bims-lifras 2019-09-15 papers

Issue of 2019–09–15
seven papers selected by
Joanna Zawacka-Pankau

Rare Tumors. 2018 ;10 2036361317749645

Efficacy of oral metformin in a patient with metastatic adrenocortical carcinoma: Examination of mechanisms and therapeutic implications.

R D Peixoto, L M Gomes, T T Sousa, D J Racy, M Shigenaga, R A Nagourney.

Although rare, adrenocortical carcinoma is among the most common tumors found in children with Li-Fraumeni syndrome and Li-Fraumeni-like syndrome, associated with germ-line mutations in the TP53 gene. In southern Brazil, one form of Li-Fraumeni syndrome, associated with childhood adrenocortical carcinoma, is caused by a mutation in the R337H TP53 tetramerisation domain and is attributed to a familial founder effect. Adrenocortical carcinoma is considered an aggressive neoplasm, usually of poor prognosis and is generally unresponsive to systemic chemotherapy. Optimal treatment regimens remain to be established. We report the case of a young woman with metastatic adrenocortical carcinoma, who achieved stable disease with mitotane, cisplatin, doxorubicin, and etoposide as first-line therapy, but then had an objective response to oral metformin that lasted 9 months. The presence of the R337H TP53 mutation suggests a mechanism for the observed response to metformin.

Keywords: Adrenocortical carcinoma; Li-Fraumeni syndrome; metformin

DOI: https://doi.org/10.1177/2036361317749645

JCO Precis Oncol. 2019 ;3

Identification and Confirmation of Potentially Actionable Germline Mutations in Tumor-Only Genomic Sequencing.

Dana Farengo Clark, Kara N Maxwell, Jacquelyn Powers, David B Lieberman, Jessica Ebrahimzadeh, Jessica M Long, Danielle McKenna, Payal Shah, Angela Bradbury, Jennifer J D Morrissette, Katherine L Nathanson, Susan M Domchek.

PURPOSE: Tumor-only genomic profiling (TGP) is increasingly advocated for all patients with cancer given the possible therapeutic implications. It is critical to develop clinical algorithms to identify and address potentially actionable germline findings identified by TGP.
METHODS: A multidisciplinary team analyzed publicly available data for genes in which mutations are implicated in germline cancer susceptibility and established a pipeline to automate clinical referral for evaluation of TGP findings.
RESULTS: A total of 2,308 patients underwent TGP, with 81 patients (3.5%) identified by the automatic referral pipeline; 37 patients (1.6%) were referred outside the pipeline based on concerns by the molecular geneticist, pathologist, or oncologist regarding genotype-phenotype correlation. Thirty-one patients (38%) and 17 patients (46%) underwent germline testing from the automatic pipeline and other referrals, respectively, and of these patients, 23 (72%) and four (24%) had confirmed germline pathogenic variants (GPVs), respectively. The majority of confirmed GPVs were in automatic referral genes, with BRCA2 being most common (confirmed GPVs in 11 [85%] of 13 patients tested), followed by PALB2 (five [67%] of six patients), BRCA1 (two [40%] of five patients), MSH6 (two of three patients), and MLH1 (two of two patients). Forty-eight percent of confirmed GPVs were found in tumors known to be associated with germline mutations in the gene. Germline testing was not performed in 50 (62%) of 81 patients identified by automatic referral as a result of poor patient health or death (30%), lack of follow-up (30%), and patient refusal (30%).
CONCLUSION: Of patients undergoing TGP, 5% had somatic findings triggering referral, and implementation of an automatic referral pipeline based solely on gene versus other clinical or molecular features resulted in a 74% germline confirmation. However, only 41% of referred patients underwent germline testing. Systems-based approaches are needed to identify carriers of actionable germline cancer susceptibility mutations identified by TGP.

DOI: https://doi.org/10.1200/PO.19.00076

JCO Precis Oncol. 2018 ;2

Multigene Hereditary Cancer Panels Reveal High-Risk Pancreatic Cancer Susceptibility Genes.

Chunling Hu, Holly LaDuca, Hermela Shimelis, Eric C Polley, Jenna Lilyquist, Steven N Hart, Jie Na, Abigail Thomas, Kun Y Lee, Brigette Tippin Davis, Mary Helen Black, Tina Pesaran, David E Goldgar, Jill S Dolinsky, Fergus J Couch.

Purpose: The relevance of inherited pathogenic mutations in cancer predisposition genes in pancreatic cancer is not well understood. We aimed to assess the characteristics of patients with pancreatic cancer referred for hereditary cancer genetic testing and to estimate the risk of pancreatic cancer associated with mutations in panel-based cancer predisposition genes in this high-risk population.
Methods: Patients with pancreatic cancer (N = 1,652) were identified from a 140,000-patient cohort undergoing multigene panel testing of predisposition genes between March 2012 and June 2016. Gene-level mutation frequencies relative to Exome Aggregation Consortium and Genome Aggregation Database reference controls were assessed.
Results: The frequency of germline cancer predisposition gene mutations among patients with pancreatic cancer was 20.73%. Mutations in ATM, BRCA2, CDKN2A, MSH2, MSH6, PALB2, and TP53 were associated with high pancreatic cancer risk (odds ratio, > 5), and mutations in BRCA1 were associated with moderate risk (odds ratio, > 2). In a logistic regression model adjusted for age at diagnosis and family history of cancer, ATM and BRCA2 mutations were associated with personal history of breast or pancreatic cancer, whereas PALB2 mutations were associated with family history of breast or pancreatic cancer.
Conclusion: These findings provide insight into the spectrum of mutations expected in patients with pancreatic cancer referred for cancer predisposition testing. Mutations in eight genes confer high or moderate risk of pancreatic cancer and may prove useful for risk assessment for pancreatic and other cancers. Family and personal histories of breast cancer are strong predictors of germline mutations.

DOI: https://doi.org/10.1200/PO.17.00291

J Med Genet. 2019 Sep 07. pii: jmedgenet-2019-106272. [Epub ahead of print]

High-sensitivity microsatellite instability assessment for the detection of mismatch repair defects in normal tissue of biallelic germline mismatch repair mutation carriers.

INTRODUCTION: Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are hereditary cancer syndromes associated with mismatch repair (MMR) deficiency. Tumours show microsatellite instability (MSI), also reported at low levels in non-neoplastic tissues. Our aim was to evaluate the performance of high-sensitivity MSI (hs-MSI) assessment for the identification of LS and CMMRD in non-neoplastic tissues.
MATERIALS AND METHODS: Blood DNA samples from 131 individuals were grouped into three cohorts: baseline (22 controls), training (11 CMMRD, 48 LS and 15 controls) and validation (18 CMMRD and 18 controls). Custom next generation sequencing panel and bioinformatics pipeline were used to detect insertions and deletions in microsatellite markers. An hs-MSI score was calculated representing the percentage of unstable markers.
RESULTS: The hs-MSI score was significantly higher in CMMRD blood samples when compared with controls in the training cohort (p<0.001). This finding was confirmed in the validation set, reaching 100% specificity and sensitivity. Higher hs-MSI scores were detected in biallelic MSH2 carriers (n=5) compared with MSH6 carriers (n=15). The hs-MSI analysis did not detect a difference between LS and control blood samples (p=0.564).
CONCLUSIONS: The hs-MSI approach is a valuable tool for CMMRD diagnosis, especially in suspected patients harbouring MMR variants of unknown significance or non-detected biallelic germline mutations.

Keywords: constitutional mismatch repair deficiency; highly sensitive methodologies; lynch syndrome; microsatellite instability; next generation sequencing

DOI: https://doi.org/10.1136/jmedgenet-2019-106272

Breast Cancer Res Treat. 2019 Sep 11.

Germline investigation in male breast cancer of DNA repair genes by next-generation sequencing.

R Scarpitta, I Zanna, P Aretini, G Gambino, C Scatena, B Mei, M Ghilli, E Rossetti, M Roncella, C Congregati, F Bonci, A G Naccarato, D Palli, M A Caligo.

PURPOSE: In order to better define the breast cancer (BC) genetic risk factors in men, a germline investigation was carried out on 81 Male BC cases by screening the 24 genes involved in BC predisposition, genome stability maintenance and DNA repair mechanisms by next-generation sequencing.
METHODS: Germline DNAs were tested in a custom multi-gene panel focused on all coding exons and exon-intron boundaries of 24 selected genes using two amplicon-based assays on PGM-Ion Torrent (ThermoFisher Scientific) and MiSeq (Illumina) platforms. All variants were recorded and classified by using a custom pipeline.
RESULTS: Clinical pathological data and the family history of 81 Male BC cases were gathered and analysed, revealing the average age of onset to be 61.3 years old and that in 35 cases there was a family history of BC. Our genetic screening allowed us to identify a germline mutation in 22 patients (23%) in 4 genes: BRCA2, BRIP1, MUTYH and PMS2. Moreover, 12 variants of unknown clinical significance (VUS) in 9 genes (BARD1, BRCA1, BRIP1, CHEK2, ERCC1, NBN, PALB2, PMS1, RAD50) were predicted as potentially pathogenic by in silico analysis bringing the mutation detection rate up to 40%.
CONCLUSION: As expected, a positive family history is a strong predictor of germline BRCA2 mutations in male BC. Understanding the potential pathogenicity of VUS represents an extremely urgent need for the management of BC risk in Male BC cases and their own families.

Keywords: Breast cancer risk in men; DNA repair genes; Familial breast cancer; Male breast cancer; Next-generation sequencing

DOI: https://doi.org/10.1007/s10549-019-05429-z

JCO Precis Oncol. 2018 ;2

Genetic Testing and Clinical Management Practices for Variants in Non-BRCA1/2 Breast (and Breast/Ovarian) Cancer Susceptibility Genes: An International Survey by the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Clinical Working Group.

Sarah M Nielsen, Diana M Eccles, Iris L Romero, Fahd Al-Mulla, Judith Balmaña, Michela Biancolella, Rien Bslok, Maria Adelaide Caligo, Mariarosaria Calvello, Gabriele Lorenzo Capone, Pietro Cavalli, T L Chris Chan, Kathleen B M Claes, Laura Cortesi, Fergus J Couch, Miguel de la Hoya, Simona De Toffol, Orland Diez, Susan M Domchek, Ros Eeles, Anna Efremidis, Florentia Fostira, David Goldgar, Andreas Hadjisavvas, Thomas V O Hansen, Akira Hirasawa, Claude Houdayer, Petra Kleiblova, Sophie Krieger, Conxi Lázaro, Maria Loizidou, Siranoush Manoukian, Arjen R Mensenkamp, Setareh Moghadasi, Alvaro N Monteiro, Luigi Mori, April Morrow, Nadia Naldi, Henriette R Nielsen, Olufunmilayo I Olopade, Nicholas S Pachter, Edenir I Palmero, Inge S Pedersen, Maria Piane, Marianna Puzzo, Mark Robson, Maria Rossing, Maria Christina Sini, Angela Solano, Jana Soukupova, Gianluca Tedaldi, Manuel Teixeira, Mads Thomassen, Maria Grazia Tibiletti, Amanda Toland, Therese Törngren, Erica Vaccari, Liliana Varesco, Ana Vega, Yvonne Wallis, Barbara Wappenschmidt, Jeffrey Weitzel, Amanda B Spurdle, Arcangela De Nicolo, Encarna B Gómez-García.

Purpose: To describe a snapshot of international genetic testing practices, specifically regarding the use of multigene panels, for hereditary breast/ovarian cancers. We conducted a survey through the Evidence-Based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium, covering questions about 16 non-BRCA1/2 genes.
Methods: Data were collected via in-person and paper/electronic surveys. ENIGMA members from around the world were invited to participate. Additional information was collected via country networks in the United Kingdom and in Italy.
Results: Responses from 61 cancer genetics practices across 20 countries showed that 16 genes were tested by > 50% of the centers, but only six (PALB2, TP53, PTEN, CHEK2, ATM, and BRIP1) were tested regularly. US centers tested the genes most often, whereas United Kingdom and Italian centers with no direct ENIGMA affiliation at the time of the survey were the least likely to regularly test them. Most centers tested the 16 genes through multigene panels; some centers tested TP53, PTEN, and other cancer syndrome-associated genes individually. Most centers reported (likely) pathogenic variants to patients and would test family members for such variants. Gene-specific guidelines for breast and ovarian cancer risk management were limited and differed among countries, especially with regard to starting age and type of imaging and risk-reducing surgery recommendations.
Conclusion: Currently, a small number of genes beyond BRCA1/2 are routinely analyzed worldwide, and management guidelines are limited and largely based on expert opinion. To attain clinical implementation of multigene panel testing through evidence-based management practices, it is paramount that clinicians (and patients) participate in international initiatives that share panel testing data, interpret sequence variants, and collect prospective data to underpin risk estimates and evaluate the outcome of risk intervention strategies.

DOI: https://doi.org/10.1200/PO.18.00091

Chin Clin Oncol. 2019 Sep 03. pii: cco.2019.07.10. [Epub ahead of print]

In memory of Dr. Henry T. Lynch.

Daniel G Haller.

DOI: https://doi.org/10.21037/cco.2019.07.10