Irene Rainville

Next-Generation Sequencing for Inherited Breast Cancer Risk: Counseling through the Complexity

Next-generation sequencing technology affords an unprecedented opportunity to analyze multiple breast cancer susceptibility genes simultaneously. With the incarnation of gene panels that combine testing for moderate- and high-penetrance genes, this technology has given birth to a paradigm shift in clinical genetic test offerings. A transformation in genetic counseling for cancer susceptibility will necessarily follow, with a shift from the traditional approach of single-gene testing to considerations of testing by multi-gene panels. At the same time, however, the opportunity to identify rare lesions underlying hereditary susceptibility has introduced new challenges. Available cancer risk estimates for genes included in panel tests may not be supported by evidence, and there is increased risk of identifying variants of uncertain significance (VUS). Management of individuals with rare pathogenic mutations may be unclear. We provide a summary of available evidence for breast cancer risks conferred by pathogenic mutations in genes commonly included in breast cancer susceptibility panels, as well as a review of limitations and counseling points.

The association between germline BRCA2 variants and sensitivity to platinum‐based chemotherapy among men with metastatic prostate cancer

Breast cancer 2 (BRCA2)‐associated breast and ovarian cancers are sensitive to platinum‐based chemotherapy. It is unknown whether BRCA2‐associated prostate cancer responds favorably to such treatment.

Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study

Purpose:Implementing cancer precision medicine in the clinic requires assessing the therapeutic relevance of genomic alterations. A main challenge is the systematic interpretation of whole-exome sequencing (WES) data for clinical care.Methods:One hundred sixty-five adults with metastatic colorectal and lung adenocarcinomas were prospectively enrolled in the CanSeq study. WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples. Somatic and germ-line alterations were ranked according to therapeutic or clinical relevance. Results were interpreted using an integrated somatic and germ-line framework and returned in accordance with patient preferences.Results:At the time of this analysis, WES had been performed and results returned to the clinical team for 165 participants. Of 768 curated somatic alterations, only 31% were associated with clinical evidence and 69% with preclinical or inferential evidence. Of 806 curated germ-line variants, 5% were clinically relevant and 56% were classified as variants of unknown significance. The variant review and decision-making processes were effective when the process was changed from that of a Molecular Tumor Board to a protocol-based approach.Conclusion:The development of novel interpretive and decision-support tools that draw from scientific and clinical evidence will be crucial for the success of cancer precision medicine in WES studies.Genet Med advance online publication 26 January 2017

Exome sequencing reveals recurrent germ line variants in patients with familial Waldenström macroglobulinemia.

Familial aggregation of Waldenström macroglobulinemia (WM) cases, and the clustering of B-cell lymphoproliferative disorders among first-degree relatives of WM patients, has been reported. Nevertheless, the possible contribution of inherited susceptibility to familial WM remains unrevealed. We performed whole exome sequencing on germ line DNA obtained from 4 family members in which coinheritance for WM was documented in 3 of them, and screened additional independent 246 cases by using gene-specific mutation sequencing. Among the shared germ line variants, LAPTM5(c403t) and HCLS1(g496a) were the most recurrent, being present in 3/3 affected members of the index family, detected in 8% of the unrelated familial cases, and present in 0.5% of the nonfamilial cases and in <0.05 of a control population. LAPTM5 and HCLS1 appeared as relevant WM candidate genes that characterized familial WM individuals and were also functionally relevant to the tumor clone. These findings highlight potentially novel contributors for the genetic predisposition to familial WM and indicate that LAPTM5(c403t) and HCLS1(g496a) may represent predisposition alleles in patients with familial WM.

Genetic testing in the clinical care of patients with pheochromocytoma and paraganglioma.

Purpose of reviewParaganglioma and pheochromocytoma (PGL/PCC) are tumours of neural crest origin that can present along a clinical spectrum ranging from apparently sporadic, isolated tumours to a more complex phenotype of one or multiple tumours in the context of other clinical features and family history suggestive of a defined hereditary syndrome. Genetic testing for hereditary PGL/PCC can help to confirm a genetic diagnosis for sporadic and syndromic cases. Informative genetic testing serves to clarify future risks for the patient and family members. Recent findingsGenetic discovery in the last decade has identified new PGL/PCC susceptibility loci. We summarize a contemporary approach adopted in our programme for genetic evaluation, testing and prospective management involving biochemical monitoring and imaging for hereditary PGL/PCC. A clinical vignette is presented to illustrate our practice. SummaryCurrent estimates that up to 40% of PGL/PCC are associated with germline mutations have implications for genetic testing recommendations. Prospective management of patients with defined hereditary susceptibility is based on established guidelines for well characterized syndromes. Management of tumour risk for rare syndromes, newly defined genetic associations and undefined genetic susceptibility in the setting of significant family history presents a challenge. Sustained discovery of new PGL/PCC genes underscores the need for a practice of continued genetic evaluation for patients with uninformative results. All patients with PGL/PCC should undergo genetic testing to identify potential hereditary tumour susceptibility.

Adrenocortical carcinoma and succinate dehydrogenase gene mutations: An observational case series

OBJECTIVE Germline loss-of-function mutations in succinate dehydrogenase (SDHx) genes results in rare tumor syndromes that include pheochromocytoma, paraganglioma, and others. Here we report a case series of patients with adrenocortical carcinoma (ACC) that harbor SDHx mutations. PATIENTS AND RESULTS We report four unrelated patients with ACC and SDHx mutations. All cases presented with Cushing syndrome and large adrenal masses that were confirmed to be ACC on pathology. All four ACC specimens were found to have truncating mutations in either SDHC or SDHA, while cases 1, 2 and 3 also had the mutations confirmed in the germline: Case 1: SDHC c.397C > T, pR133X; Case 2: SDHC c.43C > T, p.R15X; Case 3: SDHA c.91C > T, p.R31X; Case 4: SDHA c.1258C > T, p.Q420X. Notably, Case 1 had a father and daughter who both harbored the same SDHC germline mutation, and the father had a paraganglioma and renal cell carcinoma. A combination of next generation sequencing, and/or immunohistochemistry, and/or mass spectroscopy was used to determine whether there was loss of heterozygosity and/or loss of SDH protein expression or function within the ACC. Potential evidence of loss of heterozygosity was observed only in Case 2. CONCLUSIONS We observed truncating mutations in SDHA or SDHC in the ACC and/or germline of four unrelated patients. Given how statistically improbable the concurrence of ACC and pathogenic germline SDHx mutations is expected to be, these observations raise the question whether ACC may be a rare manifestation of SDHx mutation syndromes. Further studies are needed to investigate the possible role of SDH deficiency in ACC pathogenesis.

Synchronous small bowel and atypical primary leiomyosarcoma of inferior vena cava in a patient with RB1 mutation

A 72-year-old Caucasian man presenting with non-specific upper abdominal pain had asymmetric soft tissue thickening of the small bowel wall on computed tomography (CT), which was pathologically proven to be leiomyosarcoma (LMS). At the same time point patient had incidentally but retrospectively detected lesion in IVC on CT scan which was subsequently imaged with PET/CT and MRI and was histologically proven to be also LMS. We present clinical and imaging features along with pedigree of this unique case of synchronous primary LMS involving the small bowel and inferior vena cava in a patient with RB1 gene mutation and a significant family history of multiple malignancies. To our knowledge, the synchronous primary LMS at two different sites has not been described. Clinicians and radiologists should keep in mind the possibility of a synchronous primary LMS in patients with genetic predisposition before making the diagnosis of a metastatic lesion or other malignancy as localized primary tumors remain potentially curable, whereas metastatic sarcoma is most often incurable.

Abstract 2417: The INHERIT EGFR study: Investigating hereditary risk from T790M.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Background: The EGFR T790M mutation, commonly associated with acquired resistance to EGFR kinase inhibitors, has also been described rarely as a germline mutation in association with familial lung cancer. In collaboration with the Addario Lung Cancer Medical Institute (www.ALCMI.net), we initiated a prospective trial to identify patients and families carrying germline EGFR mutations in order to characterize their lung cancer risk. Preliminary data: In a prior study (GR Oxnard et al, JTO, 2012), it was identified that patients with lung cancers found to harbor EGFR T790M at diagnosis have a 50% chance of carrying an underlying germline T790M mutation. This suggests that by focusing on patients already identified to carry T790M in their cancer, it is possible to enrich for a germline mutation that may be otherwise too rare to study prospectively. Subject eligibility: The following groups are eligible: (1) Patients with a cancer (lung or other) harboring an EGFR T790M mutation on tumor genotyping; lung cancers that acquired EGFR T790M only following treatment with an EGFR kinase inhibitor are ineligible. (2) First-degree relatives of patients found to carry a germline EGFR mutation. (3) Patients who already are known to carry a germline EGFR mutation on prior testing. Subjects are referred to cohort 1 based upon genotyping results from academic centers, oncology practices, or partnering commercial laboratories (e.g. Response Genetics, Los Angeles, CA). Trial design: Subjects may present at a participating cancer center or may participate remotely through a study website (www.Dana-Farber.org/T790Mstudy). Eligible patients submit a saliva and/or blood specimen for central testing in a CLIA lab. After counseling, patients carrying germline EGFR mutations have the option of inviting first-degree relatives to participate. Genetic counseling is coordinated at the participating center or offered over the phone. Chest CT scans are collected from germline carriers and analyzed centrally to study nodule prevalence and characteristics. Patients are then clinically followed for 2 years. Funding: Supported by grants from the Conquer Cancer Foundation of ASCO and the Bonnie J. Addario Lung Cancer Foundation. Citation Format: Geoffrey R. Oxnard, Elizabeth J. Root, Alicia Sable-Hunt, Irene Rainville, Suzanne E. Dahlberg, Jennifer C. Heng, David M. Jackman, Pasi A. Janne, Judy E. Garber. The INHERIT EGFR study: Investigating hereditary risk from T790M. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2417. doi:10.1158/1538-7445.AM2013-2417

Abstract 2570: An integrated germline analysis platform for comprehensive clinical cancer genomics.

Background: In order to apply massively parallel sequencing for use in clinical oncology, we have created algorithms to identify clinically actionable somatic alterations within an individual patient9s tumor exome. To fully implement comprehensive clinical sequencing for cancer patients, a parallel platform for analyzing germline genetic variants is necessary to identify 1) clinically relevant cancer risk, non-cancer disease risk, and pharmacogenomics variants, and 2) germline variants related to clinically relevant somatic alterations. Methods: Databases consisting of genes known to undergo germline alterations that may inform disease risk or pharmacogenomic variation were created by review of publically available resources (e.g. Cancer Gene Census) and augmented with literature review and expert opinion. Whole exome sequencing of normal DNA from prospectively acquired individual patient germline samples was performed using established Broad Institute pipelines for hybrid capture and variant calling. Population frequencies of all non-synonymous variants represented in our clinical germline databases were assessed with Exome Variant Server data, and all variants were cross-referenced with published lists of possibly pathogenic germline variants (e.g. HGMD). Variants with a population frequency of less than 1% that were also present in our clinical germline databases were assigned for high priority review. Integration of germline alterations with somatic data was implemented by computationally searching for germline non-synonymous variants in somatically altered clinically actionable cancer genes or pathways of such genes. All findings were incorporated into a novel web-based decision support system to maximize interpretation access for clinical genetic specialists who determined final classification of the variants. Results: Application of the germline analysis platform to whole exome sequencing data from twelve prospectively acquired clinical patient samples identified a median of 7 [range: 4-10] high priority germline variants warranting subsequent review from among thousands of variants per patient. Integrative analysis of one patient with EGFR mutant lung adenocarcinoma revealed a non-synonymous germline variant in EGFR at another site warranting further exploration. Conclusions: Our germline analysis platform facilitates prospective clinical interpretation of germline genomic variants by prioritizing and representing alterations of potential clinical significance. The platform also integrates germline variants with clinically actionable somatic alterations for enhanced understanding of potential disease drivers at the individual patient level. Implementation of clinical cancer sequencing with germline analyses may directly impact patient care and deepen our understanding of the role of germline variants in cancer epidemiology. Citation Format: Eliezer M. Van Allen, Nikhil Wagle, Adam Keizun, Gregory Kryukov, Aaron McKenna, Franklin Huang, Elaine Hiller, Irene Rainville, Daniel Auclair, Lauren Ambrogio, Stacy Gray, Steven Joffe, Gad Getz, Judy Garber, Levi Garraway. An integrated germline analysis platform for comprehensive clinical cancer genomics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2570. doi:10.1158/1538-7445.AM2013-2570