The Spectrum of FANCM Protein Truncating Variants in European Breast Cancer Cases

Germline protein truncating variants (PTVs) in the FANCM gene have been associated with a 2–4-fold increased breast cancer risk in case-control studies conducted in different European populations. However, the distribution and the frequency of FANCM PTVs in Europe have never been investigated. In the present study, we collected the data of 114 European female breast cancer cases with FANCM PTVs ascertained in 20 centers from 13 European countries. We identified 27 different FANCM PTVs. The p.Gln1701* PTV is the most common PTV in Northern Europe with a maximum frequency in Finland and a lower relative frequency in Southern Europe. On the contrary, p.Arg1931* seems to be the most common PTV in Southern Europe. We also showed that p.Arg658*, the third most common PTV, is more frequent in Central Europe, and p.Gln498Thrfs*7 is probably a founder variant from Lithuania. Of the 23 rare or unique FANCM PTVs, 15 have not been previously reported. We provide here the initial spectrum of FANCM PTVs in European breast cancer cases

Mutation Analysis of the RAD51C and RAD51D Genes in High-Risk Ovarian Cancer Patients and Families from the Czech Republic.

Recent studies have conferred that the RAD51C and RAD51D genes, which code for the essential proteins involved in homologous recombination, are ovarian cancer (OC) susceptibility genes that may explain genetic risks in high-risk patients. We performed a mutation analysis in 171 high-risk BRCA1 and BRCA2 negative OC patients, to evaluate the frequency of hereditary RAD51C and RAD51D variants in Czech population. The analysis involved direct sequencing, high resolution melting and multiple ligation-dependent probe analysis. We identified two (1.2%) and three (1.8%) inactivating germline mutations in both respective genes, two of which (c.379_380insG, p.P127Rfs*28 in RAD51C and c.879delG, p.C294Vfs*16 in RAD51D) were novel. Interestingly, an indicative family cancer history was not present in four carriers. Moreover, the ages at the OC diagnoses in identified mutation carriers were substantially lower than those reported in previous studies (four carriers were younger than 45 years). Further, we also described rare missense variants, two in RAD51C and one in RAD51D whose clinical significance needs to be verified. Truncating mutations and rare missense variants ascertained in OC patients were not detected in 1226 control samples. Although the cumulative frequency of RAD51C and RAD51D truncating mutations in our patients was lower than that of the BRCA1 and BRCA2 genes, it may explain OC susceptibility in approximately 3% of high-risk OC patients. Therefore, an RAD51C and RAD51D analysis should be implemented into the comprehensive multi-gene testing for high-risk OC patients, including early-onset OC patients without a family cancer history

The Spectrum of FANCM Protein Truncating Variants in European Breast Cancer Cases

Predisposició al càncer de mama; Factors de risc de càncer de mama; Espectre de mutacióPredisposición al cáncer de mama; Factores de riesgo de cáncer de mama; Espectro de mutaciónBreast cancer predisposition; Breast cancer risk factors; Mutation spectrumGermline protein truncating variants (PTVs) in the FANCM gene have been associated with a 2–4-fold increased breast cancer risk in case-control studies conducted in different European populations. However, the distribution and the frequency of FANCM PTVs in Europe have never been investigated. In the present study, we collected the data of 114 European female breast cancer cases with FANCM PTVs ascertained in 20 centers from 13 European countries. We identified 27 different FANCM PTVs. The p.Gln1701* PTV is the most common PTV in Northern Europe with a maximum frequency in Finland and a lower relative frequency in Southern Europe. On the contrary, p.Arg1931* seems to be the most common PTV in Southern Europe. We also showed that p.Arg658*, the third most common PTV, is more frequent in Central Europe, and p.Gln498Thrfs*7 is probably a founder variant from Lithuania. Of the 23 rare or unique FANCM PTVs, 15 have not been previously reported. We provide here the initial spectrum of FANCM PTVs in European breast cancer cases.This research was partially funded by Associazione Italiana Ricerca sul Cancro (AIRC; IG2015 no.16732) to P. Peterlongo, a fellowship from Fondazione Umberto Veronesi to G. Figlioli and by the Italian Ministry of Health with Ricerca Corrente and 5x1000 funds. E. Tham is supported by Region Stockholm (ALF). The Czech study was supported by a grant of the Ministry of Health of the Czech Republic NV16-29959A. CNIO study was partially supported by projects PI16/00440 and PI19/00640, supported by the Instituto de Salud Carlos III, cofunded by European Regional Development Fund (ERDF), the Spanish Network on Rare Diseases (CIBERER) and BRIDGES project H2020. Financial support for GENESIS resource and genotyping was provided by the Ligue Nationale contre le Cancer (grants PRE05/DSL, PRE07/DSL, PRE11/NA), the French National Institute of Cancer (INCa grant No b2008-029/LL-LC) and the comprehensive cancer center SiRIC, (Site de Recherche Intégrée sur le Cancer: Grant INCa-DGOS-4654). HEBCS was funded by Helsinki University Hospital Research Fund, Sigrid Juselius Foundation, The cancer Society of Finland. A.Vega is supported by the Spanish Health Research Foundation, Instituto de Salud Carlos III (ISCIII) through Research Activity Intensification Program (contract grant numbers: INT15/00070, INT16/00154, INT17/00133), and through Centro de Investigación Biomédica en Red de Enferemdades Raras CIBERER (ACCI 2016: ER17P1AC7112/2018); Autonomous Government of Galicia (Consolidation and structuring program: IN607B), and by the Fundación Mutua Madrileña (call 2018). This work was supported by the Australian National Health and Medical Research Council (APP1029974 and APP1074383) and by a Victorian Life Sciences Computation Initiative grant (number VR0182) on its Peak Computing Facility, an initiative of the Victorian Government. T.N-D is a Career Development Fellow of the National Breast Cancer Foundation (Australia, ECF-17-001). M.C.S. is a National Health and Medical Research Council (Australia) Senior Research Fellow. The Hungarian Breast and Ovarian Cancer Study was supported by Hungarian Research Grants KTIA-OTKA CK-80745 and NKFI OTKA K-112228 to E. Olah. Lithuanian study was supported by The Research Council of Lithuania grant SEN18/2015 and P-MIP-20-25 to R. Janavicius. The ICO was supported by the Carlos III National Health Institute funded by FEDER funds—a way to build Europe—[PI16/00563, PI19/00553 and CIBERONC]; the Government of Catalonia [Pla estratègic de recerca i innovació en salut (PERIS) Project MedPerCan, 2017SGR1282 and 2017SGR496]; and CERCA program

Criteria for the enrollment of high-risk <i>BRCA1</i>- and <i>BRCA2</i>-negative individuals in this study and number of identified mutations in each group.

<p>BC—breast cancer; HBOC—hereditary breast and ovarian cancer; HOC—hereditary ovarian cancer; OC—ovarian cancer; y/o—years old. Number of rare missense variants are in brackets.</p><p>Criteria for the enrollment of high-risk <i>BRCA1</i>- and <i>BRCA2</i>-negative individuals in this study and number of identified mutations in each group.</p

cDNA analysis of patient No.1273 uncovered with an intronic variant c.1026+5_1026+7delGTA causing RAD51C out-of-frame exon 8 skipping.

<p>The electrophoresis (left) of PCR products amplified with primers located in exon 5 and 3’ UTR sequence (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0127711#pone.0127711.s001" target="_blank">S1 Table</a>) shows two products in a patient No.1273 compared to a wild-type control (C) sample. Sequencing chromatogram of the patient’s PCR product shows the presence of aberrantly spliced mRNA with exon 8 skipping.</p

Overall survival (OS; upper panels) and progression-free survival (PFS; lower panels) in all NHL patients (regardless of histology subtype) classified according to the type of <i>CHEK2</i> alterations.

<p>Panels show: <b>A.</b> the influence of all alterations affecting the CHK2 coding sequence (cds; HR_OS = 1.6; 95% CI 0.79–3.24 and HR_PFS = 2.1; 95% CI 1.12–4.05); <b>B.</b> the influence of the I157T mutation (HR_OS = 1.5; 95% CI 0.62–3.70 and HR_PFS = 3.7; 95% CI 1.42–9.43) and <b>C.</b> the influence of the c.319+43dupA variant (HR_OS = 0.8; 95% CI 0.50–1.15 and HR_PFS = 0.6; 95% CI 0.44–0.89).</p

Association of Germline <i>CHEK2</i> Gene Variants with Risk and Prognosis of Non-Hodgkin Lymphoma

<div><p>The checkpoint kinase 2 gene (<i>CHEK2</i>) codes for the CHK2 protein, an important mediator of the DNA damage response pathway. The <i>CHEK2</i> gene has been recognized as a multi-cancer susceptibility gene; however, its role in non-Hodgkin lymphoma (NHL) remains unclear. We performed mutation analysis of the entire <i>CHEK2</i> coding sequence in 340 NHL patients using denaturing high-performance liquid chromatography (DHPLC) and multiplex ligation-dependent probe amplification (MLPA). Identified hereditary variants were genotyped in 445 non-cancer controls. The influence of <i>CHEK2</i> variants on disease risk was statistically evaluated. Identified <i>CHEK2</i> germline variants included four truncating mutations (found in five patients and no control; P = 0.02) and nine missense variants (found in 21 patients and 12 controls; P = 0.02). Carriers of non-synonymous variants had an increased risk of NHL development [odds ratio (OR) 2.86; 95% confidence interval (CI) 1.42–5.79] and an unfavorable prognosis [hazard ratio (HR) of progression-free survival (PFS) 2.1; 95% CI 1.12–4.05]. In contrast, the most frequent intronic variant c.319+43dupA (identified in 22% of patients and 31% of controls) was associated with a decreased NHL risk (OR = 0.62; 95% CI 0.45–0.86), but its positive prognostic effect was limited to NHL patients with diffuse large B-cell lymphoma (DLBCL) treated by conventional chemotherapy without rituximab (HR-PFS 0.4; 94% CI 0.17–0.74). Our results show that germ-line <i>CHEK2</i> mutations affecting protein coding sequence confer a moderately-increased risk of NHL, they are associated with an unfavorable NHL prognosis, and they may represent a valuable predictive biomarker for patients with DLBCL.</p></div

Germline intronic and silent alterations in the <i>CHEK2</i> gene in NHL patients and controls with their frequencies and related odds ratios (OR).

<p>^a New alterations</p><p>^bThe c.319+43dupA alteration also did not show a statistically significant deviation from the Hardy-Weinberg equilibrium in any of the analyzed groups (all p > 0.05).</p><p>Germline intronic and silent alterations in the <i>CHEK2</i> gene in NHL patients and controls with their frequencies and related odds ratios (OR).</p