Copy number variants (CNVs) represent a significant source of genomic structural variation. Their length ranges from 100 bp to several Megabases (up to 5 Mb) and they comprise insertions, deletions, and duplications [1-5]. CNVs were initially thought to be only associated to diseases, but genome-wide screenings have clarified that they are ubiquitous and widespread in many animal genomes [6-11].. Recent studies have shown that genomic structural variations (including CNVs) are common among normal and healthy individuals [12-14]. They account for more differences between individuals, in terms of total bases involved, and have a higher per-locus mutation rate than SNPs [15]. Understanding their distribution in the population at large is crucial in order to clarify their role in determining the phenotype and/or disease state [16]. In humans, several studies have attempted to characterize CNVs in populations using data from the International Human HapMap Consortium [1, 9, 13, 17, 18], and other ...
The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 new insertion sequences corresponding to 720 genomic loci. We found that a substantial fraction of these sequences are either missing, fragmented or misassigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determined that 18-37% of these new insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identified new exons and conserved noncoding sequences not yet represented in the reference genome. We developed a method to accurately genotype these new insertions by mapping next-generation sequencing datasets to the breakpoint, thereby providing a means to characterize copy-number status for regions ...
Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We developed a method we call Sector-Ploidy-Profiling to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization. Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that ...
The goal of this CSP is deep-sequencing of highly diverse sorghum lines to assemble and analyze the pan-genome of this important bioenergy crop. Sorghum is a promising lignocellulosic and saccharine bioenergy crop, one of the DOE-JGIs flagship species, and an important food and feed crop. In order to accelerate breeding and development of elite sorghum lines as well as determine the genetic basis of its valuable traits, such as remarkable drought and heat tolerance, we must develop a more complete understanding of the genetic diversity within sorghum as a species. To accomplish this goal, the sorghum pan-genome project will (1) select a diverse collection of sorghum lines designed to capture the majority of genomic structural variation within the species; (2) conduct whole genome sequencing and transcriptome profiling using the PacBio and Illumina platforms; and (3) de novo assemble, annotate and characterize the sequenced genomes. The de novo assembled and resequenced sorghum genomes obtained ...
Besides detecting cancer related SNV through genotyping, we also plan to identify other type of variations called fusion genes, caused by genomic structural variations, such as insertion, deletion, transversion, translocation. We use RNA-seq, an application of NGS technology on RNA, to detect the products of fusion gene -fusion transcripts. It is a very challenge work because the output from NGS, called read, is short (~30-100 bp), and may also contain splicing site. We are developing sophisticated algorithms to map those short reads and to detect the fusion events ...
Medical Research Institute of New Zealand, Wellington, New Zealand. Hespan, Voluven is controversial. Potura E, Lindner G, Biesenbach P, et al. This study also found that although 0. The main disadvantage of using a crystalloid fluid is that excessive use will cause peripheral and pulmonary oedema Bradley, We searched the Cochrane Injuries Group Specialised Register 17 October , the Cochrane Central Register of Controlled Trials The Cochrane Library Issue 10, , MEDLINE Ovid to October , EMBASE Ovid to October , ISI Web of Science: Two review authors independently extracted data and rated quality of allocation concealment. Most Popular Poor working conditions drives huge increase in number of nurses leaving NMC register. Variation Database of Genomic Structural Variation dbVar Database of Genotypes and Phenotypes dbGaP Database of Single Nucleotide Polymorphisms dbSNP SNP Submission Tool All Variation Resources Thus, from the channel-like vasopressin but as crystalloid particles draw water more ...
Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0. The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz. Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz. The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels ,50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz. The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths.. The pre-print manuscript for this data is available on biorxiv: "Whole genome resequencing of a laboratory-adapted Drosophila ...
Istituto di Informatica e Telematica (IIT) del CNR svolge attività di ricerca, valorizzazione, trasferimento tecnologico e formazione nel settore delle tecnologie dellinformazione e della comunicazione e delle scienze computazionali.
A genetic contribution to a broad range of epilepsies has been postulated, and particularly copy number variations (CNVs) have emerged as significant genetic risk factors. However, the role of CNVs in patients with epilepsies with complex phenotypes is not known. Therefore, we investigated the role of CNVs in patients with unclassified epilepsies and complex phenotypes. A total of 222 patients from three European countries, including patients with structural lesions on magnetic resonance imaging (MRI), dysmorphic features, and multiple congenital anomalies, were clinically evaluated and screened for CNVs. MRI findings including acquired or developmental lesions and patient characteristics were subdivided and analyzed in subgroups. MRI data were available for 88.3% of patients, of whom 41.6% had abnormal MRI findings. Eighty-eight rare CNVs were discovered in 71 out of 222 patients (31.9%). Segregation of all identified variants could be assessed in 42 patients, 11 of which were de novo. The ...
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV
Background Using the development of space research its important to analyze the partnership between your space environment and genome variations that may cause phenotypic shifts in microbes. stress. Evaluation of genomic structural variants uncovered one inversion 25 deletions fifty-nine insertions two translocations and six translocations with inversions. Furthermore 155 and 400 exclusive genes had been seen in LCT-KP214 and LCT-KP289 respectively like the gene encoding dihydroxyacetone kinase which creates the ATP and NADH necessary for microbial development. Furthermore a lot of mutant genes were linked to fat burning capacity and transport. Phylogenetic analysis uncovered that a lot of genes in both of these strains got a dN/dS worth higher than 1 indicating that any risk of strain variety elevated after spaceflight. Evaluation of drug-resistance phenotypes uncovered that any risk of strain LCT-KP289 was resistant to sulfamethoxazole whereas the control stress LCT-KP214 had not been; both ...
Idiopathic generalized epilepsies account for 30% of all epilepsies. Despite a predominant genetic aetiology, the genetic factors predisposing to idiopathic generalized epilepsies remain elusive. Studies of structural genomic variations have revealed a significant excess of recurrent microdeletions at 1q21.1, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 in various neuropsychiatric disorders including autism, intellectual disability and schizophrenia. Microdeletions at 15q13.3 have recently been shown to constitute a strong genetic risk factor for common idiopathic generalized epilepsy syndromes, implicating that other recurrent microdeletions may also be involved in epileptogenesis. This study aimed to investigate the impact of five microdeletions at the genomic hotspot regions 1q21.1, 15q11.2, 16p11.2, 16p13.11 and 22q11.2 on the genetic risk to common idiopathic generalized epilepsy syndromes. The candidate microdeletions were assessed by high-density single nucleotide polymorphism arrays ...
Cancer cells are intrinsically heterogeneous. Multiple clones with their unique variants co-exist in tumor tissues. The variants include point mutations and structural variations. Point mutations, or single nucleotide variants are those variants on one base; structural variations are variations involving sequence with length not smaller than 50 bases. Approaches to estimate the number of clones and their respective percentages from point mutations have been recently proposed. However, structural variations, although involving more reads than point mutations, have not been quantitatively studied in characterizing cancer heterogeneity. I describe in this thesis a maximum likelihood approach to estimate variant allele fraction of a putative structural variation, as a step towards the characterization of tumor heterogeneity. A software tool, BreakDown, implemented in Perl realizing this statistical model is publicly available. I studied the performance of BreakDown through both simulated and real ...
The common goal for structural genomic centers and consortiums is to decipher as quickly as possible the three-dimensional structures for a multitude of recombinant proteins derived from known genomic sequences. Since X-ray crystallography is the foremost method to acquire atomic resolution for macromolecules, the limiting step is obtaining protein crystals that can be useful of structure determination. High-throughput methods have been developed in recent years to clone, express, purify, crystallize and determine the three-dimensional structure of a protein gene product rapidly using automated devices, commercialized kits and consolidated protocols. However, the average number of protein structures obtained for most structural genomic groups has been very low compared to the total number of proteins purified. As more entire genomic sequences are obtained for different organisms from the three kingdoms of life, only the proteins that can be crystallized and whose structures can be obtained ...
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints ...
KromaTiD, Inc. announced today that it has joined the National Institutes of Standards and Technology Genome Editing Consortium, a newly launched public/private partnership (https://www.nist.gov/programs-projects/nist-genome-editing-consortium). The Consortium supports the emerging gene editing market and regulatory agency needs for standardized measurements of gene edits, editing by-products and the risks of utilizing genome editing technologies in research, commercial and therapeutic products.. KromaTiDs dGH™ is a commercial structural genomic platform uniquely capable of de novo detection of random, low frequency and complex structural variations in batches of gene edited cells. By directly reading the genomic structure of individual edited cells, dGH provides definitive, quantitative data for on- and off-target structural variation. By combining dGH with a technique such as Guide-seq (http://vedtopkar.com/pdf/guide-seq.pdf), it is now possible to measure the entire range of editing ...
I raised a number of areas where long reads, or paired reads, really pay off, but most were brushed aside. De novo genome sequencing is interesting, but not where they see a large market. This isnt an instrument designed for amplicon sequencing. Three that are harder to bat down are alternative splicing discovery in RNA-Seq (a target) and fusion transcript discovery (again, RNA-Seq) and structural variant discovery in genomic sequencing. Id tack onto that one more Ive thought up since our meeting, discovering deletions which are larger than a few base, such as the 15 base deletions in EGFR that show up in lung cancer. Its not that you cant detect any of these with short reads, but algorithmically they are quite challenging when there is so little to go on ...
Author: Sudmant, Peter H. et al.; Genre: Journal Article; Published in Print: 2015-10-01; Open Access; Keywords: Genomics, Structural variation|br/||br/|; Title: An integrated map of structural variation in 2,504 human genomes
What codes would be used for the Ifuse implant system when doing a sacroiliac fusion???? I have looked at the reimbusement guidelines from the SI-Bone
SAN JOSE, Calif., Aug. 24, 2016 /PRNewswire/ -- SI-BONE, Inc. Announces Two-Year Results from a Randomized Controlled Trial of the iFuse Implant System®...
Fragment screening is an efficient way of establishing initial points for drug discovery. However, seemingly simple small molecules dont necessarily mean that their chemistry is not complex. Quite the contrary, fragment hits may be challenging to follow up. Synthesis routes can be long and rigid not allowing making small specific changes while growing, linking or merging the hit.. It was shown by Cox et al., in Chem. Sci. 2016 that the compounds synthesised from a robust and general synthetic reaction can be prioritized for building fragment library. Identification of so-called "poised" bonds in a fragment means that a library of analogues can be rapidly elaborated using standard parallel chemistry. First poised library was developed at Diamond Light Source, UK (Diamond) and Structural Genomic Consortium, UK (SGC) in the frame of one of the iNEXT Joint Research Activities. Enamine collaborated with the joint research alliance in design of a next generation of DSI-poised Library. DSI stands for ...
BACKGROUND: Structural variation (SV) plays a pivotal role in genetic disease. The discovery of SVs based on short DNA sequence reads from next-generation DNA sequence methods is error-prone, with low sensitivity and high false discovery rates. These shortcomings can be partially overcome with extensive orthogonal validation methods or use of long reads, but the current cost precludes their application for routine clinical diagnostics. In contrast, SV genotyping of known sites of SV occurrence is relatively robust and therefore offers a cost-effective clinical diagnostic tool with potentially few false-positive and false-negative results, even when applied to short-read DNA sequence data.. RESULTS: We assess 5 state-of-the-art SV genotyping software methods, applied to short-read sequence data. The methods are characterized on the basis of their ability to genotype different SV types, spanning different size ranges. Furthermore, we analyze their ability to parse different VCF file subformats and ...
TY - JOUR. T1 - Multi-platform discovery of haplotype-resolved structural variation in human genomes. AU - Chaisson, Mark J.P.. AU - Sanders, Ashley D.. AU - Zhao, Xuefang. AU - Malhotra, Ankit. AU - Porubsky, David. AU - Rausch, Tobias. AU - Gardner, Eugene J.. AU - Rodriguez, Oscar L.. AU - Guo, Li. AU - Collins, Ryan L.. AU - Fan, Xian. AU - Wen, Jia. AU - Handsaker, Robert E.. AU - Fairley, Susan. AU - Kronenberg, Zev N.. AU - Kong, Xiangmeng. AU - Hormozdiari, Fereydoun. AU - Lee, Dillon. AU - Wenger, Aaron M.. AU - Hastie, Alex R.. AU - Antaki, Danny. AU - Anantharaman, Thomas. AU - Audano, Peter A.. AU - Brand, Harrison. AU - Cantsilieris, Stuart. AU - Cao, Han. AU - Cerveira, Eliza. AU - Chen, Chong. AU - Chen, Xintong. AU - Chin, Chen Shan. AU - Chong, Zechen. AU - Chuang, Nelson T.. AU - Lambert, Christine C.. AU - Church, Deanna M.. AU - Clarke, Laura. AU - Farrell, Andrew. AU - Flores, Joey. AU - Galeev, Timur. AU - Gorkin, David U.. AU - Gujral, Madhusudan. AU - Guryev, ...
NextGenMap-LR is a long-read mapper desigend to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was desigend to correctly align reads stemming from (complex) structural variations. NextGenMap-LR uses an SV aware k-mer search to find approximate mapping locations for a read and a banded Smith-Waterman alignment algorithm with a non-affine gap model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows NextGenMap-LR to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from (complex) structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling NextGenMap-LR to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions). Currently NextGenMap-LR ...
Part A The effects of the structural variation and the relative stability by the hydration of Alanine dipeptide in $C_7^eq$, $C_7^ax$, $C_5$, $α_R$, and $P_Ⅱ$ conformations were investigated by the method of SUMSL(Secant-type Unconstrained Minimization Solver) energy minimization technique with the empirical potential energy function of the solute, and ST2 water model. The binding sites of water molecules in the solute were selected from spherical interaction energy maps. As a function of the number of added water molecules, we traced the structural variations mainly in the (φ, ψ) torsion angle space, and calculated the total internal energies of each solute-water systems to evaluate the relative probabilities between those five conformers. The results indicate that the conformers having no intramolecular hydrogen-bondings, such as $α_R$, $C_5$, and $P_Ⅱ$, show larger structural variations than the conformers of $C_7^ax$, and $C_7^eq$ that have intramolecular hydrogen-bondings. The ...
Fairwell Athabasca 01 B.T.B - Our Tears (Silence From The Sol mix) 02 ALXSIX - Stellar Movements 03 Martin Non Static - Inside 04 Axoplasma - Stratocumulus 05 S0N0 - Sphingidae 06 Shammen Delly - Orange Haze 07 The Association - Machine1 08 Nikea Bustla - Androids Cradlesong 09 Baby Arm Sound System - Fat…
We have used massively parallel paired end sequencing strategies to reconstruct the genomic landscape of 24 breast cancer genomes, through the identification and characterization of 2166 somatically acquired genomic rearrangements. These studies have revealed considerable complexity in the patterns of structural variation, identified novel fusion genes and unveiled new insights into the complex structure of amplicons. ...
A nationwide consortium has completed the first sequence-based map of structural variations in the human genome, giving scientists an overall picture of the large-scale differences in DNA between individuals. The... ...
The AUAs Clinical Practice Guidelines provide evidence-based guidance with an explicit clinical scope and purpose. AUA also provides Policy Statements, Best Practice Statements, Position Statements and White Papers to provide urology professionals with the best in peer-reviewed treatment recommendations and research.
Flax (Linum usitatissimum L.) is a major fiber and oil yielding crop grown in northeastern China. Identification of flax molecular markers is a key step toward improving flax yield and quality via marker-assisted breeding. Simple sequence repeat (SSR) markers, which are based on genomic structural variation, are considered the most valuable type of genetic marker for this purpose. In this study, we screened 1,574 microsatellites from Linum usitatissimum L. obtained using reduced representation genome sequencing (RRGS) to systematically identify SSR markers. The resulting set of microsatellites consisted mainly of trinucleotide (56.10%) and dinucleotide (35.23%) repeats, with each motif consisting of 5 to 8 repeats. We then evaluated marker sensitivity and specificity based on samples of 48 flax isolates obtained from northeastern China. Using the new SSR panel, the results demonstrated that fiber flax and oilseed flax varieties clustered into two well separated groups. The novel SSR markers developed in
In todays edition of The Heartland Daily Podcast, Research Fellow Isaac Orr talks with Dave Quast. Quast is the California Director of Energy In Depth. Quast and Orr discuss the a range of issues pertaining to Californias water supply.. It seems like everyone is talking about the drought in California. Environmental groups have been quick to blame hydraulic fracturing for Californias water woes. Last year, fracking used 70 million gallons of water, but this amount is miniscule when compared to the amount of water used for residential and agricultural purposes.. In this podcast, Quast and Orr talk about Californias water supply, including the impact of hydraulic fracturing, agriculture, diverting rivers for wildlife habitat restoration, and watering lawns in the desert have on the states water resources.. [Subscribe to the Heartland Daily Podcast for free at this link.]. ...
TY - JOUR. T1 - Loss of maternal ANNEXIN A10 via a 34-kb deleted-type copy number variation is associated with embryonic mortality in Japanese Black cattle. AU - Sasaki, Shinji. AU - Ibi, Takayuki. AU - Akiyama, Takayuki. AU - Fukushima, Moriyuki. AU - Sugimoto, Yoshikazu. PY - 2016/11/24. Y1 - 2016/11/24. N2 - Background: Conception is a fundamental trait for successful cattle reproduction. However, conception rates in Japanese Black cattle have been gradually declining over the last two decades. Although conception failures are mainly caused by embryonic mortality, the role of maternal genetic factors in the process remains unknown. Copy number variation (CNV), defined as large-scale genomic structural variants, contributes to several genetic disorders. To identify CNV associated with embryonic mortality in Japanese Black cattle, we evaluated embryonic mortality as a categorical trait with a threshold model and conducted a genome-wide CNV association study for embryonic mortality using 791 ...
Schizophrenia (SCZ) is a common, complex and severe psychiatric disorder associated with many different genetic and environmental risk factors. Evidence from genetic studies has revealed the role of genome structural variations, specifically copy number variants (CNVs), in the etiology of SCZ. Nevertheless, the occurrence of CNVs and their relation to SCZ has remained relatively unstudied in the diverse Han Chinese population. We used a case/control paradigm, including 476 cases and 1023 controls. All samples were genotyped using the Axiom® Exome Genotyping Arrays. Four CNVs, including two deletions and two duplications, were detected in this study. Notably, the 16p11.2 duplication from 29.3 Mb to 29.6 Mb was detected in four cases (0.84%) and one control (0.098%) (p = 0.0377). The results highlight the potential role of these deletions and duplications in the development of SCZ. Clearly, larger sample sized studies are needed for a careful localization of these CNVs and to possibly detect more
Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays. However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs ...
S E M I N A R: "Computational Methods for Detecting Structural Variants in the Next Generation Sequencing data and its applications" by Asst. Prof. Dr. Emre Karakoç, Medipol University. Despite the ease at which genome sequence data can be generated, most studies and standard computational pipelines to date, focus on the detection of single nucleotide variants and small insertions and deletions(indels). The main reason for this situation is that there are no robust methods for detecting larger indels and structural variations. Here I present novel computational methods for detecting these under estimated variants. In addition I developed computational system biology models using this more complete view of the variant landscape, to detect molecular pathways associated with complex diseases and to understand their etiology. Genomic variants especially structural variants, also contribute significantly to the adaptive evolution and introgression across closely related species. I applied ...
Evidence-based recommendations on iFuse titanium implant joint fusion system for treating chronic sacroiliac (SI) joint pain (lower back pain)
Copy numbers. When we discuss structural genomic variants in the human genome on the Channelopathist blog, we usually refer to regions where simple deletions or duplications exert a pathogenic effect. However, there are also genes that are highly copy number variable, sometimes present at 80 copies or more. Copy numbers of a few of these genes have expanded during human evolution recently, turning these genes into potential candidate genes for human disease. A recent paper in PLOS Genetics now examines the role of DUF1220, which encodes a protein domain of the NBPF genes. This domain shows an unusually broad range of copy number variation in the human genome. Interestingly, this gene resides right next to the 1q21.1 region that is implicated in various neurodevelopmental disorders.. Lineage and breakpoints. When gene expression in humans and chimpanzees was compared for the first time in 2005 and when the first chromosomes of the chimpanzee genome were first sequenced, I was a little ...
Abstract: Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple ...
... (JIB) is an international open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics. Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Currently, there are about 1,000 database systems and various analytical tools available via the Internet which are directed at solving various biological tasks. The challenge we have is to integrate these list-parts and relationships from genomics and proteomics at novel levels of understanding. Integrative Bioinformatics is a new area of research using the ...
1NI7: High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Mulvey, Robert and Andrews, P.C. and Clegg, W. and ONeil, P.A. (1992) Structural variations in alkali-metal amide chemistry and their influence on reactivity. [Review] Full text not available in this repository.Request a copy from the Strathclyde author ...
Genomic rearrangements or structural variants (SVs) are one of the most common classes of mutations in cancer. An integrated DNA sequencing and transcriptional profiling (RNA sequence and microarray gene expression data) analysis was performed on six ovarian cancer patient samples. Matched sets of control (whole blood) samples from these same patients were used to distinguish cancer SVs of germline origin from those arising somatically in the cancer cell lineage. We detected 10,034 ovarian cancer SVs (5518 germline derived; 4516 somatically derived) at base-pair level resolution. Only 11 % of these variants were shown to have the potential to form gene fusions and, of these, less than 20 % were detected at the transcriptional level. Collectively our results are consistent with the view that gene fusions and other SVs can be significant factors in the onset and progression of ovarian cancer. The results further indicate that it may not only be the occurrence of these variants in cancer but their
These bench-verified assays provide scientists guaranteed success when measuring structural variations in the genome. The structural variations may occur either in the germline (CNV) or be acquired somatically (CNA) and represent a major source of genetic diversity. Copy number variations and alterations can be either amplifications of genomic segments that increase the number of copies of genes or deletions that remove a copy of a gene from the genome. Now with access to the highest resolution copy number assay solution, researchers can refine and verify their genomewide copy number experiments and associate these findings with observed phenotypes ...
You need SRA Toolkit to operate on SRA runs. Default toolkit configuration enables it to find and retrieve SRA runs by accession. It also downloads (and cache) only the part of data you really need. For example quality scores represent a majority of data volume and you may not need them if you dump fasta only (versus fastq). Or if you are looking at particular gene you may not need reads aligned to other regions or not aligned at all. Same way if you use GATK with enabled SRA support you need only SRA run accessions to fire your process. fastq-dump will dump reads in a number of "standard" fastq and fasta formats. vdb-dump is also capable of producing fasta and fastq (beside other formats). It dumps data much faster then fastq-dump but ordering of reads may be different and it does not produce split-read multi-file output. Prefetch tool will help you cache all data in advance if you plan to run data analysis in environment where getting data from NCBI at run time is unfeasible. To select a list ...
This view is a gene level view. To access the transcript level displays select a Transcript ID in the table above and then navigate to the information you want using the menu at the left hand side of the page. To return to viewing gene level information click on the Gene tab in the menu bar at the top of the page. ...
A series of palladium(ii) complexes incorporating di-NHC-amine ligands has been prepared and their structural, dynamic and catalytic behaviour investigated. The complexes [trans-(κ2-tBuCN(Bn)CtBu)PdCl2] (12) and [trans-(κ2-MesCN(H)CMes)PdCl2] (13) do not exhibit interaction between the amine nitrogen and pal
Endo-β-N-Acetylglucosaminidases (ENGases) are highly useful biocatalysts that can be used to synthetically access a wide variety of defined homogenous N-linked glycoconjugates in a convergent manner. The synthetic efficiency of a selection of family GH85 ENGases was investigated as the structure of
Ionescu, D., Siebert, C., Polerecky, L., Munwes, Y.Y., Lott, C., Häusler, S., Bižić-Ionescu, M., Quast, C., Peplies, J., Glöckner, F.O., Ramette, A., Rödiger, T., Dittmar, T., Oren, A., Geyer, S., Stärk, H.-J., Sauter, M., Licha, T., Laronne, J.B., de Beer, D., (2012 ...
This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. The method does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity, polyploidy, etc. Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account. ...
This tool to detect structural variations is specifically designed to cluster short-read paired-end data into possibly overlapping predictions for deletions and insertions. The method does not make any assumptions on the composition of the data, such as the number of samples, heterogeneity, polyploidy, etc. Taking paired ends mapped to a reference genome as input, it iteratively merges mappings to clusters based on a similarity score that takes both the putative location and size of an indel into account. ...