CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools
Por:
Moreno-Cabrera, JM, Del Valle, J, Castellanos, E, Feliubadalo, L, Pineda, M, Serra, E, Capella, G, Lazaro, C and Gel, B
Publicada:
15 nov 2021
Ahead of Print:
13 may 2021
Resumen:
A Summary: Germline copy-number variants (CNVs) are relevant mutations for multiple genetics fields, such as the study of hereditary diseases. However, available benchmarks show that all next-generation sequencing (NGS) CNV calling tools produce false positives. We developed CNVfilteR, an R package that uses the single-nucleotide variant calls usually obtained in germline NGS pipelines to identify those false positives. The package can detect both false deletions and false duplications. We evaluated CNVfilteR performance on callsets generated by 13 CNV calling tools on three whole-genome sequencing and 541 panel samples, showing a decrease of up to 44.8% in false positives and consistent F1-score increase. Using CNVfilteR to detect false-positive calls can improve the overall performance of existing CNV calling pipelines.
Filiaciones:
Moreno-Cabrera, JM:
Germans Trias & Pujol Res Inst PMPPC IGTP, Hereditary Canc Grp, Program Predict & Personalized Med Canc, Campus Can Ruti, Badalona 08916, Spain
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
Del Valle, J:
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
:
Germans Trias & Pujol Res Inst PMPPC IGTP, Hereditary Canc Grp, Program Predict & Personalized Med Canc, Campus Can Ruti, Badalona 08916, Spain
Germans Trias & Pujol Univ Hosp HUGTiP, Clin Genet Serv, Clin Genom Unit, Northern Metropolitan Clin Lab, Campus Can Ruti, Badalona 08916, Spain
Feliubadalo, L:
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
Pineda, M:
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
:
Germans Trias & Pujol Res Inst PMPPC IGTP, Hereditary Canc Grp, Program Predict & Personalized Med Canc, Campus Can Ruti, Badalona 08916, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
Capella, G:
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
Lazaro, C:
Hosp Llobregat, Inst Invest Biomed Bellvitge IDIBELL, Joint Program Hereditary Canc, Hereditary Canc Program,Catalan Inst Oncol, Barcelona 08908, Spain
Ctr Invest Biomed Red Canc CIBERONC, Inst Salud Carlos 3, Madrid 28029, Spain
:
Germans Trias & Pujol Res Inst PMPPC IGTP, Hereditary Canc Grp, Program Predict & Personalized Med Canc, Campus Can Ruti, Badalona 08916, Spain
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