Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Peter EbertPeter A AudanoQihui ZhuBernardo Rodriguez-MartinDavid PorubskyMarc Jan BonderArvis SulovariJana EblerWeichen ZhouRebecca Serra MariFeyza YilmazXuefang ZhaoPingHsun HsiehJoyce LeeSushant KumarJiadong LinTobias RauschYu ChenJingwen RenMartin SantamarinaWolfram HöpsHufsah AshrafNelson T ChuangXiaofei YangKatherine M MunsonAlexandra P LewisSusan FairleyLuke J TallonWayne E ClarkeAnna O BasileMarta Byrska-BishopAndré CorveloUday S EvaniTsung-Yu LuMark J P ChaissonJunjie ChenChong LiHarrison BrandAaron M WengerMaryam GhareghaniWilliam T HarveyBenjamin RaederPatrick HasenfeldAllison A RegierHaley J AbelIra M HallPaul FlicekOliver StegleMark B GersteinJose M C TubioZepeng MuYang I LiXinghua ShiAlex R HastieKai YeZechen ChongAshley D SandersMichael C ZodyMichael E TalkowskiRyan E MillsScott E DevineCharles LeeJan O KorbelTobias MarschallEvan E EichlerPublished in: Science (New York, N.Y.) (2021)
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.