Advancing Evidence Generation for Circulating Tumor DNA: Lessons Learned from A Multi-Assay Study of Baseline Circulating Tumor DNA Levels across Cancer Types and Stages

Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across ctDNA assays has not been widely studied. Friends of Cancer Research formed a collaboration across multiple commercial ctDNA assay developers to assess baseline ctDNA levels across five cancer types in early- and late-stage disease. This retrospective study included eight commercial ctDNA assay developers providing summary-level de-identified data for patients with non-small cell lung cancer (NSCLC), bladder, breast, prostate, and head and neck squamous cell carcinoma following a common analysis protocol. Baseline ctDNA levels across late-stage cancer types were similarly detected, highlighting the potential use of ctDNA as a biomarker in these cancer types. Variability was observed in ctDNA levels across assays in early-stage NSCLC, indicative of the contribution of assay analytical performance and methodology on variability. We identified key data elements, including assay characteristics and clinicopathological metadata, that need to be standardized for future meta-analyses across multiple assays. This work facilitates evidence generation opportunities to support the use of ctDNA as a biomarker for clinical response.

ERBB2 (HER2) amplifications and co-occurring KRAS alterations in the circulating cell-free DNA of pancreatic ductal adenocarcinoma patients and response to HER2 inhibition

Purpose

Despite accumulating data regarding the genomic landscape of pancreatic ductal adenocarcinoma (PDAC), olaparib is the only biomarker-driven FDA-approved targeted therapy with a PDAC-specific approval. Treating ERBB2(HER2)-amplified PDAC with anti-HER2 therapy has been reported with mixed results. Most pancreatic adenocarcinomas have KRAS alterations, which have been shown to be a marker of resistance to HER2-targeted therapies in other malignancies, though the impact of these alterations in pancreatic cancer is unknown. We describe two cases of ERBB2-amplified pancreatic cancer patients treated with anti-HER2 therapy and provide data on the frequency of ERBB2 amplifications and KRAS alterations identified by clinical circulating cell-free DNA testing.

Methods

De-identified molecular test results for all patients with pancreatic cancer who received clinical cell-free circulating DNA analysis (Guardant360) between 06/2014 and 01/2018 were analyzed. Cell-free circulating DNA analysis included next-generation sequencing of up to 73 genes, including select small insertion/deletions, copy number amplifications, and fusions.

Results

Of 1,791 patients with pancreatic adenocarcinoma, 36 (2.0%) had an ERBB2 amplification, 26 (72.2%) of whom had a KRAS alteration. Treatment data were available for seven patients. Two were treated with anti-HER2 therapy after their cell-free circulating DNA result, with both benefiting from therapy, including one with a durable response to trastuzumab and no KRAS alteration detected until progression.

Conclusion

Our case series illustrates that certain patients with ERBB2-amplified pancreatic adenocarcinoma may respond to anti-HER2 therapy and gain several months of prolonged survival. Our data suggests KRAS mutations as a possible mechanism of primary and acquired resistance to anti-HER2 therapy in pancreatic cancer. Additional studies are needed to clarify the role of KRAS in resistance to anti-HER2 therapy.

Pan-Tumor Analytical Validation and Osimertinib Clinical Validation in EGFR Mutant Non-Small-Cell Lung Cancer, Supporting the First Next-Generation Sequencing Liquid Biopsy in Vitro Diagnostic

Comprehensive genotyping is necessary to identify therapy options for patients with advanced cancer; however, many cancers are not tested, partly because of tissue limitations. Next-generation sequencing (NGS) liquid biopsies overcome some limitations, but clinical validity is not established and adoption is limited. Herein, clinical bridging studies used pretreatment plasma samples and data from FLAURA (NCT02296125; n = 441) and AURA3 (NCT02151981; n = 450) pivotal studies to demonstrate clinical validity of Guardant360 CDx (NGS LBx) to identify patients with advanced EGFR mutant non-small-cell lung cancer who may benefit from osimertinib. The primary end point was progression-free survival (PFS). Patients with EGFR mutation as identified by NGS LBx had significant PFS benefit with first-line osimertinib over standard of care (15.2 versus 9.6 months; hazard ratio, 0.41; P < 0.0001) and with later-line osimertinib over chemotherapy (8.3 versus 4.2 months; hazard ratio, 0.34; P < 0.0001). PFS benefits were similar to the original trial cohorts selected by tissue-based EGFR testing. Analytical validation included accuracy, precision, limit of detection, and specificity. Analytical validity was established for EGFR mutation detection and pan-tumor profiling. Panel-wide limit of detection was 0.1% to 0.5%, with 98% to 100% per-sample specificity. Patients with EGFR mutant non-small-cell lung cancer by NGS LBx had improved PFS with osimertinib, confirming clinical validity. Analytical validity was established for guideline-recommended therapeutic targets across solid tumors. The resulting US Food and Drug Administration approval of NGS LBx demonstrated safety and effectiveness for its intended use and is expected to improve adherence to guideline-recommended targeted therapy use.

Real-World Treatment Patterns in Patients With HER2-Amplified Metastatic Colorectal Cancer: A Clinical-Genomic Database Study

BACKGROUND

HER2 amplification (HER2+) occurs in approximately 3% of patients with metastatic colorectal cancer (mCRC). Despite the recent addition of HER2-directed therapies to treatment recommendations in the NCCN Guidelines, until more recently there were no FDA-approved treatments. This study examined real-world treatment patterns in patients with HER2+ mCRC in the United States before and after the emerging awareness of HER2-directed therapies in 2018.

METHODS

This was a retrospective observational study of patients with HER2+ mCRC from the GuardantINFORM database, which contains claims data for patients with Guardant360 genomic testing results. Patients were aged ≥18 years, were diagnosed with mCRC between January 2014 and September 2020, and had confirmed ERBB2 amplification via the blood-based Guardant360 test. Treatment patterns and real-world time to next treatment (rwTTNT) were evaluated.

RESULTS

This study included 142 patients with a median age of 59 years; 31 (21.8%) patients with ERBB2 amplifications also had ERBB2 mutations. Treatment patterns were heterogeneous and evolved over time; before 2018, the most common regimen prescribed after detection of ERBB2 amplification was anti-VEGF therapy with or without chemotherapy (31.6%; n=25), and after 2018, HER2-directed therapies were the most commonly prescribed (36.5%; n=23). Median rwTTNT among the overall cohort was 8.4 months (95% CI, 6.5-10.0); rwTTNT was numerically longer in patients who received HER2-directed therapy compared with those who received non-HER2-directed therapies (11.0 months [95% CI, 6.3-12.3] vs 7.2 months [95% CI, 5.8-9.6]).

CONCLUSIONS

This real-world study of the largest clinically annotated dataset of patients with HER2+ mCRC showed that many patients do not receive HER2-directed therapy despite its inclusion in NCCN Guidelines, with heterogeneous treatment patterns suggesting that standard of care remains undefined and targeted therapy remains underutilized. Greater awareness of the unmet need in this patient population, together with new effective therapies, will facilitate strategies for improved, targeted treatment approaches.

Impact of STK11 mutation on first-line immune checkpoint inhibitor (ICI) outcomes in a real-world KRAS G12C mutant lung adenocarcinoma cohort

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Background: The introduction of KRAS G12C inhibitors into clinical trials has demonstrated promise and may provide a new therapeutic option for patients (pts) harboring KRAS G12C mutations. Recent data has also indicated that immune checkpoint inhibitors (ICI) have shown benefit in KRAS G12C mutant lung adenocarcinoma (LUAD); however, data on the impact of co-occurring STK11 mutations on outcomes are conflicting. We utilized the Guardant INFORM real-world clinical-genomic database to assess the impact of co-occurring STK11 mutations on outcomes in pts with KRAS G12C mutant LUAD treated with a first-line ICI containing regimen. Methods: This retrospective matched cohort observational study was conducted in a nationally representative clinical-genomic database covering over 137,000 pts with comprehensive ctDNA results and associated clinical information. Adult pts with metastatic LUAD who received ≥ 1 dose of first-line anti-PD1/PD-L1 ± chemotherapy and had at least 90 days follow-up after first KRAS G12C detection were included. A cohort of pts without KRAS G12C, including KRAS wildtype pts and pts with other KRAS mutations, were matched 3:1 for age, gender, year of index and baseline comorbidity. Time to next treatment (TTNT), time to discontinuation (TTD), real-world overall survival (rwOS) were compared with vs. without STK11 mutations for both cohorts using cox proportional-hazards model. Results: Among 330 pts in the KRAS G12C cohort, 21% (n = 70) had an STK11 mutation. Among the matched cohort (n = 938), 754 pts were KRAS wildtype, of whom 6% (n = 49) had STK11 mutations. Within the KRAS G12C cohort, pts with STK11 mutations had statistically significant shorter TTNT (hazard ratio [HR] 2.7, 95% confidence internal [CI] 1.8-4.0, p < 0.0001), TTD (HR 1.4, 95% CI 1.0-2.0, p < 0.04) and rwOS (HR 3.2, 95% CI 2.0-5.1, p < 0.0001) than pts without STK11 mutations. Within the matched KRAS wildtype cohort, the differences in TTD (HR 1.4, 95% CI = 1.0-2.0, p = 0.08) and rwOS (HR 1.4, 95% CI = 0.8-2.4, p = 0.3) in patients with vs. without STK11 mutation did not reach statistical significance (Table). Conclusions: This study provides real-world evidence that STK11 co-mutations are associated with worse outcomes among pts with KRAS G12C mutant LUAD treated with first-line ICI. These inferior outcomes indicate a high unmet medical need among LUAD pts harboring co-occurring KRAS G12C and STK11 mutations and demonstrate the need for effective targeted and/or combination therapies in this patient population.[Table: see text]

Serial Monitoring of Circulating Tumor DNA by Next-Generation Gene Sequencing as a Biomarker of Response and Survival in Patients With Advanced NSCLC Receiving Pembrolizumab-Based Therapy

Although the majority of patients with metastatic non-small-cell lung cancer (mNSCLC) lacking a detectable targetable mutation will receive pembrolizumab-based therapy in the frontline setting, predicting which patients will experience a durable clinical benefit (DCB) remains challenging.

MATERIALS AND METHODS

Patients with mNSCLC receiving pembrolizumab monotherapy or in combination with chemotherapy underwent a 74-gene next-generation sequencing panel on blood samples obtained at baseline and at 9 weeks. The change in circulating tumor DNA levels on-therapy (molecular response) was quantified using a ratio calculation with response defined by a > 50% decrease in mean variant allele fraction. Patient response was assessed using RECIST 1.1; DCB was defined as complete or partial response or stable disease that lasted > 6 months. Progression-free survival and overall survival were recorded.

RESULTS

Among 67 patients, 51 (76.1%) had > 1 variant detected at a variant allele fraction > 0.3% and thus were eligible for calculation of molecular response from paired baseline and 9-week samples. Molecular response values were significantly lower in patients with an objective radiologic response (log mean 1.25% v 27.7%, P < .001). Patients achieving a DCB had significantly lower molecular response values compared to patients with no durable benefit (log mean 3.5% v 49.4%, P < .001). Molecular responders had significantly longer progression-free survival (hazard ratio, 0.25; 95% CI, 0.13 to 0.50) and overall survival (hazard ratio, 0.27; 95% CI, 0.12 to 0.64) compared with molecular nonresponders.

CONCLUSION

Molecular response assessment using circulating tumor DNA may serve as a noninvasive, on-therapy predictor of response to pembrolizumab-based therapy in addition to standard of care imaging in mNSCLC. This strategy requires validation in independent prospective studies.

Novel Genomic Differences in Cell-Free Circulating DNA Profiles of Young- Versus Older-Onset Colorectal Cancer

We present the first analysis examining molecular alterations detected utilizing a clinically available cell-free circulating tumor DNA (cfDNA) assay in a cohort of patients with advanced colorectal cancer (aCRC) diagnosed <50 versus ≥50 years of age. Patient characteristics and mutation frequencies were compared using cfDNA tests from 5873 patients. Patients <50 had more sequence alterations in APC, CTNNB1, and SMAD4, as well as a higher frequency of focal BRAF and ERBB2(HER2) amplifications. Our study adds further evidence suggesting that young- versus older-onset CRC may have distinct molecular underpinnings, with prognostic and therapeutic implications.

Spectrum of driver mutations and clinical impact of circulating tumor DNA analysis in non-small cell lung cancer: Analysis of over 8000 cases

BACKGROUND

Circulating cell-free tumor DNA (ctDNA)-based mutation profiling, if sufficiently sensitive and comprehensive, can efficiently identify genomic targets in advanced lung adenocarcinoma. Therefore, the authors investigated the accuracy and clinical utility of a commercially available digital next-generation sequencing platform in a large series of patients with non-small cell lung cancer (NSCLC).

METHODS

Plasma-based comprehensive genomic profiling results from 8388 consecutively tested patients with advanced NSCLC were analyzed. Driver and resistance mutations were examined with regard to their distribution, frequency, co-occurrence, and mutual exclusivity.

RESULTS

Somatic alterations were detected in 86% of samples. The median variant allele fraction was 0.43% (range, 0.03%-97.62%). Activating alterations in actionable oncogenes were identified in 48% of patients, including EGFR (26.4%), MET (6.1%), and BRAF (2.8%) alterations and fusions (ALK, RET, and ROS1) in 2.3%. Treatment-induced resistance mutations were common in this cohort, including driver-dependent and driver-independent alterations. In the subset of patients who had progressive disease during EGFR therapy, 64% had known or putative resistance alterations detected in plasma. Subset analysis revealed that ctDNA increased the identification of driver mutations by 65% over standard-of-care, tissue-based testing at diagnosis. A pooled data analysis on this plasma-based assay demonstrated that targeted therapy response rates were equivalent to those reported from tissue analysis.

CONCLUSIONS

Comprehensive ctDNA analysis detected the presence of therapeutically targetable driver and resistance mutations at the frequencies and distributions predicted for the study population. These findings add support for comprehensive ctDNA testing in patients who are incompletely tested at the time of diagnosis and as a primary option at the time of progression on targeted therapies.

Duration of Targeted Therapy in Patients With Advanced Non-small-cell Lung Cancer Identified by Circulating Tumor DNA Analysis

BACKGROUND

Outcomes of therapy targeting molecular driver alterations detected in advanced non-small-cell lung (NSCLC) using circulating tumor DNA (ctDNA) have not been widely reported in patients who are targeted therapy-naive.

PATIENTS AND METHODS

We performed a multicenter retrospective review of patients with unresectable stage IIIB to IV NSCLC who received matched therapy after a targetable driver alteration was identified using a commercial ctDNA assay through usual clinical care. Eligible patients must not have received targeted therapy prior to ctDNA testing (prior chemotherapy or immunotherapy was permitted). Kaplan-Meier analysis was used to estimate the median duration of targeted therapy. Patients still on targeted therapy were censored at last follow-up.

RESULTS

Seventy-six patients met inclusion criteria. The median age of diagnosis of NSCLC was 64.5 years (range, 31-87 years), 67% were female, 74% were never-smokers, and 97% had adenocarcinoma histology. Twenty-one (28%) patients received systemic treatment prior to targeted therapy, including chemotherapy (n = 17), immunotherapy (n = 5), and/or a biologic (n = 4). Thirty-three (43%) patients remain on targeted therapy at the time of data analysis. The median time on targeted therapy was similar to what has been reported for tissue-detected oncogenic driver mutations in the targeted therapy-naive setting.

CONCLUSIONS

Patients with ctDNA-detected drivers had durable time on targeted therapy. These treatment outcomes data compliment previous studies that have shown enhanced targetable biomarker discovery rates and high tissue concordance of ctDNA testing when incorporated at initial diagnosis of NSCLC. Identification of NSCLC driver mutations using well-validated ctDNA assays can be used for clinical decision-making and targeted therapy assignment.

Clinical performance of a comprehensive novel liquid biopsy test for identifying non-small cell lung cancer (NSCLC) patients for treatment with osimertinib

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Background: Genotyping is required to identify cancer patients (pts) eligible for targeted therapy; however, many do not receive biomarker testing, in part due to limitations associated with tissue-only genotyping practices and the growing list of biomarkers recommended to be tested. Liquid biopsy overcomes many of these limitations but is not yet fully adopted. We report here the clinical performance of a comprehensive liquid biopsy test based on next generation sequencing (NGS) of circulating tumor DNA (ctDNA) for the identification of NSCLC patients with EGFR exon 19 deletions (ex19del) or L858R mutations ( EGFRm) or EGFR T790M, eligible for treatment with osimertinib. Methods: 441 (79%) of 556 pts randomized in FLAURA (NCT02296125; first-line osimertinib vs comparator EGFR TKI in EGFRm NSCLC) and 300 (72%) of 419 pts from AURA3 (NCT012151981; osimertinib vs chemotherapy in NSCLC pts with T790M at progression on EGFR TKI) were retrospectively tested with Guardant360 (G360), a 74-gene ctDNA NGS assay assessing single nucleotide variants, insertion-deletions, amplifications, and fusions in genes relevant to targeted therapy selection as well as microsatellite instability. Progression-free survival (PFS) of pts with EGFRm or T790M detected by G360 was compared to pts detected by the cobas EGFR Mutation Test (cobas) using tissue or plasma with an unadjusted cox model. Results: Treatment with osimertinib was associated with a significant PFS benefit relative to control therapy in NSCLC pts with EGFRm (FLAURA) and T790M (AURA3) detected using G360 (Table). Observed clinical benefit for pts with EGFRm or T790M detected by G360 was similar to that for pts with EGFRm or T790M identified by cobas using tissue or plasma specimens. Conclusions: This analysis demonstrates that G360 accurately identifies pts for osimertinib therapy while simultaneously providing comprehensive genotyping for other therapeutic molecular targets. The application of NGS liquid biopsy has the potential to increase rates of pts genotyped and access to precision medicine. [Table: see text]

ctDNA resistance landscape of lazertinib, a third-generation EGFR tyrosine kinase inhibitor (TKI)

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Background: While EGFR mutant ( EGFRm) non-small cell lung cancer (NSCLC) patients usually experience improved clinical benefit with EGFR TKIs, most eventually progress. Understanding mechanisms of resistance (MoR) may allow for more personalized treatment. Lazertinib is an irreversible third generation EGFR TKI for which MoR are unknown. Obtaining sufficient tumor tissue for genotyping at progression is often difficult. Therefore, we utilized plasma ctDNA from patients treated with lazertinib to explore MoR. Methods: Plasma samples from 47 NSCLC patients in the phase 2 trial of lazertinib (NCT03046992) were collected at screening and progressive disease (PD) and underwent ctDNA NGS of 74 genes using Guarant360. All patients were positive for an EGFR Ex19del or L858R ( EGFRm) and T790M by tissue testing at screening. Acquired, nonsynonymous, characterized mutations detected in a PD sample but not in the screening sample from the respective patient were considered putative MoR, excluding aneuploidy. Patients with detectable plasma EGFRm and/or T790M at screening were evaluable. Results: ctDNA was detected in 47 (100%) screening samples and 43/45 (96%) PD samples (two failed sequencing). An EGFRm was detected in 85% of patients at screening (n = 40), 38 of which had PD ctDNA results and were included in analysis. T790M was detected in 30 patients at screening and subsequently not detected at PD in 21 of these patients, 55% of all 38 included patients. Among the ten patients with T790M detected at PD, on-target MoR were detected in 7 (18% of all included patients) including EGFR C797S (n = 3, 8%), EGFR amplification (n = 3, 8%), and EGFR T854A (n = 1, 3%). All C797S were in cis with T790M. No on-target MoR were detected in patients without T790M detected at PD. Off-target MoR were seen in 34% of patients (13/38) including mutations in PIK3CA (13%; 2 E545K, 2 E542K, 1 E81K), ERBB2 (5%; 1 D769H, 1 V777L), KRAS (3%; 1 G12C), and BRAF (3%; 1 G469A). Gene amplifications were detected in CCND1 (n = 1, 3%) , CCNE1 (n = 2, 5%) , ERBB2 (n = 1, 3%) , FGFR1 (n = 1, 3%) , MET (n = 4, 11%) , and PIK3CA (n = 1, 3%), with some patients having multiple MoR. Conclusions: The spectrum of MoR identified in this cohort of patients treated with lazertinib is similar to that reported in other third generation EGFR TKIs, but with some differences in frequencies. The most common resistance mechanisms are T790M loss and PIK3CA alterations which may address the mechanism of action. Our findings suggest putative MoR of lazertinib and show that ctDNA NGS is an effective way to identify MoR in patients progressing on targeted therapy. Clinical trial information: NCT03046992 .

Abstract B028: Pan-cancer landscape of somatic BRCA1 and BRCA2 mutations detected in circulating tumor DNA

Background: Frequencies of germline mutations in BRCA1 and BRCA2 (BRCA1/2) are well-described; however, existing data are incomplete regarding the cancer specific spectrum of somatic BRCA1/2 (sBRCA) mutations and co-occurrence of microsatellite instability (MSI), particularly when detected in circulating tumor DNA (ctDNA). To better elucidate potential target populations for PARP inhibitor (PARPi) monotherapy and combination PARPi-immunotherapy trials and provide data on the frequency of sBRCA mutations detected in ctDNA, we conducted a retrospective, IRB approved analysis of de-identified genomic results of advanced solid tumor patients (pts) who had clinical liquid biopsy testing (Guardant360) from 06-2018 to 05-2019. METHODS Cancer specific sBRCA inactivating mutation frequencies were calculated for cancer types with &gt;50 patients tested; histological sub-types were compared to available TCGA inactivating sBRCA frequencies using Fisher’s exact or Chi-square test as appropriate. RESULTS Overall, 3388 pts were found to have one or more variant of uncertain significance (n=2338) and/or inactivating mutation (n=1050) in BRCA1/2. Of the 1050, 352 (33.5%) had only germline mutation(s) (gBRCA), 24 (2.3%) had both gBRCA and sBRCA, and 674 (64.2%) had sBRCA mutations only. Further analyses were limited to the 674 pts with sBRCA mutations only. Cancer specific sBRCA frequencies in uterine (5.1%), ovarian (5.0%), colorectal (CRC, 3.3%), lung squamous (3.1%), head and neck (2.9%), gastroesophageal (2.6%), melanoma (2.4%), urothelial (2.3%), breast (2.3%), lung adenocarcinoma (2.1%), and pancreatic (2.1%) cancers were not significantly different from TCGA while frequencies in prostate (3.7%, p=0.004) and renal cell (2.1%, p=0.02) cancers were significantly higher than TCGA. The mean (median) number of sBRCA mutations per pt was 1.1 (1) with 47 pts having &gt;1 sBRCA mutation. Multiple sBRCA mutations were seen in pts with CRC (n=14), prostate (n=9), non-small cell lung (n=7), breast (n=6), uterine (n=3), ovarian (n=2), and other (n=5) cancers. Co-occurring MSI was detected in 44/468 (9.4%) pts with sBRCA inactivating mutation(s) tested. CONCLUSIONS ctDNA detected sBRCA mutations at frequencies consistent with, or above TCGA, indicating it is an effective method for identifying pts eligible for PARPi trials. Additional studies are ongoing to assess the clonality of the sBRCA mutations which may further impact PARPi trial considerations. Our cohort consists of advanced cancer pts, so the identification of sBRCA mutations in prostate cancer at a higher frequency than TCGA supports what is known about the association between gBRCA mutations and more aggressive, advanced stage cancer and suggests the possibility of a similar association for sBRCA in prostate and renal cell cancers. The co-occurrence of defective homologous recombination and mismatch repair has previously been reported in tissue sequencing studies, but numbers in those and the current study are small. Still, this co-occurrence sub-population may represent a unique molecular subtype in which to investigate combination PARPi-immunotherapy. In a one year period, standard of care ctDNA testing identified 1050 advanced cancer pts with BRCA mutations, two-thirds of which were somatic, occurring in over 30 cancer types, suggesting that PARPi therapies may have relevance in a broad range of cancers.

Citation Format: Carin R Espenschied, Jennifer L Yen, Tracy Nance, Richard B Lanman, Kimberly C Banks. Pan-cancer landscape of somatic BRCA1 and BRCA2 mutations detected in circulating tumor DNA [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B028. doi:10.1158/1535-7163.TARG-19-B028

Abstract 450: Novel genomic differences in cell-free circulating tumor DNA (cfDNA) profiles of early versus older onset colorectal cancer (CRC)

Background

The incidence of early onset CRC, defined as a diagnosis under age 50 (&lt;50), is steadily rising without an established cause. Small cohort studies have reported on tumor tissue sequencing results from patients (pts) &lt;50 versus &gt;50 and have included all cancer stages and grouped all mutation types. These studies found significant yet inconsistent genomic differences between cohorts concluding &lt;50 CRC may have higher mutation rates and better survival. This study aimed to compare the cfDNA results in a large cohort of &lt;50 versus &gt;50 advanced CRC pts, which to our knowledge has not been reported.

Methods

Consecutive advanced CRC pts who received clinical cfDNA testing (Guardant360™) between 10/15-10/18 were analyzed. cfDNA analysis included next generation sequencing of 70-73 genes, assessing single nucleotide variants (SNVs), insertion/deletion alterations (indels), fusions, and amplifications (amps). High microsatellite instability (MSI-H) status was available for a subset of cases. Characteristics and mutation frequencies were compared between &lt;50 and &gt;50 groups, excluding variants of uncertain significance and synonymous alterations. Gene specific mutation frequencies were compared with Fisher’s exact test.

Results

Of 5341 stage IIIB-IV CRC pts tested, 4706 (88.1%) had alterations detected in cfDNA of which 984 (20.9%) were &lt;50 and 3722 (79.1%) were &gt;50. The &lt;50 cohort was 51.7% male and the &gt;50 cohort was 57.6% male. Both cohorts had a median of five alterations per pt (&lt;50 range 1-207, &gt;50 range 1-112). The median maximum variant allele fraction, including co-occurring amps, was 6.9% for the &lt;50 cohort (range 0.02-94.9%) and 4.4% for the &gt;50 cohort (range 0.03-97.1%). Of 2327 tested pts, MSI-H was detected in 3.3% (17/512) of &lt;50 cases and 3.5% (64/1815) of &gt;50 cases (not significant). In both cohorts SNVs and indels were most frequent in TP53, APC, KRAS, and PIK3CA. However, mutations in APC, KRAS, SMAD4, and ARID1A were more frequent in &lt;50 CRC while &gt;50 CRC had more TP53, ERBB2, and ATM mutations (all p&lt;0.05). The most common amps in both cohorts were EGFR, BRAF, and CDK6 which may reflect aneuploidy, and MYC. BRAF, MYC, CCNE1, and CCND1 amps were more frequently observed in the &lt;50 cohort (all p&lt;0.03). RET, FGFR3, ALK, NTRK1, and FGFR2 fusions were seen in about 1% of both cohorts.

Conclusions

In the first comparison of cfDNA findings between &lt;50 and &gt;50 advanced CRC, significant differences in mutation and amp frequencies of several genes were observed, including genes important for prognosis and therapy selection such as KRAS and ERBB2. Rare but targetable biomarkers such as MSI-H and fusions were present in both age groups. Our previously unreported findings may be due to the strengths of this cfDNA analysis including a larger sample size, more uniform cancer stage, and stratification by mutation type. These results may help improve understanding and treatment of &lt;50 CRC.

Citation Format: Afsaneh Barzi, Carin R. Espenschied, Victoria M. Raymond, Richard B. Lanman, Heinz-Josef Lenz. Novel genomic differences in cell-free circulating tumor DNA (cfDNA) profiles of early versus older onset colorectal cancer (CRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 450.

Clinical germline diagnostic exome sequencing for hereditary cancer: Findings within novel candidate genes are prevalent

Clinical diagnostic exome sequencing (DES) has been effective in diagnosing individuals with suspected genetic conditions; nevertheless little has been described regarding its clinical utility in individuals with a personal and family history of cancer. This study aimed to assess diagnostic yield and clinical characteristics of pediatric and adult patients undergoing germline DES for hereditary cancer. We retrospectively reviewed 2171 patients referred for DES; cases with a personal and/or family history of cancer were further studied. Of 39 cancer patients, relevant alterations were found in eight individuals (21%), including one (3%) positive pathogenic alteration within a characterized gene, two (5%) uncertain findings in characterized genes, and five (13%) alterations in novel candidate genes. Two of the 5 pediatric patients, undergoing testing, (40%) had findings in novel candidate genes, with the remainder being negative. We include brief case studies to illustrate the variety of challenging issues related to these patients. Our observations demonstrate utility of family-based exome sequencing in patients for suspected hereditary cancer, including familial co-segregation analysis, and comprehensive medical review. DES may be particularly useful when traditional approaches do not result in a diagnosis or in families with unique phenotypes. This work also highlights the importance and complexity of analysis of uncharacterized genes in exome sequencing for hereditary cancer.

Unexpected CDH1 Mutations Identified on Multigene Panels Pose Clinical Management Challenges

Purpose

Mutations in the CDH1 gene confer up to an 80% lifetime risk of diffuse gastric cancer and up to a 60% lifetime risk of lobular breast cancer. Testing for CDH1 mutations is recommended for individuals who meet the International Gastric Cancer Linkage Consortium (IGCLC) guidelines. However, the interpretation of unexpected CDH1 mutations identified in patients who do not meet IGCLC criteria or do not have phenotypes suggestive of hereditary diffuse gastric cancer is clinically challenging. This study aims to describe phenotypes of CDH1 mutation carriers identified through multigene panel testing (MGPT) and to offer informed recommendations for medical management.

Patients and Methods

This cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimate CDH1 mutation prevalence and associated clinical phenotypes. CDH1 mutation carriers were classified as IGCLC positive (met criteria), IGCLC partial phenotype, and IGCLC negative.

Results

In the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenic CDH1 mutation. In the clinic cohort, four (1.26%) of 318 had a pathogenic CDH1 mutation. Overall, 65% of mutation carriers did not meet the revised testing criteria published in 2015. All three CDH1 mutation carriers who had risk-reducing gastrectomy had pathologic evidence of diffuse gastric cancer despite not having met IGCLC criteria.

Conclusion

The majority of CDH1 mutations identified on MGPT are unexpected and found in individuals who do not fit the accepted diagnostic testing criteria. These test results alter the medical management of CDH1-positive patients and families and provide opportunities for early detection and risk reduction.

Advances in the diagnosis of hereditary kidney cancer: Initial results of a multigene panel test

BACKGROUND

Panel testing has been recently introduced to evaluate hereditary cancer; however, limited information is available regarding its use in kidney cancer.

METHODS

The authors retrospectively reviewed test results and clinical data from patients who underwent targeted multigene panel testing of up to 19 genes associated with hereditary kidney cancer from 2013 to 2016. The frequency of positive (mutation/variant likely pathogenic), inconclusive (variant of unknown significance), and negative results was evaluated. A logistic regression analysis evaluated predictive factors for a positive test.

RESULTS

Patients (n = 1235) had a median age at diagnosis of 46 years, which was significantly younger than the US population of individuals with kidney cancer (P < .0001). Overall, 6.1%, 75.5%, and 18.4% of individuals had positive, negative, and inconclusive results, respectively. The most commonly altered genes included folliculin (FLCN) and fumarate hydratase (FH), which were altered in 1.8% and 1.3% of patients, respectively. Tuberous Sclerosis Complex 2 (TSC2), mesenchymal epithelial transition factor proto-oncogene (MET), and PMS1 homolog 2 (PMS2) had the highest rates of variants of unknown significance, which were identified in 2.7%, 2.2%, and 1.7% of patients, respectively. Early age of onset was the only factor that was identified as predictive of a positive test on multivariate analysis (odds ratio, 0.975; P = .0052) and may be the only identifying characteristic of low-penetrant syndromes, such as those associated with MITF (melanogenesis-associated transcription factor) mutations, which do not have singular histology or a family history of kidney cancer.

CONCLUSIONS

Panel tests may be particularly useful for patients who lack distinguishing clinical characteristics of known hereditary kidney cancer syndromes. The current results support the use of early age of onset for genetic counseling and/or testing. Cancer 2017;123:4363-71. © 2017 American Cancer Society.

Multigene Panel Testing Provides a New Perspective on Lynch Syndrome

Purpose Most existing literature describes Lynch syndrome (LS) as a hereditary syndrome leading to high risks of colorectal cancer (CRC) and endometrial cancer mainly as a result of mutations in MLH1 and MSH2. Most of these studies were performed on cohorts with disease suggestive of hereditary CRC and population-based CRC and endometrial cancer cohorts, possibly biasing results. We aimed to describe a large cohort of mismatch repair (MMR) mutation carriers ascertained through multigene panel testing, evaluate their phenotype, and compare the results with those of previous studies. Methods We retrospectively reviewed clinical histories of patients who had multigene panel testing, including the MMR and EPCAM genes, between March 2012 and June 2015 (N = 34,981) and performed a series of statistical comparisons. Results Overall, MSH6 mutations were most frequent, followed by PMS2, MSH2, MLH1, and EPCAM mutations, respectively. Of 528 patients who had MMR mutations, 63 (11.9%) had breast cancer only and 144 (27.3%) had CRC only. When comparing those with breast cancer only to those with CRC only, MSH6 and PMS2 mutations were more frequent than MLH1 and MSH2 mutations ( P = 2.3 × 10^-5). Of the 528 patients, 22.2% met BRCA1 and BRCA2 ( BRCA1/2) testing criteria and not LS criteria, and 5.1% met neither BRCA1/2 nor LS testing criteria. MSH6 and PMS2 mutations were more frequent than MLH1 and MSH2 mutations among patients who met BRCA1/2 testing criteria but did not meet LS testing criteria ( P = 4.3 × 10^-7). Conclusion These results provide a new perspective on LS and suggest that individuals with MSH6 and PMS2 mutations may present with a hereditary breast and ovarian cancer phenotype. These data also highlight the limitations of current testing criteria in identifying these patients, as well as the need for further investigation of cancer risks in patients with MMR mutations.

Spectrum of mismatch repair gene mutations and clinical presentation of Hispanic individuals with Lynch syndrome

Lynch syndrome (LS), the most common hereditary colorectal cancer syndrome, is caused by mismatch repair (MMR) gene mutations. However, data about MMR mutations in Hispanics are limited. This study aims to describe the spectrum of MMR mutations in Hispanics with LS and explore ancestral origins. This case series involved an IRB-approved retrospective chart review of self-identified Hispanic patients (n = 397) seen for genetic cancer risk assessment at four collaborating academic institutions in California, Texas, and Puerto Rico who were evaluated by MMR genotyping and/or tumor analysis. A literature review was conducted for all mutations identified. Of those who underwent clinical genetic testing (n = 176), 71 had MMR gene mutations. Nine mutations were observed more than once. One third (3/9) of recurrent mutations and two additional mutations (seen only once) were previously reported in Spain, confirming the influence of Spanish ancestry on MMR mutations in Hispanic populations. The recurrent mutations identified (n = 9) included both previously reported mutations as well as unique mutations not in the literature. This is the largest report of Hispanic MMR mutations in North America; however, a larger sample and haplotype analyses are needed to better understand recurrent MMR mutations in Hispanic populations.

Abstract P2-02-07: Predicting germline mutations in BRCA1/2 and beyond: A comparison of women with single and multiple breast primaries

Synchronous or metachronous breast primaries are a well-known indication of hereditary breast cancer, particularly within BRCA1/2 mutation carriers. However, the frequency of gene mutations within this patient group has not been well defined, especially in the setting of multi-gene panel testing (MGPT). We conducted a retrospective review of mutation carrier status in a population of females with breast cancer(s), but no other reported cancer diagnoses, and who had MGPT at a single diagnostic laboratory. Among 31,864 females tested, the following were excluded from analysis: 5389 (17%) had variants of unknown significance (VUS), 133 (0.4%) had moderate risk mutations and 316 (1.0%) had MUTYH monoallelic mutations. For the remaining 26,026 females, we evaluated whether mutation status is associated with risk of multiple breast primaries using Fisher's exact test and logistic regression analysis adjusting for age at testing, age at first breast cancer diagnosis, and mutations in other genes. The number of genes analyzed ranged from 5-49, depending on the panel ordered. Gene-specific analyses were limited to with 10 or more mutations in this cohort (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHEK2, MRE11A, MUTYH, MSH6, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, and TP53).

In this cohort the average age of first breast cancer diagnosis was 47.7 (range 12-95) and the average age of second diagnosis was 56 years (range 17-89). A positive result (pathogenic mutation or variant, likely pathogenic) in any gene was more likely for women with three or more breast cancer primaries (p=0.007) and two or more primaries (p=1.2e-08) than those with one breast primary.

Overall, women with a mutation in any gene were more likely to have multiple primary breast cancers than those without mutations. Specifically, women with mutations in ATM, BRCA1, CDH1, PALB2, PTEN, and TP53 mutations were more likely to have multiple breast primaries than non-carriers of mutations in those genes (table 1).

Table 1: Risk of multiple breast primaries in mutation carriers versus non-carriers No. (%) with multiple primaries  GeneCarrierNon-CarrierOR (95% CI)p-valueATM55/262 (21%)2189/15057 (15%)1.6 (1.1, 2.2)0.006BRCA1100/526 (19%)3104/24117 (13%)1.9 (1.5, 2.4)3.2e-07CDH16/24 (25%)3338/25016 (13%)2.8 (1.0, 1.7)0.04PALB245/218 (21%)2199/15101 (15%)1.7 (1.2, 2.4).004PTEN7/28 (25%)3429/25788 (13%)3.8 (1.5, 8.9)0.003TP5319/96 (20%)3419/25787 (13%)2.4 (1.3, 4.0)0.002

Our results show that women with multiple breast primaries are more likely to have mutations in some genes than others. Interestingly, all genes with significant odds ratios are well-described and most are known to cause high risk for breast cancer, with the exception of ATM. Additional studies are needed to confirm these results and quantify risks for second primary breast cancers. With further work defining the risks of multiple primary breast cancers, this information could be implemented into clinical practice to aid women in risk management following a positive result.

Citation Format: Panos Smith L, Tian Y, Qian D, McFarland R, Espenschied CR. Predicting germline mutations in BRCA1/2 and beyond: A comparison of women with single and multiple breast primaries [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 P2-02-07.

Closing the loop: action research in a multimodal hereditary cancer patient conference is an effective tool to assess and address patient needs

This paper describes the use of action research in a patient conference to provide updated hereditary cancer information, explore patient and family member needs and experiences related to genetic cancer risk assessment (GCRA), elicit feedback on how to improve the GCRA process, and inform future research efforts. Invitees completed GCRA at City of Hope or collaborating facilities and had a BRCA mutation or a strong personal or family history of breast cancer. Action research activities were facilitated by surveys, round table discussions, and reflection time to engage participants, faculty, and researchers in multiple cycles of reciprocal feedback. The multimodal action research design effectively engaged conference participants to share their experiences, needs, and ideas for improvements to the GCRA process. Participants indicated that they highly valued the information and resources provided and desired similar future conferences. The use of action research in a patient conference is an innovative and effective approach to provide health education, elicit experiences, identify and help address needs of high-risk patients and their family members, and generate research hypotheses. Insights gained yielded valuable feedback to inform clinical care, future health services research, and continuing medical education activities. These methods may also be effective in other practice settings.

Reflex immunohistochemistry and microsatellite instability testing of colorectal tumors for Lynch syndrome among US cancer programs and follow-up of abnormal results

PURPOSE

Immunohistochemistry (IHC) for MLH1, MSH2, MSH6, and PMS2 protein expression and microsatellite instability (MSI) are well-established tools to screen for Lynch syndrome (LS). Although many cancer centers have adopted these tools as reflex LS screening after a colorectal cancer diagnosis, the standard of care has not been established, and no formal studies have described this practice in the United States. The purpose of this study was to describe prevalent practices regarding IHC/MSI reflex testing for LS in the United States and the subsequent follow-up of abnormal results.

MATERIALS AND METHODS

A 12-item survey was developed after interdisciplinary expert input. A letter of invitation, survey, and online-survey option were sent to a contact at each cancer program. A modified Dillman strategy was used to maximize the response rate. The sample included 39 National Cancer Institute-designated Comprehensive Cancer Centers (NCI-CCCs), 50 randomly selected American College of Surgeons-accredited Community Hospital Comprehensive Cancer Programs (COMPs), and 50 Community Hospital Cancer Programs (CHCPs).

RESULTS

The overall response rate was 50%. Seventy-one percent of NCI-CCCs, 36% of COMPs, and 15% of CHCPs were conducting reflex IHC/MSI for LS; 48% of the programs used IHC, 14% of the programs used MSI, and 38% of the programs used both IHC and MSI. One program used a presurgical information packet, four programs offered an opt-out option, and none of the programs required written consent.

CONCLUSION

Although most NCI-CCCs use reflex IHC/MSI to screen for LS, this practice is not well-adopted by community hospitals. These findings may indicate an emerging standard of care and diffusion from NCI-CCC to community cancer programs. Our findings also described an important trend away from requiring written patient consent for screening.