Whole Genome Variant Dataset for Enriching Studies across 18 Different Cancers

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• Whole genome sequencing (WGS) offers significant biological insights but presents computational challenges.
• The Cancer Genome Atlas (TCGA) has generated a substantial WGS dataset.
• Analysis has historically focused on exomic regions, limiting comprehensive genomic understanding.

Purpose of the Study:

• To present cancer-associated variants from the TCGA WGS dataset.
• To enable cancer researchers to extend genomic analysis beyond exomic regions.
• To provide a valuable resource for expanding cancer genomic studies.

Main Methods:

• Processed 1342 WGS alignments from the TCGA consortium using VarScan2.
• Deposited processed data to the NCI Cancer Cloud.
• Integrated the dataset into BigQuery for efficient data access and cross-mapping.

Main Results:

• Identified 157,313,519 pooled cancer-associated single-nucleotide variations (SNVs) across 18 cancer types.
• Observed an average of 117,223 SNVs per sample (range: 1111 to 775,470).
• The dataset covers a wide spectrum of cancer-associated genomic variations.

Conclusions:

• The TCGA WGS variant dataset is now accessible for broader genomic analysis.
• This resource facilitates deeper investigation into cancer biology by including non-exomic regions.
• Researchers can leverage this data to enrich current studies with comprehensive genomic information.