RT Journal
A1 Koenig, Zan
A1 Yohannes, Mary T.
A1 Nkambule, Lethukuthula L.
A1 Zhao, Xuefang
A1 Goodrich, Julia K.
A1 Kim, Heesu Ally
A1 Wilson, Michael W.
A1 Tiao, Grace
A1 Hao, Stephanie P.
A1 Sahakian, Nareh
A1 Chao, Katherine R.
A1 Walker, Mark A.
A1 Lyu, Yunfei
A1 gnomAD Project Consortium
A1 Rehm, Heidi L.
A1 Neale, Benjamin M.
A1 Talkowski, Michael E.
A1 Daly, Mark J.
A1 Brand, Harrison
A1 Karczewski, Konrad J.
A1 Atkinson, Elizabeth G.
A1 Martin, Alicia R.
T1 A harmonized public resource of deeply sequenced diverse human genomes
JF Genome Research 
JO Genome Research 
YR 2024 
FD May 01 
VO 34 
IS 5 
SP 796 
OP 809 
DO 10.1101/gr.278378.123 
UL http://genome.cshlp.org/content/34/5/796.abstract 
AB Underrepresented populations are often excluded from genomic studies owing in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high-quality set of 4094 whole genomes from 80 populations in the HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also show substantial added value from this data set compared with the prior versions of the component resources, typically combined via liftOver and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared with previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality-control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.