Multi-gene Hereditary Cancer Panel Research Articles

An Individual with Both MUTYH-Associated Polyposis and Lynch Syndrome Identified by Multi-Gene Hereditary Cancer Panel Testing: A Case Report.

The utilization of next-generation sequencing technology to interrogate multiple genes simultaneously is being utilized more frequently in hereditary cancer testing. While this has benefits of reducing cost and allowing clinicians to cast a wide net in the elucidation of their patient's cancer, panel testing has the potential to reveal unexpected information. We report on a proband with pathogenic variants resulting in two different hereditary colon cancer syndromes. A 39-year-old male with a history of colon cancer, more than 20 colon polyps and a family history of colon cancer presented for genetic counseling. Testing with a 7-gene high-risk hereditary colon cancer panel identified a homozygous pathogenic variant, c.1187G>A (p.Gly396Asp) in MUTYH, and a likely pathogenic duplication of exon 7 in MSH2. Since this test result, the proband's mother was diagnosed with colon cancer; subsequent genetic testing confirmed she also carries the likely pathogenic duplication in the MSH2 gene. Although the cancer risk in individuals who carry multiple pathogenic variants has not been established for combined biallelic MUTYH-associated polyposis and Lynch syndrome, the identification of multiple pathogenic variants does allow for screening for cancers associated with both syndromes and has implications for cancer risk for family members. In particular, this has significant impact on those who test negative for a known familial pathogenic variant, yet could be still be at risk for cancer due to a second pathogenic variant in a family. More information is needed on the frequency of occurrence of multiple pathogenic variants, as well as the phenotypic spectrum when multiple pathogenic variants are present.

Abstract P4-12-16: Teasing out the PALB2 phenotype

Abstract Background: Biallelic mutations in PALB2 (Partner and Localizer of BRCA2) are known to cause Fanconi Anemia Type N. Multiple reports have demonstrated an increased risk for cancer in individuals heterozygous for PALB2 mutations. For example, a recent study by Antoniou et al reported a 33-58% lifetime risk for breast cancer in PALB2 mutation carriers, with 30% of carriers reporting triple negative breast cancer (TNBC). Other studies have suggested associations between PALB2 heterozygosity and pancreatic cancer, ovarian cancer, male breast cancer, and prostate cancer as well. We aimed to better define PALB2 phenotypes by assessing clinical history of TNBC, pancreatic, ovarian, and prostate cancers amongst PALB2 mutation carriers identified via multigene panel testing. Methods: We reviewed clinical histories of 11,007 individuals who underwent PALB2 sequence and deletion/duplication analysis as part of a multigene hereditary cancer panel. Descriptive statistics were utilized for clinical histories of PALB2 carriers, and chi square analysis was used to compare clinical histories of PALB2 mutation carriers to mutation-negative controls. Individuals with mutations in other cancer susceptibility genes were excluded from analysis. Results: A total of 98 PALB2 mutation carriers identified among 9610 individuals were included in our analysis. The majority of mutation carriers were Caucasian (80%) and female (92.8%). All identified mutations were truncating (nonsense, frameshift, or gross deletions). No pathogenic missense mutations were identified in this cohort. 77.6% (n=76) of mutation carriers had breast cancer, diagnosed at a mean age of 48. Hormone receptor status was available for 48 mutation carriers and 2469 controls. 37.5% (18/48) of breast cancers in mutation carriers were reported as triple negative, compared to 17.1% (423/2469) of breast cancers in controls (OR: 2.9 ; p= 0.0002). 7.8% (n= 8) of PALB2 mutation carriers had ovarian cancer. There was no significant difference in the incidence of ovarian cancer between PALB2 mutation carriers and controls (OR: 0.65 ; p= 0.25). Additionally, mutation carriers were significantly less likely to have a family history of ovarian cancer than controls (OR: 0.5; p= 0.02). 5.9% (n=6) of mutation carriers had pancreatic cancer, diagnosed at a mean age of 57.8, compared to 61 for controls. PALB2 mutation carriers were 1.3 times more likely to have personal and/or family history of pancreatic cancer, although this was not statistically significant (p= 0.22). Similarly, PALB2 mutation carriers were 1.5 times more likely to have a family history of prostate cancer, although this was not statistically significant (p= 0.09). Conclusions: Our data supports existing literature associating PALB2 mutations with TNBC. We did not observe significant associations between PALB2 carrier status and a clinical history of pancreatic, prostate, or ovarian cancers. However, this data should be interpreted with caution, as it is possible that unidentified genetic factors contributed to the clinical history of cancer in our mutation-negative controls. Investigation of PALB2-associated cancer risks in an unselected prospective cohort would help to further elucidate the PALB2 phenotype. Citation Format: Emily K Dalton, Rachel McFarland, Holly Laduca, Shuwei Li, Chia-Ling Gau. Teasing out the PALB2 phenotype [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-12-16.

Abstract 14: Identification of probands with multiple mutations in cancer susceptibility genes using a multigene panel approach

Abstract The multi-gene hereditary cancer panel testing approach allows for the identification of probands carrying multiple mutations in hereditary cancer predisposition genes. The purpose of this study is to assess the frequency and phenotypes of individuals in our hereditary cancer panel cohort carrying multiple mutations in hereditary cancer predisposition genes. From March 2012 through October 2013, results were reported for 4382 individuals who underwent hereditary cancer panel testing at our laboratory. Panels included comprehensive analysis of 14-24 genes, depending on the panel ordered. Genes analyzed on each panel included both genes associated with defined hereditary cancer syndromes and genes not yet associated with a defined hereditary cancer syndrome, with moderate to high penetrance estimates. Panel results were reviewed to determine the number of probands carrying multiple pathogenic mutations or likely pathogenic variants in the genes analyzed, and retrospective test requisition form review was used to obtain clinician-reported clinical history information. Biallelic MUTYH mutation carriers were not counted as multiple mutation cases, nor were individuals carrying a monoallelic MUTYH mutation in combination with a mutation in a different gene. Nine probands (0.2%) were identified to carry two cancer-predisposing mutations. Mutations included 7 small insertions/deletions, 1 nonsense, 4 missense, 3 splicing, and 3 gross deletions. Five individuals carried two mutations in moderately-penetrant cancer susceptibility genes not associated with a defined hereditary cancer syndrome. Mutated gene combinations included CHEK2/CHEK2 (confirmed to be in trans), ATM/RAD50, ATM/CHEK2 (identified in two probands), and MRE11A/PALB2. Two individuals carried one mutation in a moderately-penetrant gene and one mutation in a highly-penetrant gene associated with a defined hereditary cancer syndrome (ATM/MSH6 and MLH1/CHEK2). The remaining two individuals carried two mutations in highly-penetrant genes (MSH6/MSH6 (phase unknown) and MSH2/MSH6). The average age at first primary cancer diagnosis was 42 years (range 16-66 years). All probands had a history of cancer, including six of the nine probands with a reported history of more than one primary cancer diagnosis. Results from this study indicate that a minority of probands undergoing hereditary cancer panel testing are identified to carry multiple mutations in cancer susceptibility genes. This data highlights the need for further research to determine the clinical implications of carrying multiple mutations in cancer susceptibility genes, particularly for those with mutations in moderately-penetrant genes. Detailed pedigree analysis, co-segregation analysis, and longitudinal follow-up will be helpful in clarifying cancer risks in these probands and the significance of multiple mutations in cancer susceptibility genes. Citation Format: Chia-Ling Gau, Holly LaDuca, Hong Lu, AJ Stuenkel, Tina Pesaran, Elaine Chen, Jill Siegfried, Sharon Mexal, Robert Hoiness, Jill Cook, John Copenhaver, Elizabeth Chao. Identification of probands with multiple mutations in cancer susceptibility genes using a multigene panel approach. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 14. doi:10.1158/1538-7445.CANSUSC14-14

Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients

Purpose:The aim of this study was to determine the clinical and molecular characteristics of 2,079 patients who underwent hereditary cancer multigene panel testing.Methods:Panels included comprehensive analysis of 14–22 cancer susceptibility genes (BRCA1 and BRCA2 not included), depending on the panel ordered (BreastNext, OvaNext, ColoNext, or CancerNext). Next-generation sequencing and deletion/duplication analyses were performed for all genes except EPCAM (deletion/duplication analysis only). Clinical histories of ColoNext patients harboring mutations in genes with well-established diagnostic criteria were assessed to determine whether diagnostic/testing criteria were met.Results:Positive rates were defined as the proportion of patients with a pathogenic mutation/likely pathogenic variant(s) and were as follows: 7.4% for BreastNext, 7.2% for OvaNext, 9.2% for ColoNext, and 9.6% for CancerNext. Inconclusive results were found in 19.8% of BreastNext, 25.6% of OvaNext, 15.1% of ColoNext, and 23.5% of CancerNext tests. Based on information submitted by clinicians, 30% of ColoNext patients with mutations in genes with well-established diagnostic criteria did not meet corresponding criteria.Conclusion:Our data point to an important role for targeted multigene panels in diagnosing hereditary cancer predisposition, particularly for patients with clinical histories spanning several possible diagnoses and for patients with suspicious clinical histories not meeting diagnostic criteria for a specific hereditary cancer syndrome.