Clinical Contribution of Next-Generation Sequencing Multigene Panel Testing for BRCA Negative High-Risk Patients With Breast Cancer

Published:April 12, 2021DOI:



      Breast cancer is the most common malignancy in women and thought to be hereditary in 10% of patients. Recent next-generation sequencing studies have increased the detection of pathogenic or likely pathogenic (P/LP) variants in genes other than BRCA1/2 in patients with breast cancer. This study evaluated pathogenic variants, likely pathogenic variants, and variants of unknown significance in 18 hereditary cancer susceptibility genes in patients with BRCA1/2-negative breast cancer.

      Patients and Methods

      This retrospective study included 188 high-risk BRCA1/2-negative patients with breast cancer tested with a multigene cancer panel using next-generation sequencing.


      Among 188 proband cases, 18 variants in 21 patients (11.1%) were classified as P/LP in PALB2 (n = 6), CHEK2 (n = 5), MUTYH (n = 4), ATM (n = 3), TP53 (n = 2), BRIP1 (n = 1), and MSH2 (n = 1). Three novel P/LP variants were identified. An additional 28 variants were classified as variants of unknown significance and detected in 30 different patients (15.9%).


      This is one of the largest study from Turkey to investigate the mutation spectrum in non-BRCA hereditary breast cancer susceptibility genes. A multigene panel test increased the likelihood of identifying a molecular diagnosis in patients with BRCA 1/2-negative breast cancer at risk for a hereditary breast cancer syndrome. More studies are needed to enable the clinical interpretation of these P/LP variants in hereditary patients with breast cancer.


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        • Siegel RL
        • Miller KD
        • Jemal A.
        Cancer statistics, 2017.
        CA Cancer J Clin. 2017; 67: 7-30
        • Bray F
        • Ferlay J
        • Soerjomataram I
        • Siegel RL
        • Torre LA
        • Jemal A.
        Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.
        CA Cancer J Clin. 2018; 68: 394-424
        • Lux MP
        • Fasching PA
        • Beckmann MW.
        Hereditary breast and ovarian cancer: review and future perspectives.
        J Mol Med. 2006; 84: 16-28
        • Maxwell KN
        • Domchek SM.
        Cancer treatment according to BRCA1 and BRCA2 mutations.
        Nat Rev Clin Oncol. 2012; 9: 520-528
      1. Daly MB PR, Berry M et al (2019) NCCN Clinical practice guide- lines in oncology. In: Genetic/familial high-risk assessment: breast and ovarian version 3. Accessed 17 Jan, 2019.

        • Laduca H
        • Stuenkel AJ
        • Dolinsky JS
        • et al.
        Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients.
        Genet Med. 2014; 16: 830-837
        • Eliade M
        • Skrzypski J
        • Baurand A
        • et al.
        The transfer of multigene panel testing for hereditary breast and ovarian cancer to healthcare: what are the implications for the management of patients and families?.
        Oncotarget. 2017; 8: 1957-1971
        • Reap L
        • Ahsan S
        • Saleh M.
        Beyond BRCA: a case series examining the advent of multigene panel testing.
        Clin Breast Cancer. 2018; 18: e431-e439
        • Akçay IM
        • Celik E
        • Agaoglu NB
        • et al.
        Germline pathogenic variant spectrum in 25 cancer susceptibility genes in Turkish breast and colorectal cancer patients and elderly controls.
        Int J Cancer. 2020;; 148: 285-295
        • Kraus C
        • Hoyer J
        • Vasileiou G
        • et al.
        Gene panel sequencing in familial breast/ovarian cancer patients identifies multiple novel mutations also in genes others than BRCA1/2.
        Int J Cancer. 2017; 140: 95-102
        • Yadav S
        • Reeves A
        • Campian S
        • Paine A
        • Zakalik D.
        Outcomes of retesting BRCA negative patients using multigene panels.
        Fam Cancer. 2017; 16: 319-328
        • Aloraifi F
        • McDevitt T
        • Martiniano R
        • et al.
        Detection of novel germline mutations for breast cancer in non- BRCA1 /2 families.
        FEBS J. 2015; 282: 3424-3437
        • Tung N
        • Lin NU
        • Kidd J
        • et al.
        Frequency of germline mutations in 25 cancer susceptibility genes in a sequential series of patients with breast cancer.
        J Clin Oncol. 2016; 34: 1460-1468
        • den Dunnen JT
        • Dalgleish R
        • Maglott DR
        • et al.
        HGVS recommendations for the description of sequence variants: 2016 update.
        Hum Mutat. 2016; 37: 564-569
        • Moran O
        • Nikitina D
        • Royer R
        • et al.
        Revisiting breast cancer patients who previously tested negative for BRCA mutations using a 12-gene panel.
        Breast Cancer Res Treat. 2017; 161: 135-142
        • Jarhelle E
        • Riise Stensland HMF
        • GÅM Hansen
        • et al.
        Identifying sequence variants contributing to hereditary breast and ovarian cancer in BRCA1 and BRCA2 negative breast and ovarian cancer patients.
        Sci Rep. 2019; 9: 19986
        • Pinto P
        • Paulo P
        • Santos C
        • et al.
        Implementation of next-generation sequencing for molecular diagnosis of hereditary breast and ovarian cancer highlights its genetic heterogeneity.
        Breast Cancer Res Treat. 2016; 159: 245-256
        • Schubert S
        • van Luttikhuizen JL
        • Auber B
        • et al.
        The identification of pathogenic variants in BRCA1/2 negative, high risk, hereditary breast and/or ovarian cancer patients: high frequency of FANCM pathogenic variants.
        Int J Cancer. 2019; 144: 2683-2694
        • Buys SS
        • Sandbach JF
        • Gammon A
        • et al.
        A study of over 35,000 women with breast cancer tested with a 25-gene panel of hereditary cancer genes.
        Cancer. 2017; 123: 1721-1730
        • Tedaldi G
        • Tebaldi M
        • Zampiga V
        • et al.
        Multiple-gene panel analysis in a case series of 255 women with hereditary breast and ovarian cancer.
        Oncotarget. 2017; 8: 47064-47075
        • Singh J
        • Thota N
        • Singh S
        • et al.
        Screening of over 1000 Indian patients with breast and/or ovarian cancer with a multi-gene panel: prevalence of BRCA1/2 and non-BRCA mutations.
        Breast Cancer Res Treat. 2018; 170: 189-196
        • Slavin TP
        • Maxwell KN
        • Lilyquist J
        • et al.
        The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk.
        npj Breast Cancer. 2017; 3: 1-10
        • Castéra L
        • Harter V
        • Muller E
        • et al.
        Landscape of pathogenic variations in a panel of 34 genes and cancer risk estimation from 5131 HBOC families.
        Genet Med. 2018; 20: 1677-1686
        • Rahman N
        • Seal S
        • Thompson D
        • et al.
        PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene.
        Nat Genet. 2007; 39: 165-167
        • Fernandes PH
        • Saam J
        • Peterson J
        • et al.
        Comprehensive sequencing of PALB2 in patients with breast cancer suggests PALB2 mutations explain a subset of hereditary breast cancer.
        Cancer. 2014; 120: 963-967
        • Wu Y
        • Ouyang T
        • Li J
        • et al.
        Spectrum and clinical relevance of PALB2 germline mutations in 7657 Chinese BRCA1/2-negative breast cancer patients.
        Breast Cancer Res Treat. 2020; 179: 605-614
        • Apostolou P
        • Papasotiriou I.
        Current perspectives on CHEK2 mutations in breast cancer.
        Breast Cancer Targets Ther. 2017; 9: 331-335
        • Southey MC
        • Goldgar DE
        • Winqvist R
        • et al.
        PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS.
        J Med Genet. 2016; 53: 800-811
        • Jerzak KJ
        • Mancuso T
        • Eisen A.
        Ataxia–telangiectasia gene (ATM) mutation heterozygosity in breast cancer: a narrative review.
        Curr Oncol. 2018; 25: e176-e180
        • Maxwell KN
        • Wubbenhorst B
        • D’Andrea K
        • et al.
        Prevalence of mutations in a panel of breast cancer susceptibility genes in BRCA1/2-negative patients with early-onset breast cancer.
        Genet Med. 2015; 17: 630-638
        • Kurian AW
        • Hare EE
        • Mills MA
        • et al.
        Clinical Evaluation of a multiple-gene sequencing panel for hereditary cancer risk assessment.
        J Clin Oncol. 2014; 32: 2001-2009
        • Tung N
        • Battelli C
        • Allen B
        • et al.
        Frequency of mutations in individuals with breast cancer referred for BRCA 1 and BRCA 2 testing using next-generation sequencing with a 25-gene panel.
        Cancer. 2015; 121: 25-33
        • Damineni S
        • Rao VR
        • Kumar S
        • et al.
        Germline mutations of TP53 gene in breast cancer.
        Tumor Biol. 2014; 35: 9219-9227
        • Couch FJ
        • Shimelis H
        • Hu C
        • et al.
        Associations between cancer predisposition testing panel genes and breast cancer.
        JAMA Oncol. 2017; 3: 1190
        • Weber-Lassalle N
        • Hauke J
        • Ramser J
        • et al.
        BRIP1 loss-of-function mutations confer high risk for familial ovarian cancer, but not familial breast cancer.
        Breast Cancer Res. 2018; 20: 7
        • Catucci I
        • Milgrom R
        • Kushnir A
        • et al.
        Germline mutations in BRIP1 and PALB2 in Jewish high cancer risk families.
        Fam Cancer. 2012; 11: 483-491
        • Vysotskaia V
        • Kaseniit KE
        • Bucheit L
        • Ready K
        • Price K
        • Johansen Taber K
        Clinical utility of hereditary cancer panel testing: impact of PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D results on patient management and adherence to provider recommendations.
        Cancer. 126. 2020: 549-558
        • De Nicolo A
        • Tancredi M
        • Lombardi G
        • et al.
        A novel breast cancer-associated BRIP1 (FANCJ/BACH1) germ-line mutation impairs protein stability and function.
        Clin Cancer Res. 2008; 14: 4672-4680
        • Ali M
        • Delozier CD
        • Chaudhary U.
        BRIP-1 germline mutation and its role in colon cancer: presentation of two case reports and review of literature.
        BMC Med Genet. 2019; 20: 75
        • Win AK
        • Young JP
        • Lindor NM
        • et al.
        Colorectal and other cancer risks for carriers and noncarriers from families with a DNA mismatch repair gene mutation: a prospective cohort study.
        J Clin Oncol. 2012; 30: 958-964
        • Harkness EF
        • Barrow E
        • Newton K
        • et al.
        Lynch syndrome caused by MLH1 mutations is associated with an increased risk of breast cancer: a cohort study.
        J Med Genet. 2015; 52: 553-556
        • Goldberg M
        • Bell K
        • Aronson M
        • et al.
        Association between the Lynch syndrome gene MSH2 and breast cancer susceptibility in a Canadian familial cancer registry.
        J Med Genet. 2017; 54: 742-746
        • Dorling L
        • Carvalho S
        • Allen J
        • et al.
        Breast cancer risk genes — association analysis in more than 113,000 women.
        N Engl J Med. 2021; 384: 428-439
        • Aloraifi F
        • McDevitt T
        • Martiniano R
        • et al.
        Detection of novel germline mutations for breast cancer in non-BRCA1/2 families.
        FEBS J. 2015; 282: 3424-3437
        • Hu C
        • Hart SN
        • Gnanaolivu R
        • et al.
        A population-based study of genes previously implicated in breast cancer.
        N Engl J Med. 2021; 384: 440-451
        • Piccinin C
        • Panchal S
        • Watkins N
        • Kim RH.
        An update on genetic risk assessment and prevention: the role of genetic testing panels in breast cancer.
        Expert Rev Anticancer Ther. 2019; 19: 787-801
        • Catana A
        • Apostu AP
        • Antemie R-G.
        Multi gene panel testing for hereditary breast cancer - is it ready to be used?.
        Med Pharm Reports. 2019; 92: 220-225