Development and validation of the PREMMplus clinical prediction model for multigene hereditary cancer risk assessment

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Background: Current clinical prediction models provide syndrome-specific numeric estimates of an individual's likelihood of having a specific hereditary cancer syndrome (e.g., PREMM5 for Lynch syndrome; BRCAPRO for BRCA1/2). With the emergence of multigene panel testing (MGPT), there is a need to evaluate individuals' risk of carrying a pathogenic variant in a diverse array of cancer susceptibility genes in parallel. This study’s aim was to develop and validate the PREMMplus clinical prediction model for multigene cancer risk assessment. Methods: PREMMplus was developed in a cohort of 7296 individuals who had undergone germline MGPT at a single center. Logistic regression models were used to examine candidate predictive variables – including age, sex, ethnicity, and personal/family history of cancer – to provide a numeric estimate of an individual’s likelihood of carrying a pathogenic/likely pathogenic germline variant in one of 18 cancer susceptibility genes (11 high- [ APC, BRCA1/2, CDH1, EPCAM, MLH1, MSH2, MSH6, biallelic MUTYH, PMS2, and TP53] and 7 moderate-penetrance [ ATM, CDKN2A, CHEK2, PALB2, PTEN, RAD51C, and RAD51D]). Model performance was validated in an independent dataset of 14845 individuals who had undergone MGPT at a commercial laboratory. Results: Using clinical characteristics, including personal/family history of 18 cancers plus colorectal adenoma burden, PREMMplus demonstrated an excellent ability to predict pathogenic variants in high penetrance genes at 90% sensitivity. PREMMplus had acceptable performance with the addition of 7 moderate penetrance genes. PREMMplus was well-calibrated and demonstrated comparable performance in the external validation dataset. Conclusions: PREMMplus is the first validated risk assessment model to quantify an individual’s likelihood of carrying pathogenic variants in a wide diversity of cancer risk genes, and can be used to select individuals who should undergo MGPT. As expected, PREMMplus’s discriminatory capacity was reduced with the inclusion of moderate penetrance cancer risk genes. [Table: see text]

Improving cascade genetic testing for families with inherited pancreatic cancer (PDAC) risk: The GENetic Education, Risk Assessment and TEsting (GENERATE) study

TPS779

Background: 4-10% of PDAC patients harbor pathogenic germline variants in cancer susceptibility genes, including APC, ATM, BRCA1, BRCA2, CDKN2A, EPCAM, MLH1, MSH2, MSH6, PALB2, PMS2, STK11, and TP53. For families with such pathogenic variants, the greatest potential impact of germline testing is to identify relatives with the same variant (cascade testing), thereby providing the opportunity for early detection and interception of PDAC and other associated cancers. Numerous factors limit cascade testing in real-world practice, including family dynamics, widespread geographic distribution of relatives, access to genetic services, and misconceptions about the importance of germline testing, such that the preventive benefits of cascade testing are often not fully realized. The primary aim of this study is to analyze two alternative strategies for cascade testing in families with inherited PDAC risk. Methods: 1000 individuals with a confirmed pathogenic germline variant in any of the above genes in a 1st/2nd degree relative and a 1st/2nd degree relative with PDAC will be remotely enrolled through the study website (www.GENERATEstudy.org) and randomized between two methods of cascade testing (individuals with prior genetic testing will be ineligible): Arm 1 will undergo pre-test genetic education with a pre-recorded video and live interactive session with a genetic counselor via a web-based telemedicine platform (Doxy.me), followed by germline testing through Color Genomics; Arm 2 will undergo germline testing through Color Genomics without dedicated pre-test genetic education. Color Genomics will disclose results to study personnel and directly to participants in both arms. All participants will have the option of pursuing additional telephone-based genetic counseling through Color Genomics. The primary outcome will be uptake of cascade testing. Secondary outcomes will include self-reported genetic knowledge, cancer worry, distress, decisional preparedness, familial communication, and screening uptake, which will be measured via longitudinal surveys. Enrollment is underway nationwide as of May, 2019. Clinical trial information: NCT03762590.

Implementation of systematic genetic counseling (GC) and multigene germline testing (MGT) for pancreatic cancer (PC) patients (pts)

678

Background: MGT identifies cancer susceptibility gene variants in 4-10% of unselected PC pts. Such data have prompted national guidelines to recommend GC and MGT of all PC pts, but the benefits and barriers to implementing systematic testing are unknown. This study’s aim was to study the implementation of universal GC for all PC pts seen in an academic oncology practice. Methods: In 12/2016, all Dana-Farber Cancer Institute (DFCI) gastrointestinal oncologists were recommended to refer all PC pts for GC and MGT. In 10/2018, workflows were changed such that PC patients were automatically scheduled for GC consultation on the same day as their initial oncologic evaluation (unless patients opted out), rather than relying on provider referral. Clinical and germline data were collected on a consecutive cohort of PC pts undergoing GC and MGT from 3/1/2017-3/31/2019. Two additional months (4/1/2019-5/31/2019) were collected for clinical quality assessment purposes. Results: 1305 (48.3/month) PC pts were seen for oncologic new patient visits, 318 (25.1%; 12.1/month) of whom underwent GC. Rates of GC/MGT increased significantly after the 10/2018 workflow change (8.2 PC pts/month [17.2% of all new PC pts seen] versus 20.3 PC pts/month, [40.9% of all new PC pts seen]; p<0.01). Of the 318 PC pts who underwent GC, 29 (9.1%; 95% CI 6.4-11.9%; 2.2% of all PC pts seen) were found to carry germline PC susceptibility gene mutations on MGT. Rates of mutation carrier identification increased after the clinical workflow change from 0.79 mutation carriers/month (1.6% of all new PC pts seen) to 1.75 mutation carriers/month (3.5% of all new PC pts seen). The majority of identified mutation carriers have either received therapy targeted towards their germline mutation or are undergoing first-line palliative systemic therapy with potential for future targeted therapy. Conclusions: Clinical implementation of routine GC/MGT in PC pts is feasible and results in the detection of mutations that are actionable for PC pts and at-risk family members. Systematized workflows for GC evaluation not reliant on active referral result in markedly higher uptake of MGT and mutation carrier identification. Clinical trial information: NCT03060720.

Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer

Pancreatic ductal adenocarcinoma is an aggressive cancer with limited treatment options¹. Approximately 10% of cases exhibit familial predisposition, but causative genes are not known in most families². We perform whole-genome sequence analysis in a family with multiple cases of pancreatic ductal adenocarcinoma and identify a germline truncating mutation in the member of the RAS oncogene family-like 3 (RABL3) gene. Heterozygous rabl3 mutant zebrafish show increased susceptibility to cancer formation. Transcriptomic and mass spectrometry approaches implicate RABL3 in RAS pathway regulation and identify an interaction with RAP1GDS1 (SmgGDS), a chaperone regulating prenylation of RAS GTPases³. Indeed, the truncated mutant RABL3 protein accelerates KRAS prenylation and requires RAS proteins to promote cell proliferation. Finally, evidence in patient cohorts with developmental disorders implicates germline RABL3 mutations in RASopathy syndromes. Our studies identify RABL3 mutations as a target for genetic testing in cancer families and uncover a mechanism for dysregulated RAS activity in development and cancer.

Abstract 4272: Mutations in RABL3 alter RAS prenylation and are associated with hereditary pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest solid cancers with limited treatment options despite intensive research efforts. Familial predisposition to PDAC is thought to occur in ~10% of cases, but causative genes have not been identified in most of these families. Uncovering the genetic basis for PDAC susceptibility has immediate prognostic implications for families and can provide precious mechanistic clues to PDAC pathogenesis. Here, we perform whole-genome sequence analysis in a family with high incidence of PDAC and identify a germline nonsense mutation in the member of RAS oncogene family-like 3 (RABL3) gene that has never before been directly associated with hereditary cancer. The truncated mutant allele (RABL3_p.Ser36*) co-segregates with cancer occurrence. To evaluate the contribution of the RABL3 mutant allele in hereditary cancer, we generated rabl3 heterozygous mutant zebrafish and found increased susceptibility to cancer formation in two independent cancer models. Complementary unbiased approaches implicate RABL3 in RAS pathway regulation. RNA-Seq and genome-set enrichment analysis of juvenile rabl3 mutants reveals a KRAS upregulation signature. Furthermore, affinity-purification mass-spectrometry for proteins associated with RABL3 or RABL3_p.Ser36* identifies Rap1 GTPase-GDP Dissociation Stimulator 1 (RAP1GDS1, SmgGDS), a chaperone that regulates prenylation of RAS GTPases. Indeed, in vitro studies demonstrate that RABL3_p.Ser36* accelerates KRAS prenylation, and this impact is lost in the absence of H/N/KRAS proteins. Whereas heterozygous rabl3 mutant zebrafish exhibit cancer predisposition, homozygous rabl3 mutant zebrafish develop severe craniofacial, skeletal, and growth defects consistent with human RASopathies, and these defects are partially rescued with the MEK inhibitor trametinib. Our findings support a gain-of-function rather than a null function typically associated with premature protein truncations. The discovered causative RABL3 germline mutation provides new diagnostic opportunities for genetic testing in other cancer families and uncovers an alternative mechanism for dysregulated RAS signaling in development and cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Sahar Nissim, Ignaty Leshchiner, Joseph D. Mancias, Matthew B. Greenblatt, Ophélia Maertens, Christopher A. Cassa, Jill A. Rosenfeld, Andrew G. Cox, John Hedgepeth, Julia Wücherpfennig, Andrew J. Kim, Jake E. Henderson, Patrick Gonyo, Anthony Brandt, Ellen Lorimer, Bethany Unger, Jeremy W. Prokop, Jeremy W. Heidel, Xiao-Xu Wang, Chinedu I. Ukaegbu, Gad Getz, Shamil R. Sunyaev, J. Wade Harper, Karen Cichowski, Alec C. Kimmelman, Yariv Houvras, Sapna Syngal, Carol Williams, Wolfram Goessling. Mutations in RABL3 alter RAS prenylation and are associated with hereditary pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4272. doi:10.1158/1538-7445.AM2017-4272

Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer

Purpose Hereditary factors play an important role in colorectal cancer (CRC) risk, yet the prevalence of germline cancer susceptibility gene mutations in patients with CRC unselected for high-risk features (eg, early age at diagnosis, personal/family history of cancer or polyps, tumor microsatellite instability [MSI], mismatch repair [MMR] deficiency) is unknown. Patients and Methods We recruited 1,058 participants who received CRC care in a clinic-based setting without preselection for age at diagnosis, personal/family history, or MSI/MMR results. All participants underwent germline testing for mutations in 25 genes associated with inherited cancer risk. Each gene was categorized as high penetrance or moderate penetrance on the basis of published estimates of the lifetime cancer risks conferred by pathogenic germline mutations in that gene. Results One hundred five (9.9%; 95% CI, 8.2% to 11.9%) of 1,058 participants carried one or more pathogenic mutations, including 33 (3.1%) with Lynch syndrome (LS). Twenty-eight (96.6%) of 29 available LS CRCs demonstrated abnormal MSI/MMR results. Seventy-four (7.0%) of 1,058 participants carried non-LS gene mutations, including 23 (2.2%) with mutations in high-penetrance genes (five APC, three biallelic MUTYH, 11 BRCA1/2, two PALB2, one CDKN2A, and one TP53), 15 of whom lacked clinical histories suggestive of their underlying mutation. Thirty-eight (3.6%) participants had moderate-penetrance CRC risk gene mutations (19 monoallelic MUTYH, 17 APC*I1307K, two CHEK2). Neither proband age at CRC diagnosis, family history of CRC, nor personal history of other cancers significantly predicted the presence of pathogenic mutations in non-LS genes. Conclusion Germline cancer susceptibility gene mutations are carried by 9.9% of patients with CRC. MSI/MMR testing reliably identifies LS probands, although 7.0% of patients with CRC carry non-LS mutations, including 1.0% with BRCA1/2 mutations.

Mutation spectrum and risk of colorectal cancer in African American families with Lynch syndrome

BACKGROUND & AIMS

African Americans (AAs) have the highest incidence of and mortality resulting from colorectal cancer (CRC) in the United States. Few data are available on genetic and nongenetic risk factors for CRC among AAs. Little is known about cancer risks and mutations in mismatch repair (MMR) genes in AAs with the most common inherited CRC condition, Lynch syndrome. We aimed to characterize phenotype, mutation spectrum, and risk of CRC in AAs with Lynch syndrome.

METHODS

We performed a retrospective study of AAs with mutations in MMR genes (MLH1, MSH2, MSH6, and PMS2) using databases from 13 US referral centers. We analyzed data on personal and family histories of cancer. Modified segregation analysis conditioned on ascertainment criteria was used to estimate age- and sex-specific CRC cumulative risk, studying members of the mutation-carrying families.

RESULTS

We identified 51 AA families with deleterious mutations that disrupt function of the MMR gene product: 31 in MLH1 (61%), 11 in MSH2 (21%), 3 in MSH6 (6%), and 6 in PMS2 (12%); 8 mutations were detected in more than 1 individual, and 11 have not been previously reported. In the 920 members of the 51 families with deleterious mutations, the cumulative risks of CRC at 80 years of age were estimated to be 36.2% (95% confidence interval [CI], 10.5%-83.9%) for men and 29.7% (95% CI, 8.31%-76.1%) for women. CRC risk was significantly higher among individuals with mutations in MLH1 or MSH2 (hazard ratio, 13.9; 95% CI, 3.44-56.5).

CONCLUSIONS

We estimate the cumulative risk for CRC in AAs with MMR gene mutations to be similar to that of individuals of European descent with Lynch syndrome. Two-thirds of mutations were found in MLH1, some of which were found in multiple individuals and some that have not been previously reported. Differences in mutation spectrum are likely to reflect the genetic diversity of this population.

Therapy-associated polyposis as a late sequela of cancer treatment

Survivors of childhood cancers are at increased risk of developing secondary gastrointestinal cancers, including colorectal cancer, later in life, possibly from exposure to abdominopelvic radiotherapy and/or alkylating chemotherapy. Profuse gastrointestinal polyposis is associated with rare, inherited colorectal cancer predisposition syndromes, most commonly caused by mutations in the adenomatous polyposis coli (APC) or mutY homolog (MUTYH) genes. We describe 5 patients who developed gastrointestinal polyposis many years after radiotherapy and chemotherapy for a childhood cancer. Genetic analysis of all 5 subjects did not identify pathogenic germline mutations in APC or MUTYH. Chemotherapy and/or radiotherapy therefore might cause gastrointestinal polyposis in some patients by undiscovered mechanisms.

Cancer risks and mutation spectrum of mismatch repair genes in African American families with Lynch syndrome

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Background: Although African Americans (AA) have the highest colorectal cancer (CRC) incidence and mortality of all populations in the United States, no studies have determined cancer risk and mismatch repair (MMR) genes mutation spectrum in LS patients of AA ancestry and the contribution of this syndrome to cancer disparities. Thus, the aims of this study are: (1) to describe LS cancers in AAs; (2) to investigate the mismatch repair (MMR) gene mutation spectrum in AA families with LS; (3) to determine how Amsterdam II criteria, revised Bethesda guideline, and PREMM(1,2,6) model perform for predicting MMR gene mutations in this population. Methods: Pedigrees of AA families with deleterious mutation or suspected deleterious mutation in MMR genes from five US referral centers were analyzed for personal and familial clinical cancer histories. Results: Twenty-four AA families were identified, of which 22 had deleterious mutations (15 MLH1, 4 MSH2, 2 MSH6, 1 PMS2) and 2 had suspected deleterious mutations (1 MLH1, 1 MSH2). Three recurrent mutation were found in MLH1(677G>A, IVS1-2A>G, IVS4-1G>A), accounting for 25% of all mutations. Of 24 probands, 58% were female and 96% had personal history of cancer. The median age at first primary tumor was 42yrs (range 28-57) and 50% developed more than 1 primary tumor. The majority of probands (79%) had CRC (median age of onset – 42yrs [range 31-61]), of which 26% had at least 2 CRC primaries. Endometrial cancer developed in 50% of the women (median age of onset – 51yrs [range 32-57]). Amsterdam II and Bethesda criteria were met in 63% and 88% of the individuals, respectively. Median score by PREMM(1,2,6) model was 54% (range 12.9-99.8). Conclusions: To our knowledge, this is the largest series of AA families with LS reported to date. Earlier age of onset for CRC at 42yrs (previously reported ~45 yrs) is suggested. The majority of mutations were found in MLH1 (67%), including three recurrent mutations. A 10% cutoff for PREMM(1,2,6) predictive model identified all mutation carriers. Larger studies are warranted to confirm the differences observed in age of CRC onset in this population.