Association and performance of polygenic risk scores for breast cancer among French women presenting or not a familial predisposition to the disease

BACKGROUND

Three partially overlapping breast cancer polygenic risk scores (PRS) comprising 77, 179 and 313 SNPs have been proposed for European-ancestry women by the Breast Cancer Association Consortium (BCAC) for improving risk prediction in the general population. However, the effect of these SNPs may vary from one country to another and within a country because of other factors.

OBJECTIVE

To assess their associated risk and predictive performance in French women from (1) the CECILE population-based case-control study, (2) BRCA1 or BRCA2 (BRCA1/2) pathogenic variant (PV) carriers from the GEMO study, and (3) familial breast cancer cases with no BRCA1/2 PV and unrelated controls from the GENESIS study.

RESULTS

All three PRS were associated with breast cancer in all studies, with odds ratios per standard deviation varying from 1.7 to 2.0 in CECILE and GENESIS, and hazard ratios varying from 1.1 to 1.4 in GEMO. The predictive performance of PRS₃₁₃ in CECILE was similar to that reported in BCAC but lower than that in GENESIS (area under the receiver operating characteristic curve (AUC) = 0.67 and 0.75, respectively). PRS were less performant in BRCA2 and BRCA1 PV carriers (AUC = 0.58 and 0.54 respectively).

CONCLUSION

Our results are in line with previous validation studies in the general population and in BRCA1/2 PV carriers. Additionally, we showed that PRS may be of clinical utility for women with a strong family history of breast cancer and no BRCA1/2 PV, and for those carrying a predicted PV in a moderate-risk gene like ATM, CHEK2 or PALB2.

Diagnostic chest X-rays and breast cancer risk among women with a hereditary predisposition to breast cancer unexplained by a BRCA1 or BRCA2 mutation

Background

Diagnostic ionizing radiation is a risk factor for breast cancer (BC). BC risk increases with increased dose to the chest and decreases with increased age at exposure, with possible effect modification related to familial or genetic predisposition. While chest X-rays increase the BC risk of BRCA1/2 mutation carriers compared to non-carriers, little is known for women with a hereditary predisposition to BC but who tested negative for a BRCA1 or BRCA2 (BRCA1/2) mutation.

Methods

We evaluated the effect of chest X-rays from diagnostic medical procedures in a dataset composed of 1552 BC cases identified through French family cancer clinics and 1363 unrelated controls. Participants reported their history of X-ray exposures in a detailed questionnaire and were tested for 113 DNA repair genes. Logistic regression and multinomial logistic regression models were used to assess the association with BC.

Results

Chest X-ray exposure doubled BC risk. A 3% increased BC risk per additional exposure was observed. Being 20 years old or younger at first exposure or being exposed before first full-term pregnancy did not seem to modify this risk. Birth after 1960 or carrying a rare likely deleterious coding variant in a DNA repair gene other than BRCA1/2 modified the effect of chest X-ray exposure.

Conclusion

Ever/never chest X-ray exposure increases BC risk 2-fold regardless of age at first exposure and, by up to 5-fold when carrying 3 or more rare variants in a DNA repair gene.

Further studies are needed to evaluate other DNA repair genes or variants to identify those which could modify radiation sensitivity. Identification of subpopulations that are more or less susceptible to ionizing radiation is important and potentially clinically relevant.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-021-01456-1.

A new hybrid record linkage process to make epidemiological databases interoperable: application to the GEMO and GENEPSO studies involving BRCA1 and BRCA2 mutation carriers

BACKGROUND

Linking independent sources of data describing the same individuals enable innovative epidemiological and health studies but require a robust record linkage approach. We describe a hybrid record linkage process to link databases from two independent ongoing French national studies, GEMO (Genetic Modifiers of BRCA1 and BRCA2), which focuses on the identification of genetic factors modifying cancer risk of BRCA1 and BRCA2 mutation carriers, and GENEPSO (prospective cohort of BRCAx mutation carriers), which focuses on environmental and lifestyle risk factors.

METHODS

To identify as many as possible of the individuals participating in the two studies but not registered by a shared identifier, we combined probabilistic record linkage (PRL) and supervised machine learning (ML). This approach (named "PRL + ML") combined together the candidate matches identified by both approaches. We built the ML model using the gold standard on a first version of the two databases as a training dataset. This gold standard was obtained from PRL-derived matches verified by an exhaustive manual review. Results The Random Forest (RF) algorithm showed a highest recall (0.985) among six widely used ML algorithms: RF, Bagged trees, AdaBoost, Support Vector Machine, Neural Network. Therefore, RF was selected to build the ML model since our goal was to identify the maximum number of true matches. Our combined linkage PRL + ML showed a higher recall (range 0.988-0.992) than either PRL (range 0.916-0.991) or ML (0.981) alone. It identified 1995 individuals participating in both GEMO (6375 participants) and GENEPSO (4925 participants).

CONCLUSIONS

Our hybrid linkage process represents an efficient tool for linking GEMO and GENEPSO. It may be generalizable to other epidemiological studies involving other databases and registries.

Gene- and pathway-level analyses of iCOGS variants highlight novel signaling pathways underlying familial breast cancer susceptibility

Single‐nucleotide polymorphisms (SNPs) in over 180 loci have been associated with breast cancer (BC) through genome‐wide association studies involving mostly unselected population‐based case‐control series. Some of them modify BC risk of women carrying a BRCA1 or BRCA2 (BRCA1/2) mutation and may also explain BC risk variability in BC‐prone families with no BRCA1/2 mutation. Here, we assessed the contribution of SNPs of the iCOGS array in GENESIS consisting of BC cases with no BRCA1/2 mutation and a sister with BC, and population controls. Genotyping data were available for 1281 index cases, 731 sisters with BC, 457 unaffected sisters and 1272 controls. In addition to the standard SNP‐level analysis using index cases and controls, we performed pedigree‐based association tests to capture transmission information in the sibships. We also performed gene‐ and pathway‐level analyses to maximize the power to detect associations with lower‐frequency SNPs or those with modest effect sizes. While SNP‐level analyses identified 18 loci, gene‐level analyses identified 112 genes. Furthermore, 31 Kyoto Encyclopedia of Genes and Genomes and 7 Atlas of Cancer Signaling Network pathways were highlighted (false discovery rate of 5%). Using results from the “index case‐control” analysis, we built pathway‐derived polygenic risk scores (PRS) and assessed their performance in the population‐based CECILE study and in a data set composed of GENESIS‐affected sisters and CECILE controls. Although these PRS had poor predictive value in the general population, they performed better than a PRS built using our SNP‐level findings, and we found that the joint effect of family history and PRS needs to be considered in risk prediction models.

What's new?

Genetic studies have identified more than 180 single‐nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility, but these studies are reaching their limits. Here, the authors evaluated SNPs in the iCOGS genotyping array using a multilevel approach, including single variant, gene, and pathway analyses. They measured the contribution of the SNPs to breast cancer in patients who have a sister with breast cancer but do not carry a BRCA1/2 mutation. They showed that a pathway‐derived polygenic risk score performed poorly in the general population, and that the best predictive model must include family history.

Abstract P6-08-12: Feasibility of a nation-wide family-based study to assess cancer risks in families with a predicted pathogenic variant identified through hereditary breast and ovary multi-gene panel testing: The TUMOSPEC study

Background. Assessment of the age-dependent cancer risk conferred by germline predicted pathogenic variants (PPV) in cancer susceptibility genes is often hampered by the way the data are collected. Cohort-based data frequently contain an overrepresentation of patients carrying a gene variant of interest and an underrepresentation of cancer-free gene variant carriers. In order to overcome this problem, penetrance estimates can be grounded on family-based study designs, through the evaluation of index patients (IP) and their family relatives. The purpose of the TUMOSPEC study is to estimate the penetrance of PPV in genes whose literature data are currently inaccurate or limited and to determine their associated tumour spectrum. This will lead to an appropriate assessment of the clinical utility of testing these genes. Methods. IP are enrolled consecutively among patients who are being offered a germline genetic test in a hereditary breast and ovary cancer (HBOC) context in a participating cancer genetics clinics. A panel of 24 genes (ATM, BAP1, BARD1, BRIP1, CHEK2, FANCM, FAM175A, MRE11A, NBN, STK11, RINT1, XRCC2, PALB2, MLH1, MSH2, MSH6, PMS2, CDH1, PTEN, RAD50, RAD51B, RAD51C, RAD51D, TP53) is tested in parallel of BRCA1 and BRCA2. If a PPV is identified, the IP is asked to give her/his first- and second-degree relatives and cousins address, regardless of their health status. Each relative is then contacted by the study coordinating centre (CC) to be invited. Each participant completes an epidemiological questionnaire addressing personal medical history and exposure to various risk factors, and provides a saliva sample to determine if he/she carries the familial PPV. The CC collects questionnaires, family history, clinical and genetic data. Results. Enrolment for the feasibility study takes place between Sep. 2017 and Dec. 2019 at each of the 46 participating french clinics. In June 2019, the study included 3,298 IP. So far, the CC received 1,241 TUMOSPEC panel results (37.6%) with a mean delay of 5 months [0.7 -17.5]. Among them, 169 carried a PPV in at least one of the genes (totalizing 183 PPV). Additionally, 44 IP with PPV identified beforehand were enrolled (table 1). Relatives’ invitation of these 213 IP began in June 2018. Among the relatives of the first 29 index cases contacted so far, 4.6 relatives per family consented to participate. Conclusions. The feasibility study showed that inclusion process is well adapted and that the communication between the various partners (clinicians, biologists, investigators and study participants) is quite smooth. Rates of inclusion for invited relatives (50%), for IP questionnaire completion (45%) and relatives biological sample collection (50%) are also very satisfactory and yet underestimated due to the recent start of relatives inclusions. Overall, this study shows that it is feasible to conduct a large-scale study to gather sufficient number of positive families for each gene included in the panel in a reasonable interval of time. This on-going national effort will allow to appropriately assess cancer risks cancer in families with a PPV in a gene often included in HBOC multi-gene panels. This is an essential step to optimize clinical management guidelines specific to each gene, and will represent a valuable resource for future research on the genetics of breast and ovary cancers.

Number of PPV identified in IPGeneATMCHEK2PALB2RAD51CBRIP1RAD51DMSH6RAD50PMS2MRE11ANBNMSH2MLH1CDH1BARD1TP53STK11XRCC2RINT1BAP1RAD51BFAM175AFANCMPTENNumber of PPV512019161111111010999865544322110

Citation Format: Olivier Caron, Séverine Eon-Marchais, Sarah Bonnet-Boissinot, Juana Beauvallet, Marie-Gabrielle Dondon, Chrystelle Colas, Florence Coulet, Capucine Delnatte, Claude Houdayer, Christine Lasset, Jérôme Lemonnier, Michel Longy, Catherine Nogues, Dominique Stoppa-Lyonnet, Dominique Vaur, Fabienne Lesueur, Nadine Andrieu, TUMOSPEC Investigators Group, UNICANCER Groupe Génétique et Cancer. Feasibility of a nation-wide family-based study to assess cancer risks in families with a predicted pathogenic variant identified through hereditary breast and ovary multi-gene panel testing: The TUMOSPEC study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-12.

Familial breast cancer and DNA repair genes: Insights into known and novel susceptibility genes from the GENESIS study, and implications for multigene panel testing

Pathogenic variants in BRCA1 and BRCA2 only explain the underlying genetic cause of about 10% of hereditary breast and ovarian cancer families. Because of cost‐effectiveness, multigene panel testing is often performed even if the clinical utility of testing most of the genes remains questionable. The purpose of our study was to assess the contribution of rare, deleterious‐predicted variants in DNA repair genes in familial breast cancer (BC) in a well‐characterized and homogeneous population. We analyzed 113 DNA repair genes selected from either an exome sequencing or a candidate gene approach in the GENESIS study, which includes familial BC cases with no BRCA1 or BRCA2 mutation and having a sister with BC (N = 1,207), and general population controls (N = 1,199). Sequencing data were filtered for rare loss‐of‐function variants (LoF) and likely deleterious missense variants (MV). We confirmed associations between LoF and MV in PALB2, ATM and CHEK2 and BC occurrence. We also identified for the first time associations between FANCI, MAST1, POLH and RTEL1 and BC susceptibility. Unlike other associated genes, carriers of an ATM LoF had a significantly higher risk of developing BC than carriers of an ATM MV (OR_LoF = 17.4 vs. OR_MV = 1.6; p_Het = 0.002). Hence, our approach allowed us to specify BC relative risks associated with deleterious‐predicted variants in PALB2, ATM and CHEK2 and to add MAST1, POLH, RTEL1 and FANCI to the list of DNA repair genes possibly involved in BC susceptibility. We also highlight that different types of variants within the same gene can lead to different risk estimates.

What's new?

Pathogenic variants in BRCA1 and BRCA2 only explain the genetic cause of about 10% of hereditary breast and ovarian cancer families, and the clinical usefulness of testing other genes following the recent introduction of cost‐effective multigene panel sequencing in diagnostics laboratories remains questionable. This large case‐control study describes genetic variation in 113 DNA repair genes and specifies breast cancer relative risks associated with rare deleterious‐predicted variants in PALB2, ATM, and CHEK2. Importantly, different types of variants within the same gene can lead to different risk estimates. The results may help improve risk prediction models and define gene‐specific consensus management guidelines.

Morphology and genomic hallmarks of breast tumours developed by ATM deleterious variant carriers

Background

The ataxia telangiectasia mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear histopathological and molecular features of breast tumours occurring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumour signature may help in patient management.

Methods

To characterise hallmarks of ATM-associated tumours, we performed systematic pathology review of tumours from 21 participants from ataxia-telangiectasia families and 18 participants from HBOC families, as well as copy number profiling on a subset of 23 tumours. Morphology of ATM-associated tumours was compared with that of 599 patients with no BRCA1 and BRCA2 mutations from a hospital-based series, as well as with data from The Cancer Genome Atlas. Absolute copy number and loss of heterozygosity (LOH) profiles were obtained from the OncoScan SNP array. In addition, we performed whole-genome sequencing on four tumours from ATM loss-of-function variant carriers with available frozen material.

Results

We found that ATM-associated tumours belong mostly to the luminal B subtype, are tetraploid and show LOH at the ATM locus at 11q22–23. Unlike tumours in which BRCA1 or BRCA2 is inactivated, tumours arising in ATM deleterious variant carriers are not associated with increased large-scale genomic instability as measured by the large-scale state transitions signature. Losses at 13q14.11-q14.3, 17p13.2-p12, 21p11.2-p11.1 and 22q11.23 were observed. Somatic alterations at these loci may therefore represent biomarkers for ATM testing and harbour driver mutations in potentially ‘druggable’ genes that would allow patients to be directed towards tailored therapeutic strategies.

Conclusions

Although ATM is involved in the DNA damage response, ATM-associated tumours are distinct from BRCA1-associated tumours in terms of morphological characteristics and genomic alterations, and they are also distinguishable from sporadic breast tumours, thus opening up the possibility to identify ATM variant carriers outside the ataxia-telangiectasia disorder and direct them towards effective cancer risk management and therapeutic strategies.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-0951-9) contains supplementary material, which is available to authorized users.

GENESIS: a French national resource to study the missing heritability of breast cancer

Background

Less than 20 % of familial breast cancer patients who undergo genetic testing for BRCA1 and BRCA2 carry a pathogenic mutation in one of these two genes. The GENESIS (GENE SISter) study was designed to identify new breast cancer susceptibility genes in women attending cancer genetics clinics and with no BRCA1/2 mutation.

Methods

The study involved the French national network of family cancer clinics. It was based on enrichment in genetic factors of the recruited population through case selection relying on familial criteria, but also on the consideration of environmental factors and endophenotypes like mammary density or tumor characteristics to assess potential genetic heterogeneity. One of the initial aims of GENESIS was to recruit affected sibpairs. Siblings were eligible when index cases and at least one affected sister were diagnosed with infiltrating mammary or ductal adenocarcinoma, with no BRCA1/2 mutation. In addition, unrelated controls and unaffected sisters were recruited. The enrolment of patients, their relatives and their controls, the collection of the clinical, epidemiological, familial and biological data were centralized by a coordinating center.

Results

Inclusion of participants started in February 2007 and ended in December 2013. A total of 1721 index cases, 826 affected sisters, 599 unaffected sisters and 1419 controls were included. 98 % of participants completed the epidemiological questionnaire, 97 % provided a blood sample, and 76 % were able to provide mammograms. Index cases were on average 59 years old at inclusion, were born in 1950, and were 49.7 years of age at breast cancer diagnosis. The mean age at diagnosis of affected sisters was slightly higher (51.4 years). The representativeness of the control group was verified.

Conclusions

The size of the study, the availability of biological specimens and the clinical data collection together with the detailed and complete epidemiological questionnaire make this a unique national resource for investigation of the missing heritability of breast cancer, by taking into account environmental and life style factors and stratifying data on endophenotypes to decrease genetic heterogeneity.