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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

ABSTRACT: Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

SUBMITTER: Mallick S

PROVIDER: S-EPMC5161557 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Mallick Swapan S Li Heng H Lipson Mark M Mathieson Iain I Gymrek Melissa M Racimo Fernando F Zhao Mengyao M Chennagiri Niru N Nordenfelt Susanne S Tandon Arti A Skoglund Pontus P Lazaridis Iosif I Sankararaman Sriram S Fu Qiaomei Q Rohland Nadin N Renaud Gabriel G Erlich Yaniv Y Willems Thomas T Gallo Carla C Spence Jeffrey P JP Song Yun S YS Poletti Giovanni G Balloux Francois F van Driem George G de Knijff Peter P Romero Irene Gallego IG Jha Aashish R AR Behar Doron M DM Bravi Claudio M CM Capelli Cristian C Hervig Tor T Moreno-Estrada Andres A Posukh Olga L OL Balanovska Elena E Balanovsky Oleg O Karachanak-Yankova Sena S Sahakyan Hovhannes H Toncheva Draga D Yepiskoposyan Levon L Tyler-Smith Chris C Xue Yali Y Abdullah M Syafiq MS Ruiz-Linares Andres A Beall Cynthia M CM Di Rienzo Anna A Jeong Choongwon C Starikovskaya Elena B EB Metspalu Ene E Parik Jüri J Villems Richard R Henn Brenna M BM Hodoglugil Ugur U Mahley Robert R Sajantila Antti A Stamatoyannopoulos George G Wee Joseph T S JT Khusainova Rita R Khusnutdinova Elza E Litvinov Sergey S Ayodo George G Comas David D Hammer Michael F MF Kivisild Toomas T Klitz William W Winkler Cheryl A CA Labuda Damian D Bamshad Michael M Jorde Lynn B LB Tishkoff Sarah A SA Watkins W Scott WS Metspalu Mait M Dryomov Stanislav S Sukernik Rem R Singh Lalji L Thangaraj Kumarasamy K Pääbo Svante S Kelso Janet J Patterson Nick N Reich David D

Nature 20160921 7624

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of pre ...[more]

PMID: 27654912

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Project description:Background and purposeStroke is the leading cause of death and long-term disability worldwide. Previous genome-wide association studies identified 51 loci associated with stroke (mostly ischemic) and its subtypes among predominantly European populations. Using whole-genome sequencing in ancestrally diverse populations from the Trans-Omics for Precision Medicine (TOPMed) Program, we aimed to identify novel variants, especially low-frequency or ancestry-specific variants, associated with all stroke, ischemic stroke and its subtypes (large artery, cardioembolic, and small vessel), and hemorrhagic stroke and its subtypes (intracerebral and subarachnoid).MethodsWhole-genome sequencing data were available for 6833 stroke cases and 27 116 controls, including 22 315 European, 7877 Black, 2616 Hispanic/Latino, 850 Asian, 54 Native American, and 237 other ancestry participants. In TOPMed, we performed single variant association analysis examining 40 million common variants and aggregated association analysis focusing on rare variants. We also combined TOPMed European populations with over 28 000 additional European participants from the UK BioBank genome-wide array data through meta-analysis.ResultsIn the single variant association analysis in TOPMed, we identified one novel locus 13q33 for large artery at whole-genome-wide significance (P<5.00×10-9) and 4 novel loci at genome-wide significance (P<5.00×10-8), all of which need confirmation in independent studies. Lead variants in all 5 loci are low-frequency but are more common in non-European populations. An aggregation of synonymous rare variants within the gene C6orf26 demonstrated suggestive evidence of association for hemorrhagic stroke (P<3.11×10-6). By meta-analyzing European ancestry samples in TOPMed and UK BioBank, we replicated several previously reported stroke loci including PITX2, HDAC9, ZFHX3, and LRCH1.ConclusionsWe represent the first association analysis for stroke and its subtypes using whole-genome sequencing data from ancestrally diverse populations. While our findings suggest the potential benefits of combining whole-genome sequencing data with populations of diverse genetic backgrounds to identify possible low-frequency or ancestry-specific variants, they also highlight the need to increase genome coverage and sample sizes.

Dataset Information

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

Publications

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.

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