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Rare variants in XRCC2 as breast cancer susceptibility alleles
  1. Florentine S Hilbers1,
  2. Juul T Wijnen1,2,
  3. Nicoline Hoogerbrugge3,
  4. Jan C Oosterwijk4,
  5. Margriet J Collee5,
  6. Paolo Peterlongo6,7,
  7. Paolo Radice6,7,
  8. Siranoush Manoukian8,
  9. Irene Feroce9,
  10. Fabio Capra6,10,
  11. Fergus J Couch11,
  12. Xianshu Wang11,
  13. Lucia Guidugli11,
  14. Kenneth Offit12,
  15. Sohela Shah12,
  16. Ian G Campbell13–15,
  17. Ella R Thompson13,14,
  18. Paul A James14,16,
  19. Alison H Trainer14,16,
  20. Javier Gracia17,
  21. Javier Benitez17,
  22. Christi J van Asperen2,
  23. Peter Devilee1
  1. 1Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
  2. 2Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
  3. 3Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
  4. 4Department of Genetics, University Medical Center, University of Groningen, Groningen, The Netherlands
  5. 5Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
  6. 6Fondazione Istituto FIRC di Oncologia Molecolare (IFOM), Milan, Italy
  7. 7Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
  8. 8Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
  9. 9Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia (IEO), Milan, Italy
  10. 10Cogentech Cancer Genetic Test Laboratory, Milan, Italy
  11. 11Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
  12. 12Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, USA
  13. 13Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
  14. 14Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
  15. 15Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
  16. 16Familial Cancer Centre, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
  17. 17Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
  1. Correspondence to Florentine S Hilbers, Department of Human Genetics, Leiden University Medical Centre, Albinusdreef 2, Leiden 2333 ZA, The Netherlands; f.s.m.hilbers{at}lumc.nl

Abstract

Background Recently, rare germline variants in XRCC2 were detected in non-BRCA1/2 familial breast cancer cases, and a significant association with breast cancer was reported. However, the breast cancer risk associated with these variants needs further evaluation.

Methods The coding regions and exon–intron boundaries of XRCC2 were scanned for mutations in an international cohort of 3548 non-BRCA1/2 familial breast cancer cases and 1435 healthy controls using various mutation scanning methods. Predictions on functional relevance of detected missense variants were obtained from three different prediction algorithms.

Results The only protein-truncating variant detected was found in a control. Rare non-protein-truncating variants were detected in 20 familial cases (0.6%) and nine healthy controls (0.6%). Although the number of variants predicted to be damaging or neutral differed between prediction algorithms, in all instances these categories were evenly represented among cases and controls.

Conclusions Our data do not confirm an association between XRCC2 variants and breast cancer risk, although a relative risk smaller than two could not be excluded. Variants in XRCC2 are unlikely to explain a substantial proportion of familial breast cancer.

  • Cancer: breast
  • Genetic epidemiology
  • Genetics
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Recently, Park and colleagues identified germline variants in x-ray repair cross-complementing gene-2 (XRCC2 (MIM 600375; NM_005431.1)) in a small number of breast cancer cases with a positive family history for the disease.1 The overall difference in the prevalence of protein-truncating and potentially deleterious rare missense variants between cases and controls was reported to be statistically significant. XRCC2 is involved in the repair of double-strand breaks via homologous recombination. In addition, a homozygous protein-truncating variant in XRCC2 has been detected in a Fanconi anaemia patient with consanguineous parents.2 Since most known high- and moderate-risk breast cancer genes have a function in DNA damage repair, and some are also Fanconi anaemia genes, it seems plausible that mutations in XRCC2 represent breast cancer susceptibility alleles. In order to evaluate the association between XRCC2 variants and breast cancer risk, we analysed the coding regions of XRCC2 in a cohort of 3548 non-BRCA1/2 familial breast cancer cases and 1435 healthy controls derived from various geographical locations. A more detailed description of the study population and mutations-scanning methods can be found in the online supplementary table S1.

We detected only one protein-truncating variant, a one-base-pair deletion, c.343T[8]>[7], present in a 41-year-old Italian control. Rare non-protein-truncating variants in XRCC2 were detected in 20 familial cases (0.6%) and nine healthy controls (0.6%). Polyphen2,3 SIFT4 and AlignGVGD5 were used to predict the effect of detected missense variants on XRCC2 protein function. Although the number of variants predicted to be damaging or neutral differed between the prediction algorithms (table 1), in all instances these categories were evenly represented among cases and controls. The only common variant in the coding region of XRCC2, c.563G>A (rs3218536), was found to have equal minor allele frequencies in familial cases (0.085) and healthy controls (0.086).

Table 1

Rare variants detected in the coding region of XRCC2

Thus, our data do not confirm an association between XRCC2 variants and breast cancer risk. It is possible that the study by Park et al represents a false-positive finding, or, alternatively, our data are a false-negative finding. The association reported by Park et al was based on six likely pathogenic variants in 1308 cases and zero in 1120 controls, which was significant in Fisher's exact test. However, it should be noted that of these six variants, four were considered possibly or probably damaging, based on in silico prediction. Moreover, the number of positives in cases and controls is extremely small, and the statistic is, therefore, likely to be very unstable. In the NHLBI ESP Exome Variant Server,6 a publicly available database describing variants found in exomes of patients with heart, lung and blood disease and healthy controls, rare variants in the coding region of XRCC2 are reported in 0.5% of all exomes, interestingly including two variants resulting in a gained stop codon. Whereas an allele frequency of 0.5% corresponds quite well with our findings, and with the frequency found by Park et al in their cases, it seems at odds with what they detect in controls. Even when including the innocuous missense change, Park et al found one rare XRCC2 variant in 1120 controls (0.09%). This frequency might have been an underestimation given that the study employed High Resolution Melting Curve analyses for mutation detection rather than direct sequencing. Indeed, when specifically testing two truncating variants in another 1436 controls, they found one of them to be positive, indicating that the frequency of pathogenic variants among controls is greater than what is suggested by their finding of zero out 1120.

Our study had 80% power to detect a relative risk of at least 2.1 (p<0.05) for a variant with an allele frequency of 0.5% (see online supplementary figure S1). Our results could, therefore, represent a false-negative finding if the relative risk associated with XRCC2 variants would be lower than two. We note that variants in a number of other DNA damage repair genes, such as CHEK2 and BRIP1, have been associated with breast cancer with such low risks.7 ,8 Park et al did not provide a quantitative estimate of the risk, but in the two families with an XRCC2 variant for which other family members were also available for DNA analysis, cosegregation of the variant with breast cancer was incomplete. This suggests that if an association between XRCC2 and breast cancer exists at all, it may not be very strong. A much larger sample than that studied by us here would need to be analysed to address this.

Another potential source of controversy is the selection criteria used for constituting the case- and control-series. Park and colleagues analysed 1308 breast cancer cases diagnosed before age 45 years and 1120 healthy controls recruited through population-based sampling by the Australian Breast Cancer Family Registry. In addition, they scanned 689 index cases from multicase breast cancer families and 150 male breast cancer cases. The current study included mostly clinic-based cohorts of cases that were forwarded for BRCA-mutation analysis because the prior probability of detecting a BRCA1 or BRCA2 mutation exceeded 10%.9 Hence, both studies attempted to enrich for ‘genetic’ familial breast cancer cases, but in slightly different ways, perhaps leading to different representations of certain case subgroups. Ethnic backgrounds of the cohorts may also differ proportionally between the studies, although European ancestry was represented in both, and variants were detected in comparable frequencies among individuals of Italian, Spanish, Dutch and US origin.

Neither group studied the effect of missense variants on protein function other than by in silico prediction algorithms. Whereas truncating variants are likely to cause reduction in activity of XRCC2 in homologous recombination, the effect of missense variants (if any) may be subtler. If and how loss of XRCC2 function translates into breast cancer risk will be difficult to assess, but the existence of an effect cannot be excluded at this moment. In mice, complete loss of Xrcc2 is embryonic lethal, and leads to increased genetic instability at the cellular level,10 ,11 a hallmark of many breast cancers.

In summary, our data do not confirm an association between XRCC2 variants and breast cancer risk, although a relative risk smaller than two could not be excluded. Our inability to reproduce the previously reported association might point at a more general obstacle in applying exome sequencing in order to find new genes involved in common complex diseases. Exome sequencing, typically, yields many rare candidate variants. Accordingly, the prior odds that any of these variants are truly associated with disease are small, even when such a variant has been detected in two independent exomes. In any case, our data suggest that variants in XRCC2 are unlikely to explain a substantial proportion of familial breast cancer.

Acknowledgments

The LUMC was supported by the Dutch Cancer Society (grant UL 2009-4388). MBCSG thanks Bernard Peissel and Daniela Zaffaroni of Fondazione IRCCS Istituto Nazionale Tumori; Bernardo Bonanni and Monica Barile of Istituto Europeo di Oncologia, and the personnel of the CGT laboratory at IFOM-IEO Campus. MBCSG was funded by grants from Fondazione Italiana per la Ricerca sul Cancro (Special Project ‘Hereditary tumors’), Italian Ministry of Health (‘Progetto Tumori Femminili’), and by Italian citizens who allocated the 5×1000 share of their tax payment in support of the Fondazione IRCCS Istituto Nazionale Tumori, according to Italian laws (INT-Institutional strategic projects ‘5×1000’). The CNIO was partially supported by the Spanish Association against Cancer and FIS08-1120 from the Health Ministry. At MSKK support was from the Breast Cancer Research Fund and Miele Fund.

References

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Supplementary materials

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Footnotes

  • Contributors DNA samples were collected by JTW, NH, JCO, MJC, PP, PR, SM, IF, FJC, XW, KO, IGC, PJ, AHT, JB and CJvA. Genotyping was performed by FSH, FC, LG, SS, ERT and JG. FSH, PP, PR, FJC, KO, IGC, JB, CJvA and PD were involved in the design of the study. FSH and PD coordinated the study.

  • Competing interests None.

  • Ethics approval For each centre, this study was approved by the local ethical committee.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data sharing statement Additional information on the mutation scanning methods are available on request.

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