Site-saturation functional screens identify PALB2 missense variants associated with increased breast cancer risk

Nature Communications, vol. 17, pp. 775

Abstract

Loss-of-function variants in PALB2 give rise to defects in DNA damage repair by homologous recombination (HR), increasing the risk of breast cancer in female carriers. However, genetic testing frequently reveals missense variants of uncertain significance (VUS) for which the impact on protein function and cancer risk are unclear. Here we assay 84% of all possible missense variants in 11 out of 13 PALB2 exons using site-saturation functional screens with PARP inhibitor sensitivity as a readout for HR. These exons encode the coiled-coil and WD40 domains, which we identify as the minimal regions required for HR. Furthermore, we reveal the functional impact of 6718 missense variants, classifying 3904 variants as functional (58%), 2422 as intermediate (36%), and 392 as damaging (6%). A burden-type analysis shows that damaging missense variants in PALB2 are associated with a significantly increased risk of breast cancer, similar to that observed for truncating variants. These results will be valuable for the classification of PALB2 missense VUS and clinical management of carriers. The impact of variants of uncertain significance (VUS) on protein function and cancer risk remain unclear. Here, the authors focus on the functional impact of VUS of the PALB2 gene and identify defects in DNA damage repair by homologous recombination associated with increased risk of breast cancer.

Authors 61

1. Rick A.C.M. Boonen Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

2. Sabine Knaup Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

3. Roberta Menafra Aachen Leiden Genome Technology Center Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

4. Merel E. Braspenning Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

5. Magdalena B. Rother Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

6. Petra Kleiblová

   Charles University · General University Hospital in Prague

   Affiliation as printed

   Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic

   Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic

7. Markéta Janatová

   Charles University · General University Hospital in Prague

   Affiliation as printed

   Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic

8. Dina Ruano Aachen Department of Pathology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands

9. Chunling Hu

   Mayo Clinic

   Affiliation as printed

   Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA

10. Huaizhi Huang

    Mayo Clinic

    Affiliation as printed

    Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA

11. Vijai Joseph

    Memorial Sloan Kettering Cancer Center · Cornell University · Weill Cornell Medical Center

    Affiliation as printed

    Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA

    Department of Medicine, Weill Cornell Medical Center, Cornell University, New York, NY, USA

12. Michael T. Conry

    Memorial Sloan Kettering Cancer Center

    Affiliation as printed

    Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA

13. Stephan Heijl

    Bio-Prodict (Netherlands)

    Affiliation as printed

    Bio-Prodict, Nijmegen, The Netherlands

14. Bas Vroling

    Bio-Prodict (Netherlands)

    Affiliation as printed

    Bio-Prodict, Nijmegen, The Netherlands

15. Jelle J. Goeman Aachen Department of Biomedical Data Sciences

    Leiden University Medical Center

    Affiliation as printed

    Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands

16. Matthew J. Varga

    Ambry Genetics (United States)

    Affiliation as printed

    Ambry Genetics, Aliso Viejo, CA, USA

17. Zdeněk Kleibl

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

18. Marta Černá

    University Hospital Plzen · General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

19. Barbora Konecna

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

20. Kateřina Matějková

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

21. Petr Nehasil

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

22. Taťána Ptáčková

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

23. Jana Soukupová

    General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

24. Lenka Foretova

    Masaryk Memorial Cancer Institute

    Affiliation as printed

    Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic

25. Eva Macháčková

    Masaryk Memorial Cancer Institute

    Affiliation as printed

    Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic

26. Vera Krutilkova
    Affiliation as printed

    Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic

27. Spiros Tavandzis
    Affiliation as printed

    Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic

28. Monika Koudová

    Gennet

    Affiliation as printed

    Centre for Medical Genetics and Reproductive Medicine, GENNET, Prague, Czech Republic

29. Leona Černá

    Gennet

    Affiliation as printed

    Centre for Medical Genetics and Reproductive Medicine, GENNET, Prague, Czech Republic

30. Štěpán Chvojka

    Gennet

    Affiliation as printed

    Centre for Medical Genetics and Reproductive Medicine, GENNET, Prague, Czech Republic

31. Ondřej Havránek

    General University Hospital in Prague

    Affiliation as printed

    Institute of Biology and Medical Genetics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

32. Jan Novotny

    General University Hospital in Prague

    Affiliation as printed

    Institute of Biology and Medical Genetics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

33. Kamila Veselá

    General University Hospital in Prague

    Affiliation as printed

    Institute of Biology and Medical Genetics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

34. Michal Vočka

    General University Hospital in Prague

    Affiliation as printed

    Department of Oncology, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

35. Renata Michalovska
    Affiliation as printed

    GHC Genetics, Prague, Czech Republic

36. Lucie Hrušková
    Affiliation as printed

    GHC Genetics, Prague, Czech Republic

37. Helena Paszeková
    Affiliation as printed

    GHC Genetics, Prague, Czech Republic

38. Denisa Schwetzova
    Affiliation as printed

    GHC Genetics, Prague, Czech Republic

39. Zdeňka Vlčková
    Affiliation as printed

    GHC Genetics, Prague, Czech Republic

40. Ivan Šubrt

    University Hospital Plzen

    Affiliation as printed

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

41. Monika Černá

    University Hospital Plzen · General University Hospital in Prague

    Affiliation as printed

    Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

42. Markéta Hejnalová

    University Hospital Plzen

    Affiliation as printed

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

43. Nikol Jedlickova

    University Hospital Plzen

    Affiliation as printed

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

44. Tomas Zavoral

    University Hospital Plzen

    Affiliation as printed

    Institute of Medical Genetics, University Hospital Pilsen, Pilsen, Czech Republic

45. Marcela Kosařová
    Affiliation as printed

    Department of Medical Genetics, Pronatal, Prague, Czech Republic

46. Gabriela Vacínová
    Affiliation as printed

    Department of Medical Genetics, Pronatal, Prague, Czech Republic

47. Mária Janíková

    University Hospital Olomouc · Palacký University Olomouc

    Affiliation as printed

    Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic

48. Romana Kratochvílová

    University Hospital Olomouc · Palacký University Olomouc

    Affiliation as printed

    Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic

49. Václava Curtisová

    University Hospital Olomouc · Palacký University Olomouc

    Affiliation as printed

    Department of Medical Genetics, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic

50. Ondřej Scheinost

    Nemocnice České Budějovice

    Affiliation as printed

    Laboratory of Molecular Biology and Genetics, Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic

51. Petra Duskova

    Nemocnice České Budějovice

    Affiliation as printed

    Laboratory of Molecular Biology and Genetics, Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic

52. Miroslav Fišer
    Affiliation as printed

    PRENET - Laboratore Lekarske Genetiky s.r.o., Pardubice, Czech Republic

53. Daniel Panchártek
    Affiliation as printed

    PRENET - Laboratore Lekarske Genetiky s.r.o., Pardubice, Czech Republic

54. Martin Schwartz
    Affiliation as printed

    PRENET - Laboratore Lekarske Genetiky s.r.o., Pardubice, Czech Republic

55. Lucie Faldynová

    University Hospital Ostrava

    Affiliation as printed

    Department of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava, Czech Republic

56. Michaela Nečesánková
    Affiliation as printed

    Genetika Plzen, Pilsen, Czech Republic

57. Marcy E. Richardson

    Ambry Genetics (United States)

    Affiliation as printed

    Ambry Genetics, Aliso Viejo, CA, USA

58. Susan L. Kloet Aachen Leiden Genome Technology Center Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

59. Fergus J. Couch

    Mayo Clinic

    Affiliation as printed

    Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA

60. Maaike P.G. Vreeswijk Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

61. Haico van Attikum corresponding Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. h.van.attikum@lumc.nl