High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
By M. Byrska-Bishop, U. S. Evani, Xuefang Zhao, A. Basile, Haley Abel, Allison A. Regier, A. Corvelo, Wayne E. Clarke, R. Musunuri, Kshithija Nagulapalli and 11 more. bioRxiv, 2021
932 citations recorded by the source corpus.
The 1000 Genomes Project (1kGP) is the largest fully open resource of whole genome sequencing (WGS) data consented for public distribution of raw sequence data without access or use restrictions. The final release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low coverage WGS. Here, we present a new, high coverage 3,202-sample WGS 1kGP resource, sequenced to a targeted depth of 30X using the Illumina NovaSeq 6000 system, which now includes 602 complete trios. We performed SNV/INDEL calling against the GRCh38 reference using GATK’s HaplotypeCaller, and generated a comprehensive set of SVs by integrating multiple analytic methods through a sophisticated machine learning model. We make all the data generated as part of this project publicly available and we envision it to become the new de facto public resource for the worldwide genomics and genetics community.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/bcc9e41b7c6d678c73272d72a6750521a86d2ace
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In Molecular Biology
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Citations in the corpus
- Haplotype-resolved diverse human genomes and integrated analysis of structural variation (2021, background): “graph framework (12–14) into a diversity panel of human genomes now deeply sequenced (>30-fold) with short-read data from the 1000 Genomes Project (1000GP) (15, 16).”
- The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics (2024, methodology): “Specifically, we downloaded the variant calling format (VCF) files(2) from the 1000 Genomes project [41], which aims at recording genetic variants occurring at a frequency of at least 1% in the human population.”