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A structural variation reference for medical and population genetics

Ryan L. Collins, Genome Aggregation Database Production Team, Harrison Brand, Konrad J. Karczewski, Xuefang Zhao, Jessica Alföldi, Laurent C. Francioli, Amit V. Khera, Chelsea Lowther, Laura D. Gauthier, Harold Wang, Nicholas A. Watts (+36 others)
2020 Nature  
As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD  ...  Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD.  ...  Life sciences Behavioural & social sciences Ecological, evolutionary & environmental sciences For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf  ... 
doi:10.1038/s41586-020-2287-8 pmid:32461652 pmcid:PMC7334194 fatcat:26dckx45vrdxxegdjij6q2tpq4

Genetic diversity in black South Africans from Soweto

Andrew May, Scott Hazelhurst, Yali Li, Shane A Norris, Nimmisha Govind, Mohammed Tikly, Claudia Hon, Keith J Johnson, Nicole Hartmann, Frank Staedtler, Michèle Ramsay
2013 BMC Genomics  
Limited reference data for these individuals hampers medical research and prevents thorough understanding of the underlying population substructure.  ...  Our data represent a suitable reference set for southeastern Bantu-speakers, on par with a HapMap type reference population, and constitute a prelude to the Southern African Human Genome Programme.  ...  The National Health Laboratory Service and the Bioinformatics unit at the University of the Witwatersrand provided the infrastructure for AM, SH and MR.  ... 
doi:10.1186/1471-2164-14-644 pmid:24059264 pmcid:PMC3850641 fatcat:3c2yt33eznc4hdtv4denneomxm

The population genetics of structural variation

Donald F Conrad, Matthew E Hurles
2007 Nature Genetics  
Population genetics is central to our understanding of human variation, and by linking medical and evolutionary themes, it enables us to understand the origins and impacts of our genomic differences.  ...  We summarize recent dramatic advances, describe the diverse mutational origins of chromosomal rearrangements and argue that their complexity necessitates a re-evaluation of existing population genetic  ...  Coop and C. Tyler-Smith for their comments on an earlier manuscript and to D. Andrews for data processing.  ... 
doi:10.1038/ng2042 pmid:17597779 pmcid:PMC2716079 fatcat:qtr7ttpfdjefrhepjm4nlevvia

The Sri Lankan Genome Variation Database

Pubudu S. Samarakoon, Rohan W. Jayasekara, Vajira H.W. Dissanayake
2011 Sri Lanka Journal of Bio-Medical Informatics  
There is therefore a need for a central repository of this data. The SLGVD was created to fulfill this void. The SLGVD offers web based access to genetic variation information of Sri Lankan people.  ...  The Sri Lankan Genome Variation Database (SLGVD) is a database of single nucleotide polymorphisms found in Sinhalese, Sri Lankan Tamils and Moors -the three major ethnic groups in Sri Lanka.  ...  Acknowledgement The SLGVD was funded by funds from the Human Genetics Unit Development Fund, Faculty of Medicine, University of Colombo, Sri Lanka.  ... 
doi:10.4038/sljbmi.v2i1.2861 fatcat:sfkvy4vpjfchjlgofmy5a5huja

Human genetic admixture

Katharine L. Korunes, Amy Goldberg, Gregory S. Barsh
2021 PLoS Genetics  
This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within  ...  medical genetics.  ...  Despite their ubiquity and importance, admixed populations remain understudied in population and medical genetics [11] [12] [13] , especially from a theoretical perspective.  ... 
doi:10.1371/journal.pgen.1009374 pmid:33705374 fatcat:5prc4rr7qveejmunmw2i2lzlpa

The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design

Paul Lacaze, Mark Pinese, Warren Kaplan, Andrew Stone, Marie-Jo Brion, Robyn L. Woods, Martin McNamara, John J. McNeil, Marcel E. Dinger, David M. Thomas
2018 European Journal of Human Genetics  
Aged and healthy populations are more likely to be selectively depleted of pathogenic alleles and therefore particularly suitable as a reference population for the major diseases of clinical and public  ...  Allele frequency data from human reference populations is of increasing value for the filtering, interpretation, and assignment of pathogenicity to genetic variants.  ...  as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1038/s41431-018-0279-z pmid:30353151 pmcid:PMC6336775 fatcat:stg2ewiycrar3k5zo4j2nleyia

Use of GeIS for Early Diagnosis of Alcohol Sensitivity

José Fabián Reyes Román, Óscar Pastor López
2016 Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies  
Also, we integrate the association of genes/variations with population studies, for this way providing an early diagnosis for any disease of genetic origin. 284  ...  With SILE we perform a selective loading of genes and variations found for a specific disease from different data sources like: NCBI, dbSNP and others.  ...  ACKNOWLEDGEMENTS The author thanks Ainoha Martín Mayordomo, Mercedes Rossana Fernández Alcalá, David Roldán Martínez and Edgars Groza for critically reading this manuscript.  ... 
doi:10.5220/0005822902840289 dblp:conf/biostec/RomanL16 fatcat:tkr5ds2lsnc6fpqwxo6lk5sqw4

Trends in Next-Generation Sequencing and a New Era for Whole Genome Sequencing

Sang Tae Park, Jayoung Kim
2016 International Neurourology Journal  
First, NGS methods do not require a bacterial cloning procedure and prepare libraries for sequencing in a cell free system.  ...  lower cost and enable population-scale genome research.  ...  By comparing sequencing results to reference genomes, researchers can see the genetic variation such as single nucleotide polymorphisms (SNPs), structural variations, copy number variations, and other  ... 
doi:10.5213/inj.1632742.371 pmid:27915479 pmcid:PMC5169091 fatcat:utshiiliyzazlg75zpn7deryje

Different differences: The use of 'genetic ancestry' versus race in biomedical human genetic research

Joan H. Fujimura, Ramya Rajagopalan
2010 Social Studies of Science  
This article presents findings from our ethnographic research on biomedical scientists' studies of human genetic variation and common complex disease.  ...  We introduce the concept of 'genome geography', to analyze how some researchers studying human genetic variation 'locate' stretches of DNA in different places and times.  ...  Nevertheless, there are disciplinary differences that made for sometimes tense interactions in the collaborations between the medical geneticists and population geneticists around EIGENSTRAT and around  ... 
doi:10.1177/0306312710379170 pmid:21553638 pmcid:PMC3124377 fatcat:nnl2ejdli5efxlxtfsvafa32ii

Meeting on big mutations addresses big questions in human genetics

Donald F Conrad
2011 Genome Medicine  
Common CNVs e mapping and characterization of common germline structural variation is quickly becoming a mature field.  ...  With sample sizes over 45,000 and over 15,000, respectively, these medical genetics projects have moved into a scale previously only obtained by the largest GWAS meta-analyses.  ... 
doi:10.1186/gm226 pmid:21345244 pmcid:PMC3092097 fatcat:ya7mij7y4rhrjni22qel2cvxfm

Genome diversity in Ukraine

Taras K Oleksyk, Walter W Wolfsberger, Alexandra M Weber, Khrystyna Shchubelka, Olga T Oleksyk, Olga Levchuk, Alla Patrus, Nelya Lazar, Stephanie O Castro-Marquez, Yaroslava Hasynets, Patricia Boldyzhar, Mikhailo Neymet (+18 others)
2021 GigaScience  
To our knowledge, this study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for medical research in a large understudied  ...  The genome data have been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, copy number variations, single-nucletide  ...  Acknowledgements We thank all the Ukrainian volunteers who contributed their data for the project.  ... 
doi:10.1093/gigascience/giaa159 pmid:33438729 pmcid:PMC7804371 fatcat:ja7wazt6bzamhc7unihbjkdzla

The Medical Genome Reference Bank: a whole-genome data resource of 4,000 healthy elderly individuals. Rationale and cohort design [article]

Paul Lacaze, Mark Pinese, Warren Kaplan, Andrew Stone, Marie-Jo Brion, Robyn L Woods, Martin McNamara, John J McNeil, Marcel E Dinger, David M Thomas
2018 bioRxiv   pre-print
Allele frequency data from human reference populations is of increasing value for filtering and assignment of pathogenicity to genetic variants.  ...  Aged and healthy populations are more likely to be selectively depleted of pathogenic alleles, and therefore particularly suitable as a reference populations for the major diseases of clinical and public  ...  Reference populations are powerful filters to distinguish pathogenic from population-based genetic variation; both clinically for Mendelian disorders [1, 2] , and in research for studies of genetic disease  ... 
doi:10.1101/274019 fatcat:hung7ywkijhhtb4inxoi4jqjja

Finding the global in the local [chapter]

2020 Global health and the new world order  
Acknowledgements The research for this chapter was funded by a Wellcome  ...  It reveals an important slippage: from thinking about populations and population structure in the instrumental language of epidemiology -referring simply to those individuals who together make up a study  ...  so-called 'population structure' in the search for correlations between diseases and genes.  ... 
doi:10.7765/9781526149688.00012 fatcat:dq6krsnjmrendozfnxaf2ur46a

Magnitude of Human Genetic Variations: A Mini Review

2017 International Journal of Research Studies in Medical and Health Sciences  
It is quite interesting to know how and when these genetic variations offer to a population the survival benefit under the altered situations and at what extent over time.  ...  These variations are adaptive i.e. they ensure flexibility and survival of a population in the changing environment over time.  ...  Use of SNPs in drug designing has offered wide applications in medical and health. 9, 11,12,13,14 Structural Variation (SV) Structural variation is generally defined as a region of DNA approximately  ... 
doi:10.22259/ijrsmhs.0202004 fatcat:imgqmugkoneoza7f4bfa4t36ky

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese

Pengyu Chen, Jian Wu, Li Luo, Hongyan Gao, Mengge Wang, Xing Zou, Yingxiang Li, Gang Chen, Haibo Luo, Limei Yu, Yanyan Han, Fuquan Jia (+1 others)
2019 Frontiers in Genetics  
Our population genetic results from five different reference datasets indicated that Shanxi Han shares a closer phylogenetic relationship with northern-neighbors and southern ethnically close groups than  ...  We addressed genetic legacy, population structure and phylogenetic relationship of northern-Han Chinese via various analyses.  ...  High-Density Genetic Variations of Modern and Ancient Genomes Show Fine-Scale Population Structure of Northern Han We additionally investigated the fine-scale genetic structure of Shanxi Han by determining  ... 
doi:10.3389/fgene.2019.01045 pmid:31737039 pmcid:PMC6832103 fatcat:aehcdkgyjvgghbg6qb4ifmy5b4
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