Genome sequence deletion. Medical search. Frequent questions

Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. (nature.com)
Boldface indicates genes at the border of SG33 deletion. (cdc.gov)
Subsequent screening for structural variants in candidate genes located in the same regions identified a homozygous deletion that includes exons 17 to 23 of the integrin beta 4 ( ITGB4 ), a gene that was previously associated with the same defect in humans. (biomedcentral.com)
An influenza virus' genome consists of all genes that make up the virus. (cdc.gov)
A, C, G and T/U) in each of the genes present in the virus's genome. (cdc.gov)
Full genome sequencing can reveal the approximately 13,500-letter sequence of all the genes of the influenza virus' genome. (cdc.gov)
The sequences deposited into these databases allow CDC and other researchers to compare the genes of currently circulating influenza viruses with the genes of older influenza viruses and those used in vaccines. (cdc.gov)
In a comparison excluding the composite sequencing data, the genomes and the open reading frames are fairly well conserved with differences only in 2, out of 80, genes. (usda.gov)
Comparison of the genome sequences of phenotypically different strains could help to identify genes involved in virulence. (usda.gov)
Exclusive to the genomes of the Serva vaccine strains, 7 non-synonymous mutation were identified in the predicted translation products of the genes encoding glycoproteins gB, gE, gL and gM and three nonstructural proteins UL28 (DNA packaging protein), UL5 (helicase-primase) and the immediate early protein ICP4. (usda.gov)
The lack of restorer lines for the newly identified male-sterility led us to predict that it might be a complete cytoplasmic male-sterility without restorer-of-fertility genes in nuclear genomes. (springer.com)
Genes on chromosome 9 are among the estimated 20,000 to 25,000 total genes in the human genome. (news-medical.net)
Some mutations shuffle the genetic code, others come from the deletion of key genes. (news-medical.net)
As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. (columbia.edu)
In addition there are some clustered hot-spots for HPV integrations into the human genome and there are important cancer-related genes at or around HPV integration sites [ 9 ]. (biomedcentral.com)
Hence, important human genes could be contributing to carcinogenesis, and thus the site(s) of integration into the human genome may be more important than initially realized. (biomedcentral.com)
Within the resulting 77 million base pair hybrid bladderwort genome assembly, the team tracked down a whopping 28,500 or so predicted protein-coding genes - far more than anticipated from its size alone. (genomeweb.com)
That coding capacity comes at the cost of non-coding repetitive sequences, jumping genes, and other mobile genetic elements, which together make up just 3 percent or so of the bladderwort genome. (genomeweb.com)
Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA," Albert and co-authors wrote. (genomeweb.com)
Nevertheless, they noted that the genome seems to house a full complement of the plant genes and microRNAS tasked with retrotransposon silencing. (genomeweb.com)
This surprisingly rich history of duplication, paired with the current small size of the bladderwort genome, is further evidence that the plant has been prolific at deleting non-essential DNA," co-corresponding author Luis Herrera-Estrella, with Mexico's Laboratorio Nacional de Genómica para la Biodiversidad, said in a statement, "but at the same time maintaining a functional set of genes similar to those of other plant species. (genomeweb.com)
The NCBI RefSeq Genes composite track shows zebrafish protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). (ucsc.edu)
As early as 1993, Martin and Palumbi found that smaller animals, both endotherms and ectotherms, harbor more changes in the DNA sequences of certain genes than do larger animals. (eurekalert.org)
1q23.1 homozygous deletion and downregulation of Fc receptor-like family genes confer poor prognosis in chronic lymphocytic leukemia. (cancerindex.org)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
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)
A deletion anywhere in the mitochondrial genome may affect transcription or translation of genes that were not affected by the deletion. (medscape.com)

In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). (nature.com)
The speed and accuracy of identifying small insertions and deletions of sequence, collectively termed INDELs, can be improved by calling variants while aligning sequence reads. (usda.gov)
The positive (disease-causing) insertion and deletion dataset consists of 9007 variants, 2667 frameshift (FS) insertions and deletions and 6340 non frame-shift (NFS) insertions and deletions. (lu.se)
The neutral dataset contains 8861 micro-insertions and deletions from the 1,000 Genomes Project (20101123 release). (lu.se)
There are 2587 FS insertions and deletions and 6274 NFS-insertions and deletions. (lu.se)
The pathogenic dataset contains 6513 frameshift (FS) and 5023 non frameshift (NFS) insertions and deletions from ClinVar database. (lu.se)
The training datasets from the 1000 Genomes Project phase 3 contains 366 FS and 3171 NFS insertions and deletions. (lu.se)
The neutral datasets from ESP6500 consists of 1604 FS and 181 NFS insertions and deletions. (lu.se)
Insertions and deletions that have a length divisible by 3 cause amino acid insertions/deletions or block substitutions are called 3n changes. (lu.se)
This dataset contains 9710 3n neutral insertions and deletions identified from UCSC mammalian alignments, chosen so that there is one random insertion or deletion per gene. (lu.se)
Subset of 474 3n neutral insertions and deletions was used for method training and cross-validation. (lu.se)
Dataset for training predictor for frameshifting insertions and deletions. (lu.se)

Analysis of high coverage sequencing data (more than 30x) from 10,000 individuals showed that each newly analyzed genome added roughly 0.7MB of new sequences to the human reference genome and contributed an average of 8,579 new SNVs to the existing human variation data set 13 . (nature.com)
The algorithm uses a string pattern hash to store the entire reference genome in a rapidly accessed table. (usda.gov)
Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. (columbia.edu)
RefSeq Diffs - alignment differences between the zebrafish reference genome(s) and RefSeq curated transcripts. (ucsc.edu)
The amount of actual nucleotide sequence in the latest version of the reference genome ( GRCh38.p13 ) is 3,110,748,599 bp and the estimated total size is 3,272,116,950 bp based on estimating the size of the remaining gaps. (blogspot.com)
DNA from a patient is compared to a reference genome using many oligonucleotide probes. (msdmanuals.com)

Overall our comparative sequence analysis of virulent GaHV-1 strains has identified both intragenic and intergenic deletions as well as single nucleotide polymorphism mutations that differentiate the Serva vaccine genome from the genomes of 4 virulent strains. (usda.gov)
Although SGBS is mainly a disorder caused by point mutations, this report shows that deletions of Xq26.3 affecting the GPC3 gene also may cause this condition. (chromodisorder.org)
Whole genome sequencing studies can directly identify causative mutations for subsequent use in genomic evaluations, but sequence variant identification is a lengthy and sometimes inaccurate process. (usda.gov)
Analysis of the remaining (88 percent of) non-induced proviruses showed that all were defective, possessing genetic deletions and mutations that would forestall viral replication. (hopkinsmedicine.org)
Deep sequencing discovery of causal mtDNA mutations in a patient with unspecific neurological disease. (ucu.edu.uy)
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. (doe.gov)
For example, instead of studying changes in base pairs of DNA sequences, the current researchers looked at a suite of genomic attributes that may represent mutations generated by different processes. (eurekalert.org)
The VOC differ from the original Wuhan virus as they have mutations across the genome. (who.int)
Mutations in other regions of the genome may also be informative for known VOI/VOC detection. (who.int)
Overall, these assays and approaches detect specific mutations or features such as insertions, deletions and point mutations in the SARS CoV-2 genome that are characteristic of a particular VOC/VOI using PCR. (who.int)
Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. (lu.se)

To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. (asm.org)
Deletion in the genomes of certain strains localized to the 5' genomic termini and the ICP4 loci. (usda.gov)
BGI-Research and the Maternal and Child Health Hospital of Hubei Province (MCHH) published whole-genome sequencing research results in npj Genomic Medicine. (news-medical.net)
However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. (columbia.edu)
I]n contrast to recent publications that highlight a crucial functional role of non-coding DNA in complex organisms such as animals," he and his colleagues argued, "the necessary genomic content required to make a flowering plant may not require substantial hidden regulators in the non-coding 'dark matter' of the genome. (genomeweb.com)
With advances in genome sequencing technology and rich long-term data accumulated about the life history traits of birds, scientists are now able to tackle this issue from a slightly different genomic perspective. (eurekalert.org)
Since transposable elements and DNA deletions also drive the expansion and contraction of genome size, the researchers also studied the relationship between these two genomic traits and variation in genome size. (eurekalert.org)
Array comparative genomic hybridization (aCGH) is a type of microarray now routinely used to identify deleted or duplicated regions of DNA sequence in specific chromosomes on a genome-wide basis. (msdmanuals.com)
These challenges may be solved, at least in part, by supplementing genomic DNA samples with in silico (electronic) reference materials to develop and validate the informatics pipeline used to analyze the data generated during the physical sequencing of the patient sample. (cdc.gov)

While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. (frontiersin.org)
Compared to whole genome sequencing (WGS), exome sequencing covers only the 1% of the genome that is translated into protein, greatly reducing the technical burden of data collection and analysis. (frontiersin.org)
Whole exome or whole genome sequencing is typically used when single gene or panel testing has not provided a diagnosis, or when the suspected condition or genetic cause is unclear. (medlineplus.gov)
Whole exome or whole genome sequencing is often more cost- and time-effective than performing multiple single gene or panel tests. (medlineplus.gov)
This technology involves breaking the entire genome into small segments, sequencing the segments, and then reassembling the sequences using intensive computational techniques to provide the base-by-base sequence of the entire genome or more limited regions, such as the expressed portion of the genome known as the exome. (msdmanuals.com)
However, the sheer volume of information generated by sequencing the exome or genome results in a variety of interpretive problems that complicate understanding of the results. (msdmanuals.com)
We performed exome sequencing (seq), RNA-seq, assay for transposase-accessible chromatin-seq, chromatin immunoprecipitation-seq, high-throughput chromosome conformation capture, and phenotypic analyses with short hairpin RNA or clustered regularly interspaced short palindromic repeats interference. (bvsalud.org)
In silico reference materials are truly scalable and can be tailored to meet the needs of any NGS assay regardless of size, including whole exome/whole genome. (cdc.gov)

Nucleotide changes with position in Lausanne genome, or identity percentage if too many. (cdc.gov)
Filtering of variants located in these regions for (i) homozygous polymorphisms observed in the WGS data from eight healthy Charolais animals and (ii) homozygous or heterozygous polymorphisms found in the genomes of 234 animals from different breeds did not reveal any deleterious candidate SNPs (single nucleotide polymorphisms) or small indels. (biomedcentral.com)
nucleotide of the inserted sequence. (ethz.ch)
The nucleotide sequences of four virulent strains of gallid herpesvirus type 1, the causative agent of infectious laryngotracheitis, were determined. (usda.gov)
Sanger dideoxy sequencing, 454 pyrosequencing and Illumina sequencing were used to determine the nucleotide sequences of four groups of virulent GaHV-1 strains (groups I, III, V and VI). (usda.gov)
This process helps identify single or multiple nucleotide variations as well as areas of insertion or deletion. (msdmanuals.com)

We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. (nature.com)
Accuracy of detection was examined using reads simulated from cattle reference map UMD3.1 for 10 animals with 10x coverage and including 38,062,190 SNPs, 532,179 insertions, and 1,127,620 deletions from run5 of the 1,000 bull genomes project. (usda.gov)

Whole-genome sequencing (WGS) analyses of this tumor type are limited, and we therefore interrogated eight ATCs using WGS and RNA sequencing. (lu.se)
However, compared to other flaviviruses, USUV has received less research attention and there is therefore limited access to whole-genome sequences and also to in-depth phylogenetic and phylodynamic analyses. (frontiersin.org)
In addition, despite the compressed genome found in bladderworts today, researchers reported, their analyses suggest that genome duplication events are not uncommon in the plant's history. (genomeweb.com)

Genome sequencing reveals the sequence of the nucleotides in a gene, like alphabet letters in words. (cdc.gov)
WGS reveals that there is a great complexity in both HPV sequences present and the HPV integrations events in HPV positive OPSCCs tumors. (biomedcentral.com)

Results: A genome wide association study (GWAS) was performed using the Axiom 670 k Equine Genotyping array (MNEc670k) utilizing 14 cases and 38 controls phenotyped for distichiasis. (uu.nl)
DNA microarrays can be used in genome-wide association studies (GWAS) to compare patient and control populations to identify DNA variants that can contribute to disease risk. (msdmanuals.com)

Twenty-five of the 213 non-induced isolates, when sequenced, had fully intact genomes when compared to those that did reactivate. (hopkinsmedicine.org)
Complete Genome Sequences of Four Macrolide-Resistant Nondiphtheritic Corynebacterium Isolates. (cdc.gov)
Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions. (cdc.gov)

When they compared the bladderwort genome to those of other sequenced plants, for instance, the researchers saw signs of at least three historical genome duplications in the bladderwort lineage since a split from a shared ancestor with tomato and grape plants. (genomeweb.com)
The key idea in these methods is that deletions/duplications will result in more/fewer fetal reads within a window, and this difference can be identified using statistical methods. (genomeweb.com)

The changes to the proteins can come in the form of amino acid substitutions, insertions, or deletions. (cdc.gov)
78 synonymous and 118 non-synonymous amino acid substitutions were identified in a comparison that included ORFs encoded within the genomes of the Serva and group I, III, V and VI strains. (usda.gov)

Genome sequence alignments were used to identify two regions (5' terminus and the unique short/repeat junction) that contained various intragenic deletions. (usda.gov)
They were manually curated, based on publications describing transcripts and manual reviews of evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites and any other evidence available in databases or the scientific literature. (ucsc.edu)
They were predicted based on protein, cDNA, EST and RNA-seq alignments to the genome assembly by the NCBI Gnomon prediction software. (ucsc.edu)
RefSeq Alignments - alignments of RefSeq RNAs to the zebrafish genome provided by the RefSeq group, following the display conventions for PSL tracks . (ucsc.edu)

Current technologies and methods are largely limited to coding regions of the genome. (frontiersin.org)

Only two ORFs, ICP4 and the US2 differed in amino acid (a.a.) lengths among the newly sequenced genomes. (usda.gov)
2013) SIFT Indel: Predictions for the Functional Effects of Amino Acid Insertions/Deletions in Proteins. (lu.se)

Meanwhile, the PCR amplification profile of molecular markers for the classification of radish mitochondrial genome types revealed that the new MS radish contained a novel mitotype. (springer.com)
Abdelnoor RV, Yule R, Elo A, Christensen AC, Meyer-Gauen G, Mackenzie SA (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. (springer.com)
Albert B, Godelle B, Gouyon PH (1998) Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences. (springer.com)
Bellaoui M, Martin-Canadell A, Pelletier G, Budar F (1998) Low-copy-number molecules are produced by recombination, actively maintained and can be amplified in the mitochondrial genome of Brassicaceae: relationship to reversion of the male sterile phenotype in some cybrids. (springer.com)
The mitochondrial genome is a 16569 base-pair closed circular loop of double-stranded DNA found in multiple copies within the mitochondrial matrix. (medscape.com)
The mitochondrial genome encodes the genetic information for the 13 polypeptide subunits essential for the process of oxidative phosphorylation. (medscape.com)
[ 2 ] The mitochondrial genome is remarkably concise, containing little noncoding capacity and no introns. (medscape.com)
[ 5 ] The deletions vary in size and location on the mitochondrial genome in different individuals, although a common deletion of 4.9kB is present in at least a third of patients with Kearns-Sayre syndrome. (medscape.com)

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. (nature.com)
As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. (nature.com)
KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations. (nature.com)
The completion of the human genome marked the beginning of our concerted efforts to understand and catalogue genetic variation across human populations. (nature.com)
These efforts laid the groundwork for approximately 1,800 genome-wide association (GWA) studies that investigated the genetic basis of complex diseases such as diabetes, cancer, and heart disease 6 . (nature.com)
Here, we present a suite of tools for genetic manipulation in the tomato pathogen C. michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. (biorxiv.org)
The vector pSelAct-KO is a recombination based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. (biorxiv.org)
In the latest study, researchers sequenced, or spelled out, the entire genetic code of HIV proviruses that reactivated and those that could not be induced to do so. (hopkinsmedicine.org)
We have employed whole genome sequencing, RNA sequencing, and functional assays in a large cohort of primary patient samples to understand the genetic basis of CTCLs. (hhs.gov)
The software is designed to analyze whole-genome sequence data from samples of cell-free DNA (cfDNA) extracted from maternal blood plasma, one of the newer and less invasive forms of prenatal genetic testing that are becoming more commonly used to screen fetuses for heritable genetic diseases and identify abnormalities. (genomeweb.com)
Deletions, an important type of SVs, have been suggested in association with genetic diseases. (omictools.com)
building blocks (nucleotides) in an individual's genetic code, a process called DNA sequencing. (medlineplus.gov)
Next-generation sequencing technologies have dramatically changed the approach to genetic diagnosis. (msdmanuals.com)
This revolutionary and rapidly evolving technology has moved a significant portion of the technical aspects of genetic diagnosis to next-generation sequencing and has become the mainstay of genetic diagnosis. (msdmanuals.com)
To address these issues, the Centers for Disease Control and Prevention's Genetic Testing Reference Material Program ( GeT-RM ) has partnered with the Clinical Genome Resource ( ClinGen ) to develop a publicly available list of expert curated variants. (cdc.gov)

Recent advances in sequencing technology have produced sequence data covering the repetitive regions in the gaps and the first complete sequence of a human chromosome (X) was published in 2019 [ First complete sequence of a human chromosome ]. (blogspot.com)

To ease future molecular studies, this study compares first- (partial sequencing via Sanger), second- (Illumina), and third-generation (MinION Nanopore) sequencing platforms for USUV. (frontiersin.org)
The method used most frequently by laboratories (7) was targeted DNA sequencing (58%), including pyrosequencing and Sanger sequencing. (cdc.gov)
For the current study, the researchers used a combination of Roche 454, Illumina, and Sanger approaches to sequence the bladderwort's 82 million base genome. (genomeweb.com)

The deletion was classified as pathogenic based on guidelines for interpretation of sequence variants.ConclusionThis first successful application of genome LRS to identify a pathogenic variant in a patient suggests that LRS has significant potential for the identification of disease-causing structural variation. (nih.gov)
Hum Genome Variation" 2022, v.9:23. (chromodisorder.org)
In addition, we accurately identified small-scale (2-40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. (columbia.edu)

PurposeCurrent clinical genomics assays primarily utilize short-read sequencing (SRS), but SRS has limited ability to evaluate repetitive regions and structural variants. (nih.gov)
Filtering for variants that are absent in an unrelated control and overlap a disease gene coding exon identified three deletions and three insertions. (nih.gov)
Accuracy is improved by accounting for DNA variants while aligning sequence data. (usda.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)

As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. (frontiersin.org)
First, this article summarizes the history of massively parallel next-generation sequencing (NGS) in the context of cancer genomics and reviews recent research and clinical applications. (frontiersin.org)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
are applicable to biobanks associated with genome, and the development of genomics population-based studies coordinated by databases and new bioinformatics tools. (who.int)

Interestingly, none of the 16 animals genotyped for the deletion carried the mutation, which suggests a rather recent origin for the mutation. (biomedcentral.com)
In conclusion, we successfully identified the causative mutation for a very rare autosomal recessive mutation with only one case by exploiting the most recent DNA sequencing technologies. (biomedcentral.com)
[ 19 ] The apparent lack of a second-hit mutation in the genome of FLCs supports the role of DNAJB1-PRACA fusion protein as a major driver of this tumor and as a key diagnostic and therapeutic target. (medscape.com)
GPC3 mutation/deletion and Simpson-Golbai-Behmel syndrome (SGBS). (chromodisorder.org)
Given the possibility of an unknown recessive or de novo dominant mutation, whole-genome sequencing was conducted on the trio of individuals. (unl.edu)

Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. (asm.org)
Pioneering work in the late 1990s through early 2010s resulted in vectors for gene deletion and expression in Clavibacter , but there is still reliance on these tools despite known limitations. (biorxiv.org)
introduces a novel de-novo case featuring a 240 kb gene deletion, which includes a part of GPC3 and manifests endocrinological complications of precocious puberty and advanced bone aging not seen in previous SGBS patients. (chromodisorder.org)

This track is only available on the human genomes hg19 and hg38. (ucsc.edu)

This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. (frontiersin.org)
The complete genome of an individual by massively parallel DNA sequencing. (columbia.edu)
Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. (columbia.edu)

These methods - which use low-coverage WGS of cfDNA and a lot of samples - first map reads to the genome, divide the genome into bins, and identify the CNVs by comparing the number of reads mapped to each bin, according the paper. (genomeweb.com)
Furthermore, the other open source [programs] are better at identifying larger CNVs that are around 10 megabases, for example, he said, but are not as effective at calling smaller deletions involved in conditions such as DiGeorge syndrome, which are on the order of one to five megabases long. (genomeweb.com)

We concluded that depending on the focus of a research project, amplicon-based MinION Nanopore sequencing can be an ideal cost- and time-effective alternative to Illumina in producing optimal genome coverage. (frontiersin.org)

Kearns Sayre Syndrome (OMIM #530000) occurs as a result of large-scale single deletions (or rearrangements) of mitochondrial DNA (mtDNA), which are usually not inherited but occur spontaneously, probably at the germ-cell level or very early in embryonic development. (medscape.com)

One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon of PRKAR1A, which is implicated in autosomal dominant Carney complex. (nih.gov)

In this study, using over 200 whole-genome sequences that the Bird 10,000 Genomes Project produced over the past decade, the researchers investigated the length of orthologous microsatellites, transposable elements, and DNA deletions. (eurekalert.org)

Whole-genome sequencing data from 3 cases and 2 controls identified a 16 kb deletion within the ECA13 associated haplotype (ECA13:g.178714_195130del). (uu.nl)
1 Mb) were identified after analysing the whole-genome sequencing (WGS) data from the only case available for DNA sampling at the beginning of the study. (biomedcentral.com)
CDC contributes gene sequences to public databases, such as GenBank and the Global Initiative on Sharing Avian Influenza Data (GISAID) , for use by researchers and public health scientists. (cdc.gov)
Analysis of the sequencing data revealed numerous discrepancies with the published sequence of a composite genome. (usda.gov)
A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
We then examined the sequencing data to characterize the HPV copy number and HPV physical status to determine what effect they have on both HPV and human genome structural changes. (biomedcentral.com)
It is expected to improve confidence in and clarify scientific communication, data reporting, and data interpretation in the genome editing field. (nist.gov)
Advances of next generation sequencing technologies and availability of short read data enable the detection of structural variations (SVs). (omictools.com)
Furthermore, finding deletions from sequencing data remains challenging. (omictools.com)

The new report is from the first sub-study from the CCGA, in which three prototype sequencing assays were performed on blood samples from approximately 1,700 participants. (dana-farber.org)
Two (17%) laboratories reported use of the Cepheid Xpert MTB/RIF assay, two (17%) reported results for line probe assays, Genotype MTBDR plus and MTBDR sl by Bruker, and one (8%) reported results from whole genome sequencing. (cdc.gov)
This is recapitulated in our functional assays with primary patient samples where CTCLs with PD1 deletion displayed increased proliferation ex vivo. (hhs.gov)

This deletion was associated with distichiasis, as 18 of the 19 cases were homozygous (p = 4.8 × 10− 13). (uu.nl)

Whole-genome sequencing revealed that the fusion resulted from a ∼400-kilobase (kb) deletion on chromosome 19 (chr19). (medscape.com)
The genome of T. maritima consists of a single circular 1.8 megabase chromosome encoding for 1877 proteins. (eol.org)
First, a full-length functional ZIKV cDNA clone was engineered as a bacterial artificial chromosome, with each reporter gene under the cap-independent translational control of a cardiovirus-derived internal ribosome entry site inserted downstream of the single open reading frame of the viral genome. (mdpi.com)
The identification of chromosome 1 translocations and deletions is a rare and poorly investigated event in chronic lymphocytic leukemia (CLL). (cancerindex.org)
The best average estimate was 3,286 Gb based on the sequence of 22 autosomes, one X chromosome, and one Y chromosome (Morton 1991). (blogspot.com)
For example, Williams syndrome is caused by a deletion of a section of chromosome 7 . (medlineplus.gov)

Proteins are made of sequences of amino acids. (cdc.gov)
Together with other patterns in the genome, those events suggest that the organism is especially apt to toss out sequences that don't directly code for proteins, study authors said. (genomeweb.com)
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). (lu.se)

Independent of HPV copy number, most tumors had either a small or a very large deletion in the viral genome. (biomedcentral.com)

WGS determined the HPV copy number across the viral genome. (biomedcentral.com)
Another was the non-integrating Sendai virus, which uses as viral delivery but the Sendai virus isn't capable of integrating into the genome, so it's a transient expression of the transcription factors (involved in reprogramming). (embs.org)

WGS revealed that ~ 70% of these tumors had HPV integrations within the human genome and HPV integration occurred independent of HPV copy number. (biomedcentral.com)

The findings, from one of the first studies to explore whether sequencing blood-borne DNA is a feasible approach to the early cancer detection, will be featured in a press briefing today and presented at the 2018 American Society of Clinical Oncology (ASCO) Annual Meeting. (dana-farber.org)
The last two types are very common in the human genome, but they pose difficulty for the detection. (omictools.com)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)
CoV-2 genome and can be targeted as a region for detection of VOC/VOI. (who.int)

Genome Insider: Methane Makers in Yosemite's Lakes Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work. (doe.gov)
But with two projects, communities are forming to generate high quality genomes to benefit researchers. (doe.gov)

The Toronto method requires whole-genome sequences from the mother and the father in addition to the fetal genome sequence extracted from the cfDNA. (genomeweb.com)

Ch 12 Human Genetics - Ch 12 Human Genetics By Miss Dreher 12.1 The nucleus contains an information rich genome Genome: an organism s complete set of DNA. (powershow.com)

Genotyping the deletion in 955 horses from 54 different breeds identified the deletion in only 11 non-Friesians, all of which were carriers, suggesting that this could be causal for this Friesian disorder. (uu.nl)

Genome Insider: A Shrubbier Version of Rubber Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant. (doe.gov)
International Cancer Genome Consortium. (cancerindex.org)
International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. (blogspot.com)

However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. (columbia.edu)
This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. (columbia.edu)
Overall, these results agree well with recent results of sequencing of a single individual by traditional methods. (columbia.edu)

Genome sequencing is a process that determines the order, or sequence, of the nucleotides (i.e. (cdc.gov)

Conclusions: This study identified a 16 kb deletion on ECA13 in an intergenic region that was associated with distichiasis in Friesian horses. (uu.nl)

The first cancer exomes were sequenced soon after the completion of the Human Genome Project in 2001. (frontiersin.org)
Human Genome and Human Genome Project - Human Genome Project: Background. (powershow.com)
We discovered that these deletions were the result of either HPV integration into the human genome or HPV-HPV sequence junctions. (biomedcentral.com)
According to the model it is believed that the integration of HPV into the human genome is an important step in carcinogenesis as a frequent site of disruption is the HPV E2 gene which is a transcriptional repressor of the HPV-specific oncogenes: E6 and E7. (biomedcentral.com)
An examination of a large number of HPV16 and HPV18-positive cervical cancers has revealed that while most HPV18-positive cervical cancers have HPV integrated somewhere within the human genome, this only occurs in about 75% of HPV16-positive cervical cancers [ 8 ]. (biomedcentral.com)
The integration event is also associated with differential amplification of HPV18 sequences, and the nearby human sequences, and the entire size of the region of disruption caused by that integration is over 300 kb [ 10 ]. (biomedcentral.com)
The resulting sequences can differ from the genome, they exist independently from a particular human genome build, and so must be aligned to the genome to create a track. (ucsc.edu)
Sandwalk: The 20th anniversary of the human genome sequence: 2. (blogspot.com)
It's been 20 years since the first drafts of the human genome sequence were published. (blogspot.com)
These first drafts from the International Human Genome Project (IHGP) and Celera were far from complete. (blogspot.com)
We've known for many decades that the correct size of the human genome is close to 3,200,000 kb or 3.2 Gb. (blogspot.com)
It's now possible to complete the human genome reference sequence by sequencing at least one individual but I'm not sure that the effort and the expense are worth it. (blogspot.com)
Morton, N.E. (1991) Parameters of the human genome. (blogspot.com)
That's what led me by the nose to genetics-because if you're going to focus on something, the best lens to use initially is human genetics, and from human genetics to IPSC and the genome editing tools that we use today in the lab. (medscape.com)

Second, we highlight the importance and potential of complete or 100% genome sequencing, i.e., the ability to sequence highly repetitive non-coding sequences beyond the reach of current NGS technologies. (frontiersin.org)
As I understand it the 5% that is remaining as unsequenced gaps are difficult to sequence primarily because they're highly repetitive in nature, is that correct? (blogspot.com)
Highly repetitive regions are unstable in plasmid/cosmids/BACs so their length and sequences couldn't be accurately determined. (blogspot.com)
In addition, it's difficult to sequence highly repetitive DNA because of stuttering and stammering during the DNA polymerase reaction. (blogspot.com)

How can a heterogeneous group of mitochondrial deletions lead to a similar phenotype? (medscape.com)
Neither size nor location of the deletion alone determines clinical phenotype. (medscape.com)

CDC and other public health laboratories around the world have been sequencing the gene segments of influenza viruses since the 1980s. (cdc.gov)

Anatomy9

Organisms24

Diseases4

Chemicals and Drugs29

Analytical, Diagnostic and Therapeutic Techniques and Equipment27

Phenomena and Processes115

Disciplines and Occupations5

Technology, Industry, Agriculture2

Information Science12

Health Care3

Geographicals1

Genes29

Insertions and deletions12

Reference genome6

Mutations11

Genomic9

Exome8

Nucleotide6

1,0002

Analyses3

Reveals2

GWAS2

Isolates3

Duplications2

Substitutions2

Alignments4

Regions of the genome1

Amino acid2

Mitochondrial genome8

Genetic15

20191

Sanger3

Variation3

Variants5

Genomics4

Mutation5

Gene deletion3

Hg191

Massively parallel3

CNVs2

Illumina1

MtDNA1

Heterozygous1

10,0001

Data9

Assays3

Homozygous1

Chromosome6

Proteins3

Large deletion1

Viral2

Tumors1

Detection4

Researchers2

Fetal1

Organism1

Causal1

Consortium3

Methods3

Nucleotides1

Intergenic1

Human14

Highly repetitive4

Phenotype2

1980s1