Establishment of reference standards for multifaceted mosaic variant analysis

Area of Science:

• Genomics
• Molecular Biology

Background:

• Detecting somatic mosaicism in non-proliferative cells is challenging due to the absence of a ground truth.
• Current detection strategies for mosaic variants lack validated accuracy.

Purpose of the Study:

• To create a reference standard dataset for evaluating somatic mosaicism detection.
• To provide ultra-deep sequenced data for optimizing variant detection algorithms.

Main Methods:

• Generated reference standards using mixtures of cell lines with known genotypes.
• Performed ultra-deep whole-exome sequencing (WES).
• Included a comprehensive set of mosaic single-nucleotide variants (SNVs), insertion-deletion mutations (INDELs), non-variant sites, and germline variants.

Main Results:

• Cataloged 386,613 mosaic SNVs and INDELs with variant allele frequencies (VAFs) from 0.5% to 56%.
• Included 35,113,417 non-variant sites and 19,936 germline variant sites as controls.
• Identified 741 potential inter-sample relationships based on variant sharing and VAF asymmetry.

Conclusions:

• The generated reference data is crucial for optimizing current mosaic variant detection methods.
• This dataset will facilitate the development of improved algorithms for future somatic mosaicism studies.