Research Article| Volume 262, P118-133, April 2022

Download started.


Evaluation of hereditary/familial breast cancer patients with multigene targeted next generation sequencing panel and MLPA analysis in Turkey


      • Pathogenic variants in BRCA1 and BRCA2 genes, the genes most affected in hereditary breast and ovarian cancer, are detected in ∼15% of women with familial breast cancer. However, disease causing variants in high and moderate risk genes exact frequency is unknown in Turkey.
      • Pathogenic gene variants’ frequency in high and moderate risk genes was found in 17.8% of 495 unrelated individuals diagnosed with breast cancer who are selected for genetic testing according to NCCN criteria for hereditary breast cancer. BRCA1/2 genes were the most affected ones.
      • Gene panel approach for hereditary breast cancer is an effective method for identifying disease causing variants in breast cancer susceptibility genes.
      • MLPA analysis of BRCA1/2 genes should be complementary method of gene panels.


      Breast cancer, a worldwide leading cause of cancer in women, may occur in familial cases. Germline mutations in BRCA1/2 genes are responsible for 15% of the familial cases. With the power of next generation sequencing (NGS) analysis, it is possible to analyze genes related to hereditary susceptibility to breast cancer and investigate the genetic etiology more thoroughly.
      In this study, we investigated 30 genes identified frequent pathogenic alleles in Turkish population. The study includes 495 unrelated individuals diagnosed with breast cancer who are selected for genetic testing according to NCCN criteria for hereditary breast cancer. All patients were analyzed by NGS for BRCA1/2 genes. Deletion/duplication investigation by Multiplex ligation-dependent probe amplification (MLPA) and massive sequencing of 30 breast cancer-related genes (Oncorisk Gene Panel) were performed in a stepwise manner.
      BRCA1/2 variants are the most frequent pathogenic variants which are found in 45 of 495 (9.1%) patients. Four previously unreported, novel, pathogenic variants of BRCA2 gene are identified. In four cases, exonic deletions of BRCA1/2 genes are determined and there is no duplication of these genes. NGS panel investigation involving other moderate-high risk genes contributed genetic diagnosis in an extra 39 out of 419 (9.3%) cases.
      Our study presents the cost effectiveness of the gene panel approach. We suggest that gene panels should be the first-tier genetic testing for hereditary breast cancer and MLPA analysis of BRCA1/2 genes should be investigated as a complementary method of NGS analysis.


      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'


      Subscribe to Cancer Genetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect


        • Ozmen V
        • Ozmen T
        • Dogru V.
        Breast cancer in Turkey; An analysis of 20,000 patients with breast cancer.
        Eur J Breast Health. 2019; 15: 141-146
        • Özmen V
        • Gürdal SÖ
        • Cabioğlu N
        • Özcinar B
        • Özaydın AN
        • Kayhan A
        • et al.
        Cost-effectiveness of breast cancer screening in Turkey, a developing country: results from bahçeşehir mammography screening project.
        Eur J Breast Health. 2017; 13: 117-122
        • Harbeck N
        • Penault-Llorca F
        • Cortes J
        • Gnant M
        • Houssami N
        • Poortmans P
        • et al.
        Breast cancer.
        Nat Rev Dis Prim. 2019; 5: 66
      1. Peshkin BN, Isaacs C. Overview of hereditary breast and ovarian cancer syndromes associated with genes other than BRCA1 /2. In: Post TedW, editor. UpToDate, UpToDate in Waltham, MA.; 2021.

        • Lynch JA
        • Venne V
        • Berse B.
        Genetic tests to identify risk for breast cancer.
        Semin Oncol Nurs. 2015; 31: 100-107
        • Karami F
        • Mehdipour P.
        A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer.
        BioMed Res Int. 2013; 2013: 1-21
        • Fackenthal JD
        • Olopade OI.
        Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations.
        Nat Rev Cancer. 2007; 7: 937-948
        • Couch FJ
        • Shimelis H
        • Hu C
        • Hart SN
        • Polley EC
        • Na J
        • et al.
        Associations between cancer predisposition testing panel genes and breast cancer.
        JAMA Oncol. 2017; 3: 1190-1196
        • Zelli V
        • Compagnoni C
        • Cannita K
        • Capelli R
        • Capalbo C
        • Di Vito
        • Nolfi M
        • et al.
        Applications of next generation sequencing to the analysis of familial breast/ovarian cancer.
        High-Throughput. 2020; 9: 1
        • Couch FJ
        • Nathanson KL
        • Offit K.
        Two decades after BRCA: setting paradigms in personalized cancer care and prevention.
        Science. 2014; 343: 1466-1470
        • Balci A
        • Huusko P
        • Pääkkönen K
        • Launonen V
        • Uner A
        • Ekmekçi A
        • et al.
        Mutation analysis of BRCA1 and BRCA2 in Turkish cancer families: a novel mutation BRCA2 3414del4 found in male breast cancer.
        Eur J Cancer. 1999; 35 (Oxford, England 1990): 707-710
        • Ozdag H
        • Tez M
        • Sayek I
        • Müslümanoglu M
        • Tarcan O
        • Içli F
        • et al.
        Germ line BRCA1 and BRCA2 gene mutations in Turkish breast cancer patients.
        Eur J Cancer. 2000; 36 (Oxford, England : 1990): 2076-2082
        • Yazici H
        • Bitisik O
        • Akisik E
        • Cabioglu N
        • Saip P
        • Muslumanoglu M
        • et al.
        BRCA1 and BRCA2 mutations in Turkish breast/ovarian families and young breast cancer patients.
        Br J Cancer. 2000; 83: 737-742
        • Manguoglu AE
        • Lüleci G
        • Ozçelik T
        • Colak T
        • Schayek H
        • Akaydin M
        • et al.
        Germline mutations in the BRCA1 and BRCA2 genes in Turkish breast/ovarian cancer patients.
        Hum Mutat. 2003; 21: 444-445
        • Güran S
        • Ozet A
        • Dede M
        • Gille JJP
        • Yenen MC.
        Hereditary breast cancer syndromes in a Turkish population. Results of molecular germline analysis.
        Cancer Genet Cytogenet. 2005; 160: 164-168
        • Egeli U
        • Cecener G
        • Tunca B
        • Tasdelen I.
        Novel germline BRCA1 and BRCA2 mutations in Turkish women with breast and/or ovarian cancer and their relatives.
        Cancer Investig. 2006; 24: 484-491
        • Manguoğlu E
        • Güran S
        • Yamaç D
        • Colak T
        • Simşek M
        • Baykara M
        • et al.
        Germline mutations of BRCA1 and BRCA2 genes in Turkish breast, ovarian, and prostate cancer patients.
        Cancer Genet Cytogenet. 2010; 203: 230-237
        • Manguoğlu E
        • Güran S
        • Yamaç D
        • Simşek M
        • Akdeniz S
        • Colak T
        • et al.
        Genomic large rearrangement screening of BRCA1 and BRCA2 genes in high-risk Turkish breast/ovarian cancer patients by using multiplex ligation-dependent probe amplification assay.
        Cancer Investig. 2011; 29: 73-77
        • Aydin F
        • Akagun T
        • Yildiz B
        • Fidan E
        • Ozdemir F
        • Kavgaci H.
        Clinicopathologic characteristics and BRCA-1/BRCA-2 mutations of Turkish patients with breast cancer.
        Bratislavske Lekarske Listy. 2011; 112: 521-523
        • Cecener G
        • Egeli U
        • Tunca B
        • Erturk E
        • Ak S
        • Gokgoz S
        • et al.
        BRCA1/2 germline mutations and their clinical importance in Turkish breast cancer patients.
        Cancer Investig. 2014; 32: 375-387
        • Cecener G
        • Guney Eskiler G
        • Egeli U
        • Tunca B
        • Alemdar A
        • Gokgoz S
        • et al.
        Association of PALB2 sequence variants with the risk of early-onset breast cancer in patients from Turkey.
        Mol Biol Rep. 2016; 43: 1273-1284
        • Yazıcı H
        • Kılıç S
        • Akdeniz D
        • Şükrüoğlu Ö
        • Tuncer ŞB
        • Avşar M
        • et al.
        Frequency of rearrangements versus small indels mutations in BRCA1 and BRCA2 genes in Turkish patients with high risk breast and ovarian cancer.
        Eur J Breast Health. 2018; 14: 93-99
        • Bisgin A
        • Boga I
        • Yalav O
        • Sonmezler O
        • Tug Bozdogan S
        BRCA mutation characteristics in a series of index cases of breast cancer selected independent of family history.
        Breast J. 2019; 25: 1029-1033
        • Geredeli C
        • Yasar N
        • Sakin A.
        Germline mutations in BRCA1 and BRCA2 in breast cancer patients with high genetic risk in turkish population.
        Int J Breast Cancer. 2019; 20199645147
        • Demir S
        • Tozkir H
        • Gurkan H
        • Atli EI
        • Yalcintepe S
        • Atli E
        • et al.
        Genetic screening results of individuals with high risk BRCA-related breast/ovarian cancer in Trakya region of Turkey.
        J BUON : Off J Balkan Union Oncol. 2020; 25: 1337-1347
        • Bahsi T
        • Erdem HB.
        Spectrum of BRCA1/BRCA2 variants in 1419 Turkish breast and ovarian cancer patients: a single center study.
        Turkish J Biochem. 2020; 45: 83-90
        • Cecener G
        • Sabour Takanlou L
        • Sabour Takanlou M
        • Egeli U
        • Eskiler GG
        • Aksoy S
        • et al.
        Clinicopathologic features and genetic characteristics of the BRCA1/2 mutation in Turkish breast cancer patients.
        Cancer Genet. 2020; 240: 23-32
        • Peker Eyüboğlu İ
        • Yenmiş G
        • Bingöl EN
        • Yüksel Ş
        • Tokat F
        • Özbek P
        • et al.
        Next-generation sequencing identifies BRCA1 and/or BRCA2 mutations in women at high hereditary risk for breast cancer with shorter telomere length.
        OMICS: J Integr Biol. 2020; 24: 5-15
        • Akcay IM
        • Celik E
        • Agaoglu NB
        • Alkurt G
        • Kizilboga Akgun T
        • Yildiz J
        • et al.
        Germline pathogenic variant spectrum in 25 cancer susceptibility genes in Turkish breast and colorectal cancer patients and elderly controls.
        Int J Cancer. 2021; 148: 285-295
        • Atcı MM
        • Geredeli Ç
        • Ay S
        • Sakin A
        • Ertürk B
        • Seçmeler Ş
        • et al.
        Clinical and pathological characteristics of patients with high-risk breast cancer based on BRCA mutation profiles: a retrospective study.
        Eur J Breast Health. 2021; 17: 123-127
      2. National Comprehensive Cancer Network. Genetic/familial high-risk assessment: breast, ovarian, and pancreatic (Version 2.2021) 2021. (accessed June 18, 2021).

        • Petrucelli N
        • Daly MB
        • Pal T.
        BRCA1- and BRCA2-associated hereditary breast and ovarian cancer.
        University of Washington, Seattle (WA)2021 (Seattle1993-2021)
        • Richards S
        • Aziz N
        • Bale S
        • Bick D
        • Das S
        • Gastier-Foster J
        • et al.
        Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American college of medical genetics and genomics and the association for molecular pathology.
        Genet Med. 2015; 17: 405-423
        • Kalia SS
        • Adelman K
        • Bale SJ
        • Chung WK
        • Eng C
        • Evans JP
        • et al.
        Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.
        Genet Med. 2017; 19: 249-255
      3. Abbadessa B, Early DS, Friedman M, Giardiello FM, Glaser K, Halverson AL, et al. Continue NCCN guidelines panel disclosures NCCN guidelines version 2.2020 colorectal cancer screening. 2020.

      4. T.C. Sağlık Bakanlığı Sağlık Hizmetleri Genel Müdürlüğü. Meme Kanseri Korunma, Tarama, Tanı, Tedavi ve İzlem Klinik Rehberi (Versiyon 1.0). 2020.

        • Ewald IP
        • Cossio SL
        • Palmero EI
        • Pinheiro M
        • Nascimento IL de O
        • Machado TMB
        • et al.
        BRCA1 and BRCA2 rearrangements in Brazilian individuals with hereditary breast and ovarian cancer syndrome.
        Genet Mol Biol. 2016; 39: 223-231
        • Palma MD
        • Domchek SM
        • Stopfer J
        • Erlichman J
        • Siegfried JD
        • Tigges-Cardwell J
        • et al.
        The relative contribution of point mutations and genomic rearrangements in BRCA1 and BRCA2 in high-risk breast cancer families.
        Cancer Res. 2008; 68: 7006-7014
        • Judkins T
        • Rosenthal E
        • Arnell C
        • Burbidge LA
        • Geary W
        • Barrus T
        • et al.
        Clinical significance of large rearrangements in BRCA1 and BRCA2.
        Cancer. 2012; 118: 5210-5216
        • Kang P
        • Mariapun S
        • Phuah SY
        • Lim LS
        • Liu J
        • Yoon S-Y
        • et al.
        Large BRCA1 and BRCA2 genomic rearrangements in Malaysian high risk breast-ovarian cancer families.
        Breast Cancer Res Treatm. 2010; 124: 579-584
        • Hu C
        • Hart SN
        • Gnanaolivu R
        • Huang H
        • Lee KY
        • Na J
        • et al.
        A population-based study of genes previously implicated in breast cancer.
        N Engl J Med. 2021; 384: 440-451
        • Tsaousis GN
        • Papadopoulou E
        • Apessos A
        • Agiannitopoulos K
        • Pepe G
        • Kampouri S
        • et al.
        Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations.
        BMC Cancer. 2019; 19: 535
        • Dorling L
        • Carvalho S
        • Allen J
        • González-Neira A
        • Luccarini C
        • et al.
        Breast cancer risk genes - association analysis in more than 113,000 women.
        N Engl J Med. 2021; 384: 428-439
        • Richardson ME
        • Hu C
        • Lee KY
        • LaDuca H
        • Fulk K
        • Durda KM
        • et al.
        Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance.
        Am J Hum Genet. 2021; 108: 458-468