Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures

(c) The Author/sCarriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers.Published onlin

Abstract PD4-11: Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers

Abstract Hormone receptor positive breast cancer remains an ongoing therapeutic challenge. Despite optimal anti-endocrine therapies, most breast cancer deaths follow a diagnosis of early luminal cancer. Data describing molecular events in breast cancer has yet to be translated into actionable information to inform medical management and benefit patients. To understand the impact of multiple aberrations in the context of current therapy, we assessed the prognostic ability of genomic signatures as a putative stratification tool to targeted therapies. The analysis was performed based on an a priori hypothesis relating to molecular pathways which might predict response to targeted therapies currently under evaluation in late-stage clinical trials. In a case-control fashion, 420 patients from the Tamoxifen vs Exemstane Adjuvant Multinational Trial (TEAM) pathology cohort, were analysed to determine the prognostic, ability for these mutational and copy-number biomarkers representing the CCND/CDK, FGFR/FGF and AKT/PIK3CA to inform potential response to therapies targeting these pathways. Copy number analysis was performed using the Affymetrix Oncoscan™ Assay. Targeted sequencing was performed in a subset of samples for genes based on signaling cassettes mined from the ICGC. Pathways were identified as aberrant if there were copy number aberrations (CNAs) and/or mutations in any of the predetermined pathway genes: 1) CCND1/CCND2/CCND3/CDK4/CDK6 2) FGFR1/FGFR2/FGFR2/FGFR4 and 3) AKT1/AKT2/PIK3CA/PTEN. Kaplan Meier and log rank analyses were used for DRFS between groups. Hazard ratios were calculated using the Cox proportional hazard models adjusted for age, tumour size, grade, lymph node and HER2 status. 390/420 samples passed informatics QC filters. For the CCND/CDK pathway, patients with no CNA changes experienced a better DRFS (HR=1.94, 95% CI 1.45-2.61, p&amp;lt; 0.001). For the FGFR/FGF pathway, a similar outcome is seen among patients without CNAs (HR = 1.43, 95% CI 1.07-1.92 p=0.017). For AKT/PIK3CA, a decrease in DRFS was seen in those with aberrations (H=1.34, 95% CI 1.00-1.81, p=0.053). We demonstrated that CNAs of genes within CDK4/CCND, PIK3CA/AKT and FGFR pathways are independently linked to high risk of relapse following endocrine treatment. In this way, improving the clinical management of early breast cancers could be made, firstly by identifying those patients for whom current endocrine therapies are sufficient, thus reducing unnecessary treatment; and secondly, identifying those patients who are at high-risk for recurrence despite optimal endocrine therapy and the linking molecular features driving these cancers to treatment with targeted therapies. Citation Format: Bayani J, Kornaga EN, Crozier C, Jang GH, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Boutros PC, Spears M, Stein LD, Rea D, Bartlett JMS. Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers [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 PD4-11.</jats:p

Body mass index and molecular subtypes of colorectal cancer

BACKGROUND: Obesity is an established risk factor for colorectal cancer (CRC), but the evidence for the association is inconsistent across molecular subtypes of the disease. METHODS: We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype status, BRAF and KRAS mutations, and Jass classification types for 11 872 CRC cases and 11 013 controls from 11 observational studies. We used multinomial logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for covariables. RESULTS: Higher BMI was associated with increased CRC risk (OR per 5 kg/m2 = 1.18, 95% CI = 1.15 to 1.22). The positive association was stronger for men than women but similar across tumor subtypes defined by individual molecular markers. In analyses by Jass type, higher BMI was associated with elevated CRC risk for types 1-4 cases but not for type 5 CRC cases (considered familial-like/Lynch syndrome microsatellite instability-H, CpG island methylator phenotype-low or negative, BRAF-wild type, KRAS-wild type, OR = 1.04, 95% CI = 0.90 to 1.20). This pattern of associations for BMI and Jass types was consistent by sex and design of contributing studies (cohort or case-control). CONCLUSIONS: In contrast to previous reports with fewer study participants, we found limited evidence of heterogeneity for the association between BMI and CRC risk according to molecular subtype, suggesting that obesity influences nearly all major pathways involved in colorectal carcinogenesis. The null association observed for the Jass type 5 suggests that BMI is not a risk factor for the development of CRC for individuals with Lynch syndrome

Identifying colorectal cancer caused by biallelic <i>MUTYH</i> pathogenic variants using tumor mutational signatures

Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk of colorectal cancer. We test 5649 colorectal cancers to evaluate the discriminatory potential of a tumor mutational signature specific to MUTYH for identifying biallelic carriers and classifying variants of uncertain clinical significance (VUS). Using a tumor and matched germline targeted multi-gene panel approach, our classifier identifies all biallelic MUTYH carriers and all known non-carriers in an independent test set of 3019 colorectal cancers (accuracy = 100% (95% confidence interval 99.87-100%)). All monoallelic MUTYH carriers are classified with the non-MUTYH carriers. The classifier provides evidence for a pathogenic classification for two VUS and a benign classification for five VUS. Somatic hotspot mutations KRAS p.G12C and PIK3CA p.Q546K are associated with colorectal cancers from biallelic MUTYH carriers compared with non-carriers (p = 2 × 10-23 and p = 6 × 10-11, respectively). Here, we demonstrate the potential application of mutational signatures to tumor sequencing workflows to improve the identification of biallelic MUTYH carriers