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Establishment of reference standards for multifaceted mosaic variant analysis
- Source :
- Scientific Data, Vol 9, Iss 1, Pp 1-10 (2022)
- Publication Year :
- 2022
- Publisher :
- Springer Science and Business Media LLC, 2022.
-
Abstract
- Detection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of ultra-deep sequenced WES data based on reference standards generated by cell line mixtures, providing a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition such as in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference data will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.
- Subjects :
- Statistics and Probability
Genotype
Science
High-Throughput Nucleotide Sequencing
Reference Standards
Library and Information Sciences
Polymorphism, Single Nucleotide
Cell Line
Computer Science Applications
Education
INDEL Mutation
Animals
Humans
Statistics, Probability and Uncertainty
Information Systems
Subjects
Details
- ISSN :
- 20524463
- Volume :
- 9
- Database :
- OpenAIRE
- Journal :
- Scientific Data
- Accession number :
- edsair.doi.dedup.....7289b19a98e26af2e3bcb2adb6a252d1