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An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice
Author(s) -
Ellison Gillian,
Ahdesmäki Miika,
Luke Sally,
Waring Paul M.,
Wallace Andrew,
Wright Ronnie,
Röthlisberger Benno,
Ludin Katja,
MerkelbachBruse Sabine,
Heydt Carina,
Ligtenberg Marjolijn J.L.,
Mensenkamp Arjen R.,
Castro David Gonzalez,
Jones Thomas,
Vivancos Ana,
Kondrashova Olga,
Pauwels Patrick,
Weyn Christine,
Hahnen Eric,
Hauke Jan,
Soong Richie,
Lai Zhongwu,
Dougherty Brian,
Carr T. Hedley,
Johnson Justin,
Mills John,
Barrett J. Carl
Publication year - 2018
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.23375
Subject(s) - biology , amplicon , germline , genetic testing , computational biology , genotype , genetics , polymerase chain reaction , gene
Abstract Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with poly ADP ribose polymerase (PARP) inhibitors. Tumor BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin‐fixed paraffin embedded (FFPE), the tumor genome is complex, and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumors to compare different approaches to identify clinically important variants within FFPE tumor DNA samples. This was not a proficiency study but an inter‐laboratory comparison to identify common issues. Each laboratory received the same tumor DNA samples ranging in genotype, quantity, quality, and variant allele frequency (VAF). Each laboratory performed their preferred next‐generation sequencing method to report on the variants. No false positive results were reported in this small study and the majority of methods detected the low VAF variants. A number of variants were not detected due to the bioinformatics analysis, variant classification, or insufficient DNA. The use of hybridization capture or short amplicon methods are recommended based on a bioinformatic assessment of the data. The study highlights the importance of establishing standards and standardization for t BRCA testing particularly when the test results dictate clinical decisions regarding life extending therapies.