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DNA Sequence Variants and Risk of Breast Cancer


Impact of Moderate and High-Risk DNA Sequence Variants in Breast Cancer Risk and Relevance to Anti-Cancer Therapy

Tech Area / Field

  • BIO-CGM/Cytology, Genetics and Molecular Biology/Biotechnology
  • BIO-INF/Bioinformatics/Biotechnology

3 Approved without Funding

Registration date

Leading Institute
Center of Medical Genetics of NAS RA, Armenia, Yerevan


  • University of Montreal, Canada, QC, Montreal\nInstitut Curie, France, Paris\nDanish Cancer Society, Denmark, Copenhagen\nAsper Biotech Ltd., Estonia, Tartu\nInstitute Curie and University Paris Descartes, France, Paris

Project summary

Breast cancer (BC, MIM #114480) is the most frequent malignant tumor among women with approximately one million new cases per year around the world. The understanding of BC genetic predisposition has advanced dramatically by the identification of high-penetrance genes BRCA1 and BRCA2, as well as four other genes, CHEK2, ATM, BRIP1, and PALB2, conferring intermediate risk to BC. About 5% of all BC cases are considered to be due to the segregation of a germline mutation within a family. The two major BC-susceptibility genes BRCA1 and BRCA2 are estimated to be involved in 20% of familial BC, whereas mutations in other high-susceptibility genes PTEN, STK11, P53 or in intermediate-susceptibility genes explain only about 3% of familial BC. Therefore, despite these findings, most of genetic fraction of BC risk remains unexplored. The majority of the unknown fraction of familial risk is likely to be explained by a polygenic model implying a combination of many inpidual DNA sequence variants in weak associations with BC risk. There is a growing list of reports from genome-wide association studies on identification of single nucleotide polymorphisms (SNPs) in genes or chromosomal loci that are associated with an increased risk of BC, each expected to impact only to a minor extent on the inpidual risk. Most of these variants are common and associated with 5% of the increases in BC risk (so-called low-penetrant variants).
On the other side, most of the BRCA1&2 variants have been reported only a few times, and are considered of unknown significance (unclassified variants; UVs) due to the uncertainty of BC risk attributed to these sequence variants. In this regard, prediction and further clinical classification of UVs are of high interest. Notably, a special connection of basal-like breast carcinomas (BLCs) with mutations in BRCA1 is apparent. Firstly, BLCs represent the majority of BCs developing in BRCA1 mutation carriers, while representing less than 20% in the sporadic context. Secondly, high level of genomic instability observed in BLCs goes in line with involvement of BRCA1 gene in double strand break (DSB) signaling and repair by homologous recombination (HR). HR-deficiency (so called BRCAness) has been proposed as a general feature of BLCs explaining their high level of genomic instability, and being the basis of proposed treatments exploiting HR deficiency. However, disappointing clinical trials using PARP inhibitors highlighted the necessity for a better classification of BLC. Considering its importance in diagnosis and therapeutic stratification, numerous approaches have been searched for clinically relevant surrogate markers of BRCAness. As BRCA1 is mandatory for genome stability, it is likely that tumor genome profiling could give clues on BRCA1 status and more generally on HR proficiency or deficiency.
Although many additional loci are yet to be discovered, the currently identified loci provide low discriminatory accuracy to distinguish between common and rare DNA sequence variants in a specific population, and the combination of loci may prove useful in population screening strategies. Thus, there is a clear discontinuity in the risks associated with the three groups of BC predisposition genes/loci. None of the studies has been able to distinguish strictly between rare mutations in genes involved in DNA repair associated with high and intermediayte BC risk on the one side and common low-pentrance sequence variants associated with a slightly increased BC risk. Little attention has been paid to the genetic population attributable fractions (gPAFs) conferred by each BC predisposition gene.
The impact of rare (high- and intermediate-penetrance) and common (low-penetrance) genetic variants to the genetic component of BC risk is the major objective of this study. The attractive aspects of considering gPAFs of each BC susceptibility genes include the possibility to compare with gPAFs of known genes and their interactions with other gene in interest. In contrast to “common disease: common variant” hypothesis of association studies’ design, two approaches, “common disease: common variant” and “common disease: rare variant” hypotheses will be used in the proposed case-control study.
To contribute to the solution of the general question of this proposal, several new approaches of case-control study will be applied. This includes selection of cases with high-risk to BC and from a homogenous and ethnically-unique (ethno-national) population. This project is going to be the first focused on BC cases of Armenian ethnicity as a genetically relatively homogenous population with annual increase of younger BC cases and disease incidence similar to many of the European populations and higher than many others.
Given the general question of this project proposal, the specific objectives are the following:
1) To identify BRCA1&2 sequence variants (mutations and unclassified variants),
2) To evaluate unclassified BRCA1&2 sequence variants,
3) To correlate SNP-array status as a surrogate marker of HR-deficiency with UVs found in BRCA1 or BRCA2 genes,
4) To search and evaluate rare sequence variants in intermediate-susceptibility genes,
5) To identify the profile of known common sequence variants in low-susceptibility genes/loci, and
6) To calculate BC susceptibility risk relevant to each gene and each group of DNA sequence variants.
The study consists of five consecutive stages: 1) full mutation screening of high-susceptibility genes BRCA1 and BRCA2 in all cases and their further clinical classification, 2) evaluation of genomic profile of tumor samples by human whole-genome SNP-array analysis, 3) case-control full mutation screening of intermediate-penetrance genes, 4) case-control genotyping of low-risk sequence variants, and 5) analysis of the genotyping and mutation screening data which will answer the main question of this study. Achievement of the objectives of the proposed project depends on the combination of approaches and application of modern methods of genetics, genomics, immunohistochemistry, bioinformatics, and statistics. Molecular analysis includes mutation screening by high-resolution melt curve analysis followed by resequencing analysis and genotyping. Genomic profiling of the tumor samples will be performed on Affymetrix platform using human genome-wide SNP-arrays followed by bioinformatics analysis of created genome alteration print. To distinguish and evaluate unclassified variants a multifactorial likelihood scoring wiil be applied which combines several genetic and bioinformatics methods. Several statistical methods will be applied to calculate the role of each gene and each group of sequence variants for the determination of their impact on BC risk (gPAF).
The expected results will provide a clear picture of the role of common low-susceptibility sequence variants compared to rare high- and intermediate-risk sequence variants, and will contribute to better knowledge of genetic susceptibility factors in BC risk. The results obtained will help to identify inpidual and combined role of genetic variants of the three tiers of genes/loci and their profile with different level of penetrance to BC. The calculated gPAF of each gene, common and rare variants will have potential benefit for BC targeted preventive intervention and early detection programs when considering genetic susceptibility burden in the population. The expecting results also will have commercial significance with a direct consequence to the public health, especially for the development of a genetic risk assessment program and a genetic test which in turn will have a huge impact to detect and reduce hereditary burden of BC in a specific population. The analysis of common low-susceptibility variants or UVs would also influence response to therapy and could prove useful in the clinical management of patients. Thus, the calculation of the joint gPAF of BC risk through screening of all susceptibility genes/loci may lead to improvements in prevention and early detection of BC on the one part, and the study of genomic profile in tumors with unknown genetic variant could shed light on new mechanisms of the disease, and thus could become targets for therapy or prevention on the other part.
Inpidual participants of different categories are working in BC research, diagnostics, and treatment, and have many years of working experience in different research projects and foreign institutions. They have strong skilled-experience in all the techniques and methods which will be applied during the course of the project. Main participants are co-authors of several publications in BC genetics and in adjacent fields of medical genetics. The foreign collaborators of this proposal have expressed their willingness to provide professional information exchange, comments to the technical reports, cross-checks of results, as well as equipment provision during the visits of the project participants in their labs.
The scientists and the specialists connected with weapon will have the opportunity for reorientation of the capabilities aimed to peaceful activities for the implementation of the aims and problems of ISTC. There will be huge support to fundamental and applied research in peaceful aims. The project will promote to the solution of national and international scientific problems having a huge impact on the population, environment and for the development of public health.


The International Science and Technology Center (ISTC) is an intergovernmental organization connecting scientists from Kazakhstan, Armenia, Tajikistan, Kyrgyzstan, and Georgia with their peers and research organizations in the EU, Japan, Republic of Korea, Norway and the United States.


ISTC facilitates international science projects and assists the global scientific and business community to source and engage with CIS and Georgian institutes that develop or possess an excellence of scientific know-how.

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