Somatic Variant Calling and Mutational Signature Analysis
Raw variants called by Strelka2 in WGS data were also the basis for the mutational signature analysis. Since normal pairs were not available, we applied a series of filters to approximate a somatic callset: we filtered out the variants with a population frequency (AF_popmax) higher than 1%, called in more than one cell line, with a variant allele frequency (VAF) lower than 0.1 and, variants in highly variable genes (MUC3A, MUC5AC, OR52E5, OR52L1, SMPD1, PRAMEF and LILR). We also filtered out the variants in dbSNP except for those present in COSMIC and ICGC. We used this call set enriched in somatic variants with the mutSignatures68 (link) R package to estimate the contribution of each of the thirty COSMIC mutational signatures to the mutational profile of each cell line.
Magallón-Lorenz M., Terribas E., Ortega-Bertran S., Creus-Bachiller E., Fernández M., Requena G., Rosas I., Mazuelas H., Uriarte-Arrazola I., Negro A., Lausová T., Castellanos E., Blanco I., DeVries G., Kawashima H., Legius E., Brems H., Mautner V., Kluwe L., Ratner N., Wallace M., Fernández-Rodriguez J., Lázaro C., Fletcher J.A., Reuss D., Carrió M., Gel B, & Serra E. (2023). Deep genomic analysis of malignant peripheral nerve sheath tumor cell lines challenges current malignant peripheral nerve sheath tumor diagnosis. iScience, 26(2), 106096.
Publication 2023
Cell line Cosmic Genes variants Muc5ac Mutational Smpd1 Somatic
Corresponding Organization : Universitat de Barcelona
Other organizations :
Institut d'Investigació Biomédica de Bellvitge, Institut Català d'Oncologia, German Cancer Research Center, University Hospital Heidelberg, Hospital Universitari Germans Trias i Pujol, Edward Hines, Jr. VA Hospital, Niigata University Medical and Dental Hospital, KU Leuven, University Medical Center Hamburg-Eppendorf, Universität Hamburg, Cincinnati Children's Hospital Medical Center, University of Florida Health, Florida College, Brigham and Women's Hospital, Harvard University
Variants with a population frequency (AF_popmax) higher than 1%
Variants called in more than one cell line
Variants with a variant allele frequency (VAF) lower than 0.1
Variants in highly variable genes (MUC3A, MUC5AC, OR52E5, OR52L1, SMPD1, PRAMEF, and LILR)
Variants in dbSNP except for those present in COSMIC and ICGC
controls
No positive or negative controls were explicitly mentioned.
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