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April 25 , 2024Medical and Population Genetics PrimerBroad Institute of MIT and HarvardXuefang Zhao & Emma Pierce-HoffmanBroad InstituteStructural Variation
https://www.youtube.com/watch?v=xCPBLGt_azQ
Medical and Population Genetics PrimerFebruary 8, 2024Broad Institute of MIT and HarvardBenjamin StroberHarvard School of Public HealthIntegration of GWAS an
https://www.cell.com/cell/fulltext/S0092-8674(20)30619-X
Summary. Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations.
https://www.broadinstitute.org/videos/mpg-primer-gene-and-variant-interpretation
The Primer on Medical and Population Genetics is a series of informal weekly discussions of basic genetics topics that relate to human populations and disease. Experts from across the Broad Institute community give in-depth introductions to the basic principles of complex trait genetics, including human genetic variation, genotyping, DNA sequencing methods, statistics, data analysis, and more.
https://www.cell.com/trends/genetics/fulltext/S0168-9525(21)00185-2
Structural variation (SV) is a large difference (typically >100 bp) in the genomic structure of two genomes and includes both copy number variation and variation that does not change copy number of a genomic region, such as an inversion. Improved reference genomes, combined with widespread genome sequencing using short-read sequencing technology, and increasingly using long-read sequencing
https://www.nature.com/articles/s41467-019-08992-7
An integrated map of structural variation in 2,504 human genomes. Nature 526, 75-81 (2015). Article CAS Google Scholar ... Nature Reviews Genetics (2024)
https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/primers/primer-medical-and-pop
The Primer on Medical and Population Genetics is a series of weekly lectures on genetics topics related to human populations and disease. Experts from across the Medical and Population Genetics community at the Broad Institute give in-depth introductions to research in human genetics through overviews of core concepts and practical tutorials on tools for biostatistics, computational genomics
https://www.nature.com/articles/nature15394
The Structural Variation Analysis Group of The 1000 Genomes Project reports an integrated structural variation map based on discovery and genotyping of eight major structural variation classes in
https://www.nature.com/articles/nrg1767
New technologies have revealed widespread structural variation in the human genome, including copy-number variants, insertions, inversions and translocations. These variants are predicted to
https://www.sciencedirect.com/science/article/pii/S0092867424000047
This development represents an important tipping point for human genetics for three reasons: (1) a change from read-based variant discovery to assembly-based discovery (e.g., PAV or SVIM-asm), 55, 71, 76 (2) the potential for understanding all forms of variation simultaneously in conjunction with methylation differences (Figure 4), and (3) the development of the pangenome reference instead of
https://www.mpi-inf.mpg.de/news/spotlights/bioinformatics/structural-variation-in-genomes/
The genome is organized in chromosomes: we inherit 23 chromosomes from our mother and father, respectively. A chromosome consists of a long DNA molecule, stabilized and spatially structured by special proteins. The DNA encodes genetic information as a sequence of its constituting bases adenine (A), cytosine (C), guanine (G), and thymine (T). In
https://pubmed.ncbi.nlm.nih.gov/32460305/
Here we used a scalable pipeline 1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding
https://www.cell.com/cell/fulltext/S0092-8674(22)00784-X
Summary. Non-allelic recombination between homologous repetitive elements contributes to evolution and human genetic disorders. Here, we combine short- and long-DNA read sequencing of repeat elements with a new bioinformatics pipeline to show that somatic recombination of Alu and L1 elements is widespread in the human genome.
https://nanoporetech.com/news/news-structural-variation-human-genomics-6-things-read-right-now
The significance of structural variation in human genomics is becoming increasingly established in many fields, from cancer to neurology and the mechanisms of rare disease. ... For the ultimate primer in understanding how SVs relate to other classes of genetic variation, Evan Eichler's review delves into both historical and future-looking
https://www.hgsvc.org/publications
Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C, Lee C, Devine SE, Eichler EE, Ye K; Human Genome Structural Variation Consortium. Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants. Genomics Proteomics Bioinformatics. 2021 Jul 2:S1672-0229(21)00143-1. doi: 10.1016/j.gpb.2021.03.007.
https://www.sciencedirect.com/science/article/pii/S0092867424001211
We used these data to generate gene trees and a time-calibrated phylogeny for the nine primate species, including human (Figures 1 A and 1B; Data S2).While the majority of trees (52.7%) are consistent with the generally accepted phylogeny, the fraction of alternate topologies is, once again, greater than previous estimates 8, 9, 19, 31 (Figure 1 C; Data S2).
https://www.nature.com/articles/nature09534
Rates of variant discovery. In the trio project, with an average mapped sequence coverage of 42× per individual across six individuals and 2.3 gigabases (Gb) of accessible genome, we identified 5
https://www.broadinstitute.org/blog/structural-variation-goes-extreme
Speaking at a MPG primer lecture last month, Handsaker described the team's recent work, published in Nature Genetics, uncovering extreme forms of copy number variation by analyzing whole-genome sequence data from thousands of genomes at once. The team identified in the human genome hundreds of sites of extreme CNV, at which genes varies in
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080742/
Structural variations are widespread in the human genome and can serve as genetic markers in clinical and evolutionary studies. With the advances in the next-generation sequencing technology, recent methods allow for identification of structural variations with unprecedented resolution and accuracy. They also provide opportunities to discover
https://www.pacb.com/publications/an-integrated-map-of-structural-variation-in-2504-human-genomes/
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611/
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.
https://www.cell.com/cell/fulltext/S0092-8674(10)01197-9
Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation. We develop a resource based on capillary end sequencing of 13.8 million fosmid clones from 17 human genomes and characterize the complete sequence of 1054 large structural variants
https://vivo.weill.cornell.edu/display/pubid26432246
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
https://jnanobiotechnology.biomedcentral.com/articles/10.1186/s12951-024-02647-6
The gut microbiota is one of the essential contributors of the pathogenesis and progress of inflammatory bowel disease (IBD). Compared with first-line drug therapy, probiotic supplementation has emerged as a viable and secure therapeutic approach for managing IBD through the regulation of both the immune system and gut microbiota. Nevertheless, the efficacy of oral probiotic supplements is
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10517-6
Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201903/
Each segment of structural proteins that are implicated in viral life cycle processes such as assembly, replication, encapsidation, immunological evasion, and transit carries genetic information. These structural proteins comprise the polyprotein and ribonucleoprotein complex: RNA polymerase, nucleoprotein precursors (GPC), and NP.
https://www.biorxiv.org/content/10.1101/2024.06.25.599715.full.pdf
In this study, we reconstruct nine full and two partial Human betaherpesvirus 6 genomes from individuals dating between the 8th-6th century BCE to the 14th century CE, expanding our knowledge to more than 2500 years of these viruses' evolutionary histories. The genomes originate from individuals of all ages and both
https://pubs.rsc.org/en/content/articlelanding/2024/np/d4np00009a
Time span in literature: 1985-early 2024. Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties.
https://www.nature.com/articles/s41564-024-01751-5
The human vagina harbours diverse microorganisms—bacteria, viruses and fungi—with profound implications for women's health. Genome-level analysis of the vaginal microbiome across multiple