Identification of KRASG12C Mutations in Circulating Tumor DNA in Patients With Cancer

KRAS is the most mutated proto-oncogene that has been identified in cancer, and treatment of patients with KRAS mutations remains an arduous challenge. Recently, KRAS^G12C mutation has attracted special interest because it is now considered potentially druggable with recently developed covalent small-molecule KRAS^G12C inhibitors. Nevertheless, to date, there have been no large-scale analyses of liquid biopsy that include testing for KRAS^G12C. Here, we performed a comprehensive analysis of KRAS^G12C mutations in multiple cancer types, as detected by circulating tumor DNA.

Development of oxaalkyne and alkyne fatty acids as novel tracers to study fatty acid beta-oxidation pathways and intermediates

Fatty acid beta-oxidation is a key process in mammalian lipid catabolism. Disturbance of this process results in severe clinical symptoms, including dysfunction of the liver, a major beta-oxidizing tissue. For a thorough understanding of this process, a comprehensive analysis of involved fatty acid and acyl-carnitine intermediates is desired, but capable methods are lacking. Here, we introduce oxaalkyne and alkyne fatty acids as novel tracers to study the beta-oxidation of long- and medium-chain fatty acids in liver lysates and primary hepatocytes. Combining these new tracer tools with highly sensitive chromatography and mass spectrometry analyses, this study confirms differences in metabolic handling of fatty acids of different chain length. Unlike longer chains, we found that medium-chain fatty acids that were activated inside or outside of mitochondria by different acyl-CoA synthetases could enter mitochondria in the form of free fatty acids or as carnitine esters. Upon mitochondrial beta-oxidation, shortened acyl-carnitine metabolites were then produced and released from mitochondria. In addition, we show that hepatocytes ultimately also secreted these shortened acyl chains into their surroundings. Furthermore, when mitochondrial beta-oxidation was hindered, we show that peroxisomal beta-oxidation likely acts as a salvage pathway, thereby maintaining the levels of shortened fatty acid secretion. Taken together, we conclude that this new method based on oxaalkyne and alkyne fatty acids allows for metabolic tracing of the beta-oxidation pathway in tissue lysate and in living cells with unique coverage of metabolic intermediates and at unprecedented detail.

Therapeutic Actionability of Circulating Cell-Free DNA Alterations in Carcinoma of Unknown Primary

Cancer of unknown primary (CUP) is a metastatic disease with unidentifiable primary tumor. Somatic alterations can be assessed noninvasively via liquid biopsies interrogating cell-free DNA (cfDNA).

METHODS

We evaluated 1,931 patients with CUP with a cfDNA next-generation sequencing panel (73-74 genes).

RESULTS

Overall, 1,739 patients (90%) had ≥ 1 cfDNA alteration. We then explored alteration actionability (per the levels of evidence from the OncoKB database); 825 patients (47.4% of 1,739) had level 1, level 2, or resistance/R1 alterations. Among 40 clinically annotated patients with CUP who had cfDNA evaluated, higher degrees of matching treatment to alterations (Matching Score > 50% v ≤ 50%) was the only variable predicting improved outcome: longer median progression-free survival (10.4 v 2.5 months; P = .002), overall survival (13.4 v 5.7 months; P = .07, trend), and higher clinical benefit rate (stable disease ≥ 6 months/partial response/complete response; 83% v 25%; P = .003).

CONCLUSION

In summary, cfDNA frequently reveals strong level-of-evidence actionable alterations in CUP, and high degrees of matching to therapy correlates with better outcomes.

Multigene assessment of genetic risk for women for two or more breast cancers

PURPOSE

The prevalence, penetrance, and spectrum of pathogenic variants that predispose women to two or more breast cancers is largely unknown.

METHODS

We queried clinical and genetic data from women with one or more breast cancer diagnosis who received multigene panel testing between 2013 and 2018. Clinical data were obtained from provider-completed test request forms. For each gene on the panel, a multivariable logistic regression model was constructed to test for association with risk of multiple breast cancer diagnoses. Models accounted for age of diagnosis, personal and family cancer history, and ancestry. Results are reported as odds ratios (ORs) with 95% confidence intervals (CIs).

RESULTS

This study included 98,979 patients: 88,759 (89.7%) with a single breast cancer and 10,220 (10.3%) with ≥ 2 breast cancers. Of women with two or more breast cancers, 13.2% had a pathogenic variant in a cancer predisposition gene compared to 9.4% with a single breast cancer. BRCA1, BRCA2, CDH1, CHEK2, MSH6, PALB2, PTEN, and TP53 were significantly associated with two or more breast cancers, with ORs ranging from 1.35 for CHEK2 to 3.80 for PTEN. Overall, pathogenic variants in all breast cancer risk genes combined were associated with both metachronous (OR 1.65, 95% CI 1.53-1.79, p = 7.2 × 10-33) and synchronous (OR 1.33, 95% CI 1.19-1.50, p = 2.4 × 10-6) breast cancers.

CONCLUSIONS

This study demonstrated that several high and moderate penetrance breast cancer susceptibility genes are associated with ≥ 2 breast cancers, affirming the association of two or more breast cancers with diverse genetic etiologies.

Age of ovarian cancer diagnosis among BRIP1, RAD51C, and RAD51D mutation carriers identified through multi-gene panel testing

BACKGROUND

Professional society guidelines recommend risk-reducing salpingo-oophorectomy (RRSO) for women with pathogenic variants (PVs) in ovarian cancer-risk genes. Personalization of that intervention is based on gene-specific phenotypes; however, the age of ovarian cancer diagnosis in women with PVs in moderate penetrance ovarian cancer-risk genes is not well characterized. Women who had hereditary cancer panel testing from September 2013-May 2019 were included (N = 631,950). Clinical/demographic information was compared for women with a PV in BRIP1, RAD51C, or RAD51D versus in BRCA1 or BRCA2.

RESULTS

PVs in BRIP1, RAD51C, or RAD51D were identified in 0.5% of all tested women but in 1.6% of women with a history of ovarian cancer (~ 3-fold increase). PVs in BRCA1 or BRCA2 were identified in 2.4% of all tested women but in 6.1% of women with a history of ovarian cancer (~ 2.5-fold increase). The proportion of women with a personal or family history of ovarian cancer was similar among women with a PV in BRIP1, RAD51C, RAD51D, BRCA1, or BRCA2. The median age at ovarian cancer diagnosis was 53 years for BRCA1, 59 years for BRCA2, 65 years for BRIP1, 62 years for RAD51C, and 57 years for RAD51D.

CONCLUSIONS

These data reinforce the importance of identifying PVs in moderate penetrance ovarian cancer-risk genes. The age at ovarian cancer diagnosis was older for women with PVs in BRIP1, RAD51C, or RAD51D, suggesting that it is safe to delay RRSO until age 45-50 in RAD51D PV carriers and possibly until age 50-55 in BRIP and RAD51C PV carriers.

Cell-Free Circulating Tumor DNA Improves Standard Genotyping of Non-Small-Cell Lung Cancer and Increases Detection of Targetable Alterations in a Selected Hispanic Cohort

BACKGROUND

Several studies have shown that the non-small-cell lung cancer (NSCLC) genomic background among Hispanics differs from other populations. The finding of low-frequency genomic alterations in cell-free DNA (cfDNA) can increase diagnostic accuracy and could improve treatment in NSCLC.

METHODS

Data from 54 Hispanic patients with advanced NSCLC with high clinical suspicion for ALK, EGFR, and ROS1 mutations were collected (including young age, female sex, and non-smokers). cfDNA was extracted from plasma and analyzed using a commercial next-generation sequencing test (Guardant360) which detects genomic alterations in 74 genes.

RESULTS

The median age was 56 years (range 31-83). Most patients were female (661.1%) and never smokers (72.3%). Among the patients included, 96% (52/54) had cfDNA detectable alterations with a mean number of 3.37 cfDNA alterations per test (range 1-10). cfDNA was able to detect some genomic alterations previously undetected by tissue biopsy. Among patients with insufficient or unavailable tissue to perform testing, mutations in EGFR and ALK which led to a change in therapy were determined using cfDNA in 28.8 and 3.8% of cases, respectively. Among patients with cfDNA alterations, 46.1% (n = 24) were switched to a targeted therapy with a median progression-free survival of 11.1 months (95% CI 7.6-14.6) and an overall survival of 40.3 months (95% CI 27.1-53.6). Concurrent genetic mutations with TP53 and KRAS negatively impacted the prognosis.

CONCLUSIONS

In a selected population of NSCLC Hispanic patients, comprehensive cfDNA analysis allowed a treatment change in 46.1% of the cases. Guardant360 allows the identification of genomic alterations to improve treatment selection and increase prognosis.

Abstract PS2-09: Next generation sequencing (NGS) in older adults with breast cancer using tissue-based and circulating tumor DNA (ctDNA) assays

Background: With advances in next generation sequencing (NGS) and now approved targeted therapy in breast cancer, genomic testing to identify potentially actionable mutations has become a common practice in patients (pts) with advanced breast cancer using both ctDNA and traditional tissue-based assays. Less is known regarding physician practice patterns in obtaining NGS testing and the practical implications of testing in older adults with breast cancer.Methods: Pts with advanced breast cancer underwent molecular profiling using a plasma-based ctDNA NGS assay (Guardant360® or Tempus®) between 5/2015 and 5/2020 at Siteman Cancer Center. Pts with advanced breast cancer who underwent genomic profiling using a tissue-based NGS assay (Tempus®) between 12/2017 and 5/2020 at this institution were also included. Clinicopathological histories were obtained from the medical record. Correlations were examined using a Fisher’s exact test.Results: During 5/15-5/20, 244 pts underwent ctDNA testing and 147 pts had a tissue-based NGS assay performed. There was no significant difference between the number of pts ≥ 65 years-old who underwent ctDNA testing (n=78, 32.0%) and tissue testing (n=37, 25.2%). There was no statistically significant difference between date of metastatic diagnosis and date of NGS testing between the older and younger cohorts. In pts who underwent tissue-based NGS testing, there was no significant difference between site of tissue tested (distant recurrence vs local) in the older and younger cohorts. The most common clinical managements following both ctDNA and tissue-based testing are presented in Table 1. Out of the 391 pts who underwent testing, 27 pts had both ctDNA and tissue-based NGS performed. Pts ≥ 65 were less likely to have both assays performed (n=3, 11.1%; p<0.05). In pts undergoing both assays, there were high concordance rates of ESR1 (81.5%) and PIK3CA (81.5%) mutations. Mean time between tissue and plasma collection for NGS testing in pts undergoing both assays was 356.4 days.

Conclusion: Older adults, who are typically less likely to be included in clinical trials, may still benefit from NGS to reveal potentially targetable mutations. It is reassuring in our cohort that older adults had ctDNA and tissue-based NGS performed at similar rates as part of standard of care treatment. The clinical management following NGS testing was also not significantly different in the older adult cohort. Older adults were less likely to have both tissue and ctDNA testing performed however, given the high concordance rates between tests, this may be less clinically relevant.

Table 1clinical management following NGS testing≥65 years-old<65 years-oldp valueno actionable mutations41 (35.7%)123 (44.6%)p=0.1testing results saved for potential future use27 (23.5%)45 (16.3%)p=0.1change in management15 (13.0%)41 (14.9%)p=0.6

Citation Format: Katherine K Clifton, Jingqin Luo, Yu Tao, Jennifer Saam, Thereasa Rich, Timothy Rearden, Anna Roshal, Ashley Frith, Caron Rigden, Foluso Ademuyiwa, Katherine Weilbaecher, Leonel Hernandez Aya, Lindsay Peterson, Nusayba Bagegni, Rama Suresh, Ron Bose, Tanya Wildes, Mateusz Opyrchal, Cynthia Ma. Next generation sequencing (NGS) in older adults with breast cancer using tissue-based and circulating tumor DNA (ctDNA) assays [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-09.

Mutation profile differences in younger and older patients with advanced breast cancer using circulating tumor DNA (ctDNA)

PURPOSE

Little is known regarding the mutation profiles of ctDNA in the older adult breast cancer population. The objective of this study is to assess differences in mutation profiles in the older adult breast cancer population using a ctDNA assay as well as assess utilization of testing results.

METHODS

Patients with advanced breast cancer underwent molecular profiling using a plasma-based ctDNA NGS assay (Guardant360) between 5/2015 and 10/2019 at Siteman Cancer Center. The profiling results of a multi-institutional database of patients with advanced breast cancer who had undergone molecular profiling were obtained. Associations between mutations and age group (≥ 65 vs. < 65) were examined using a Fisher's exact test.

RESULTS

In the single-institutional cohort, 148 patients (69.2%) were < 65 years old and 66 patients (30.8%) ≥ 65 years old. ATM, BRAF, and PIK3CA mutations were found more frequently in older patients with ER + HER2- breast cancers (p < 0.01). In the multi-institutional cohort, 5367 (61.1%) were < 65 years old and 3417 (38.9%) ≥ 65 years old. ATM, PIK3CA, and TP53 mutations were more common in the older cohort (p < 0.0001) and MYC and GATA3 mutations were less common in the older cohort (p < 0.0001). CtDNA testing influenced next-line treatment management in 40 (19.8%) patients in the single-institutional cohort.

CONCLUSION

When controlling for subtype, results from a single institution were similar to the multi-institutional cohort showing that ATM and PIK3CA were more common in older adults. These data suggest there may be additional molecular differences in older adults with advanced breast cancers.

Family history of breast cancer in men with non-BRCA male breast cancer: implications for cancer risk counseling

PURPOSE

The role of genetic predisposition in male breast cancer (MBC) patients who test negative for a BRCA mutation is unclear. The aim of this study is to define the association between MBC and family history of breast cancer in patients without mutations in BRCA1 or BRCA2.

METHODS

We conducted an unmatched case-control study with men who received commercial testing for germline mutations in cancer susceptibility genes, including 3,647 MBC cases who tested negative for deleterious mutations in BRCA1/BRCA2, and 4,269 men with a personal history of colorectal cancer who tested negative for mutations in DNA mismatch repair genes to serve as controls. Associations between family history of breast cancer and MBC were estimated using unconditional multivariable logistic regression with adjustment for age, race/ethnicity and year of testing.

RESULTS

Breast cancer in a first- or second-degree relative was associated with a four-fold increased odds of MBC (OR 4.7; 95% CI 4.1, 5.3). Associations with MBC were strongest for family history of breast cancer in 2 or more first-degree relatives (FDR) (OR 7.8; 95% CI 5.2, 11.6), for probands and FDR diagnosed at age < 45 years (OR 6.9; 95% CI 3.9, 12.4), and for family history of MBC (OR 17.9; 95% CI 7.6, 42.1). Findings were confirmed in a sensitivity analysis of MBC cases who tested negative on a 25-gene pan-cancer panel.

CONCLUSIONS

MBC patients without mutations in BRCA1/2 have significantly higher odds of a family history of breast cancer, suggesting the existence of unidentified MBC susceptibility alleles.

Abstract 729: Landscape of homologous recombination repair (HRR) mutations in prostate cancer profiled by ctDNA next-generation sequencing

Background: PARP inhibition can cause synthetic lethality and increased therapeutic sensitivity in patients with HRR deficiency (HRD), which can be detected through the molecular profiling of HRR genes. Prostate cancer has a high prevalence of HRD (20-25%, Athie 2019). High failure rates for tissue biopsy in metastatic prostate cancer patients (25-75%) (Ross 2005, Spritzer 2013) pose challenges for HRD profiling, underscoring the need for a non-invasive, ctDNA alternative. Copy number loss, a frequent cause of HRD, is further difficult to call due to signal dilution by cell-free leukocytic DNA. We developed a pipeline that detects loss-of-function SNV/Indels, structural rearrangements, and gene deletions to identify HRD on GuardantOMNITM, a 500-gene liquid biopsy panel. We present its performance across &gt;620 prostate cancer GuardantOMNITM samples.

Methods: Samples from 627 prostate cancer patients were processed on GuardantOMNITM RUO, with median unique coverage of 4982 molecules sequenced to 20,000x read depth. Somatic and germline SNVs and small indels were called using the Guardant bioinformatics pipeline (Helman 2018). A novel HRD module was developed to annotate pathogenic SNV/Indels and identify structural rearrangements, gene-level homozygous deletions, loss-of-heterozygosity (LOH) and genome-wide LOH, comprising of a novel CNV (Barbacioru 2019) and de-novo fusion caller (Gnerre, submitted). Loss-of-function variants were analyzed in 24 HRD genes.

Results: Pathogenic alterations in HRD genes were called in 260/620 (42%) prostate cancer samples with ctDNA detected: 28% of all samples had a pathogenic somatic or germline SNV/Indel, 20% had a homozygous deletion, 3.4% had a rearrangement involving an HRD gene. The majority of SNV/Indels occurred in BRCA2 (31% of all 158 SNV/Indels) and ATM (22%), similar to tissue (Dahwan 2016), but mutations also occurred across an additional 21 genes, including CDK12 (8%), CHEK2 (5%) and NBN (3.8%). Of prostate patients with a germline BRCA1/2 SNV/Indel and sufficient tumor shedding for LOH detection (max MAF&gt;10%), 10/19 (52%) also had LOH, compared to 86% in tissue (Jonsson 2019). Homozygous deletions were enriched in BRCA2 (6.9% of all samples), ATM (4.4%) and CHEK1 (2.3%). Rearrangements, including fusions and multi-exonic deletions, accounted for 6.5% of inactivating HRD mutations detected. In total, 24% of prostate samples had a biallelic inactivation involving an SNV, Indel or deletion.

Conclusion: We demonstrate in a prostate cancer cohort that GuardantOMNITM ctDNA profiling calls all classes of mutations contributing to HRD, with relative prevalence of alterations consistent with those in tissue. CfDNA presents a potential alternative for identifying patients who may benefit from PARP or cisplatin/platinum therapies, expanding the prevalence from 28% using small variants to 42% with the complete HRD biomarker set.

Citation Format: Jennifer Yen, Sante Gnerre, Catalin Barbacioru, Elena Helman, Ohad Manor, Arielle Yablonovitch, Ravi Vijaya Satya, Leo Liu, Jennifer Saam, Stephen Fairclough, Becky Nagy, Richard Lanman, Darya Chudova, AmirAli Talasaz. Landscape of homologous recombination repair (HRR) mutations in prostate cancer profiled by ctDNA next-generation sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 729.

Mutation profile differences in younger and older patients with advanced breast cancer using circulating tumor DNA (ctDNA)

1089

Background: Although the noninvasive nature of ctDNA testing is attractive in an older adult population, less is known regarding the mutation profiles of ctDNA in the older adult breast cancer population as this population is often excluded from studies. Previous tissue testing has shown differences in mutation profiles between older and younger adults with breast cancer. The objective of this study is to assess differences in mutation profiles in the older and younger adult breast cancer population using a ctDNA assay. Methods: Patients (pts) with advanced breast cancer underwent molecular profiling using a plasma-based ctDNA NGS assay (Guardant360) between 5/2015-10/2019 at Siteman Cancer Center. Clinicopathological histories were obtained from the medical record. The results of a multicenter database of pts with advanced breast cancer who had undergone molecular profiling using Guardant360 were obtained. Associations between mutations and age were measured using a Fisher’s exact test. Results: In the single institution cohort, of the 214 patients who underwent testing, 148 (69.16%) were < 65 and 66 (30.84%) ≥ 65 years-old. The most frequently mutated genes in age < 65 pts were TP53 (48.65%), PIK3CA (35.81%), and ESR1 (30.41%) while the most frequently mutated genes in age≥65 pts were PIK3CA (56.06%), TP53 (51.52%), ESR1 (25.76%), and ATM (21.21%). ATM, BRAF and PIK3CA mutations were found more frequently in age≥ 65 pts with ER+ HER2- breast tumors (p < 0.01). MYC and ESR1 mutations were not significantly associated with age, overall or within subtype. Overall ctDNA resulted in change in management in 19.8% pts (40/202). In the larger multicenter cohort, of the 8803 pts who underwent testing, 5367 (61.0%) were < 65 and 3417 (38.8%) ≥ 65 years-old. ATM, ESR1 and PIK3CA mutations were more common in age≥65 pts (p < 0.0001) and MYC mutations were less common in age≥65 pts (p < 0.0001). Conclusions: This study found that ctDNA is a feasible, attractive alternative to traditional biopsies and may identify actionable mutations in older adults with breast cancer. When controlling for subtype, results from a single institution were similar to the larger multicenter cohort showing ATM and PIK3CA were more common in the older adult population. This data suggests there may be additional molecular differences between breast cancer in older compared to younger adults that warrants further investigation.

Utility of circulating cell-free DNA (cfDNA) analysis in patients with carcinoma of unknown primary (CUP) in identifying alterations with strong evidence for response or resistance to targeted therapy

105

Background: CUP is a rare, heterogeneous group of cancers with an overall poor prognosis; the standard treatment remains chemotherapy. The OncoKB database is a curated list of somatic molecular alterations. Alterations with the highest classification must be an FDA-recognized biomarker associated with response to an FDA-approved drug (Level 1), be recommended by major guidelines or expert panels as predictive of response to an FDA-approved drug (Level 2) or be predictive of resistance to an FDA-approved drug (R1). We explored the landscape of alterations classified as Level 1, 2 or R1 based on the OncoKB scale in a large cohort of CUP patients tested via a well-validated cfDNA assay. Methods: We queried consecutive samples from advanced cancer patients with a listed diagnosis of CUP who underwent testing via a commercially available liquid biopsy assay (Guardant360) between November 2016 and November 2019. The cfDNA assay included targeted next-generation sequencing of 73- to 74-genes specifically curated to include genes with potential targeted therapy options. Alterations were classified based on their ranking in the OncoKB database as of January 2020. Results: In total we identified 2,022 samples with a diagnosis of CUP, and 90.0% of these samples had >1 cfDNA alteration detected. The median age of patients was 68 years and 51% were female. Overall, 20.7% of patients had a Level 1 alteration, 9.5% had a Level 2 alteration, and 23.9% had an R1 alteration (select alterations outlined in Table). Conclusions: cfDNA analysis of patients with advanced CUP identified a significant number of patients with alterations associated with strong evidence for either response or resistance to treatment based on the OncoKB classification schema. While many of these alterations are associated with approvals in specific cancer types, the identification of these alterations suggests many CUP patients may have targeted therapy options. We will present case examples illustrating patient outcomes from CUP patients who received targeting therapy based on cfDNA results. [Table: see text]

The prevalence of KRASG12C mutations utilizing circulating tumor DNA (ctDNA) in 80,911 patients with cancer

3547

Background: Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most commonly mutated proto-oncogene identified in cancer and still remains an arduous therapeutic challenge. Recently, KRASG12C mutation has become special interest since it has now been considered potentially druggable after the introduction of covalent small-molecule KRASG12C inhibitors. Advances in next-generation sequencing (NGS) and embracing utilization of ctDNA have uncovered more genetic alterations in many cancers. We present a comprehensive analysis on the prevalence of KRASG12C mutations identified by ctDNA. Methods: We conducted a 5-year (July 2014 to June 2019) retrospective review of ctDNA NGS analysis in the Guardant360 CLIA database inclusive of treatment-naïve and previously treated patients with metastatic solid tumors. Data were retrieved from the 80,911 unique patients with ctDNA detected. Clonality and co-occurrence of cancer type were analyzed. Clonality was defined as variant allele fraction(AF) / maximum somatic AF in the sample. Results: 80,911 patients, which included more than 100 tumor histologies, were identified. 2,985 patients (3.7%) with > 40 tumor types had KRASG12C mutations identified in ctDNA. KRASG12C prevalence by cancer type were as follows: sarcomatoid lung carcinoma (13.5%), lung cancer NOS (9%), large cell lung carcinoma (9%), lung adenocarcinoma (7.4%), NSCLC (6.9%), carcinoma of unknown primary (CUP) (4.1%), lung carcinoid (4%), CRC (3.5%), squamous cell lung carcinoma (2%), small cell lung carcinoma (1.5%), pancreatic ductal adenocarcinoma (PDAC) (1.2%), cholangiocarcinoma (1.2%), bladder cancer (0.6%), ovarian cancer (0.6%) and breast cancer (0.3%). 53 additional patients with KRASG12C were identified across 24 other tumor types. The KRASG12C mutation was found to be clonal (clonality > 0.9%) in the majority of patients with lung adenocarcinoma, NSCLC, CUP, squamous cell lung carcinoma, and PDAC, compared to patients with CRC and breast cancer who had bimodal distribution of clonal and sub clonal mutations. Conclusions: To our knowledge, this is the largest analysis on the prevalence of KRASG12C mutations identified by ctDNA. Our study demonstrated the feasibility of utilizing ctDNA to identify KRASG12C mutations across solid tumors with the highest prevalence in lung cancer as previously reported in tissue. The clonality information available from ctDNA-based genotyping may provide insights into the clinical efficacy of targeting KRASG12C in different tumor types.

Prevalence and association of ARID1A with driver alterations and immune checkpoint inhibitor (ICPi) biomarkers in cell-free circulating tumor DNA (ctDNA) from 27,000 non-small cell lung cancer (NSCLC) patients

9523

Background: Recent data suggest that the tumor suppressor gene ARID1A is associated with high anti-tumor immunity and may have value as a predictive biomarker for response to ICPi therapy in NSCLC. We examined ARID1A alterations detected in ctDNA from a large cohort of advanced NSCLC patients using a commercially available liquid biopsy assay and explored associations of ARID1A with lung cancer driver alterations and other putative ICPi mutational biomarkers. Methods: Consecutive samples from stage IIIB/IV NSCLC patients tested from March 2016 - August 2019 using a 73- to 74-gene targeted next-generation sequencing ctDNA assay (Guardant360) were queried. Testing included analysis of single nucleotide variants, insertions/deletions, fusions, and amplifications ( KEAP1 not tested). Mutation frequencies were compared using Fisher’s exact test, with variants of uncertain significance and synonymous variants excluded. Results: Of 27,776 NSCLC patients with >1 ctDNA alteration detected, 1,094 (3.9%) had >1 functional ARID1A (f ARID1A) mutation. f ARID1A mutations were significantly more common in patients with squamous histology compared to adenocarcinoma (5.1% vs 3.8%, p = 0.0007). There were significantly fewer EGFR exon 19 deletion mutations (4.9% vs 11.1%; p < 0.0001) and EGFR L858R mutations (4.0% vs 7.0%; p < 0.0001), and significantly more BRAF V600E alterations (2.2% vs 1.4%; p = 0.0338) in patients with f ARID1A. There was no significant difference in the frequency of ALK and ROS1 fusions, nor STK11 mutations between patients with and without f ARID1A (8.0% vs 6.8%; p = 0.126). Activating KRAS mutations were significantly more frequent in patients with f ARID1A (31.1% vs 19.4%; p < 0.0001), including KRAS G12C (10.9% vs 7.0%; p < 0.0001). Conclusions: These data provide a mutational landscape for f ARID1A mutations in NSCLC. f ARID1A was associated with significant differences in the frequency of multiple lung cancer driver alterations, of particular interest in the EGFR-mutated cohort, where ICPi efficacy is low. The frequency of STK11 mutations, a possible negative predictor of ICPi efficacy, was not significantly different. KRAS mutations were significantly more frequent in patients with f ARID1A, notable given recent data reporting that KRAS mutations, particularly KRAS G12C, may be a positive predictor of ICPi response in NSCLC. Determination of ICPi efficacy in patients with f ARID1A is in-process.

Circulating tumor (ct) DNA-based comprehensive genomic profiling to identify microsatellite instability (MSI) and defective DNA damage repair (DDR) in prostate cancer (PCa) patients

190

Background: Recent trials in PCa have shown efficacy of PARP inhibitors (PARPi) in patients (pts) with mutations in DDR genes such as BRCA1/2 (TOPARP-B, GALAHAD), as well as efficacy of immunotherapy (IO) in PCa pts with MSI. The combination of PARPi + IO is currently being evaluated in the KEYNOTE-365 trial. This analysis explored the utility of ctDNA in identifying PCa pts who may benefit from PARPi, IO, or a combination. Methods: ctDNA-based comprehensive genomic profiling (Guardant360) of 2,165 PCa pts was performed between 10/2018-08/2019. Frequency of pathogenic somatic BRCA1/ 2 mutations and MSI are reported. Results: Out of 2,165 PCa pts tested, Guardant360 identified 24 (1.1%) and 59 (2.7%) pts harboring pathogenic somatic BRCA1 or BRCA2 variants, respectively; MSI was detected in 40 (1.8%) PCa pts. Of the 40 MSI samples, 9 (22.5%) pts also had a somatic pathogenic BRCA1 and/or BRCA2 mutation . One pt harbored pathogenic somatic mutations in both BRCA1 and BRCA2. The variant allele frequency (VAF) for somatic pathogenic BRCA1 (N=2) ranged from 0.2-0.88%, and BRCA2 (N=8) ranged from 0.05-12.4%. There were no BRCA1/2 mutations at VAFs suspicious for germline in MSI PCa pts. A median of 19 genomic alterations (range 8-28) was identified among the 9 pts with pathogenic BRCA1/2 variants. The most frequent co-occurring aberrations were found in TP53, APC, AR, BRCA2, ARID1A, PTEN, RB1, and PIK3CA. An 82yo male with recurrent metastatic PCa underwent Guardant360 testing which identified BRCA2 T3085fs at 7.9% VAF and MSI. He was treated with pembrolizumab for 3 cycles and remains in remission. Another 51yo with MSI was treated with pembrolizumab for 4 cycles. He also remains in remission. Subsequent analysis shows clearance of ctDNA and MSI. Conclusions: ctDNA-based comprehensive genomic profiling can be used to detect PCa pts eligible to receive PARPi, IO, or a combination, improving clinical treatment decision making and pt outcomes, especially when a tissue biopsy is not feasible or sufficient for comprehensive genomic profiling. PSA and objective responses to IO have been observed in PCa pts with MSI detected by ctDNA.

Hereditary cancer genetic testing among patients with pancreatic cancer

4134

Background: Pancreatic cancer (PC) is typically diagnosed at a late, untreatable stage, with a 5-year survival rate of only ~8%. Genetic testing for individuals with PC may aid in therapy decisions, as those with a germline or somatic pathogenic variant (PV) in a DNA-repair gene may benefit from PARP inhibitors. In addition, germline genetic testing for unaffected family members can identify high risk individuals who may be appropriate for surveillance studies. We assessed the results of hereditary cancer genetic testing among individuals with a personal history of PC and evaluated several possible risk factors. Methods: Individuals with PC who had germline testing for 25-29 cancer-susceptibility genes between September 2013 and November 2018 were included in this analysis (N = 1,676). Clinical characteristics were obtained from provider-completed test request forms and included personal cancer history (PHx), family cancer history (FHx), and age at diagnosis. Results: Overall, 12.6% (212/1676) of patients with PC carried a PV, most commonly in BRCA2 (3.8%), ATM (2.7%), and PALB2 (1.2%). PVs were more common in men and for individuals who had a PHx of additional cancer(s) (see Table). Age at PC diagnosis did not impact the positive PV rate. The PV positive rate was elevated among individuals with PC and at least two relatives with PC (15.1%) and for individuals with a FHx of cancer at an early age (14.2%). The PV positive rate remained > 10% regardless of nearly all other FHx characteristics evaluated, including the absence of any FHx (see Table). Conclusions: In this cohort, a substantial proportion of individuals with a PHx of PC carried PVs, regardless of age at diagnosis and personal and family cancer history. [Table: see text]

Inherited germline mutations in men with prostate cancer

357

Background: Recent studies have demonstrated a high prevalence of pathogenic variants (PVs) in genes that confer hereditary cancer risk among men with metastatic prostate cancer (PC); however, PC does not currently receive attention as an indication for genetic testing. We assessed the clinical features of men with PC who received clinical testing as well as the distribution of PVs identified. Methods: Men with PC who underwent testing with a multi-gene hereditary cancer panel (Myriad Genetic Laboratories) from September 2013–September 2017 were included. Clinical information was obtained from provider-completed test request forms. Individuals with PC only were evaluated separately from those who had ≥1 additional malignancy. Personal/family history was evaluated relative to the 2013 NCCN guidelines for hereditary breast and ovarian cancer (HBOC) testing. Results: Overall, 1004 men with a personal history of PC were identified: 606 (60.4%) with only PC and 398 (39.6%) with PC and ≥1 additional malignancy. The most common additional malignancies were breast (136) and colorectal cancer (134). The median age of diagnosis in men with only PC was 59, which is younger than tested men who had an additional malignancy (63) and the SEER data (2009-2013) for all men with PC (66). HBOC testing criteria were met by 78.0% of men, including 68 (6.8%) who met based only on a personal/family history of PC and 330 (32.9%) who met in part due to a personal/family history of PC. PVs were identified in 12.9% of all men: 11.2% of men with PC only and 15.4% of men with PC and a second malignancy (Table). Conclusions: PC patients selected for genetic testing here were younger than men diagnosed with PC from the general population (SEER), and about a third had a diagnosis of an additional malignancy. They also have a high positive mutation rate across a broad spectrum of genes. [Table: see text]

Inherited germline mutations in men with prostate cancer

e16564

Background: Recent studies have demonstrated a high prevalence of pathogenic variants (PVs) in genes that confer hereditary cancer risk among men with metastatic prostate cancer (PC); however, PC does not currently receive attention as an indication for genetic testing. We assessed the clinical features of men with PC who received clinical testing as well as the distribution of PVs identified. Methods: A commercial laboratory database was queried to identify men with PC who underwent testing with a multi-gene hereditary cancer panel from September 2013–September 2016. Clinical information was obtained from provider-completed test request forms. Individuals with PC only were evaluated separately from those who had ≥1 additional malignancy. Personal/family history was evaluated relative to the 2013 NCCN guidelines for hereditary breast and ovarian cancer (HBOC) testing. Results: Overall, 700 men with a personal history of PC were identified: 384 (54.9%) with only PC and 316 (45.1%) with PC and ≥1 additional malignancy. The most common additional malignancies were colorectal (115) and breast cancer (105). The median age of diagnosis in men with only PC was 57.5, which is younger than tested men who had an additional malignancy (62) and the SEER data (2009-2013) for all men with PC (66). HBOC testing criteria were met by 75.9% of men, including 44 (6.3%) who met based only on a personal/family history of PC and 202 (28.9%) who met in part due to a personal/family history of PC. PVs were identified in 14.0% of all men: 11.5% of men with PC only and 17.1% of men with PC and a second malignancy (see Table). Conclusions: PC patients selected for genetic testing here were younger than men diagnosed with PC from the general population (SEER), and almost half had a diagnosis of an additional malignancy. They also have a high positive mutation rate across a broad spectrum of genes. [Table: see text]

Family history of breast cancer in non-BRCA male breast cancer: A case-control study

e13032

Background: Approximately 85% of male breast cancer (MBC) patients test negative for a BRCA mutation, and the role of genetic predisposition is unclear. Cancer risk counseling for unaffected relatives of BRCA-negative MBC patients relies on accurate cancer risk estimates, but there is limited data on the risk of breast cancer (BC) for relatives of these men. We characterized the association between MBC and family history of BC in patients who test negative for BRCA mutations in order to facilitate cancer risk counseling and to explore the possibility of unidentified MBC susceptibility alleles. Methods: We performed a case-control study of patients who had full length sequencing and large-rearrangement analysis for germline mutations in BRCA1/2 or the mismatch repair (MMR) genes at a commercial laboratory from 2006-2012. Cases were MBC patients who tested negative for a BRCA1/2 mutation (n = 3,647); controls were male colon cancer patients who tested negative for mutations in MMR genes (n = 4,269). Information on family history of BC was ascertained from test request forms completed by the ordering healthcare provider at the time of testing. Unconditional multivariable logistic regression models estimated odds ratios (OR) and 95% confidence intervals (CI) for associations between family history of BC in first- (FDR) and second-degree relatives (SDR) and MBC with adjustment for potential confounders (age, ethnicity, year of testing). Results: Compared to controls, MBC cases had higher odds of BC in a FDR or SDR (OR = 4.7; 95% CI 4.1, 5.3). Associations were strongest for family history of BC in 1 female FDR (OR = 3.9; 95% CI: 3.3, 4.6), ≥2 female FDR (OR = 7.5; 95% CI 5.0, 11.4), BC in a FDR < 45 years old (for cases diagnosed < 45, OR = 6.9; 95% CI 3.9, 12.4), a male FDR or SDR with BC (OR = 17.9; 95% CI 7.6, 42.1), and both a male and female FDR or SDR with BC (OR = 15.7; 95%CI 4.4, 55.3). Conclusions: MBC patients who test negative for a BRCA mutation have significantly higher odds of reporting family members affected by breast cancer, particularly with affected FDR < 45 years old, multiple affected relatives, and male relatives with BC. This data can guide risk counseling in MBC families, and suggests the existence of unidentified MBC susceptibility alleles.

Multi-gene hereditary cancer testing among men with breast cancer

1532

Background: All men with a personal diagnosis of breast cancer (BC) are candidates for BRCA1/2 genetic testing, as pathogenic variants (PVs) in these genes have a known association with BC risk in both men and women. As additional genes with known BC risk in women are now routinely included in multi-gene panel testing, we evaluated the outcomes of multi-gene panel testing in a large cohort of men with BC. Methods: This analysis includes the results of commercial genetic testing for 1,358 men with BC usinga multi-gene pan-cancer panel between September 2013 and January 2017. Clinical information was obtained from provider-completed test request forms. Age at diagnosis, personal, and family history were compared for men with PVs in BRCA1/2 versus non- BRCA1/2 genes. Results: Overall, 207 (15.2%) men with BC were found to carry a PV, where 147 (10.8%) men had a PV in BRCA1/2 ( BRCA1, 0.7%; BRCA2, 10.2%) and 60 (4.4%) men had a PV in a non- BRCA1/2 gene ( CHEK2, 2.0%; ATM, 1.0%; PALB2, 1.0%; BARD1, 0.2%; NBN, 0.2%; MSH6, 0.1%; BRIP1, 0.1%; CDH1, 0.1%; CDKN2A, 0.1%; MLH1, 0.1%, TP53, 0.1%). There were no substantial differences in the median age-at-diagnosis for men without a PV (65) compared to those with a BRCA1/2 PV (66) or a non- BRCA1/2 PV (63). Prostate cancer was the most common additional malignancy among all men with BC (9.0%), with a similar incidence among men with a BRCA1/2 PV (9.2%) and a non- BRCA1/2 PV (8.3%). In addition, 1.4% of men with a BRCA1/2 PV and 3.3% of men with a non- BRCA1/2 PV had a second BC. A family history of breast and/or ovarian cancer was present in 44.4% of the testing cohort, 66.7% of men with a BRCA1/2 PV, and 48.3% of men with a non- BRCA1/2 PV. This is consistent with the relative penetrance of BRCA1/2 and other genes included here. There were no other substantial differences in family history among BRCA1/2 PV carriers versus non- BRCA1/2 PV carriers. Conclusions: Close to a third of all PVs identified here in men with BC were in a gene other than BRCA1/2. There were no obvious differences in the clinical presentation of men with a BRCA1/2 PV compared to men with a PV in another gene or no PV at all. Collectively, this suggests that multi-gene panel testing is appropriate for all men with BC, regardless of other personal or family history.

Ancestry-based differences in hereditary cancer genetic testing

e13107

Background: Ancestry-based disparities in genetic testing for the hereditary breast and ovarian cancer (HBOC) genes BRCA1/2 have been well documented, but it is unclear whether this extends to other cancer-risk genes. Given reduced costs and broader access to multi-gene panels, we evaluated ancestry-based differences in the utilization and outcomes of HBOC and pan-cancer panel testing. Methods: Individuals who had genetic testing for BRCA1/2only (2006-2016) or with a multi-gene pan-cancer panel (2013-2016) were assessed. Clinical information was obtained from provider-completed test request forms. The most commonly reported ancestries [European (EU), Latin American/Caribbean (LA/C), African (AF), Asian (AS)] were evaluated. Individuals of Ashkenazi Jewish ancestry were not included in the EU group. Results: The relative utilization of HBOC testing in 2013-2016 increased in AF and LA/C individuals (vs 2006-2013) and was similar to panel testing in all ancestries (Table). The positive mutation rate for panel testing was 6.7%; AF (6.4%), LA/C (6.6%), AS (7.1%), EU (7.1%). The positive rate for HBOC testing from 2006-2013 was 5.7%. Of significance, the HBOC positive rate from 2013-2016 dropped to 4.1% and ancestry-specific positive rates were much lower relative to panel testing (Table). Gene-specific mutation prevalence differed by ancestry, but mutations were identified in a wide range of genes for all ancestries. Possible founder mutations were identified in BRCA1/2 and other genes. Conclusions: In this cohort, broader access to genetic testing has reduced disparities in recent years and panel testing shows improved clinical utility relative to HBOC testing in all ancestries. [Table: see text]

Abstract P3-10-06: Genetic testing for HBOC among women with a personal diagnosis of breast cancer in patients with Medicaid as compared to patients with private insurance

Introduction: National guidelines recommend that women diagnosed with early-onset breast cancer and/or a strong family history receive BRCA1/2 testing to guide treatment decisions. Among newly diagnosed patients, a positive test result will often prompt more aggressive surgical treatment to minimize the risk of second primary cancers. Currently, coverage for genetic counseling and testing for Hereditary Breast and Ovarian Cancer (HBOC) under the Medicaid expansion program of the Affordable Care Act has varied by state, where some states require a copayment for this service. Similarly, there is no mandate to cover risk-reducing surgery for patients found to carry a genetic mutation despite research showing cost-effectiveness. This analysis sought to determine whether genetic testing for HBOC among patients with breast cancer is different for those with Medicaid compared to those with private insurance.

Methods: A commercial laboratory database was analyzed for patients with a personal history of breast cancer who underwent testing with a 25-gene hereditary cancer panel from September 2013-February 2016. Patients were eligible for inclusion if they were between ages 18 and 64 at the time of testing and had not undergone previous genetic testing. A total of 17,020 patients with either Medicaid (N=4,313) or one of 5 private payers (N=12,707) were tested during this period. Descriptive statistics, including means for continuous variables and proportions for categorical variables, were calculated. Chi-square tests were used to test associations and differences of positive rates between insurance provider category. Two-tailed p-values are reported, and any p-value less than 0.05 is considered statistically significant.

Results: Medicaid patients had a median age of breast cancer diagnosis of 45 compared to 47 for patient with private insurance. Among women with Medicaid insurance, a higher proportion were of African (13.3% vs 6.4%) and Latin American ancestry (16.4% vs 5.3%). The mutation positive rate among patients with Medicaid was 13.0%, which was statistically higher than patients with private insurance (9.5%) (p&lt;0.001). The positive rate was higher among Medicaid patients of all ancestries suggesting that this discrepancy was not due to ancestry difference among the two testing populations.

Positive rate by ancestry MedicaidPrivateOverallAfrican80 (13.9%)72 (8.9%)152 (11.0%)Ashkenazi3 (17.6%)20 (15.3%)23 (15.5%)Asian26 (13.3%)40 (7.5%)66 (9.1%)Caucasian201 (12.9%)171 (9.9%)918 (10.4%)Latin American/Caribbean98 (13.8%)65 (9.6%)163 (11.8%)Native American7 (13.7%)9 (7.9%)16 (9.7%)Neareast/Mideast10 (17.9%)8 (9.3%)18 (12.7%)Multiple49 (12.3%)77 (9.0%)126 (10.0%)None Specified85 (11.3%)199 (8.8%)284 (9.4%)Total559 (13.0%)1207 (9.5%)1766 (10.4%)

Conclusions: Overall, the positive mutation rate among individuals with Medicaid insurance was higher than those with private insurance, suggesting the testing requirements applied to this population may be more stringent than those applied to the private insurance population. Consistent genetic testing insurance criteria are necessary for all patients to receive care in line with guidelines following a breast cancer diagnosis.

Citation Format: Baron P, Johnson-Isidore K, Miller L, Brown K, Kidd J, Saam J, Lancaster J. Genetic testing for HBOC among women with a personal diagnosis of breast cancer in patients with Medicaid as compared to patients with private insurance [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-10-06.

Abstract PD7-03: Characterization of Li-Fraumeni syndrome diagnosed using a 25-gene hereditary cancer panel

Background: Clinical diagnostic criteria for Li-Fraumeni syndrome (LFS) have evolved with increased utilization of TP53 germline testing and subsequent improved understanding of the diversity of the associated cancer phenotypes. However, data on LFS still suffer from ascertainment bias as patients are typically selected to undergo TP53 testing based on the presence of hallmark features of LFS. Analyzing TP53 mutation carriers identified from multi-gene panel testing, for which the diagnosis of LFS may not have been suspected or was included in a longer differential diagnosis, affords an opportunity to characterize additional TP53 carriers who might not otherwise have been ascertained.

Methods: Patients with a deleterious or suspected deleterious germline TP53 mutation were identified from 80,748 consecutive cases that underwent a 25-gene hereditary cancer panel test between September 2013 and March 2015 at a commercial diagnostic laboratory. Patient clinical data were obtained by healthcare provider report on test requisition forms. Each TP53 mutation carrier was evaluated to determine whether the National Comprehensive Cancer Network's (NCCN) guidelines were met for TP53 testing.

Results: Eighty-one TP53 mutation carriers were identified and had a total of 115 cancers (0.1% overall prevalence). Among the 76 carriers with at least one cancer, the average age at first diagnosis was 42 years (range 11-76 years) and 24% were first diagnosed older than age 50 years. The most common first cancers were of the breast (n=45), ovary (n=9), and gastrointestinal tract (n=8). Fifty-two of the 75 (69%) women had breast cancer, 44% of which were first diagnosed at 35 years or younger, and 21% were first diagnosed at 50 years or older. Only 27 TP53 carriers met NCCN criteria for TP53 testing, 14 of whom only met based on having early-onset breast cancer. An additional 8 did not meet criteria themselves but had a first- or second-degree relative who did. Among the 28 individuals with more than one primary cancer, 21 (75%) developed their second primary at a site for which increased surveillance is recommended in LFS, but only 4 would have met NCCN criteria for TP53 testing at their first cancer diagnosis. The most common second cancers were of the breast (n=16), gastrointestinal tract (n=4), or kidney (n=2) and occurred an average of 11 years after the first cancer (range 0-36 years).

Conclusion: In this analysis, a large proportion of carriers would not have been identified as TP53 testing candidates based on NCCN guidelines. Our data are consistent with other studies demonstrating high second primary cancer risks in LFS, and highlight the value of multigene panel testing in identifying individuals who may be candidates for increased surveillance and/or cancer risk-reducing management options.

Citation Format: Rich T, Lotito M, Kidd J, Saam J, Lancaster J. Characterization of Li-Fraumeni syndrome diagnosed using a 25-gene hereditary cancer panel. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr PD7-03.

Lynch Syndrome Patients with Limited Family History Identified in a Laboratory Setting: A Descriptive Study

OBJECTIVE

Patients diagnosed with colorectal cancer before the age of 50 years are recommended for Lynch syndrome (LS) testing according to current clinical guidelines. However, many patients are not identified because of the stringent guidelines on existing diagnostic criteria. The aim of this analysis was to evaluate the ability of existing criteria to adequately ascertain patients appropriate for LS genetic testing.

METHOD

To determine whether existing clinical diagnostic criteria underascertain individuals who would be appropriate candidates for hereditary cancer risk assessment, we stratified the detection rate of deleterious mismatch repair (MMR) mutations in 9,109 patients with a personal history of colorectal cancer who were diagnosed between the ages of 30 and 74 years with little or no family history suggestive of LS by 5-year age-at-detection intervals.

RESULTS

There was little difference in the aggregate positive mutation rate in individuals diagnosed between the ages of 50 and 59 years compared to the positive mutation rate in patients diagnosed before the age of 50 years.

CONCLUSION

These results suggest that cancer diagnosis under the age of 50 years is an insufficiently sensitive predictor of hereditary cancer susceptibility.

Abstract P1-03-03: Experience in the community oncology practice with a 25-gene hereditary cancer panel

Introduction:

The identification of patients with an inherited cancer syndrome is becoming increasingly relevant in the treatment and prevention of cancer. Testing with a panel of genes provides the opportunity to rapidly identify or rule out deleterious mutations in several genes simultaneously and, thus, has the potential to streamline the testing process and more efficiently and accurately provide results. We report on the experience of panel-based testing in the community oncology setting.

Objectives:

To evaluate the performance of a 25-gene hereditary cancer test in the community oncology setting and describe the patient characteristics and test findings.

Methods:

We retrospectively evaluated the 25-gene panel testing data obtained between September 2013 and February 2014 in 6 large community oncology practices. The gene panel was based on next generation sequencing and rearrangement analysis of 25 genes with cancer risk data: BRCA1, BRCA2, MLH1, MSH2, MSH6, PMS2, EPCAM, APC, MUTYH, CDKN2A, CDK4, PALB2, CHEK2, SMAD4, BMPR1A, STK11, TP53, CDH1, PTEN, ATM, NBN, BARD1, BRIP1, RAD51C, and RAD51D. Personal and family history was obtained by health care provider report on test requisition forms.

Results:

The panel test was performed on 359 individuals during the time period. 69.9% of these patients had a phx of at least one of the eight panel cancers: breast, ovarian, colorectal, endometrium, pancreas, melanoma, prostate, and/or stomach. cancer diagnosis. 97.8% of the patients tested met the 2013 NCCN guideline criteria for HBOC, 2012 NCCN guideline criteria for Lynch Syndrome, or both. 37 pathogenic mutations were found in 34 distinct patients. The variant rate in this population was 35.4%. Mutations were identified in 16 different genes, and only 20 of the 37 mutations (54.1%) were found to be in the 6 genes included in HBOC and Lynch Syndrome testing (BRCA1, BRCA2, MSH6, MLH1, MSH2, PMS2).

Conclusion:

The 25-gene hereditary cancer panel increased the identification of deleterious mutations which would otherwise not have been detected. The variant rate in this setting is similar to the rate reported previously in both community and academic centers where panel testing is used. Use of a hereditary cancer panel in the community oncology practice may improve detection rates and provide an opportunity for enhanced cancer management.

Citation Format: Sami Diab, Patricia Rodriguez, Anna Leininger, Lisa Clark, Mike F Janicek, Ellen B Smith, John Sandbach, Jennifer Saam, Lucy Langer. Experience in the community oncology practice with a 25-gene hereditary cancer panel [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 P1-03-03.

Comprehensive sequencing of PALB2 in patients with breast cancer suggests PALB2 mutations explain a subset of hereditary breast cancer

BACKGROUND

This study sought to determine the prevalence of PALB2 mutations in a cohort referred for diagnostic testing for hereditary breast cancer.

METHODS

Sanger sequencing was used to analyze the entire coding region and flanking introns of PALB2 in anonymized DNA samples from 1479 patients. Samples were stratified into a "high-risk" group, 955 samples from individuals predicted to have a high probability of carrying a mutation in BRCA1 or BRCA2 based on their personal and family history, and a "lower-risk" group consisting of 524 samples from patients with breast cancer, but fewer risk factors for being a BRCA1 or BRCA2 mutation carrier. All patients were known to be negative for deleterious sequence mutations and large rearrangements in BRCA1 and BRCA2.

RESULTS

We identified 12 disease-associated PALB2 mutations among the 1479 patients (0.8%). The PALB2 mutations included 8 nonsense, 3 frameshift mutations and a splice-site mutation. The mutation prevalence for the high-risk population was 1.05% (95% CI = 0.5-1.92), whereas that for the lower-risk population was 0.38% (95% CI = 0.05-1.37). We identified 59 PALB2 variants of uncertain significance (VUS) among 57 of the 1479 patients (3.9%).

CONCLUSIONS

These results suggest that PALB2 mutations occur at a frequency of ~1% in patients with hereditary breast cancer.

A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes

Genetic testing has the potential to guide the prevention and treatment of disease in a variety of settings, and recent technical advances have greatly increased our ability to acquire large amounts of genetic data. The interpretation of this data remains challenging, as the clinical significance of genetic variation detected in the laboratory is not always clear. Although regulatory agencies and professional societies provide some guidance regarding the classification, reporting, and long-term follow-up of variants, few protocols for the implementation of these guidelines have been described. Because the primary aim of clinical testing is to provide results to inform medical management, a variant classification program that offers timely, accurate, confident and cost-effective interpretation of variants should be an integral component of the laboratory process. Here we describe the components of our laboratory's current variant classification program (VCP), based on 20 years of experience and over one million samples tested, using the BRCA1/2 genes as a model. Our VCP has lowered the percentage of tests in which one or more BRCA1/2 variants of uncertain significance (VUSs) are detected to 2.1% in the absence of a pathogenic mutation, demonstrating how the coordinated application of resources toward classification and reclassification significantly impacts the clinical utility of testing.

BRCA1/2 mutation prevalence among triple-negative breast cancer patients from a large commercial testing cohort

1544

Background: BRCA1/2 deleterious mutation identification among triple-negative breast cancer (TNBC) patients has gained importance due to cancer-risk management implications for patients and their relatives, and also has an emerging role in guiding treatment selection for therapies such as PARP inhibitors. The National Comprehensive Cancer Network (NCCN) currently recommends BRCA1/2 testing for TNBC patients diagnosed at age <60. Mutation prevalence among TNBC patients has previously been studied only in small regionalized cohorts. A recent study in unselected patients using the updated definitive criteria for TNBC reported mutation prevalence as 10.6%. Methods: Following the 2011 NCCN Hereditary Breast and Ovarian Cancer (HBOC) Testing Criteria update, serial cohorts of > 5,000 Ashkenazi Jewish and > 65,000 non-Ashkenazi Jewish breast cancer patients undergoing commercial BRCA1/2 testing were analyzed. Age at diagnosis, ethnicity, and provider-reported TN status were obtained from test requisition forms completed by ordering providers, and correlated with test results. Neither the accuracy nor definitive criteria used for TN status reported was independently verified. Results: Incidence of TNBC was reported as 9.7% among non-Ashkenazi patients and 16.5% within the subset with African ancestry. Incidence of TNBC was reported as 4.5% among Ashkenazi patients, but this is likely affected by test ordering for this population. The Table displays the BRCA1/2mutation rates classified by ethnicity and age-group. Conclusions: This study provides the most robust estimate to date of BRCA1/2 mutation prevalence among TNBC patients of all ages. The mutation rates seen among TNBC patients diagnosed after age 60 also illustrate the importance of testing such patients who may not meet the current NCCN HBOC testing criteria. [Table: see text]

Stratification of risk for patients with prostate cancer at biopsy using CCP score

127

Background: In the US, most prostate cancers are treated with surgery or radiation, despite many having low malignant potential. If low cancer progression risk can be established, some men can be spared treatment. PSA, Gleason score and clinical stage work well for population risk assessment but lack precision for individuals. Molecular analysis can refine risk assessment as demonstrated by a cell cycle progression score (CCP) predictive of prostate cancer aggressiveness in 4 separate cohorts. In these studies, CCP typically ranged from −2 to +3 with each 1−unit increase corresponding to approximately a doubling of risk. We characterized the CCP distribution using recent samples from a typical US urology multi−centered clinical setting and determined the analytic success rate of the assay. Methods: Formalin fixed, prostate biopsy tissue from 300 patients diagnosed with adenocarcinoma within the last 12 months was analyzed. CCP is calculated by measuring the relative RNA expression of 31 cell cycle progression genes. Patients were recruited from 15 geographically diverse community urology practices. Results: CCP could be measured for 98% of samples (294/300). This study showed a normal distribution for the CCP ranging from −2 to 3.2 (median = −0.3, SD=0.92). There was little correlation of CCP with PSA, age, or body mass index. Correlation with Gleason score was similar to those in prior studies (r=0.494). A relative classification of cancer aggressiveness based on CCP of ~ 1200 patients from multiple cohorts has been developed. The 294 evaluable patients were cross−classified by AUA risk and cancer aggressiveness (see table). CCP further stratified patients within each AUA risk classification. Conclusions: CCP is a novel assay that can facilitate risk stratification for men with prostate adenocarcinoma. [Table: see text]

Prevalence of DPYD gene mutations among patients receiving 5-FU therapy

447

Background: Dihydropyrimidine dehydrogenase (DPYD) is the major enzyme that metabolizes 5-Fluoruracil (5-FU), a component of many chemotherapy regimens. Patients with a DPYD gene mutation have higher 5-FU plasma levels, leading to a 50-60% risk of a grade 3-4 toxicity. DPYD mutations have an estimated prevalence of 3-5% in the general population, but full sequencing is rarely performed in published studies. Analyses of the largest set of full DPYD gene sequencing test results from a commercial laboratory database are presented. Methods: A set of 3,083 patients was analyzed. Patient demographics (age, gender, ethnicity) and pre-test grade 3-4 toxicity status (none, 5-FU related, other) were obtained from the test request form. Descriptive analyses were performed to estimate mutation prevalence overall, and by toxicity and ancestry classifications, as well as to characterize mutations of interest. A subset of 24 patients tested for DPYD mutations in response to high 5-FU exposure levels was also analyzed. Results: The overall DPYD mutation prevalence was 7.3%. Mutations were present in 4.7% and 10.3% of patients experiencing none and at least one 5-FU related toxicity pre-test, respectively. Among patients with toxicities pre-test, the prevalence increased from 7.8% to 31.6% for those experiencing a single to all four toxicity types. Among 5-FU related toxicities, mutation prevalence was highest (18.5%) for hematopoietic events. The previously reported founder mutation IVS14+1G>A had a relative prevalence 42.7%, but 30.9% of these mutations were seen in patients not reporting a Western/Northern European ancestry. Among the subset of patients with high 5-FU exposure levels, 29% had a DPYD mutation showing a genetic causality. Conclusions: 5-FU in chemotherapy regimens remains widespread, yet DPYD gene testing utilization remains minimal. Most testing occurs post-treatment in response to a severe toxicity rather than pre-treatment, which would permit physicians to adapt treatment and reduce toxicity risk. Compared to previous studies, this study using full sequencing data from 3083 patients provides robust estimates of DPYD mutation prevalence and helps characterize DPYD mutations of particular interest.

ZEN-4/MKLP1 is required to polarize the foregut epithelium

BACKGROUND

Epithelial tubes are a key component of organs and are generated from cells with distinct apico-basolateral polarity. Here, we describe a novel function during tubulogenesis for ZEN-4, the Caenorhabditis elegans ortholog of mitotic kinesin-like protein 1 (MKLP1), and CYK-4, which contains a RhoGAP (GTPase-activating protein) domain. Previous studies revealed that these proteins comprise centralspindlin (a complex that functions during mitosis to bundle microtubules), construct the spindle midzone, and complete cytokinesis.

RESULTS

Our analyses demonstrate that ZEN-4/MKLP1 functions postmitotically to establish the foregut epithelium. Mutants that lack ZEN-4/MKLP1 express polarity markers but fail to target these proteins appropriately to the cell cortex. Affected proteins include PAR-3/Bazooka and PKC-3/atypical protein kinase C at the apical membrane domain, and HMR-1/cadherin and AJM-1 within C. elegans apical junctions (CeAJ). Microtubules and actin are disorganized in zen-4 mutants compared to the wild-type.

CONCLUSION

We suggest that ZEN-4/MKLP1 and CYK-4/RhoGAP regulate an early step in epithelial polarization that is required to establish the apical domain and CeAJ.