal genomic ζ-crystallin clone revealed that the missing 102-bp fragment corresponds to an entire exon (exon 7). (elsevier.com)
The predicted sensitivity of Next-Generation Sequencing is approximately 98% for the detection of nucleotide base changes or homozygous deletions in the coding exons and exon/intron boundaries of the five genes analyzed. (cincinnatichildrens.org)
One patient had an in-frame deletion of exon 13, while the second patient had a c.592_593dup frameshift mutation. (wustl.edu)

This condition is described as a contiguous gene deletion syndrome because it results from the loss of many genes that are close together. (medlineplus.gov)
Researchers are working to identify all of the genes that contribute to the features of 22q11.2 deletion syndrome. (medlineplus.gov)
The loss of additional genes in the deleted region likely contributes to the varied features of 22q11.2 deletion syndrome. (medlineplus.gov)
Microdeletion - a relatively small amount of deletion (up to 5Mb that could include a dozen genes). (wikipedia.org)
large deletions are usually fatal - there are always variations based on which genes are lost. (wikipedia.org)
Molecular characterization of the virus was done by using polymerase chain reaction amplification, cloning, and DNA sequencing of conserved orthopoxvirus genes such as the vaccinia growth factor (VGF), thymidine kinase (TK), and hemagglutinin. (cdc.gov)
Gene sequences showed 99% homology with vaccinia virus genes and were clustered together with the isolated virus in the phylogenetic tree. (cdc.gov)
The objectives of this study were to clone, sequence and cytogenetically map RGAs and to analyze their associations with resistance genes. (usda.gov)
Although conservation of DNA sequences is largely confined to protein coding regions, conservation of short flanking sequences has been shown to correlate with promoter expression studies in the case of some genes. (sfu.ca)
Use of sequence conservation between C. elegans and other species to deduce regulatory sequences and to study the effect of selection on the arrangement of genes. (sfu.ca)
Alpha thalassemia typically results from deletions involving the HBA1 and HBA2 genes. (medlineplus.gov)
Less commonly, changes to the DNA sequence in or near these genes cause alpha thalassemia. (medlineplus.gov)
With a high spectrum of the clinical manifestations due to environmental factors, the disease has a genetic heterogeneity that goes from a point mutation to a large deletion involving several genes to produce a contiguous gene syndrome. (wjgnet.com)
Large deletions involving entire single exons or multiple exons, large insertions and other complex genetic events have been reported in many of these genes and will not be identified using this test methodology. (cincinnatichildrens.org)
RNA was sequenced and 63 wheat genes were identified that showed varying expression in response to the six races. (globalrust.org)
Over the last decade, genetic testing has evolved from examining a few well-defined variants in one or a few genes to the capability to examine much of the human genome using next generation sequencing (NGS). (cdc.gov)
Use of genomic DNA reference materials has generally worked well for tests targeting one or a few genes but presents challenges for assuring the quality of sequencing tests with more than a few genes. (cdc.gov)
It can be challenging for individual laboratories to recognize the clinically relevant variant spectrum and have knowledge of difficult to sequence genomic regions, such as those with high GC content, highly homologous genes, or repetitive sequences for all genes included in the test. (cdc.gov)
These transcriptomic data of A. davidianus should open the door to molecular evolution studies based on the entire transcriptome or targeted genes of interest to sequence. (rna-seqblog.com)
Exome sequencing was carried out in gemistocytic astrocytomas, and homozygous deletion of genes was identified at 19q13, i.e. (who.int)
Available hearing loss gene panels include analysis by next-generation sequencing (NGS), deletion and duplication testing, and targeted sequencing of common variants of many genes associated with both non-syndromic and syndromic hearing loss. (concertgenetics.com)
Sanger sequencing or DNA-enrichment methods and massively parallel nucleotide sequencing) and quantitative deletion/duplication (e.g., multiple ligation-dependent probe amplification (MLPA), quantitative PCR, or array comparative genomic hybridization) methodologies to identify disease-associated, protein-coding variants in genes associated with this clinical spectrum. (concertgenetics.com)

Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)
There is a clear consensus in studies in which tumor genomes have been sequenced and analyzed that hypoxia is associated with tumor genomic instability. (frontiersin.org)
sequences from the reference genomes using blastp. (cdc.gov)
Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. (bioseek.eu)
Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. (wurmlab.com)

propensity for homoplasy, we used only those indels with 2 If deliberate release of the organism is suspected, the need allelic variants and devoid of substantial sequence repeats. (cdc.gov)
Assessment of TMB involves next-generation sequencing (NGS) of tumor samples using one of several available platforms and may also involve sequencing of normal patient tissue for germline variants. (springer.com)
Deletions and nondeletion variants in one or more alleles reduce the amount of alpha-globin cells produce. (medlineplus.gov)
Nondeletion variants tend to reduce alpha-globin more than deletions. (medlineplus.gov)
Because nondeletion variants are usually more severe than deletions, nondeletion variants in two of the four alpha-globin alleles can result in HbH disease. (medlineplus.gov)
The plurality consensus sequence is very useful when used with the BAM file to look at minor variants, since the most frequent allele will appear in the reference. (cdc.gov)
Some SARS-CoV-2 variants, including the Omicron variant, have Δ69-70 deletion in the spike (S) gene. (cdc.gov)
Such assays can be used as a screen to presumptively identify SARS-CoV-2 variants that have the Δ69-70 deletion, including the Omicron variant. (cdc.gov)
Analytic validation studies are designed to demonstrate that a test can reliably analyze clinically relevant sequences and identify disease-associated variants. (cdc.gov)
In silico reference materials are created by electronically adding variants to NGS sequencing files. (cdc.gov)

To avoid confusion, this condition is usually called 22q11.2 deletion syndrome, a description based on its underlying genetic cause. (medlineplus.gov)
Microsatellite analysis has shown that comparison of the boundaries of this large deletion with other reported rearrangements of the region reduces the critical region for Duane syndrome (an eye movement disorder) to between markers D8S553 and D8S1797, a genetic distance of approximately 1 cM. (nih.gov)
Deletions can be caused by errors in chromosomal crossover during meiosis , which causes several serious genetic diseases . (wikipedia.org)
Deletions that do not occur in multiples of three bases can cause a frameshift by changing the 3-nucleotide protein reading frame of the genetic sequence. (wikipedia.org)
Deletions are responsible for an array of genetic disorders, including some cases of male infertility , two thirds of cases of Duchenne muscular dystrophy , [1] and two thirds of cases of cystic fibrosis (those caused by ΔF508 ). (wikipedia.org)
[1] Deletions in the SMN -encoding gene cause spinal muscular atrophy , the most common genetic cause of infant death. (wikipedia.org)
Coronaviruses use a complex strategy to express their genetic information [ 5 , 6 ], involving a process of discontinuous transcription during minus-strand RNA synthesis that is regulated by defined transcription regulatory sequences (TRS) [ 7 ]. (biomedcentral.com)
Sarah Elsea, PhD, associate professor of pediatrics and human and molecular genetics at the Virginia Commonwealth University School of Medicine in Richmond, and colleagues assembled a collaborative team of clinical diagnostic laboratories and research facilities in Canada, Europe, and the United States to characterize the genetic content and phenotypic outcomes associated with a spectrum of genetic alterations with the 2q23.1 deletion syndrome region. (medscape.com)
encoding the methyl-CpG-binding domain 5 protein, is a clear causal locus within the 2q23.1 deletion region and represents a previously unrecognized contributor to the genetic etiology of ASD," they report. (medscape.com)
Genetic and phenotypic analyses suggest that the majority of individuals affected by the 2q23.1 deletion syndrome exhibit autistic-like behaviors. (medscape.com)
It is also ounique in that the markers were cloned using genetic sequences from other plant species. (usda.gov)
Development of tools that makes possible the genetic exploitation of the sequenced C. elegans genome. (sfu.ca)
Heterozygous deletions, insertions, genetic recombination events, as well as mutations in regulatory regions or other untranslated regions are not detected by this test. (cincinnatichildrens.org)
Genetic changes in the form of amplifications and deletions are observed predominantly in the 12p11.2-p12.1 chromosomal region. (medscape.com)
This can be determined using the Revised International Prognostic Scoring System (IPSS-R) in addition to evaluation of a patient's performance status, symptoms, care goals, cytopenias, and molecular genetic testing (eg, for 5q31 deletion or SF3B1 mutations). (medscape.com)
And when that happens, usually the cases are escalated and the specimens are sent to state laboratories that have some advanced strategies to do things like real- time RT-PCR testing or even sequence analysis of the genetic material in the clinical specimen. (cdc.gov)
Deletion of sequences of nucleic acids from the genetic material of an individual. (bvsalud.org)
In this study, we show that for a given collection of HIV sequences from different hosts, the HIV sequences are not selected randomly but with a certain bias.Association of genetic polymorphism of the angiotensin-converting enzyme gene with hypertension. (royalmarloiesport.com)
Hearing loss genetic testing typically consists of sequencing (e.g. (concertgenetics.com)

Here we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase III clinical trial. (springer.com)
Nonpaternity was considered but ruled out by whole exome sequencing analysis. (hindawi.com)

Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) among mutant strains, which simplifies forward genetics approaches. (wustl.edu)

More specifically, it's a library for dealing with all kinds of nucleotide sequences, including degenerate nucleotides . (github.com)
Nt.MatchMap allows you to find all ungapped alignments between two degenerate nucleotide sequences, ordered by the number of matches . (github.com)
We used VGF-homologous and TK gene nucleotide sequences to construct a phylogenetic tree for comparison with other poxviruses. (cdc.gov)
GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. (unix.com)

We conclude that a combination of techniques capable of detecting both single base mutations and small insertions / deletions and large genomic rearrangements is necessary in order to accurately analyze the BRCA1 gene in patients at high risk of carrying a germline mutation as determined by their family history. (biomedcentral.com)

7- 9 All reported mutations are single nucleotide alterations leading to splice site, missense, nonsense, or frameshift mutations, or intra-exonic deletions and insertions of up to four nucleotides, which have been detected through exonic PCR amplifications and sequencing. (bmj.com)
We report the first intragenic deletion and frameshift mutations identified in RAD21 in two patients presenting with atypical CdLS. (wustl.edu)
This results in in-frame amino acid deletions, insertions or frameshift mutations leading to premature stop codons within the targeted gene. (galaxyproject.org)

Sequencing of rpoB allows for clarification of the result and understanding of possible discordance between rapid molecular and growth-based testing results. (cdc.gov)
Expression of the HRP2 antigen can be evaluated using point-of-care RDTs or laboratory-based immunoassays, but confirmation of a deletion (or mutation) of pfhrp2 requires more intensive laboratory molecular assays, and new tools and strategies for rigorous but practical data collection are particularly needed for large surveys. (biomedcentral.com)
Abstract Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. (nsf.gov)
Abstract Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. (nsf.gov)
[ 38 ] Molecular testing for homozygous deletion or mutation of the SMN1 gene allows efficient and specific diagnosis. (medscape.com)

Initially the clones were physically mapped to chromosomes using wheat nulli-tetrasomic deletion lines. (usda.gov)
Although a majority of chromosomal duplication-deletion cases have resulted from a parental pericentric inversion, the parents of our case have normal chromosomes. (hindawi.com)
Analysis revealed deletion of DNA fragments with collinear gene order on chromosomes 1A, 2D, 5A, 5B, 5D and 7D of Chara HII mutants. (globalrust.org)
Recently published research papers are now demonstrating how Human cells can rewrite RNA sequences into DNA Chromosomes. (ethealing.com)

Testing for this gene is available as part of the Cholestasis and Jaundice panels by next-generation sequencing. (cincinnatichildrens.org)
Selection was based upon lowest cycle threshold values (i.e., highest viral nucleic acid concentration), such that cost-effective next generation sequencing could be performed by batching (at most) a dozen specimens. (cdc.gov)
3. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. (cdc.gov)

The sensitivity of Sanger sequencing is over 99% for the detection of nucleotide base changes, small deletions and insertions in the regions analyzed. (cincinnatichildrens.org)
However, there have been approximately 50 reported cases with the deletions ranging from 6q26 and 6q27 [ 5 ] (decipher.sanger.ac.uk). (hindawi.com)
Targeted sequencing of the S gene, using either NGS or Sanger sequencing, or whole genome sequencing using NGS will provide positive identification of Omicron. (who.int)

Missense mutations and whole gene deletions in RAD21 have been identified in children with growth retardation, minor skeletal anomalies and facial features that overlap findings in individuals with CdLS. (wustl.edu)

Based on homology to other known coronaviruses [ 3 , 4 ], the genome sequence was used for viral transcript prediction and the annotation of ORFs. (biomedcentral.com)

KEY-WORDS : Oligonucleotide Array Sequence Analysis. (academie-medecine.fr)

Francisella tularensis, a potent human pathogen and a pu- needed, not only because of their use in clinical and public tative bioterrorist agent, we combined analysis of insertion- health work but also because of a rising concern associated deletion (indel) markers with multiple-locus variable-number with risks for bioterrorism ( 4 , 8 ). (cdc.gov)
keithwhor/NtSeq: JavaScript (node + browser) bioinformatics library for nucleotide sequence manipulation and analysis. (github.com)
NtSeq is an open source Bioinformatics library written in JavaScript that provides DNA sequence manipulation and analysis tools for node and the browser. (github.com)
Therefore, in this analysis read pair methods (BreakDancer in particular) were the best performing approaches for the identification of deletions =1?kb, balancing accuracy and sensitivity. (pacb.com)
This dosage assay, combined with microsatellite marker analysis, has identified de novo deletions of the EYA1 gene and surrounding region in two patients with complex phenotypes involving features of BOR syndrome. (nih.gov)
Current efforts in mapping and sequencing will soon facilitate the high throughput analysis of gene function. (sfu.ca)
Further sequence analysis of the α-crystallin gene disclosed a dinucleotide delection of the universal AG at the acceptor splice-site of intron 6 of the mutant gene. (elsevier.com)
Single gene sequencing, deletion/duplication analysis and familial mutation analysis are also available for this gene. (cincinnatichildrens.org)
Deletion mutation analysis revealed a putative polarization domain at the N terminus of caveolin-1, between amino acids 32-60. (cdc.gov)
Two samples were randomly selected for repeat extraction, library preparation and sequencing to evaluate reproducibility of whole genome analysis. (cdc.gov)
Blueprint Genetics' Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis. (blueprintgenetics.com)
We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile . (biomedcentral.com)
Our techniques are based on a delicate design and analysis of hard distributions of insertion and deletion errors, which depart significantly from typical techniques used in analyzing Hamming LDCs. (nsf.gov)
Mechanistically, RNA sequencing analysis indicated that DCLK1 mediates oxLDL-induced inflammation via NF-κB signaling pathway in primary macrophages. (bvsalud.org)

We introduce an alignment-integrated ASR approach that combines information from many different sequence alignments. (nsf.gov)
References Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. (ucsc.edu)
The multiple sequence alignments were concatenated, and a maximum-likelihood phylogenetic tree was inferred using RAxML ( 9 ) (model parameter set to PROTGAMMAGTR). (cdc.gov)
Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept. (ucsc.edu)

The aim of this study was to evaluate the efficiency of each of these main approaches in detecting germline deletions.WGS data and high confidence deletion calls for the individual NA12878 from the Genome in a Bottle consortium were the benchmark dataset. (pacb.com)
Patients with gemistocytic astrocytoma with oligodendroglial differentiation, IDH1 samples from a Li-Fraumeni family with and secondary glioblastoma with RRAS mutation, and 1p/19q loss, suggesting a TP53 germline mutation and multiple deletion tended to have shorter survival that FUBP1 immunohistochemistry is nervous system tumours revealed times than those without deletion. (who.int)

22q11.2 deletion syndrome has many possible signs and symptoms that can affect almost any part of the body. (medlineplus.gov)
People with 22q11.2 deletion syndrome commonly have heart abnormalities that are often present from birth, recurrent infections caused by problems with the immune system, and distinctive facial features. (medlineplus.gov)
Many children with 22q11.2 deletion syndrome have developmental delays, including delayed growth and speech development, and some have mild intellectual disability or learning disabilities. (medlineplus.gov)
Additionally, affected children are more likely than children without 22q11.2 deletion syndrome to have attention-deficit/hyperactivity disorder (ADHD) and developmental conditions such as autism spectrum disorder that affect communication and social interaction. (medlineplus.gov)
Because the signs and symptoms of 22q11.2 deletion syndrome are so varied, different groupings of features were once described as separate conditions. (medlineplus.gov)
In addition, some children with the 22q11.2 deletion were diagnosed with the autosomal dominant form of Opitz G/BBB syndrome and Cayler cardiofacial syndrome. (medlineplus.gov)
22q11.2 deletion syndrome affects an estimated 1 in 4,000 people. (medlineplus.gov)
Small intragenic deletions of the 3' region of the gene have also been reported in patients with BOR syndrome. (nih.gov)
One patient with OFC syndrome carried a large deletion of the EYA1 gene region, confirming that OFC syndrome is allelic with BOR syndrome. (nih.gov)
[10] Some syndromes, including Angelman syndrome and Prader-Willi syndrome, are associated with both microdeletions and genomic imprinting, meaning that same microdeletion can cause two different syndromes depending on which parent the deletion came from. (wikipedia.org)
Regardless of the size of the deletion, the MBD5 gene is the primary contributor to the core features of the syndrome, she added. (medscape.com)

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels. (blueprintgenetics.com)

To investigate the evolutionary pattern of HIV sequences, we have reconstructed a phylogenetic tree of HIV sequences from the IAS (International AIDS Society) Data Set. (royalmarloiesport.com)

Also, ERCC1 homozygous deletion or et al. (who.int)

A high-throughput method to produce deletions of non-coding DNA is needed. (nature.com)
We report a high-throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. (nature.com)
Our high-throughput pgRNA genome deletion method will enable rapid identification of functional mammalian non-coding elements. (nature.com)

For the first time there is evidence that polymerase theta has the ability for reverse-transcription, that is mRNA products with sequencing complimentary to the DNA template can replace and encode genomic DNA strands permanently into newly formed cells. (ethealing.com)
The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide. (ucsc.edu)

The method capitalizes subspecies into 2 major groups of isolates, which differ in on differences among strains in copy numbers of sequence virulence and geographic distribution ( 5 - 7 ). (cdc.gov)
A comparison of polymorphisms in the imp3 strain and the other 15 strains allowed us to identify a deletion of the last three amino acids, Y 313 F 314 L 315 , in a protein phosphatase 2A catalytic subunit (PP2A3) in the imp3 strain. (wustl.edu)
Complete genome sequence of four strains of Leptospira borgpetersenii serovar Hardjo isolated from cattle in the Central United States. (usda.gov)
DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. (biomedcentral.com)
When we analyze the present-day HIV sequences, we observe one dominant variant with numerous subpopulations consisting of many strains. (royalmarloiesport.com)

This study builds on work done in 2007 by Mills' colleague Michael Wigler and others, who discovered that some autistic children have deletions in the 16p11.2 chromosomal region. (genomeweb.com)

CDC has recommended that RMP resistance detected by the Xpert ® MTB/RIF assay be confirmed by DNA sequencing [7] . (cdc.gov)

In contrast, they found no deletions of the 2q23.1 segment, the full MBD5 locus, or any MBD5 coding exons in 7878 control subjects with no psychiatric diagnosis. (medscape.com)

Evaluation of the performance of copy number variant prediction tools for the detection of deletions from whole genome sequencing data. (pacb.com)
Whole genome sequencing (WGS) has increased in popularity and decreased in cost over the past decade, rendering this approach as a viable and sensitive method for variant detection. (pacb.com)
The performance of BreakDancer, CNVnator, Delly, FermiKit, and Pindel was assessed by comparing the accuracy and sensitivity of each software package in detecting deletions exceeding 1?kb.There was considerable variability in the outputs of the different WGS CNV detection programs. (pacb.com)
Concordance across software packages was poor, with only 27 of the total 612 benchmark deletions identified by all five methodologies.The WGS based CNV detection tools evaluated show disparate performance in identifying deletions =1?kb, particularly those utilising different input data characteristics. (pacb.com)
Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein, a leading vaccine target, shows that this and other regions of SARS-CoV-2 proteins may readily mutate. (biomedcentral.com)
Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table). (blueprintgenetics.com)

Use of the genomic sequence of C. elegans as a tool in the investigation of the human genome. (sfu.ca)
This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. (ucsc.edu)

Probabilistic modeling of insertion and deletion events has the potential to radically improve ASR accuracy when the model reflects the true underlying evolutionary history, but further studies are required to thoroughly evaluate the reliability of these approaches under realistic conditions. (nsf.gov)
In this work we study LDCs for insertion and deletion errors, called Insdel LDCs. (nsf.gov)

The deletion does not interfere with the reading frame but results in a protein 34 amino acids shorter. (elsevier.com)
Interestingly, deletion of amino acids 1-60 did not prevent the polarization of caveolin-1 in human umbilical vein endothelial cells or wild-type mouse embryonic fibroblasts because of an interaction of Cav(61-178) mutant with endogenous caveolin-1. (cdc.gov)

Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. (biomedcentral.com)
During homologous recombination, sequences are exchanged between homologous DNA fragments. (biomedcentral.com)

DNA isolation, genotyping of simple tandem repeat polymorphisms, PCR amplification and sequencing were performed using standard techniques 2 and all simple tandem repeat polymorphisms were amplified in the presence of 10% glycerol and 5% DMSO after labelling one oligonucleotide primer with 32 P and analysed on a 6% polyacrylamide gel. (bmj.com)

At the species level, however, the reported nuclear ITS and LEAFY intron II sequences failed to resolve the phylogenetic and species identification problems in this genus. (frontiersin.org)

Plasmodium falciparum parasites with deletion of the pfhrp2 gene encoding this antigen have now been identified in dozens of countries across Asia, Africa, and South America, with new reports revealing a high prevalence of deletions in some selected regions. (biomedcentral.com)
The relative prevalence of each mutation in Omicron sequences in not yet known as the sequencing data at the present time is limited. (who.int)

The Human Genome Variation Society (HGVS) has established a sequence variant nomenclature , an international standard used to report variation in genomic, transcript and protein sequences. (ucsc.edu)

The team also found that partial or complete deletion of the same gene was associated with haploinsufficiency of messenger RNA expression, "meaning individuals with this microdeletion disorder have only 1 functioning copy of the gene, so there is only 50% function. (medscape.com)

MutS beta recognizes large insertion-deletion loops (IDL) up to 13 nucleotides long. (affbiotech.com)

We used direct RNA sequencing to determine the transcriptome of SARS-CoV-2 grown in Vero E6 cells which is widely used to propagate the novel coronavirus. (biomedcentral.com)

We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. (biomedcentral.com)
Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. (biomedcentral.com)
Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. (biomedcentral.com)
Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. (biomedcentral.com)

Some medium-sized deletions lead to recognizable human disorders, e.g. (wikipedia.org)
Distal 6q deletions are also rare chromosomal disorders. (hindawi.com)

Recent work suggests that some deletions of highly conserved sequences (CONDELs) may be responsible for the evolutionary differences present among closely related species. (wikipedia.org)
To better understand the mutation patterns in the chloroplast genome of Machilus , the complete plastomes of two species were sequenced. (frontiersin.org)
This raises the question, are there any useful sequences for the phylogenetic classification of Machilus species in the chloroplast genome? (frontiersin.org)

The samples were sequenced on an Illumina Hiseq 4000 at the Beijing Genomics Institute, China. (globalrust.org)
Pools were sequenced on a HiSeq 2500 (Illumina) to obtain roughly 20 million reads per sample. (cdc.gov)

Sequences of ARF-GAP domains show no recognizable similarity to those of other GAPs, and contain a characteristic Cys-X(2)-Cys-X(16-17)-Cys-X(2)-Cys motif. (embl.de)

Amplicon dropouts can sometimes leave zero coverage regions where no in-read deletions were detected. (cdc.gov)

Figure 1: Lentivirally delivered paired-guide RNAs create large-fragment deletion with high efficiency in human cells stably expressing Cas9. (nature.com)
A large amount of deletion would result in immediate abortion (miscarriage). (wikipedia.org)
Individuals with very large deletions in the region are more severely affected with additional manifestations. (medscape.com)
Joel reported long preempt and irq off sequence in newidle_balance because of a large number of cgroups in used and having to be updated. (lkml.org)

Organisms1

Diseases1

Analytical, Diagnostic and Therapeutic Techniques and Equipment4

Phenomena and Processes10

Information Science3

Transformation mediated by RhoA requires activity of ROCK kinases. (1/14225)

Deletion analysis of the Drosophila Inscuteable protein reveals domains for cortical localization and asymmetric localization. (2/14225)

Superimposed histologic and genetic mapping of chromosome 9 in progression of human urinary bladder neoplasia: implications for a genetic model of multistep urothelial carcinogenesis and early detection of urinary bladder cancer. (3/14225)

Level of retinoblastoma protein expression correlates with p16 (MTS-1/INK4A/CDKN2) status in bladder cancer. (4/14225)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (5/14225)

Over-representation of a germline RET sequence variant in patients with sporadic medullary thyroid carcinoma and somatic RET codon 918 mutation. (6/14225)

Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. (7/14225)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (8/14225)

Sequence Deletion

Molecular Sequence Data

Base Sequence

Gene Deletion

Chromosome Deletion

Mutation

Amino Acid Sequence

Phenotype

Chromosome Mapping

DNA Mutational Analysis

Plasmids

Polymerase Chain Reaction

Clonal Deletion

Exons

Cloning, Molecular

Mice, Knockout

Transformation mediated by RhoA requires activity of ROCK kinases. (1/14225)

Deletion analysis of the Drosophila Inscuteable protein reveals domains for cortical localization and asymmetric localization. (2/14225)

Superimposed histologic and genetic mapping of chromosome 9 in progression of human urinary bladder neoplasia: implications for a genetic model of multistep urothelial carcinogenesis and early detection of urinary bladder cancer. (3/14225)

Level of retinoblastoma protein expression correlates with p16 (MTS-1/INK4A/CDKN2) status in bladder cancer. (4/14225)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (5/14225)

Over-representation of a germline RET sequence variant in patients with sporadic medullary thyroid carcinoma and somatic RET codon 918 mutation. (6/14225)

Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. (7/14225)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (8/14225)

CRISPR Biosafety Guidance

NCCR Database - N-terminal deletion of prnp

generating terminal truncations of a protein

Defective Interfering Particles And Their Role In Disease Progression And Persistence

Recognition of tRNA elements by EcTrmJ. (A) A model of | Open-i

The best Side of hbr case solution

Characterization of the effects of a 7 amino-acid delet | Open-i

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Various deletion mutants of Flag-tagged NOX5 or Pyk2 and HA-tagged NOX5 or Pyk2 were cloned into a pcDNA3 - In vivo efficacy of...

Team:Calgary/Project/IbpAB - 2010.igem.org

2q33 1 Deletions And Other Deletions Between 2q31 And 2q33 - PDF Download

Deletion problems

MEDICA

MEDICA

My sons deletion - PPMD Community

Exon deletion of 63-67 - PPMD Community

Category:Candidates for deletion | Speedy deletion Wiki | FANDOM powered by Wikia

A novel DFNB1 deletion allele supports the existence of a distant **cis**-regulatory region that controls **GJB2** and **GJB6**...

Topic revision: 6 (15 Dec 2017 - 06:13:12)

Full-length KIR3DL1*01501 differing from KIR3DL1*0150201 with 10 SNPs and 2 nucleotide deletion in intron 7. © 2014 John Wiley ...

ELM - Detail for LIG EF ALG2 ABM 2

Patent US6751635 - File deletion and truncation using a zombie file space - Google Patents

BOL: Results for Deletions

Anaplastic oliodendroglioma grade 3 | Cancer Survivors Network

Final Diagnosis -- Case 243

SYNCOPE-707] ConfigurationLogic doesnt check the existence of key during deletion. - ASF JIRA

Deleting a Structure | ChemAxon Docs

Deletion log - Speedsolving.com Wiki

PATCH 02/12] dmusic/tests: Introduce compare time helper.

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Error - ZineWiki - the history and culture of zines, independent media and the small press.

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Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a...

Refinement of the critical 2p25.3 deletion region - Danish National Research Database-Den Danske Forskningsdatabase

Detection of large scale 3 deletions in the PMS2 gene amongst Colon-CFR participants: have we been missing anything? - UQ...

Effect of surface wave diffraction on radiation pattern of slot antenna etched in finite ground plane - IET Journals & Magazine

3q deletion Symptoms, Diagnosis, Treatments and Causes - RightDiagnosis.com

PRRS-Resistant Pigs Produced Using CRISPR-Cas9 For DNA Deletion

relationship to other organisms - York the smallest visible deletion(about 4Mb would represent about an 8 km gap and that on...

Fixed-Parameter Algorithms for Cluster Vertex Deletion | SpringerLink

getDeletionTolerance.Sequence: Get the deletion tolerance site-process specific parameter... in phylosim: Flexible Simulations...

Cancer may require simpler genetic mutations than previously thought

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Characterization of novel RS1 exonic deletions in juvenile X-linked retinoschisis<...

P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored. | CBCB

indelmiss-package: Insertion deletion analysis while accounting for possible... in indelmiss: Insertion Deletion Analysis While...

Chromosomal deletion | definition of chromosomal deletion by Medical dictionary

Discovery of significant variants containing large deletions in the 5UTR of human hepatitis C virus (HCV) | Virology Journal |...

Multiple Deletions in Logistic Regression Models | Korea Science

Deletion legal definition of deletion

A novel DFNB1 deletion allele supports the existence of a distant cis-regulatory region that controls GJB2 and GJB6...

Full-length KIR3DL101501 differing from KIR3DL10150201 with 10 SNPs and 2 nucleotide deletion in intron 7. © 2014 John Wiley ...

$Effect of surface wave diffraction on radiation pattern of slot antenna etched in finite ground plane - IET Journals & Magazine$ Effect of surface wave diffraction on radiation pattern of slot antenna etched in finite ground plane - IET Journals & Magazine