Potentially pathogenic germline CHEK2 c.319+2T>A among multiple early-onset cancer families

  • Mev Dominguez-Valentin
  • Sigve Nakken
  • Hélène Tubeuf
  • Daniel Vodak
  • Per Olaf Ekstrøm
  • Anke M. Nissen
  • Monika Morak
  • Elke Holinski-Feder
  • Alexandra Martins
  • Pål Møller
  • Eivind Hovig
Original Article

Abstract

To study the potential contribution of genes other than BRCA1/2, PTEN, and TP53 to the biological and clinical characteristics of multiple early-onset cancers in Norwegian families, including early-onset breast cancer, Cowden-like and Li-Fraumeni-like syndromes (BC, CSL and LFL, respectively). The Hereditary Cancer Biobank from the Norwegian Radium Hospital was used to identify early-onset BC, CSL or LFL for whom no pathogenic variants in BRCA1/2, PTEN, or TP53 had been found in routine diagnostic DNA sequencing. Forty-four cancer susceptibility genes were selected and analyzed by our in-house designed TruSeq amplicon-based assay for targeted sequencing. Protein- and RNA splicing-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as the more likely to affect splicing were experimentally analyzed by minigene assay. We identified a CSL individual carrying a variant in CHEK2 (c.319+2T>A, IVS2), here considered as likely pathogenic. Out of the five VUS (BRCA2, CDH1, CHEK2, MAP3K1, NOTCH3) tested in the minigene splicing assay, only NOTCH3 c.14090C>T (p.Ser497Leu) showed a significant effect on RNA splicing, notably by inducing partial skipping of exon 9. Among 13 early-onset BC, CSL and LFL patients, gene panel sequencing identified a potentially pathogenic variant in CHEK2 that affects a canonical RNA splicing signal. Our study provides new information on genetic loci that may affect the risk of developing cancer in these patients and their families, demonstrating that genes presently not routinely tested in molecular diagnostic settings may be important for capturing cancer predisposition in these families.

Keywords

Early-onset breast cancer Cowden-like syndrome Li-Fraumeni-like syndrome Gene panel testing CHEK2 RNA splicing mutations 

Abbreviations

ACMG

American College of Medical Genetics and Genomics

BC

Breast cancer

CS

Cowden syndrome

CRC

Colorectal cancer

CSL

Cowden syndrome like

LF

Li-Fraumeni syndrome

LFL

Li-Fraumeni like syndrome

MMR

Mismatch repair genes

NGS

Next generation sequencing

SNP

Single nucleotide polymorphism

SNVs

Single-nucleotide variants

VUS

Variants of unclassified significance

WT

Wild type

Supplementary material

10689_2017_11_MOESM1_ESM.docx (226 kb)
Supplementary material 1 (DOCX 226 KB)
10689_2017_11_MOESM2_ESM.docx (16 kb)
Supplementary material 2 (DOCX 16 KB)

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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Mev Dominguez-Valentin
    • 1
  • Sigve Nakken
    • 1
  • Hélène Tubeuf
    • 2
    • 3
  • Daniel Vodak
    • 1
  • Per Olaf Ekstrøm
    • 1
  • Anke M. Nissen
    • 4
    • 5
  • Monika Morak
    • 4
    • 5
  • Elke Holinski-Feder
    • 4
    • 5
  • Alexandra Martins
    • 2
  • Pål Møller
    • 1
    • 6
    • 7
  • Eivind Hovig
    • 1
    • 8
    • 9
  1. 1.Department of Tumor Biology, Institute for Cancer ResearchOslo University HospitalOsloNorway
  2. 2.Normandy Centre for Genomic and Personalized MedicineInserm-U1245, UNIROUEN, Normandie UnivRouenFrance
  3. 3.Interactive BiosoftwareRouenFrance
  4. 4.Medizinische Klinik und Poliklinik IV, Campus InnenstadtKlinikum der Universität MünchenMunichGermany
  5. 5.MGZ—Medizinisch Genetisches ZentrumMunichGermany
  6. 6.Department of Human MedicineUniversität Witten/HerdeckeWittenGermany
  7. 7.Department of Medical GeneticsOslo University HospitalOsloNorway
  8. 8.Department of InformaticsUniversity of OsloOsloNorway
  9. 9.Instituteof Cancer Genetics and InformaticsOslo University HospitalOsloNorway

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