Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association

D.M. Vossen, C.V.M. Verhagen, R. Grénman, R.J.C. Kluin, M. Verheij, M.W.M. van den Brekel, L.F.A. Wessels, C. Vens

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Background.
Large cancer genome studies continue to reveal new players in treatment response and tumorigenesis. The discrimination of functional alterations from the abundance of passenger genetic alterations still poses challenges and determines DNA sequence variant selection procedures. Here we evaluate variant selection strategies that select homozygous variants and rare SNPs and assess its value in detecting tumor cells with DNA repair defects.

Methods.
To this end we employed a panel of 29 patient-derived head and neck squamous cell carcinoma (HNSCC) cell lines, of which a subset harbors DNA repair defects. Mitomycin C (MMC) sensitivity was used as functional endpoint of DNA crosslink repair deficiency. 556 genes including the Fanconi anemia (FA) and homologous recombination (HR) genes, whose products strongly determine MMC response, were capture-sequenced.

Results.
We show a strong association between MMC sensitivity, thus loss of DNA repair function, and the presence of homozygous and rare SNPs in the relevant FA/HR genes. Excluding such selection criteria impedes the discrimination of crosslink repair status by mutation analysis. Applied to all KEGG pathways, we find that the association with MMC sensitivity is strongest in the KEGG FA pathway, therefore also demonstrating the value of such selection strategies for exploratory analyses. Variant analyses in 56 clinical samples demonstrate that homozygous variants occur more frequently in tumor suppressor genes than oncogenes further supporting the role of a homozygosity criterion to improve gene function association or tumor suppressor gene identification studies.

Conclusion.
Together our data show that the detection of relevant genes or of repair pathway defected tumor cells can be improved by the consideration of allele zygosity and SNP allele frequencies.
Original languageEnglish
Article numbere0206632
Number of pages16
JournalPLoS ONE
Volume13
Issue number11
DOIs
Publication statusPublished - 8 Nov 2018

Bibliographical note

With supplementary file

Funding

CV and MWMvdB received financial support from the Dutch Cancer Society (Design - KWF-A6C7072), the Brunel fund, the Verwelius fund and The Netherlands Cancer Institute. No grant numbers are applicable for the latter three. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

FundersFunder number
KWF KankerbestrijdingKWF-A6C7072

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