Genomic Structural Variation

Color coding in data visualization

Flap structure-specific endonuclease 1

Structural variation

List of RNA-Seq bioinformatics tools

Li Ding

Structural variation in the human genome

Jumping library

Halibut

Jan O. Korbel

End-sequence profiling

Single-cell sequencing

Comparative genomic hybridization

Short Oligonucleotide Analysis Package

Single-cell DNA template strand sequencing

Hi-C (genomic analysis technique)

Variant Call Format

Matthew Hurles

Centre for Applied Genomics

Liverpool Women's NHS Foundation Trust

Somatic evolution in cancer

Schizophrenia

Ensembl Genomes

Copy number variation

CLC bio

Steven A. Benner

GeneCards

Medulloblastoma

Linked-read sequencing

Genetic variation

Reference genome

Catalog of human genomic variation1

• Offering a glimpse of the bright gleam of victory, the 1000 Genomes Project Consortium has announced that it has accomplished its goal, the creation of a comprehensive catalog of human genomic variation. (genengnews.com)

Impact of genomic structural variation2

• Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing. (nature.com)
• The impact of genomic structural variation on meiotic pairing and segregation in Beta vulgaris subsp. (google.co.uk)

Genome20

• Here we apply population -scale whole- genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities . (bvsalud.org)
• Lupski, J. R. Structural variation mutagenesis of the human genome: impact on disease and evolution. (nature.com)
• In the main Nature study, investigators identified about 88 million sites in the human genome that vary among people, establishing a database available to researchers as a standard reference for how the genomic make-up of people varies in populations and around the world. (genome.gov)
• One of the more immediate uses of 1000 Genomes Project data is for genome-wide association studies (GWAS), which compare the genomes of people with and without a disease to search for regions of the genome that contain genomic variants associated with that disease. (genome.gov)
• Entrez is NCBI's primary text search and retrieval system that integrates the PubMed database of biomedical literature with 38 other literature and molecular databases including DNA and protein sequence, structure, gene, genome, genetic variation and gene expression. (nih.gov)
• We performed genome-wide assessment for structural abnormalities in 427 unrelated ASD cases via single-nucleotide polymorphism microarrays and karyotyping. (nih.gov)
• In the other Nature article-"An integrated map of structural variation in 2,504 human genomes"-differences in the structure of the genome were examined. (genengnews.com)
• We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. (genengnews.com)
• Optical Genome Mapping is non-sequencing technology capable of analyzing large eukaryotic genomes and their structural features at a high resolution by evaluation of patterns generated by fluorophore tags labeled to specific sequence motifs within extremely long DNA molecules, of more than 300 kb (3, 4). (mdanderson.org)
• Bionano Optical Genome Mapping directly observes structural variations by linearizing and imaging DNA in its native state using massively parallel Nano-Channels. (mdanderson.org)
• A definition of copy number variation is included in the Talking Genome Glossary from the National Human Genome Research Institute. (medlineplus.gov)
• Dr. Charles Lee is a distinguished biomedical scientist who first discovered widespread structural variation in the human genome in 2004, also known as "Copy Number Variation. (jax.org)
• Researchers create reference human genome sequences to help detect genomic variants in each sequenced human genome. (genome.gov)
• The human pangenome is a more comprehensive framework that aims to account for genomic variation across human populations, thereby reducing biases that can come with the use of a single reference human genome sequence. (genome.gov)
• Most genomic variants have no influence on the functioning of a person's genome, but a small subset of variants do have an impact. (genome.gov)
• The platform enables direct observation of native genomic structure "through imaging of extremely long molecules," which enables the detection of structural variation "and significantly improves genome assemblies and phasing haplotypes. (genomeweb.com)
• Our results resolve the outstanding question of how hybrids in native genomic contexts interact with replication to cause mutagenesis and shape genome organization. (biorxiv.org)
• His team has pioneered novel approaches, including copy number variation (CNV) and structural variation (SV) discovery, as well as whole-genome sequencing, and the development of informatics tools, to delineate loci and genes involved in these conditions. (sfari.org)
• Genomic architecture of autism from comprehensive whole-genome sequence annotation. (sfari.org)
• MACDONALD J.R., ZIMAN R., YUEN R.K., FEUK L., SCHERER S.W. The database of genomic variants: a curated collection of structural variation in the human genome. (bvsalud.org)

Functional genomic data3

• Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. (biomedcentral.com)
• Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. (biomedcentral.com)
• The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes comprehensive sets of microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. (nih.gov)

Genetic Variation8

• https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. (nih.gov)
• Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. (nature.com)
• Structural Variation (SV) describes a broad class of genetic variation greater than 50bps in size. (medrxiv.org)
• In one of the Nature articles-"A global reference for human genetic variation"-the 1000 Genomes Project identified "over 88 million variants (84.7 million single nucleotide polymorphisms, 3.6 million short insertions/deletions, and 60,000 structural variants), all phased onto high-quality haplotypes. (genengnews.com)
• Our findings diverge from previous studies of common genetic variation that show genetic risk of schizophrenia is associated with risk of psychosis in bipolar disorder. (news-medical.net)
• These observations support the notion that different classes of genetic variation contribute to different domains of psychopathology, and suggest that the combination of genetic variants in a given individual create his or her unique symptom profile," said lead author Alexander Charney, MD, PhD, Icahn School of Medicine at Mount Sinai, New York. (news-medical.net)
• The Howard Hughes Medical Institute discusses the results of recent research on copy number variation in the news release, Genetic Variation: We're More Different Than We Thought . (medlineplus.gov)
• Between-individual genetic variation is the substrate for selection. (biomedcentral.com)

Rare genomic3

• When the 1000 Genomes Project was first launched in 2008, there wasn't much understanding of how rare genomic variants were distributed among populations around the world and their relationship to other variants," said Adam Auton, Ph.D., the main study senior author and principal investigator who until recently was assistant professor of genetics at the Albert Einstein College of Medicine in New York City. (genome.gov)
• When it first mustered an international team of scientists back in 2008, the project planned to build a reference dataset that would show how rare genomic variants were distributed among populations around the world-or at least within a microcosm of 1000 individuals. (genengnews.com)
• A form of rare genomic structural variation called copy number variants (CNVs) may be more closely associated with schizophrenia than bipolar disorder. (news-medical.net)

Contain genomic1

• NCBI hosts repositories that contain genomic data from humans as well as many other organisms. (nih.gov)

Transcriptomic4

• We begin with an introduction to bioinformatics and omics data analysis, and conclude with the walkthrough of a simple bioinformatics workflow for aligning transcriptomic sequences with genomic data. (r-bloggers.com)
• What are common file formats for transcriptomic and genomic data? (r-bloggers.com)
• Become familiar with how transcriptomic and genomic data is structured. (r-bloggers.com)
• IKB contains information for human immunome genes and proteins, phylogenetic trees and evolutionary information for immunome orthologs, ortholog groups for metazoan immunome, and variation data on genomic, transcriptomic and proteomic level. (lu.se)

Analyses5

• The assembly was characterized, including analyses of the genomic structure, with the aim of providing data to support the discovery of beneficial or harmful genes and to improve our understanding of the molecular pathogenesis. (researchsquare.com)
• Structural variants were found in sufficiently high frequency influencing ASD to suggest that cytogenetic and microarray analyses be considered in routine clinical workup. (nih.gov)
• Data analyses will be performed to e.g. develop prediction models to understand likely outcomes from multifactorial genetic, environmental and treatment data, or to understand trade-offs in fish breeding (trade-off between growth and sexual maturity), or to develop predictive models based on structural genomic variation (as done here: Ruigrok, Xue et al. (findaphd.com)
• Finally, we identified aberrant methylation in multiple genes also targeted by recurring DNA copy number alterations in ALL, suggesting that these genes are inactivated far more frequently than suggested by structural genomic analyses alone. (lu.se)
• This resource includes tools for clinical, biochemical, genetic, structural and computational analyses as well as links to related information maintained by others. (lu.se)

Deletions6

• These genomic differences, many of which affected genes, include deletions (loss of DNA), insertions (added DNA), and duplications (extra DNA copies). (genengnews.com)
• Most large genomes contain thousands of large structural variants (SVs), repetitive regions composed of identical or similar stretches of sequences, mobile elements such as transposons, large insertions, deletions, translocations, and inversions up to millions of bases, with even partial or entire chromosomes altered. (mdanderson.org)
• Some SVs, such as deletions and duplications, change the dosage of DNA and are considered copy number variations (CNVs). (mdanderson.org)
• Copy number variation results from insertions, deletions, and duplications of large segments of DNA that are at least one thousand nucleotides (also called 1 kilobase or 1kb) in length. (medlineplus.gov)
• Array comparative genomic hybridization in patient one and patient two revealed copy-number variant (CNV) deletions, respectively, ~ 1.45 Mb in size involving FOXF1 and an ~ 0.7 Mb in size involving FOXF1 enhancer and leaving FOXF1 intact. (researchgate.net)
• dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. (nih.gov)

Phenotypic2

• Genomic structural variation is an important and abundant source of genetic and phenotypic variation. (usda.gov)
• NIH hosts many genomic and phenotypic data repositories. (nih.gov)

Genomics3

• The latest data and insights add to a growing understanding of the patterns of variation in individuals' genomes, and provide a foundation for gaining greater insights into the genomics of human disease. (genome.gov)
• 10X Genomics has started shipping the GemCode platform for generating long range genomic information from short read sequencing data. (genomeweb.com)
• Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants. (genomeweb.com)

Humans3

• An international team of scientists from the 1000 Genomes Project Consortium has created the world's largest catalog of genomic differences among humans, providing researchers with powerful clues to help them establish why some people are susceptible to various diseases. (genome.gov)
• The study showed that the greatest genomic diversity is in African populations, consistent with evidence that humans originated in Africa and that migrations from Africa established other populations around the world. (genome.gov)
• The 1000 Genomes Project Consortium has created the world's largest catalog of genomic differences among humans. (genengnews.com)

Genomes5

• An integrated map of structural variation in 2,504 human genomes. (nature.com)
• The 1000 Genomes Project was an ambitious, historically significant effort that has produced a valuable resource about human genomic variation," said Eric Green, M.D., Ph.D., director of NHGRI. (genome.gov)
• The 1000 Genomes Project data are a resource for any study in which scientists are looking for genomic contributions to disease, including the study of both common and rare variants. (genome.gov)
• Structural variation is responsible for a large percentage of differences in the DNA among human genomes," said Jan Korbel, Ph.D., an investigator at the European Molecular Biology Laboratory and senior author of the structural variation article. (genengnews.com)
• The differences among human genomes are called genomic variants. (genome.gov)

Single-nucleotide1

• The smallest genomic variants are single-nucleotide variants (SNVs). (genome.gov)

CNVs2

• We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes. (usda.gov)
• The findings that CNVs are not associated with bipolar disorder as a whole, but rather a subtype of the disorder, provide insight into how symptom variation arises within the disease and highlights that considering these different subgroups as a single diagnosis might overlook important differences that define them. (news-medical.net)

Datasets1

• 2019). Methods to analyse these large and complex genomic datasets include statistical and machine learning, and a host of new algorithms that can reveal structure in data, perform classifications, reveal causal patterns and make predictions. (findaphd.com)

Variants were found1

• Nearly 69,000 structural variants were found. (genengnews.com)

Genes7

• A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. (researchsquare.com)
• Genomic comparison with human and mouse revealed a triplication of a key enzyme involved in testosterone synthesis and we discovered a small group of genes involved in early development of kidney specifically expressed in the female testis. (mpg.de)
• Analysing this set [of eight structural variant classes], 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," the article indicated. (genengnews.com)
• Structural Variants (SVs) caused by the reorganization of the DNA may connect two distal fragments together leading to gene fusions and chimeric proteins when two distant genes are joined into one. (mdanderson.org)
• Variation in gene copy number can influence the activity of genes and the functioning of proteins made from them, which may affect body processes. (medlineplus.gov)
• Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. (biomedcentral.com)
• The rationale behind these prediction methods is that essential genes, with minimal inter-individual variation, are subject to purifying selection in order to maintain their sequence in the population, as alterations would lead to reduced fitness. (biomedcentral.com)

Copy number va3

• Structural variation (copy number variation [CNV] including deletion and duplication, translocation, inversion) of chromosomes has been identified in some individuals with autism spectrum disorder (ASD), but the full etiologic role is unknown. (nih.gov)
• Copy number variation accounts for a significant amount of genetic difference between people. (medlineplus.gov)
• More information about copy number variation is available in a video from Cold Spring Harbor Laboratory. (medlineplus.gov)

Diversity3

• Indigenous Australians harbour rich and unique genomic diversity. (bvsalud.org)
• Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine . (bvsalud.org)
• Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. (cdc.gov)

Molecules1

• Megabase size molecules of genomic DNA are isolated and labelled at a specific 6 or 7 base pair sequence motifs. (mdanderson.org)

Catalogue1

• A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community , underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. (bvsalud.org)

Inversions2

• In Australian zebra finches ( Taeniopygia guttata ), two polymorphic inversions are known cytogenetically and we set out to detect these two and potentially additional inversions using genomic tools and study their effects on embryo mortality and other fitness-related and morphological traits. (biomedcentral.com)
• Inversions are intrachromosomal structural mutations which result in the reversal of gene order (and no change in the genic content of a chromosome) [ 4 ]. (biomedcentral.com)

Populations around the w1

• No study has ever looked at genomic structural variation with this kind of broad representation of populations around the world. (genengnews.com)

Human5

• On the human side, we are currently focusing on the exploitation of long-read sequencing technologies for detection of structural variations in human individuals. (mpg.de)
• JAX employs 1,700 staff, and its mission is to discover precise genomic solutions for disease and empower the global biomedical community in the shared quest to improve human health. (jax.org)
• A very small subset of genomic variants contributes to human health and disease. (genome.gov)
• NIH maintains a number of human and non-human genomic data repositories at the National Center for Biotechnology Information (NCBI). (nih.gov)
• Some individual NIH Institutes and Centers (ICs) support repositories that contain human genomic as well as other types of data that are relevant to their specific area of interest. (nih.gov)

Farmington1

• To support the quickly evolving public health crisis caused by the coronavirus pandemic, The Jackson Laboratory for Genomic Medicine (JAX-GM), located in Farmington, Connecticut, is partnering with the Connecticut Department of Public Health (DPH), UConn Health and Hartford HealthCare to provide the State with significant additional coronavirus testing capacity. (jax.org)

Researchers3

• They will be a member of a highly active and collaborative group of researchers, and help develop new technological approaches and applied-genomic tools. (findaphd.com)
• Presumably, the beginning of the end of population sequencing would see researchers and clinicians leveraging genomic variant information to develop improved diagnostics and treatments, in addition to new methods of prevention. (genengnews.com)
• The researchers created a map of eight classes of structural variants that potentially contribute to disease. (genengnews.com)

Methylation2

• In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. (researchgate.net)
• First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. (researchgate.net)

Data5

• The different kinds of genomic structural variation to be identified from sequencing data. (mpg.de)
• It models and interprets genomic complexity, integrates basic research with clinical application, educates current and future scientists, and empowers the global biomedical community by providing critical data, tools and services. (jax.org)
• Some repositories store both genomic and non-genomic (for example, imaging) data. (nih.gov)
• Some repositories store open-access or unrestricted access genomic data and consequently no special credentials are required for downloading data. (nih.gov)
• IDbases are locus-specific databases for immunodeficiency-causing variations, which contain in addition to variation information also some clinical data. (lu.se)

Disorders1

• His research group studies the role of genomic alterations in autism spectrum and related neurodevelopmental disorders. (sfari.org)

Autism spectrum1

• Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci. (nature.com)

Clinicians1

• Understanding how genomic variants contribute to disease may help clinicians develop improved diagnostics and treatments, in addition to new methods of prevention. (genome.gov)

Differences among1

• This genomic variation accounts for some of the differences among people, including important aspects of their health and susceptibility to diseases. (genome.gov)

Coronavirus1

• Overall, the molecular and biologic characteristics of the strain HSR1 provide evidence that SARS-CoV forms a fourth genetic coronavirus group with distinct genomic and biologic features. (cdc.gov)

Jackson Laboratory1

• Seoul, South Korea - Six senior officials and scientists from The Jackson Laboratory (JAX) will visit EWHA Womans University in Seoul for an International Joint Symposium on Genomic Medicine on Oct. 2. (jax.org)

Sequence2

• In this study, the complete genomic sequence of Fusarium equiseti D25-1 was determined using multiple sequencing platforms. (researchsquare.com)
• Additionally, the Irys System, which the firm launched in November, does not use DNA fragmentation or amplification - typical of next-generation sequencing - resulting in sequence information over very long reads ranging from hundreds of kilobases to a megabase, where important sample structural information is preserved, BioNano said. (genomeweb.com)

Bionano1

• As a result, Bionano mapping yields hundreds of times more contiguous assembly than sequencing technologies alone can provide with unparalleled sensitivity for large structural variations (SVs) from 500 bp to mega base pair lengths. (mdanderson.org)

TP531

• The majority of osteosarcomas harbour mutations in the TP53 gene, either point mutations or structural variations that separate the promoter region from the coding parts of TP53. (lu.se)

Regions2

• Such studies generally find several genomic regions associated with a disease and many variants in each of those regions. (genome.gov)
• CONCLUSION: Integrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. (duke.edu)

Rearrangements2

• Genomic rearrangements in Arabidopsis considered as quantitative traits. (nature.com)
• Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC. (duke.edu)

Loci1

• This study also uncovered 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 likely to have formed through individual mutational events. (genengnews.com)

Landscape3

• The landscape of genomic structural variation in Indigenous Australians. (bvsalud.org)
• In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. (nature.com)
• In this study we perform tumor and normal whole exome sequencing (WES) on 32 pediatric primary MDS patients and targeted sequencing on another 14 cases through a single institution study focused on defining the genomic landscape of pediatric MDS. (nature.com)

Study2

• Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia . (bvsalud.org)
• Despite this progress, no study to date has performed comprehensive sequencing on a pediatric MDS cohort to fully understand somatic and germline variation in this neoplasm. (nature.com)

Characteristics1

• Our most compelling result discovered CNV at 16p11.2 (p = 0.002) (with characteristics of a genomic disorder) at approximately 1% frequency. (nih.gov)