RT Journal Article
SR Electronic
T1 Screening of CNVs using NGS data improves mutation detection yield and decreases costs in genetic testing for hereditary cancer
JF Journal of Medical Genetics
JO J Med Genet
FD BMJ Publishing Group Ltd
SP jmedgenet-2020-107366
DO 10.1136/jmedgenet-2020-107366
A1 José Marcos Moreno-Cabrera
A1 Jesús del Valle
A1 Lidia Feliubadaló
A1 Marta Pineda
A1 Sara González
A1 Olga Campos
A1 Raquel Cuesta
A1 Joan Brunet
A1 Eduard Serra
A1 Gabriel Capellà
A1 Bernat Gel
A1 Conxi Lázaro
YR 2020
UL http://jmg.bmj.com/content/early/2020/11/20/jmedgenet-2020-107366.abstract
AB Introduction Germline CNVs are important contributors to hereditary cancer. In genetic diagnostics, multiplex ligation-dependent probe amplification (MLPA) is commonly used to identify them. However, MLPA is time-consuming and expensive if applied to many genes, hence many routine laboratories test only a subset of genes of interest.Methods and results We evaluated a next-generation sequencing (NGS)-based CNV detection tool (DECoN) as first-tier screening to decrease costs and turnaround time and expand CNV analysis to all genes of clinical interest in our diagnostics routine. We used DECoN in a retrospective cohort of 1860 patients where a limited number of genes were previously analysed by MLPA, and in a prospective cohort of 2041 patients, without MLPA analysis. In the retrospective cohort, 6 new CNVs were identified and confirmed by MLPA. In the prospective cohort, 19 CNVs were identified and confirmed by MLPA, 8 of these would have been lost in our previous MLPA-restricted detection strategy. Also, the number of genes tested by MLPA across all samples decreased by 93.0% in the prospective cohort.Conclusion Including an in silico germline NGS CNV detection tool improved our genetic diagnostics strategy in hereditary cancer, both increasing the number of CNVs detected and reducing turnaround time and costs.