Unselected Breast Cancer Cohort Research Articles

ATM c.7570G>C is a high-risk allele for breast cancer.

ATM is generally described as a moderate-risk breast cancer susceptibility gene. However, some of ATM variants might encounter higher risk. ATM c.7570G>C, p.Ala2524Pro, (rs769142993) is a pathogenic Finnish founder variant causative for recessively inherited ataxia-telangiectasia. At cellular level, it has been reported to have a dominant-negative effect. ATM c.7570G>C has recurrently been described in Finnish breast cancer families and unselected case cohorts collected from different parts of the country, but the rarity of the allele (MAF 0.0002772 in Finns) and lack of confirming segregation analyses have prevented any conclusive risk estimates. Here, we describe seven families from genetic counseling units with ATM c.7570G>C variant showing co-segregation with breast cancer. Further analysis of the unselected breast cancer cohort from Northern Finland (n=1822), a geographical region previously indicated to have enrichment of the variant, demonstrated that c.7570G>C significantly associates with breast cancer, and the risk is estimated as high (odds ratio [OR]=8.5, 95% confidence interval [CI]=1.04-62.46, P=.018). Altogether, these results place ATM c.7570G>C variant among the high-risk alleles for breast cancer, which should be taken into consideration in genetic counseling.

Exome sequencing identifies a recurrent variant in SERPINA3 associating with hereditary susceptibility to breast cancer.

Breast cancer is strongly influenced by hereditary risk factors. Yet, the known susceptibility genes and genomic loci explain only about half of the familial component of the disease. To identify novel breast cancer predisposing gene defects, here we have performed massive parallel sequencing for Northern Finnish breast cancer cases. Ninety-eight breast cancer cases with indication of hereditary disease susceptibility were exome sequenced. Data filtering strategy focused on predictably deleterious rare variants that were still enriched in the sequenced cohort. Findings were confirmed with additional, geographically matched breast cancer cohorts. A recurrent heterozygous splice acceptor variant, c.918-1G>C, in SERPINA3, was identified, and it was significantly enriched both in the hereditary (6/201, 3.0%, p=0.006, OR 5.1, 95% CI 1.7-14.8) and unselected breast cancer cohort (26/1569, 1.7%, p=0.009, OR 2.8, 95% CI 1.3-6.2). SERPINA3 c.918-1G>C carriers were also significantly more likely to have a rare tumor subtype, medullary breast cancer, than the non-carriers (4/26, 15.4%, p=0.000014, OR 42.9, 95% CI 11.7-157.1). These findings demonstrate that c.918-1G>C germline variant in SERPINA3 gene, encoding a member of the serine protease inhibitor class, is a novel breast cancer predisposing allele.

Prevalence of BRCA1 and BRCA2 pathogenic variants in a large, unselected breast cancer cohort

Breast cancer patients with BRCA1/2‐driven tumors may benefit from targeted therapy. It is not clear whether current BRCA screening guidelines are effective at identifying these patients. The purpose of our study was to evaluate the prevalence of inherited BRCA1/2 pathogenic variants in a large, clinically representative breast cancer cohort and to estimate the proportion of BRCA1/2 carriers not detected by selectively screening individuals with the highest probability of being carriers according to current clinical guidelines. The study included 5,122 unselected Swedish breast cancer patients diagnosed from 2001 to 2008. Target sequence enrichment (48.48 Fluidigm Access Arrays) and sequencing were performed (Illumina Hi‐Seq 2,500 instrument, v4 chemistry). Differences in patient and tumor characteristics of BRCA1/2 carriers who were already identified as part of clinical BRCA1/2 testing routines and additional BRCA1/2 carriers found by sequencing the entire study population were compared using logistic regression models. Ninety‐two of 5,099 patients with valid variant calls were identified as BRCA1/2 carriers by screening all study participants (1.8%). Only 416 study participants (8.2%) were screened as part of clinical practice, but this identified 35 out of 92 carriers (38.0%). Clinically identified carriers were younger, less likely postmenopausal and more likely to be associated with familiar ovarian cancer compared to the additional carriers identified by screening all patients. More BRCA2 (34/42, 81.0%) than BRCA1 carriers (23/50, 46%) were missed by clinical screening. In conclusion, BRCA1/2 mutation prevalence in unselected breast cancer patients was 1.8%. Six in ten BRCA carriers were not detected by selective clinical screening of individuals.

Abstract P4-06-15: Targeted sequencing of BRCA1/2 across a large unselected breast cancer cohort in Sweden

Abstract Background Observed BRCA1/2 mutation frequencies can vary depending on the population screened, screening criteria, founder effects, and methods used for testing. We aimed at examining BRCA1/2 germline mutations, identified through targeted sequencing, in a large unselected breast cancer population in Sweden. Methods Sequencing libraries of germline DNA from 5122 breast cancer patients diagnosed between 2001-2008 (LIBRO1) were prepared (48.48 Fluidigm Access Array system, Fluidigm Corp, USA) and sequenced (Next-generation sequencing [NGS], Illumina HiSeq 2500, v2 chemistry, University of Cambridge, UK). A total of 5099 samples (97.8%) passed quality control and were analysed. BRCA1/2 carriers identified by NGS were compared with those who were already identified by clinical BRCA screening (n=418) performed by the BRCA Lab (Lund University). This unit carries out mutation screening for all oncogenetic clinics in Sweden using denaturing high performance liquid chromatography (DHPLC) and multiple ligation-dependent probe amplification (MLPA). Results A total of 50 BRCA1 mutation carriers were identified, of which 28 were unique pathogenic germline mutations. Frameshift insertions and deletions made up 34/50 (68%) of the BRCA1 mutations. Exon 11 harbored 33/50 (66%) of the BRCA1 mutations. The most common mutation was c.3048_3052dupTGAGA (n=8), which is a founder mutation originating from the West coast of Sweden. Three other Swedish founder mutations were also identified (c.1082_1092del [n=5], c.3626delT [n=3] and c.2475delC [n=2]). For BRCA2, 42 mutation carriers were identified; 33 unique deleterious BRCA2 mutations (27 frameshift deletions, 3 frameshift insertions, 9 truncating and 3 splice sites). More than half of the mutations (24/42, 57%) were found on exon 11. Of the 418 women who had attended clinical BRCA testing, 38 deleterious mutations were found. Our screening method confirmed 34 of these mutations, as two each of BRCA1 and BRCA2 mutations were missed, since NGS was proven unsuitable for the detection of large exon duplications. NGS did, however, identify three more carriers not previously identified by clinical testing (c.3048_3052dup, c.2577delA and c.7442delT). Overall, 55/92 BRCA1/2 mutation carriers (59.8%) identified in the present study by NGS were not clinically tested. Conclusion NGS is comparable with current BRCA testing tools for the identification of BRCA1/2 germline mutations, suggesting that the technology has the potential to be used in BRCA1/2 clinical testing in unselected breast cancer patients. Citation Format: Li J, Wen SWX, Eriksson M, Kvist A, Christensen HN, Torstensson A, Easton DF, Teo S-H, Borg Å, Grönberg H, Czene K. Targeted sequencing of BRCA1/2 across a large unselected breast cancer cohort in Sweden [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-15.

Abstract P4-06-13: BRCA1/2 mutations identified by screening a large unselected breast cancer cohort in Sweden

Abstract Background Treatment options for BRCA1/2 breast cancer include new therapeutic agents, such as poly (ADP-ribose) polymerase (PARP) inhibitors, which selectively target BRCA defective cells. According to current Swedish screening guidelines, eligibility for clinical BRCA1/2 hereditary mutation testing is mainly based on family history of breast or ovarian cancer and early age onset. We aimed at examining the prevalence and characteristics of BRCA1/2 mutation carriers by screening a large unselected breast cancer cohort in Sweden, and comparing our results with BRCA mutation carriers already identified through the national BRCA testing program. Methods Germline DNA (blood) from 5122 women diagnosed with breast cancer between 2001-2008 (LIBRO1 study) were analysed for BRCA1/2 mutations by targeted sequencing (next generation sequencing, NGS), of which 5099 samples passed quality control. All patients provided informed consent. Information on patient and tumor characteristics was collected from the LIBRO1 database. Clinical BRCA testing information was obtained from the BRCA Lab (Lund University, Sweden), which carries out mutation screening for all oncogenetic clinics in Sweden. Multinomial logit models were used to compare tumor characteristics of BRCA1 and BRCA2 versus non-BRCA carriers. Multivariable logistic regression models were used to examine for differences between BRCA carriers identified through the national BRCA testing program and additional BRCA carriers found by sequencing the entire study population (not tested or not identified under current screening guidelines). Results In total, 92 (1.8%) BRCA1/2 mutation carriers were identified retrospectively by NGS. The prevalence of BRCA1/2 mutations was 1.6% (38/2363) between years 2001-2004; and 2.0% (54/2736) between years 2005-2008. After controlling for age and year of diagnosis, BRCA2 mutation carriers were in general similar to non-BRCA carriers regarding tumor characteristics (hormone receptor status, grade, tumor size and proliferation index), except for nodal involvement. BRCA1 mutation carriers, however, had more aggressive tumor characteristics than non-BRCA breast cancer patients. Overall, 55/92 BRCA1/2 mutation carriers (59.8%) found by NGS were not already identified through the national clinical BRCA testing program. The BRCA carriers identified by clinical testing were more likely high-risk individuals, i.e. younger, less likely to have experienced menopause, and more likely to be associated with a familiar ovarian cancer compared to those not identified through clinical testing, after adjusting for year of diagnosis. A larger proportion of BRCA2 (34/42, 80%) than BRCA1 mutations (25/50, 50%) were missed by selectively testing, mainly high-risk individuals. Conclusion BRCA1/2 mutations were found in approximately 2.0% of unselected BC patients. Six out of ten BRCA mutation carriers were not identified through the national testing program, which follows the screening guidelines. Revised guidelines might be needed for the effective identification of BRCA1/2 germline mutations. Citation Format: Li J, Wen SWX, Eriksson M, Kvist A, Christensen HN, Torstensson A, Easton DF, Teo S-H, Borg Å, Grönberg H, Czene K. BRCA1/2 mutations identified by screening a large unselected breast cancer cohort in Sweden [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-13.

Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests that one-third of mutations are somatic

A mutation found in the BRCA1 or BRCA2 gene of a breast tumor could be either germline or somatically acquired. The prevalence of somatic BRCA1/2 mutations and the ratio between somatic and germline BRCA1/2 mutations in unselected breast cancer patients are currently unclear. Paired normal and tumor DNA was analyzed for BRCA1/2 mutations by massively parallel sequencing in an unselected cohort of 273 breast cancer patients from south Sweden. Deleterious germline mutations in BRCA1 (n = 10) or BRCA2 (n = 10) were detected in 20 patients (7%). Deleterious somatic mutations in BRCA1 (n = 4) or BRCA2 (n = 5) were detected in 9 patients (3%). Accordingly, about 1 in 9 breast carcinomas (11%) in our cohort harbor a BRCA1/2 mutation. For each gene, the tumor phenotypes were very similar regardless of the mutation being germline or somatically acquired, whereas the tumor phenotypes differed significantly between wild-type and mutated cases. For age at diagnosis, the patients with somatic BRCA1/2 mutations resembled the wild-type patients (median age at diagnosis, germline BRCA1: 41.5 years; germline BRCA2: 49.5 years; somatic BRCA1/2: 65 years; wild-type BRCA1/2: 62.5 years). In a population without strong germline founder mutations, the likelihood of a BRCA1/2 mutation found in a breast carcinoma being somatic was ∼1/3 and germline 2/3. This may have implications for treatment and genetic counseling.

Abstract OT2-05-01: BRCAsearch: A population based prospective study on screening for BRCA1 and BRCA2 germline mutations in patients with newly diagnosed breast cancer treated in southern Sweden

Abstract The overall purpose of the study BRCAsearch is to evaluate a new method for offering mutation analysis of BRCA1 and BRCA2 to all patients with newly diagnosed breast cancer. Patients with breast cancer in southern Sweden are offered inclusion in the SCAN-B study at the time of diagnosis pre-surgery. If they consent, a part of the tumor is sent to a lab in Lund, Sweden, for research purposes (RNA sequencing etc.). Patients that are included in the SCAN-B study are eligible for inclusion in BRCAsearch. Summary of study procedure for BRCAsearch: 1.An envelope with written information is given to the patient at the visit to the surgeon the week after surgery. This envelope contains a written genetic counseling, information about the study, an informed consent form, psychosocial questionnaires and contact information to a genetic counsellor and psycisians responsible for the study (telephone, e-mail). The patient can contact a genetic counselor for pre-test telephone genetic counseling if she wishes to. 2.BRCA1 and BRCA2 are analyzed. 3.Non-carriers are informed about the test result with a letter. Mutation carriers and VUS (variants of uncertain significance) are telephoned and given a time for an appointment at the Department of Clinical Genetics. 4.Psychosocial self-reported questionnaires are delivered at 3 times over a year. Inclusion criteria (all): 1.The patient is included in the SCAN-B study. 2.The patient is recently diagnosed with an invasive breast cancer or a ductal cancer in situ. 3.The patient has signed an informed consent form for BRCAsearch. Exclusion criteria (any of): 1.The patient is unable to understand the written information in Swedish. 2.The patient is a psychological state, due to chronic och temporary reasons, where one could suspect that information about the study substantially could be detrimental to the psychological well-beeing. Primary outcome measures: • Prevalence of BRCA1/2 mutations in an unselected breast cancer cohort in southern Sweden • Uptake of genetic testing • Proportion of the mutation carriers that do not fulfil current criteria for genetic testing Secondary outcome measures: • How many of the patients that contact us for questions and what type of questions they have • How uptake of genetic testing varies with patient, treatment, and tumor characteristics • The patients' attitudes towards the method used for identifying mutation carriers • The economic cost per QALY (quality-adjusted life year) • Psychosocial comparisons between mutation carriers and non-carriers Targeted accrual is 500 patients included in the study, which is expected to be reached by the end of 2016. The study enrolls patients from two hospitals in southern Sweden: 1.Helsingborg Hospital (study start: Febuary 2, 2015) 2.Kristianstad Hospital (study start: March 2, 2015). Citation Format: Nilsson MP, Borg Å, Henriksson K, Kristoffersson U, Kvist A, Silfverberg B, Törngren T, Loman N. BRCAsearch: A population based prospective study on screening for BRCA1 and BRCA2 germline mutations in patients with newly diagnosed breast cancer treated in southern Sweden. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT2-05-01.

Neoadjuvant epirubicin, gemcitabine and docetaxel for primary breast cancer: Long‐term survival data and major prognostic factors based on two consecutive neoadjuvant phase I/II trials

We previously reported primary endpoints of two consecutive phase I/II trials, evaluating different schedules of neoadjuvant epirubicin (E), gemcitabine (G) and docetaxel (Doc) for primary breast cancer (PBC). Here, we report mature survival data and prognostic factors. One hundred fifty-one patients were recruited into two consecutive phase I/II trials of neoadjuvant chemotherapy for T2-4 N0-2 M0 PBC. Patients received six cycles of G/E/Doc every 3 weeks with G repeated on d8 (GEDoc, n = 84) or five cycles of G/E followed by four cycles of Doc all given every two weeks (GEsDoc, n = 67). Prognostic factors were investigated using univariate and multivariate analyses. No survival differences by treatment were found. Among reported predictive factors for pathologic complete response (pCR), oestrogen receptor (ER) status was the only relevant factor in the multivariate analysis. Unexpectedly, pCR resulted in poorer survival (univariate HR for overall survival [OS] 3.11, p = 0.007). Multivariate analyses identified molecular subtype and tumour size as the most relevant prognostic factors for OS. HER2-receptor status and the CPS-EG score (Mittendorf et al., J Clin Oncol 2011;29:1956-62), based on clinical and pathological stage, ER-status and tumour grade, were particularly relevant in disease-free survival. Our findings cast doubt on the reliability of pCR as single marker for prognosis of this unselected breast cancer cohort, with an abundance of luminal subtypes. These results underline the significance of additional molecular characteristics for breast cancer survival.

Hypoxia-induced protein CAIX is associated with somatic loss of BRCA1 protein and pathway activity in triple negative breast cancer

The purpose of this study is to explore the relationship between tumor hypoxia assessed by CA IX protein expression and loss of BRCA1 function in triple negative breast cancer (TNBC). Protein expression of CA IX and BRCA1 was evaluated by AQUA™ technology on two breast cancer cohorts: an unselected cohort of 637 breast cancer patients and a TNBC cohort of 120 patients. Transcriptional profiling was performed on FFPE samples from the TNBC cohort to evaluate a gene expression signature associated with BRCA1 mutation (van't Veer et al., Nature 415(6871):530-536, 2002). CA IX is expressed in 7% of the unselected breast cancer cohort and in 25% of the TNBCs and is significantly associated with the triple negative phenotype. CA IX protein expression and BRCA1 protein expression are inversely correlated in both cohorts. Patients expressing high levels of CA IX show significantly worse overall survival (p=0.02). Importantly, high CA IX protein expression occurs in patients who show the BRCA1 mutant signature and low levels of BRCA1 protein. These data suggest that elevated CA IX protein in TNBC is associated with a BRCA1 mutant signature and loss of BRCA1 function. CA IX may be a useful biomarker to identify triple negative patients with defective homologous recombination, who might benefit from PARP inhibitor therapy.

Prognostic Significance of Stromal Platelet-Derived Growth Factor β-Receptor Expression in Human Breast Cancer

Prognostic Significance of Stromal Platelet-Derived Growth Factor β-Receptor Expression in Human Breast Cancer