Researchers Expand 1000 Genomes Project Resource

NEW YORK — Researchers at the New York Genome Center have published an expanded version of the 1000 Genomes Projects, adding parent-child sequences to the popular, open access genome sequencing resource.

Originally published seven years ago, the collection from the independent, nonprofit research institution included 2,504 samples.

Now, in collaboration with groups at the Massachusetts General Hospital, Yale University, and Human Genome Structural Variation Consortium, the researchers have expanded the resource using Illumina NovaSeq instruments. 

The study, published in Cell, presents comprehensive analyses of the high-coverage whole-genome sequencing data on the expanded 1kGP cohort which now consists of 3,202 samples, including 602 parent-child trios.

Using state-of-the-art methods and algorithms, researchers at the NYGC sequenced DNA derived from lymphoblastoid cell lines (LCLs; i.e., immortalized human B cells from peripheral blood) from the expanded cohort to a targeted depth of 30X genome coverage. 

Next, the group performed single nucleotide variant and short insertion and deletion calling, which consists of identification of variant sites from the sequence data relative to the human genome reference and genotyping of discovered variant sites across all samples in the cohort.

Additionally, a team from Harvard Medical School, Broad Institute and Massachusetts General Hospital, in collaboration with a group at Yale University and the Washington University School of Medicine, discovered and genotyped a comprehensive set of structural variants  across the 3,202 1kGP samples by integrating multiple analytic approaches.

All raw sequence data and variant call sets were immediately released to the public upon sequencing completion via several genomic data repositories, including the International Genome Sample Resource which is maintained by co-authors from the European Bioinformatics Institute at the European Molecular Biology Laboratory. 

“Our goal is to have this public resource serve as the benchmark for future population genetic studies and methods development,” said Xuefang Zhao, Ph.D., postdoctoral fellow at the Center for Genomic Medicine Massachusetts General Hospital, and the study’s co-first author.

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