Cell upgrades 1000 Genomes Project resources: high-coverage whole-genome sequencing and improved analytical methods

Researchers Expand and Upgrade 1000 Genomes Project Resources Using High-Coverage Whole-Genome Sequencing and Improved Analytical Methods

The original 2504 samples from the 1000 Genomes Project were resequenced and new relevant samples were added to generate an improved publicly available whole-genome sequencing resource

Seven years ago, the 1000 Genomes Project (1kGP) released an open-access resource based primarily on low-coverage whole-genome sequencing (WGS) data from 2504 individuals from 26 populations on five continents, the first time WGS has made it available on a large scale Work on the Catalog of Human Genetic Variation

Now, researchers at the New York Genome Center (NYGC), in collaboration with teams at Massachusetts General Hospital, Yale University, and the Human Genome Structural Variation Consortium (HGSVC), have expanded the 1kGP resource to include nearly all parent-child trios in addition to the original sample , and sequenced them with high coverage using the Illumina NovaSeq instrument

"The 1000 Genomes Project cohort is such a valuable resource, and we think it will be useful to the community to synchronize sequencing with the latest version of short-read technology, while increasing Abundance of previously missed family samples

Using state-of-the-art methods and algorithms, NYGC researchers have analyzed cell lines (LCLs) derived from lymphoblastoid cells, from expanded cohorts to a target depth of 30X genome coverage

In addition, Dr.

Overall, the study shows significant improvements in both discovery power and precision for variant calling, especially among rare SNVs, INDELs, and SVs that were previously unattainable with low-coverage sequencing

An important aspect of the original 1kGP resource is that it is used as a reference panel for variant attribution, i.

"The new attribution panel includes more loci, particularly many of the more common INDELs and SVs, expanding the GWAS," explained Marta Byrska-Bishop, Ph.

All raw sequence data and variant call sets are released to the public immediately after sequencing is complete through several genomic databases, including the International Genome maintained by co-authors at the European Institute of Bioinformatics at the European Molecular Biology Laboratory (EMBL-EBI) Sample Resource (IGSR)

"Our goal is to make this public resource a benchmark for future population genetic research and method development," added Xuefang Zhao, PhD, a postdoctoral fellow at the Massachusetts General Hospital Center for Genomic Medicine and co-first author of the study

These data are already of interest to the genetics and genomics community

article title

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios