Mutation analysis of the SLX4/FANCP gene in hereditary breast cancer

Abstract

SLX4 coordinates three structure-specific endonucleases in the DNA damage response. One subtype of Fanconi anaemia, FA-P, has recently been attributed to biallelic SLX4 gene mutations. To investigate whether monoallelic SLX4 gene defects play some role in the inherited component of breast cancer susceptibility, in this study we resequenced the whole SLX4 coding region and flanking untranslated sections in genomic DNA samples obtained from a total of 52 German or Byelorussian patients with familial breast cancer. Selected variants were subsequently screened by RFLP or TaqMan-based assays in an extended set of 965 German breast cancer cases and 985 healthy female controls. The resequencing study uncovered four new SLX4 missense substitutions, each of them in a single breast cancer patient. Three missense substitutions (p.V197A, p.G700R and p.R1034H) were not found in a subsequent screening of 240 additional breast cancer patients, while one missense substitution (p.R237Q) was more common and was detected in a total of 12 cases (1.3%) and seven controls (0.7%) in the Hannover breast cancer study. The rare missense substitution, p.G700R, resides in the conserved BTB domain and was in silico predicted to be pathogenic. Seven additional missense polymorphisms were correlated and formed one haplotype which was, however, neither associated with breast cancer risk nor with survival from breast cancer. In summary, this study did not reveal truncating or clearly pathogenic mutations, but unravelled four new unclassified missense variants at a low frequency. We conclude that there is no evidence for a major role of SLX4 coding variants in the inherited susceptibility towards breast cancer in German and Byelorussian patients, although very rare mutations such as the p.G700R substitution could make a minor contribution.

Sequencing Analysis of SLX4/FANCP Gene in Italian Familial Breast Cancer Cases

“…Our data are in line with those from a small study in 52 German and Byelorussian hereditary breast cancer cases, where extensive genetic variation was shown with lack of any clear pathogenic mutation [26], providing evidence against impact of SLX4 on breast cancer risk in the tested populations. However, SLX4 might impact on breast cancer risk in populations such as Indians, Americans, and Northern Europeans, where the FA families with SLX4 truncating mutations originated from [7], [8].…”

Low prevalence of SLX4 loss-of-function mutations in non-BRCA1/2 breast and/or ovarian cancer families

“…Previous studies conducted in non-BRCA1/2 families failed to detect such alterations. [10][11][12] Interestingly, not a single SLX4 truncating (or consensus splice) variant has been observed in 412,000 exomes from the ESP project, supporting the relevance of our finding.…”

“…Similar observations have been made previously. 10,12 Variants with MAF 40.01, and/or variants in which homozygous carriers have been reported (Supplementary Table 2) were considered likely neutral polymorphisms (not clinically relevant) and discarded for further analysis (N ¼ 23). The truncating mutation p.Glu1517X (not annotated in dbSNP135) was the only unequivocal loss-offunction SLX4 mutation detected.…”

“…So far, this hypothesis has been tested by analyzing SLX4 in 52 German/ Byelorussian, 94 Spanish and 526 Italian non-BRCA1/2 families, but obvious loss-of-function germ-line mutations (or any other evidence supporting a causative role) have not been reported. [10][11][12] To further investigate the role of SLX4 in breast/ovarian cancer susceptibility, we have performed a comprehensive scanning of germ-line mutations in a cohort of 486 index cases from Spanish non-BRCA1/2 families. …”

PALB2 sequencing in Italian familial breast cancer cases reveals a high-risk mutation recurrent in the province of Bergamo

“…2 Mutations in the RAD51C/FANCO gene were originally found in breast/ovarian cancer families. 8 [10][11][12][13] However, subsequent analyses allowed the identification of (i) three unique SLX4-truncating mutations, [14][15][16] indicating these mutations are very rare in familial cases, and (ii) a nonsense mutation in FANCM, whose frequency in cases was, however, not significantly higher than that in controls. 17 Finally, deleterious mutations in the FA gene XRCC2 were detected in families with breast cancer ascertained mainly in Australia.…”