Prediction model for detecting circulating tumor DNA (ctDNA) in metastatic colorectal cancer (mCRC)

3590

Background: While tissue-based assays have yields above 90% in solid tumors, there is less known about factors that influence the sensitivity of ctDNA for detecting mutations. Methods:We retrospectively evaluated mCRC patients (pts) who had plasma-derived NGS utilizing a highly-sensitive targeted 68-73-gene ctDNA assay. In a case-control design, pts with a known mutation on tissue and radiologic evidence of metastatic disease but no detectable ctDNA mutation were matched 1:3 with randomly selected pts with detectable mutations and compared according to clinical, laboratory, and radiologic characteristics. A prediction score for ctDNA detection was built using a binary logistic backward stepwise regression analysis and tested in two independent data sets from different institutions. Area under the curve (AUC) from receiver operating characteristics curves (ROC) were used for internal and external validation. Results: From 416 pts who met inclusion criteria, plasma-derived NGS did not find tumor mutations in 66 cases (15.9%); 198 pts with detectable alterations were selected as controls. After multivariate analysis, the detection of ctDNA was associated with increasing age (OR 1.05; 95%CI 1.02-1.09; p = .001), presence of liver (OR 5.82; 95%CI 2.55-12.49; p < .001) and lymph node metastases (OR 3.28; 95%CI 1.51-7.60; p = .004), archival TP53 mutations (OR = 2.88; 95%CI 1.37-6.17; p = .006). A key determinant was timing of collection relative to disease status: plasma collected in newly diagnosed metastatic disease or after evidence of progression was substantially more likely to have detectable alterations (OR 9.24; 95%CI 4.11-22.40; p < .001); The simplified prediction model performed well in internal (AUC = 0.88) and external validation (AUC = 0.95; 163 pts). Conclusions: Our validated prediction model provides clinicians and researchers with a tool to screen for patients in whom ctDNA testing can outperform tissue-based testing in detecting genomic alterations.

Detection of ERBB2 (HER2) Gene Amplification Events in Cell-Free DNA and Response to Anti-HER2 Agents in a Large Asian Cancer Patient Cohort

Background: HER2 antagonists have marked activity and are approved for the treatment of HER2 overexpressing breast and gastric cancers. Recent studies have shown that ERBB2 (HER2) gene amplification and overexpression may also be actionable in other tumor types. Inter- and intratumoral heterogeneity in HER2 status, however, poses a significant challenge in identifying patients that may benefit from HER2-targeted therapies. ERBB2 amplification as identified by circulating cell-free DNA (cfDNA), which circumvents tissue heterogeneity issues, is emerging as a robust biomarker predictive of response to anti-HER2 agents. Here, the prevalence and genomic landscape of ERBB2 alterations detectable by next-generation sequencing (NGS) of cfDNA was evaluated in a large cohort of Asian patients with advanced solid tumors. Methods: Results were queried for consecutive patients (n = 469) tested by a comprehensive 70/73-gene cfDNA NGS assay (Guardant360®) between November 2015 and June 2018. Patients with ERBB2 gene alterations including copy number amplifications (CNAs), single nucleotide variants (SNVs), and insertion-deletions (indels) were identified. Results: ERBB2 alterations were detected in 52 patients (11.1%); ERBB2 SNVs, CNAs, and indels were found in 27 (5.8%), 27 (5.8%), and 10 (2.1%) patients, respectively. ERBB2 amplification was most frequently identified in gastric (21.4%; 6/28), colorectal (11.1%; 5/45), lung (3.9%; 9/231), and breast (3.2%; 1/31) cancer patients. ERBB2 amplification was often mutually exclusive with other oncogenic alterations in gastric (83.3%; 5/6) and colorectal (60%; 3/5) cancer patients. ERBB2 copy number gains were also highest in gastric and colorectal cancers (median 4.8 and 6.6, respectively). We further report two cases of advanced gastric cancer patients, one treatment naïve, and the other having failed four lines of therapy, whose ERBB2 CNAs were identified by cfDNA and derived clinical benefit from HER2-based therapies. Conclusion: Our data indicate that ERBB2 amplification is a common event in solid tumors among Asian cancer patients. High ERBB2 incidence and copy number gains were observed in gastric and colorectal cancer patients, often in the absence of other oncogenic mutations, underscoring its likely role as the driver alteration in those settings. Finally, we show the potential of comprehensive cfDNA testing in identifying patients who are most likely to benefit from HER2-targeted therapies.

Analysis of cell-free circulating tumor DNA in 419 patients with glioblastoma and other primary brain tumors

Aim:

Genomically matched trials in primary brain tumors (PBTs) require recent tumor sequencing. We evaluated whether circulating tumor DNA (ctDNA) could facilitate genomic interrogation in these patients.

Methods:

Data from 419 PBT patients tested clinically with a ctDNA NGS panel at a CLIA-certified laboratory were analyzed.

Results:

A total of 211 patients (50%) had ≥1 somatic alteration detected. Detection was highest in meningioma (59%) and gliobastoma (55%). Single nucleotide variants were detected in 61 genes, with amplifications detected in ERBB2, MET, EGFR and others.

Conclusion:

Contrary to previous studies with very low yields, we found half of PBT patients had detectable ctDNA with genomically targetable off-label or clinical trial options for almost 50%. For those PBT patients with detectable ctDNA, plasma cfDNA genomic analysis is a clinically viable option for identifying genomically driven therapy options.

Discovery of targetable mutational signatures in advanced prostate cancer (aPC) using machine learning and next-generation sequencing (NGS) of circulating tumor DNA (ctDNA)

226

Background: Alterations (alts) of the AR gene are common in aPC and are associated with reduced responses to AR-axis inhibitors; optimal treatment is unknown. Genomic sequencing of ctDNA from aPCs may recapitulate truncal and branching alts across metastatic sites in heavily pretreated progressive aPC and facilitates identification of AR and other alts that contribute to aPC progression. Such data could lead to better understanding of aPC molecular biology and guide development of novel treatments. Methods: Two unsupervised machine learning algorithms, hierarchical clustering and principal components analysis, were used to evaluate mutational profiles of 2,679 plasma samples from 2,309 men with aPC. Samples were assessed by a validated ctDNA NGS panel that sequences 73 clinically relevant cancer genes (Guardant360, Redwood City, CA). Indels, amplifications, and fusions are evaluated in a subset of genes with high sensitivity and specificity. Chi-squared residual analysis and gene ontology enrichment were used to identify significantly co-altered molecular pathways. Results: Distinct, non-overlapping mutational signatures were observed in tumors with only AR amplification (amp) vs. only AR mutation (mut). Tumors with only AR amp, and those with both AR amp and mut, were strongly enriched for amps in the MAPK pathway (P = 3.62E-10, 4.92E-05, resp.). Tumors with only AR mut, and those with no AR alts, were strongly enriched for muts in negative regulators of cell proliferation (P = 1.09E-05, 3.30E-09, resp.). Muts further stratified to oxidative stress response in AR mut (P = 4.37E-05), and cell aging in no AR alts (P = 8.31E-07). Conclusions: In men with aPC, machine learning of ctDNA NGS data revealed recurrent mutational signatures that stratified according to the type of AR alts. These hypothesis-generating data require external validation but suggest that aPC may progress due to distinct mechanisms dependent on AR status. Future efforts to develop novel therapeutic approaches for aPC may need to consider the impact of the type of AR alt present and explore the interplay of AR with other altered pathways identified in this analysis.

Abstract P4-01-05: Cell free DNA analysis identifies actionable ERBB2 amplifications in patients with HER2 equivocal breast cancer

Background:

Determination of ERBB2 (HER2) expression or amplification informs eligibility of HER2-targeted therapies. ASCO and NCCN guidelines recommend evaluation of HER2 status on primary invasive breast cancers and on a metastatic site if stage IV, where possible, as treatment is based on the status of the metastasis. Reassessment of HER2 status should also be considered in patients with disease recurrence as initially HER2-negative tumors may acquire HER2 amplification at progression. HER2 status can be complicated by equivocal results from in situ hybridization (ISH) and/or immunohistochemistry (IHC). Clarification requires reflex testing on the same tissue specimen or repeat testing on a new specimen, however some patients' tissue status remains equivocal. Furthermore, metastases to bone, lung, or brain may be difficult to re-biopsy or of low DNA quality. Rapid and non-invasive blood-based cell-free DNA (cfDNA) NGS may facilitate identification of HER2 targetable disease in advanced breast cancer.

Methods:

We assessed the frequency of ERBB2 amplification detectable by a blood-based cell-free DNA (cfDNA) assay among patients with metastatic breast cancer with equivocal HER2 results in tissue. cfDNA samples were ordered as part of routine clinical care using an assay validated for the detection of copy number amplification in ERBB2 (tests run between 03/2014-04/2017 by Guardant Health, Redwood City, CA). Submitted pathology reports were reviewed for HER2 status which was categorized as positive, negative, or equivocal based on the interpretation issued by the reading pathologist at the time the test was ordered. Patients were included if they had an equivocal result on IHC and/or ISH unless both assays were performed on the same specimen and one provided a definitive negative or positive HER2 result. Additionally, 4 patients with equivocal IHC or ISH results were excluded as biopsy of another tumor site revealed a positive HER2 result around the same time as the equivocal test. For the 349 patients with multiple cfDNA samples, the earliest pathology report was referenced.

Results:

Tissue HER2 status was available for 1,853 unique patients (98.8% female, median age at testing was 58y, range 26-91y). 141 patients (7.6%) had equivocal HER2 results in tissue; 99 by IHC alone, 14 by ISH alone, and 28 were equivocal by both assays. Among these, 126 patients (89.4%) had at least one sample with ctDNA detected. 12/126 (9.5%) had amplification of ERBB2 detected in at least one cfDNA sample. Samples were drawn a median of 267 days after tissue collection (range 4 days – 11.5 years). Frequency of ERBB2 amplification was similar regardless of time between tissue and blood collection but was higher among patients with ISH results alone (4/14, 36.4%) compared to those with IHC alone (6/89, 6.7%) or both assays (6/26, 7.6%; p=0.006).

Conclusion:

cfDNA testing identifies a significant number of patients with HER2-targetable advanced breast cancer whose tissue was HER2 equivocal. cfDNA testing may supplement tissue-based methods to help clarify HER2 status in metastatic disease as well as identify patients who may acquire HER2 amplification subsequent to their initial biopsy.

Citation Format: Rich TA, Raymond VM, Ahn ER, Banks KC, Brufsky A, Lee C, Lippman M, Pluard TJ, Schwab RB, Lanman RB. Cell free DNA analysis identifies actionable ERBB2 amplifications in patients with HER2 equivocal breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-01-05.

Comprehensive landscape of gene amplifications (amps) in tissue and circulating tumor DNA (ctDNA) in metastatic colorectal cancer (mCRC)

604

Background: Amps, as oncogenic and resistance drivers, have therapeutic implications, but unlike mutations, have been sparsely described in mCRC. Functional account is piecemeal due to vague definitions, limited data on co-occurring alterations and use of primary tissue samples nonrepresentative of tumor heterogeneity. Our aim was to define the amp landscape in mCRC using tissue and ctDNA sequencing. Methods: We performed systematic analyses of copy-number variation in 2 cohorts of mCRC patients (pts) [tissue (TC) (N = 1,134) and ctDNA (BC) (N = 3,218)] who had high sensitivity targeted sequencing with MSK-IMPACT (341-468 genes) or Guardant Health (70-73 genes) panel, respectively. For BC, plasma copy number was adjusted (ApCN) to account for variable tumor DNA shedding using max allele frequency and high amp (HAmp) was defined as > 4 copies (similar to predefined tissue cutoff). Results: 166 (15%) and 405 (13%) pts in TC and BC harbored amp in at least one of 18 genes assessed by both panels (Table). Amp prevalence for individual gene was similar in both cohorts ( r = 0.9; P < .01) with RTK amps ( EGFR, ERBB2, MET, FGFR1/2, PDGFRA) seen in 8% pts. Key RTK amps were enriched in RAS/BRAF wild type (RB WT) compared to mutant (RB MUT) (OR 3.5; P < .01) pts in both cohorts, in contrast to low prevalence RTK and non-RTK amps. Median ApCN was higher for RTKs in RB WT vs MUT cases ( ERBB2: 12 vs 5; P = .02). Using validated EGFRab exposure (EGFRi) ctDNA signature, we found that EGFRi pts had higher prevalence of EGFR, MET, BRAF, KRAS, PIK3CA and FGFR1 amps compared to EGFRab naïve pts. Conclusions: While individually uncommon, amps occur across key oncogenic pathways in mCRC and after adjusting for ctDNA shedding, are seen at similar prevalence in tissue and plasma. Amps in RTKs are seen in 10-12% of RB WT tumors, suggesting clinically relevant roles as oncogenic effectors and targets. After EGFRi, a number of amps emerge, including PIK3CA and FGFR1 amps, not previously implicated in acquired resistance. [Table: see text]

Circulating tumor derived cell-free DNA (ctDNA) to predict recurrence of metastatic colorectal cancer (mCRC) following curative intent surgery or radiation: Interim results

552

Background: Over half of patients (pts) with oligometastatic CRC treated with definitive surgery or radiotherapy experience cancer recurrence. Early detection of ctDNA could identify high risk pts for additional intervention to eliminate micrometastatic disease. Here we report interim results of a prospective study aiming to determine ctDNA detection rates using a sensitive multigene assay and to correlate post-procedure ctDNA detection with radiographic mCRC recurrence. Methods: Pts with mCRC intending to undergo a curative intent procedure were prospectively recruited at a single site. ctDNA was collected pre-procedure, 3 weeks (wks) post-procedure, and at multiple follow-up timepoints. ctDNA detection utilizing a multi-gene sequencing panel (Guardant Health) included somatic variant and epigenetic assessments. A novel variant classifier was applied to differentiate tumor derived versus non-tumor derived alterations. A Simon’s two-stage design with planned interim analysis to assess 3wk post-procedure ctDNA detection rate was employed. Results: Of 25 pts enrolled, 21 (84%) had evaluable paired pre- and post-procedure samples. In these 21 pts, the 3 wks post-procedure sample was collected after surgery (N = 20) or radiation (N = 1) to address liver (N = 17), lung (N = 3), or ovarian (N = 1) metastases ± colon resection (N = 6). ctDNA was detected (+) in 15/21 (71%) pre- and 11/21 (52%) post-procedure samples. ctDNA was (+) in 8/12 (67%) pre- and 8/17 (47%) post-procedure samples with carcinoembryonic antigen < 5 ng/ml. Conclusions: In this interim analysis of pts with mCRC undergoing curative intent procedures, the post-procedure ctDNA detection rate was 52%. The similarity between the observed post-procedure ctDNA detection and expected recurrence rate suggests promise for recurrence prediction using this approach. Given post-procedure ctDNA was (+) in > 3 pts, the study will continue to enroll, and pts are being followed for future correlation of ctDNA with radiographic recurrence. [Table: see text]

Quantifying the evolution of tumor architecture using serial circulating tumor DNA

600

Background: There is limited data regarding changes in the genomic landscape in individual patients over time as serial tissue biopsy has risk and is of uncertain clinical benefit. The advent of circulating tumor DNA (ctDNA) allows for safe and repeated molecular sampling with the potential to investigate evolution of tumor architecture over the disease course. Methods: From 5/15 to 12/17, 116 patients with metastatic CRC had between three to 12 blood specimens taken over the treatment course. Plasma was tested using targeted NGS assay (Guardant360, Guardant Health, 68 gene). To account for variations in the amount of ctDNA in serial samples, a window of evaluable allele frequency was established for each patient as the fold change between the max allele frequency (mAF) and limit of detection for serial samples with the lowest mAF. Mutations not falling within this window were excluded from analysis. Substantial treatment induced selective pressure (SP) was defined as a decrease in the mutant mAF of > 50% in patients with at least an initial mAF of 1%. Results: 116 patients with a total of 317 serial blood samples were evaluable after accounting for ctDNA variations over time. Specimens were collected a median of 12 months apart, with a median of three specimens per patient. Thirteen patients (11%) did not have any changes in mutations on serial sampling, however the remainder of patients gained an average of 1.1 mutations per time point (mut/tp), and lost 1.0 mut/tp. 31% of patients demonstrated evidence of substantial treatment-induced SP. These patients were more likely to demonstrate a change in clonal architecture of the tumor (46% greater rate than those without SP, P = 0.04), predominantly through gain of new clones. In contrast, clonal hematopoiesis alterations that may be induced by chemotherapy, such as JAK2V617F, were neither gained or lost. Conclusions: After correction for variations over time in the total amount of ctDNA in circulation, we identify numerous changes in tumor architecture with serial sampling. For the first time in colorectal cancer we demonstrate that when treatment-induced SP is applied the rate of tumor evolution is increased, demonstrating potential value of monitoring changes in tumor architecture over the disease course.

Anti-EGFR-resistant clones decay exponentially after progression: implications for anti-EGFR re-challenge

BACKGROUND

Colorectal cancer (CRC) has been shown to acquire RAS and EGFR ectodomain mutations as mechanisms of resistance to epidermal growth factor receptor (EGFR) inhibition (anti-EGFR). After anti-EGFR withdrawal, RAS and EGFR mutant clones lack a growth advantage relative to other clones and decay; however, the kinetics of decay remain unclear. We sought to determine the kinetics of acquired RAS/EGFR mutations after discontinuation of anti-EGFR therapy.

PATIENTS AND METHODS

We present the post-progression circulating tumor DNA (ctDNA) profiles of 135 patients with RAS/BRAF wild-type metastatic CRC treated with anti-EGFR who acquired RAS and/or EGFR mutations during therapy. Our validation cohort consisted of an external dataset of 73 patients with a ctDNA profile suggestive of prior anti-EGFR exposure and serial sampling. A separate retrospective cohort of 80 patients was used to evaluate overall response rate and progression free survival during re-challenge therapies.

RESULTS

Our analysis showed that RAS and EGFR relative mutant allele frequency decays exponentially (r2=0.93 for RAS; r2=0.94 for EGFR) with a cumulative half-life of 4.4 months. We validated our findings using an external dataset of 73 patients with a ctDNA profile suggestive of prior anti-EGFR exposure and serial sampling, confirming exponential decay with an estimated half-life of 4.3 months. A separate retrospective cohort of 80 patients showed that patients had a higher overall response rate during re-challenge therapies after increasing time intervals, as predicted by our model.

CONCLUSION

These results provide scientific support for anti-EGFR re-challenge and guide the optimal timing of re-challenge initiation.

Genomic Assessment of Blood-Derived Circulating Tumor DNA in Patients With Colorectal Cancers: Correlation With Tissue Sequencing, Therapeutic Response, and Survival

PURPOSE

Genomic alterations in blood-derived circulating tumor DNA (ctDNA) from patients with colorectal cancers were correlated with clinical outcomes.

PATIENTS AND METHODS

Next-generation sequencing of ctDNA (54- to 73-gene panel) was performed in 94 patients with colorectal cancer.

RESULTS

Most patients (96%) had metastatic or recurrent disease at the time of blood draw. The median number of nonsynonymous alterations per patient was three (range, zero to 30). The most frequently aberrant genes were TP53 (52.1% of patients), KRAS (34%), and APC (28.7%). Concordance between tissue and blood next-generation sequencing ranged from 63.2% (APC) to 85.5% (BRAF). Altogether, 74 patients (79%) had one or more nonsynonymous alterations, 69 (73%) had one or more potentially actionable alterations, and 61 (65%) had an alteration actionable by a drug approved by the US Food and Drug Administration (on or off label). Lung metastases correlated with improved survival from diagnosis in univariable analysis. ctDNA of 5% or more from blood tests as well as EGFR and ERBB2 (HER2) nonsynonymous alterations correlated with worse survival (but only ERBB2 remained significant in multivariable analysis). No two patients had identical molecular portfolios. Overall, 65% versus 31% of patients treated with matched (n = 17) versus unmatched therapy (n = 18) after ctDNA testing achieved stable disease for 6 months or more, partial response, or complete response (P = .045); progression-free survival, 6.1 versus 2.3 months (P = .08); and survival not reached versus 9.4 months (P = .146; all by multivariable analysis).

CONCLUSION

Patients with colorectal cancer have heterogeneous ctDNA profiles, and most harbor potentially actionable ctDNA alterations. Matched therapy yielded higher rates of stable disease for 6 months or more, partial response, or complete response. ctDNA assessment may have clinical utility and merits further investigation.

Revisiting Epidermal Growth Factor Receptor (EGFR) Amplification as a Target for Anti-EGFR Therapy: Analysis of Cell-Free Circulating Tumor DNA in Patients With Advanced Malignancies

Purpose

To date, evidence for tissue epidermal growth factor receptor (EGFR) overexpression as a biomarker for anti-EGFR therapies has been weak. We investigated the genomic landscape of EGFR amplification in blood-derived cell-free tumor DNA (cfDNA) across diverse cancers and the role of anti-EGFR therapies in achieving response.

Methods

We assessed EGFR amplification status among 28,584 patients with malignancies evaluated by clinical-grade next-generation sequencing (NGS) of blood-derived cfDNA (54- to 73-gene panel). Furthermore, we curated the clinical characteristics of 1,434 patients at the University of California San Diego who had cfDNA testing by this NGS test.

Results

Overall, EGFR amplification was detected in cfDNA from 8.5% of patients (2,423 of 28,584), most commonly in colorectal (16.3% [458 of 2,807]), non–small-cell lung (9.0% [1,096 of 12,197]), and genitourinary cancers (8.1% [170 of 2,104]). Most patients had genomic coalterations (96.9% [95 of 98]), frequently involving genes affecting other tyrosine kinases (72.4% [71 of 98]), mitogen-activated protein kinase cascades (56.1% [55 of 98]), cell-cycle–associated signals (52.0% [51 of 98]), and the phosphoinositide 3-kinase pathway (35.7% [35 of 98]). EGFR amplification emerged in serial cfDNA after various anticancer therapies (n = 6), including checkpoint inhibitors (n = 4), suggesting a possible role for these amplifications in acquired resistance. Nine evaluable patients with EGFR amplification were treated with anti-EGFR–based regimens; five (55.6%) achieved partial responses, including three patients whose tissue NGS lacked EGFR amplification.

Conclusion

EGFR amplification was detected in cfDNA among 8.5% of 28,584 diverse cancers. Most patients had coexisting alterations. Responses were observed in five of nine patients who received EGFR inhibitors. Incorporating EGFR inhibitors into the treatment regimens of patients harboring EGFR amplification in cfDNA merits additional study.

Use of Low-Frequency Driver Mutations Detected by Cell-Free Circulating Tumor DNA to Guide Targeted Therapy in Non–Small-Cell Lung Cancer: A Multicenter Case Series

Purpose

To evaluate the clinical outcome of patients with non–small-cell lung cancer treated by targeting low variant allelic frequency (VAF) driver mutations identified through cell-free DNA (cfDNA) next-generation sequencing (NGS). Detection of driver mutations in cancer is critically important in the age of targeted therapy, where both tumor-based as well as cfDNA sequencing methods have been used for therapeutic decision making. We hypothesized that VAF should not be predictive of response and that low VAF alterations detected by cfDNA NGS can respond to targeted therapy.

Patients and Methods

A multicenter retrospective case review was performed to identify patients with non–small-cell lung cancer who received targeted molecular therapy on the basis of findings of low VAF alterations in cfDNA NGS. Mutations at low VAF were defined as < 0.2% mutated cfDNA molecules in a background of wild-type cfDNA.

Results

One hundred seventy-two patients underwent cfDNA NGS testing. Of the 172 patients, 12 were identified as having low VAF driver alterations and were considered for targeted therapy. The median progression-free survival (PFS) for all patients was 52 weeks (range, 17 to 88 weeks). For patients with EGFR exon 19 deletion (n = 7), the median PFS was 52 weeks (range, 17 to 60.5 weeks). For patients with EML4-ALK fusions (n = 3), the median PFS was 60 weeks (range, 18 to 88 weeks). The median overall survival for all patients after diagnosis was 57.6 weeks.

Conclusion

Targeted treatment response for driver mutations detected by cfDNA may be independent of VAF, even in relation to other higher VAF aberrations in plasma, and directly dependent on the underlying disease biology and ability to treat the patient with appropriate targeted therapy.

Preoperative Circulating Tumor DNA in Patients with Peritoneal Carcinomatosis is an Independent Predictor of Progression-Free Survival

BACKGROUND

Next-generation sequencing (NGS) is a useful tool for detecting genomic alterations in circulating tumor DNA (ctDNA). To date, most ctDNA tests have been performed on patients with widely metastatic disease. Patients with peritoneal carcinomatosis (metastases) present unique prognostic and therapeutic challenges. We therefore explored preoperative ctDNA in patients with peritoneal metastases undergoing surgery.

METHODS

Patients referred for surgical resection of peritoneal metastases underwent preoperative blood-derived ctDNA analysis (clinical-grade NGS [68-73 genes]). ctDNA was quantified as the percentage of altered circulating cell-free DNA (% cfDNA).

RESULTS

Eighty patients had ctDNA testing: 46 (57.5%) women; median age 55.5 years. The following diagnoses were included: 59 patients (73.8%), appendix cancer; 11 (13.8%), colorectal; five (6.3%), peritoneal mesothelioma; two (2.5%), small bowel; one (1.3%) each of cholangiocarcinoma, ovarian, and testicular cancer. Thirty-one patients (38.8%) had detectable preoperative ctDNA alterations, most frequently in the following genes: TP53 (25.8% of all alterations detected) and KRAS (11.3%). Among 15 patients with tissue DNA NGS, 33.3% also had ctDNA alterations (overall concordance = 96.7%). Patients with high ctDNA quantities (≥ 0.25% cfDNA, n = 25) had a shorter progression-free survival (PFS) than those with lower ctDNA quantities (n = 55; 7.8 vs. 15.0 months; hazard ratio 3.23, 95% confidence interval 1.43-7.28, p = 0.005 univariate, p = 0.044 multivariate).

CONCLUSIONS

A significant proportion of patients with peritoneal metastases referred for surgical intervention have detectable ctDNA alterations preoperatively. Patients with high levels of ctDNA have a worse prognosis independent of histologic grade.

Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non-Small Cell Lung Cancer

Purpose: Patients with advanced non-small cell lung cancer (NSCLC) whose tumors harbor anaplastic lymphoma kinase (ALK) gene fusions benefit from treatment with ALK inhibitors (ALKi). Analysis of cell-free circulating tumor DNA (cfDNA) may provide a noninvasive way to identify ALK fusions and actionable resistance mechanisms without an invasive biopsy.Patients and Methods: The Guardant360 (G360; Guardant Health) deidentified database of NSCLC cases was queried to identify 88 consecutive patients with 96 plasma-detected ALK fusions. G360 is a clinical cfDNA next-generation sequencing (NGS) test that detects point mutations, select copy number gains, fusions, insertions, and deletions in plasma.Results: Identified fusion partners included EML4 (85.4%), STRN (6%), and KCNQ, KLC1, KIF5B, PPM1B, and TGF (totaling 8.3%). Forty-two ALK-positive patients had no history of targeted therapy (cohort 1), with tissue ALK molecular testing attempted in 21 (5 negative, 5 positive, and 11 tissue insufficient). Follow-up of 3 of the 5 tissue-negative patients showed responses to ALKi. Thirty-one patients were tested at known or presumed ALKi progression (cohort 2); 16 samples (53%) contained 1 to 3 ALK resistance mutations. In 13 patients, clinical status was unknown (cohort 3), and no resistance mutations or bypass pathways were identified. In 6 patients with known EGFR-activating mutations, an ALK fusion was identified on progression (cohort 4; 4 STRN, 1 EML4; one both STRN and EML4); five harbored EGFR T790M.Conclusions: In this cohort of cfDNA-detected ALK fusions, we demonstrate that comprehensive cfDNA NGS provides a noninvasive means of detecting targetable alterations and characterizing resistance mechanisms on progression. Clin Cancer Res; 24(12); 2758-70. ©2018 AACR.

Abstract P2-02-12: Cell free DNA analysis identifies actionable ERBB2 amplifications in patients with HER2 negative breast cancer

Identification of ERBB2 (HER2) overexpression in metastatic breast cancer informs utilization of HER2 targeted therapy. The NCCN recommends HER2 expression re-evaluation at the first disease recurrence in patients with negative or equivocal tissue status given results discrepancies due to inadequate tissue biopsy, tumoral heterogeneity, biopsy technique or fixation as well as discordance in ERBB2 (HER2) expression between primary and metastatic lesions. We examined the incidence of ERBB2 (HER2) negative to positive “flips” (e.g. to ERBB2-amplified in plasma) in a cohort of patients who underwent a blood-based cell-free DNA (cfDNA) assay at a CLIA-certified/CAP-accredited/NYSDOH-approved molecular diagnostic laboratory.

Laboratory database was queried for samples from patients with a breast cancer diagnosis. The query was filtered to ensure patients with multiple cfDNA timepoints were counted only once. Patients without a pathology report submitted at any cfDNA collection timepoint or the pathology report did not include ERBB2 (HER2) status, results were inconclusive or quantity not sufficient were excluded. Between March 2014 and April 2017, 1,853 unique patients were identified with reported ERBB2 (HER2) status. For patients with more than one cfDNA timepoint collected (N=349; 18.8%), the earliest pathology report was referenced. 1,386 patient tumor samples were negative for HER2 overexpression (74.8%), 325 (17.5%) were positive, and 142 (7.7%) were equivocal. Twenty-nine of the 1,386 patients with reported tumor negative HER2 status had amplification on subsequent cfDNA analysis (2.1%).

All 29 patients were female. Most patients (N=21) had a single cfDNA timepoint collected. Median age at cfDNA blood draw was 58 years (range 28–68). Median length of time between reported tissue negative status and cfDNA blood draw was 405 days (range 21–4,060). Median plasma ERBB2 copy number was 2.44 (greater than 50th-centile per laboratory data) (range 2.15–16.5).

Clinical follow-up was obtained for 19 patients (65%). Nine patients were lost to follow-up or succumbed to disease prior to initiation of a new therapeutic regimen. One patient was known HER2 positive prior to receipt of the cfDNA results. In the remaining nine patients, six initiated targeted HER2 therapy following receipt of the cfDNA results, with five of six (83%) demonstrating a clinical response. In one patient with known ER/PR positive, HER2 negative disease, progressing through multiple lines of therapy, addition of trastuzumab and pertuzumab to her paclitaxel regimen following identification of the cfDNA ERBB2 amplification resulted in a significant reduction in CEA levels (238 to 37.9 ng/mL) by week five. In a second patient, following identification of the cfDNA ERBB2 amplification, she was treated with trastuzumab and pertuzumab along with docetaxel and had a dramatic response. She continues on trastuzumab and pertuzumab alone.

Although a modest sample size, this is the second cfDNA series demonstrating that ERBB2 (HER2) status may flip from negative to positive upon recurrence or metastasis, and that targeting plasma-detected ERBB2 amplification with anti-HER2 has clinical benefit. cfDNA is a viable alternative to tissue rebiopsy in this patient population.

Citation Format: Raymond VM, Diaz J, Banks KC, Ahn E, Brufsky A, Ellis M, Lippman M, Lee C, Pluard T, Schreeder M, Schwab R, Lanman RB. Cell free DNA analysis identifies actionable ERBB2 amplifications in patients with HER2 negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-12.

Ultrasensitive plasma ctDNA KRAS assay for detection, prognosis, and assessment of therapeutic response in patients with unresectable pancreatic ductal adenocarcinoma

Precision oncology requires sensitive and specific clinical biomarkers. Carbohydrate Antigen 19-9 (CA19-9) is widely used in pancreatic ductal adenocarcinoma (PDA) but lacks sensitivity and specificity. Nearly all PDAs harbor somatic KRAS mutations, nominating circulating tumor DNA (ctDNA) KRAS as an alternative disease biomarker, however, variable clinical performance has limited its clinical utility. We applied an ultrasensitive, PCR mutation enrichment, next generation sequencing ctDNA KRAS assay in a large cohort of patients with unresectable PDA (N = 189) recruited to the BIOPAC study between 2008-2015. Baseline and longitudinal serum CA19-9 and plasma ctDNA KRAS were correlated with time to progression (TTP) and overall survival (OS). Baseline ctDNA KRAS detection rate was 93.7% (86.4% in patients with non-elevated CA19-9). ctDNA KRAS and CA19-9 were positively correlated yet independently associated with TTP and OS (ctDNA KRAS p = 0.0018 and 0.0014; CA19-9 p = 0.0294 and 0.0007, respectively). A generated model quantitating longitudinal ctDNA KRAS correctly assessed greater than 80% of patient responses. Quantitative detection of KRAS ctDNA is an informative prognostic biomarker, complementary to CA19-9 in patients with unresectable PDA. Longitudinal ctDNA KRAS may inform therapeutic decision making and provides a kinetically dynamic and quantitative metric of patient response.

Urine test for EGFR analysis in patients with non-small cell lung cancer

Precision medicine approaches in oncology are reliant on the accurate genomic characterization of tumors. While tissue remains the mainstay specimen for molecular testing, tumor biopsies are riddled with challenges and limitations due to their invasive and site-specific nature. Tumor inaccessibility and intratumoral heterogeneity, in particular, represent significant obstacles to the identification of actionable genetic alterations and hence effective mono- and combination therapy strategies. Proof-of-concept studies indicate that circulating tumor DNA (ctDNA) released from multiple tumor regions and anatomical locations is more reflective of intra- and intertumoral heterogeneity. Non-invasive liquid biopsy approaches that allow for the analysis of ctDNA are thus being increasingly implemented in routine patient care for the detection and monitoring of cancer-associated mutations. Indeed, the use of plasma testing to screen for epidermal growth factor receptor (EGFR) T790M mutant positive non-small cell lung cancer (NSCLC) patients eligible for treatment with third-generation EGFR inhibitors was recently approved by the U.S. Food and Drug Administration and is incorporated into the most recent version of the National Comprehensive Cancer Center guidelines as an alternative to tissue biopsy. Urine represents another liquid biopsy specimen that is distinguished by its ease of collection, option for home collection, and lack of temporal and volumetric collection restrictions. Importantly, there is an accumulating body of evidence supporting the clinical validity of urinary EGFR mutant testing for the identification and stratification of patients likely to benefit from EGFR-directed therapies and as a means to assess patient response, the presence of residual disease, and emergence of resistant tumor cell populations.

Physician Experiences and Understanding of Genomic Sequencing in Oncology

The amount of information produced by genomic sequencing is vast, technically complicated, and can be difficult to interpret. Appropriately tailoring genomic information for non-geneticists is an essential next step in the clinical use of genomic sequencing. To initiate development of a framework for genomic results communication, we conducted eighteen qualitative interviews with oncologists who had referred adult cancer patients to a matched tumor-normal tissue genomic sequencing study. In our qualitative analysis, we found varied levels of clinician knowledge relating to sequencing technology, the scope of the tumor genomic sequencing study, and incidental germline findings. Clinicians expressed a perceived need for more genetics education. Additionally, they had a variety of suggestions for improving results reports and possible resources to aid in results interpretation. Most clinicians felt genetic counselors were needed when incidental germline findings were identified. Our research suggests that more consistent genetics education is imperative in ensuring the proper utilization of genomic sequencing in cancer care. Clinician suggestions for results interpretation resources and results report modifications could be used to improve communication. Clinicians' perceived need to involve genetic counselors when incidental germline findings were found suggests genetic specialists could play a critical role in ensuring patients receive appropriate follow-up.

Abstract 2737: Development of a clinically actionable, ultra-sensitive multi-oncogene panel compatible with ctDNA testing in urine and plasma

Background: Circulating tumor DNA (ctDNA) is rapidly emerging as a viable alternative to tissue molecular diagnostics for the detection of actionable oncogenic mutations. In non-small cell lung cancer, identifying the emergence of EGFR T790M in patients receiving first line EGFR tyrosine-kinase inhibitors (TKIs) is a clinical need. Obtaining a tissue biopsy to determine T790M status is associated with significant cost and patient morbidity. In a retrospective analysis of the TIGER-X trial, patients had similar therapeutic response to a 3rd generation TKI, independent of the sample type positive for T790M; tissue, plasma, or urine. This indicates that non-invasive urine liquid biopsy is a viable diagnostic option (Wakelee et al, ASCO, 2016). We report on the expansion of single mutation assays to a multiplex-panel of clinically actionable mutations having analytical properties with similar ultra-sensitive detection.

Methods: We previously developed two next generation sequencing methodologies with high sensitivity and specificity for ctDNA detection: 1) A series of individual ultrasensitive ctDNA hotspot assays capable of detecting ultra-short DNA fragments (31-45 base pairs) and a 0.01% lower limit of detection (LLoD). The short sized amplicons coupled with mutant allele enrichment enabled high clinical sensitivity for plasma and urine ctDNA (Reckamp et al, J Thorac Oncol., 2016) 2) A multiplex panel using sequence-specific synchronous coefficient of drag alteration (SCODA) technology that enriches for mutant ctDNA to obtain a LL0D of 0.001%-0.03%, (Pel et al, PNAS, 2009; Kidess et al, Oncotarget, 2015). By combining a multiplex of short amplicons with SCODA enrichment capabilities, we developed an assay enriched for over 200 clinically actionable driver and resistance mutations within 7 oncogenes.

Results: An iterative process was used to design and optimize primer and enrichment probe length and placement to produce a panel where mean coverage across hotspot regions was within 2 to 3-fold (read uniformity) and greater than 1,000-fold enrichment of mutant DNA prior to sequencing. Technical validation was performed utilizing in-house and commercially available model systems for plasma and urine demonstrating mutation detection from inputs ranging from hundreds to fewer than 10 copies and LLoD as low as 0.001%. Clinical performance evaluation of the newly developed multiplex assay is ongoing using urine and plasma ctDNA from patients with advanced cancer.

Conclusions: High sensitivity is critical when identifying targetable driver mutations as well as emergence of resistance mutations which can inform therapeutic decision making. By combining short amplicon and mutation enrichment technology, we developed an ultra-sensitive ctDNA assay for use in sample types with highly degraded and fragmented DNA.

Citation Format: Karena A. Kosco, Matthew Wiggin, Peter J. Croucher, David Broemeling, Shiloh Guerrero, Laura Mai, Kurt Krummel, Victoria M. Raymond, Mark G. Erlander, Andre Marziali, Karsten Schmidt. Development of a clinically actionable, ultra-sensitive multi-oncogene panel compatible with ctDNA testing in urine and plasma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2737. doi:10.1158/1538-7445.AM2017-2737

Development of a Streamlined Work Flow for Handling Patients' Genetic Testing Insurance Authorizations

Obtaining genetic testing insurance authorizations for patients is a complex, time-involved process often requiring genetic counselor (GC) and physician involvement. In an effort to mitigate this complexity and meet the increasing number of genetic testing insurance authorization requests, GCs formed a novel partnership with an industrial engineer (IE) and a patient services associate (PSA) to develop a streamlined work flow. Eight genetics clinics and five specialty clinics at the University of Michigan were surveyed to obtain benchmarking data. Tasks needed for genetic testing insurance authorization were outlined and time-saving work flow changes were introduced including 1) creation of an Excel password-protected shared database between GCs and PSAs, used for initiating insurance authorization requests, tracking and follow-up 2) instituting the PSAs sending GCs a pre-clinic email noting each patients' genetic testing insurance coverage 3) inclusion of test medical necessity documentation in the clinic visit summary note instead of writing a separate insurance letter and 4) PSAs development of a manual with insurance providers and genetic testing laboratories information. These work flow changes made it more efficient to request and track genetic testing insurance authorizations for patients, enhanced GCs and PSAs communication, and reduced tasks done by clinicians.

Abstract A20: Detection and quantification of ctDNA KRAS mutations from patients with unresectable pancreatic cancer

Introduction: An estimated 90% of pancreatic cancers harbor somatic KRAS G12/G13 mutations. The presence of circulating tumor DNA (ctDNA) KRAS mutations at diagnosis has prognostic implications, however, recent studies on small numbers of patients demonstrate widely variable KRAS ctDNA sensitivity (27 – 71%). Accurate identification of both the presence of ctDNA KRAS mutations and quantification of the number of ctDNA KRAS mutant copies would be an improved therapeutic response biomarker over CA19-9 which is known to be uninformative in 5-10% of patients with pancreatic cancer. A diagnostic and prognostic tool with very high analytical and clinical sensitivity, along with quantification, is needed for therapeutic response monitoring.

Patients and Methods: Pretreatment (baseline) and longitudinal plasma samples were prospectively collected from 239 patients with unresectable pancreatic cancer through the Danish Biomarkers in Patients with Pancreatic Cancer (BIOPAC) study. The median age at diagnosis was 67 years (range 42 – 89 years) and 51.9% (N = 112) of patients were male. The majority of patients were metastatic at diagnosis (79.6%; N=172). ctDNA KRAS G12A/C/D/R/S/V, and G13D mutations were PCR enriched, sequenced by next generation sequencing (NGS), quantified and standardized. This was achieved by generating standard curves from a sample set with known numbers of spike-in copies for mutant KRAS molecules. These sample sets were assayed in parallel with patient samples starting with PCR enrichment of mutant KRAS DNA followed by NGS. The number of mutant copies detected was standardized by normalizing the number of copies detected in the sample to a constant number of calculated genome equivalents (GEqs) of wild type DNA across all samples evaluated. Baseline KRAS mutant levels were assessed. Additional metrics analyzed include age, gender, stage, and CA19-9 levels.

Results: Two-hundred and sixteen patients (90.4%) had baseline plasma samples which passed quality control metrics. Baseline serum CA19-9 levels were available for 160 patients and ranged from 2.5 – 608,500 U/mL (median 202 U/mL). Eighteen patients (11.3%) had serum CA19-9 levels below the diagnostic threshold (&lt;37 U/mL), and 76 patients (47.5%) had serum CA19-9 levels below the prognostic threshold (&lt;1000 U/mL). Overall, 87% of patients were positive for a KRAS mutation at baseline by ctDNA analysis, with a median of 88.51 copies per 100,000 GEqs. Patients presenting with metastatic disease had a significantly higher median number of KRAS mutations (104.2 versus 23.9 copies per 100,000 GEqs; p&lt;0.0001) and serum CA19-9 levels (1702.0 versus 303.0 U/mL; p&lt;0.0001) at baseline than those with locally advanced cancer.

Conclusion: In this large, prospective dataset of 216 patients with unresectable pancreatic cancer, ctDNA analysis was KRAS positive in 87.0% of patients. This detection rate closely matches the published prevalence of KRAS in pancreatic cancer (90%), and out performs previous studies, demonstrating the superior assay sensitivity. ctDNA analysis offers a viable tissue biopsy alternative for determining KRAS mutation status, especially in late stage patients. Given that approximately 48% of patients had CA19-9 levels below the prognostic threshold, quantification of KRAS mutant copy load may provide a more informative biomarker. Other clinical variables, baseline and longitudinal KRAS mutant levels, and patient outcomes will be examined and presented.

Citation Format: Inna Chen, Victoria M. Raymond, Jennifer A. Geis, Sandeep Pingle, Eric A. Collisson, Vlada Melnikova, Mark G. Erlander, Julia A. Johansen, Fernando Blanco.{Authors}. Detection and quantification of ctDNA KRAS mutations from patients with unresectable pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A20.

Non-invasive urine testing of EGFR activating mutation and T790M resistance mutation in non-small cell lung cancer

Background

The increasing understanding of non-small cell lung cancer (NSCLC) biology over the last two decades has led to the identification of multiple molecular targets. This led to the development of multiple targeted therapies in the primary and secondary resistance setting and the epidermal growth factor receptor (EGFR) gene remains the most frequently observed molecular target in NSCLC. Tissue biopsies remain the standard for the identification of such EGFR mutations. Obtaining serial tissue biopsies, especially in the secondary resistance setting is associated with multiple medical and logistical challenges. Utilizing circulating tumor DNA (ctDNA) fragments for molecular analysis can overcome these challenges and aid in therapeutic decision-making.

Case presentation

Here we present a present a 72-year-old Korean woman with metastatic, EGFR L858R mutated bronchogenic adenocarcinoma. She developed skeletal progression on treatment with first and second generation tyrosine kinase inhibitors (TKIs). Repeated biopsies failed to provide informative molecular test results. A novel urine ctDNA assay was utilized and confirmed T790M positive status. The patient was started on a third generation TKI, which led to a measurable clinical response.

Conclusions

Utilization of urine liquid biopsies for EGFR diagnostics are feasible and provided critical clinical information in this patient’s case. Urine liquid biopsy represents a viable alternative to tissue biopsy, particularly in the secondary resistance setting, when tissue is not available for molecular testing.

Germline Findings in Tumor-Only Sequencing: Points to Consider for Clinicians and Laboratories

Precision oncology holds great potential to improve patient therapies and outcomes. Tumor sequencing is rapidly moving into clinical care as our understanding of the cancer genome and the availability of targeted therapies increase. Analysis of the cancer genome is most informative when paired with germline genomic DNA to delineate inherited and somatic variants. Although tumor-only analysis remains the most common methodology for numerous reasons, it holds the potential to identify clinically significant germline variants. Here, we provide anticipatory guidance and points to consider for laboratories and clinicians regarding the potential for germline findings in tumor sequencing.

Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth

IMPORTANCE

Cancer is caused by a diverse array of somatic and germline genomic aberrations. Advances in genomic sequencing technologies have improved the ability to detect these molecular aberrations with greater sensitivity. However, integrating them into clinical management in an individualized manner has proven challenging.

OBJECTIVE

To evaluate the use of integrative clinical sequencing and genetic counseling in the assessment and treatment of children and young adults with cancer.

DESIGN, SETTING, AND PARTICIPANTS

Single-site, observational, consecutive case series (May 2012-October 2014) involving 102 children and young adults (mean age, 10.6 years; median age, 11.5 years, range, 0-22 years) with relapsed, refractory, or rare cancer.

EXPOSURES

Participants underwent integrative clinical exome (tumor and germline DNA) and transcriptome (tumor RNA) sequencing and genetic counseling. Results were discussed by a precision medicine tumor board, which made recommendations to families and their physicians.

MAIN OUTCOMES AND MEASURES

Proportion of patients with potentially actionable findings, results of clinical actions based on integrative clinical sequencing, and estimated proportion of patients or their families at risk of future cancer.

RESULTS

Of the 104 screened patients, 102 enrolled with 91 (89%) having adequate tumor tissue to complete sequencing. Only the 91 patients were included in all calculations, including 28 (31%) with hematological malignancies and 63 (69%) with solid tumors. Forty-two patients (46%) had actionable findings that changed their cancer management: 15 of 28 (54%) with hematological malignancies and 27 of 63 (43%) with solid tumors. Individualized actions were taken in 23 of the 91 (25%) based on actionable integrative clinical sequencing findings, including change in treatment for 14 patients (15%) and genetic counseling for future risk for 9 patients (10%). Nine of 91 (10%) of the personalized clinical interventions resulted in ongoing partial clinical remission of 8 to 16 months or helped sustain complete clinical remission of 6 to 21 months. All 9 patients and families with actionable incidental genetic findings agreed to genetic counseling and screening.

CONCLUSIONS AND RELEVANCE

In this single-center case series involving young patients with relapsed or refractory cancer, incorporation of integrative clinical sequencing data into clinical management was feasible, revealed potentially actionable findings in 46% of patients, and was associated with change in treatment and family genetic counseling for a small proportion of patients. The lack of a control group limited assessing whether better clinical outcomes resulted from this approach than outcomes that would have occurred with standard care.

Illustrative case studies in the return of exome and genome sequencing results

Whole genome and exome sequencing tests are increasingly being ordered in clinical practice, creating a need for research exploring the return of results from these tests. A goal of the Clinical Sequencing and Exploratory Research (CSER) consortium is to gain experience with this process to develop best practice recommendations for offering exome and genome testing and returning results. Genetic counselors in the CSER consortium have an integral role in the return of results from these genomic sequencing tests and have gained valuable insight. We present seven emerging themes related to return of exome and genome sequencing results accompanied by case descriptions illustrating important lessons learned, counseling challenges specific to these tests and considerations for future research and practice.

Screening for germline mismatch repair mutations following diagnosis of sebaceous neoplasm

IMPORTANCE Sebaceous neoplasms (SNs) define the Muir-Torre syndrome variant of Lynch syndrome (LS), which is associated with increased risk for colon and other cancers necessitating earlier and more frequent screening to reduce morbidity and mortality.Immunohistochemical (IHC) staining for mismatch repair (MMR) proteins in SNs can be used to screen for LS, but data on subsequent germline genetic testing to confirm LS diagnosis are limited.OBJECTIVE To characterize the utility of IHC screening of SNs in identification of germline MMR mutations confirming LS.DESIGN, SETTING, AND PARTICIPANTS Retrospective study at 2 academic cancer centers of 86 adult patients referred for clinical genetics evaluation after diagnosis of SN.MAIN OUTCOMES AND MEASURES Results of tumor IHC testing and germline genetic testing were reviewed to determine positive predictive value and sensitivity of IHC testing in diagnosis of LS. Clinical variables, including age at diagnosis of SN, clinical diagnostic criteria for LS and Muir-Torre syndrome, and family history characteristics were compared between mutation carriers and noncarriers.RESULTS Of 86 patients with SNs, 25 (29%) had germline MMR mutations confirming LS.Among 77 patients with IHC testing on SNs, 38 (49%) had loss of staining of 1 or more MMR proteins and 14 had germline MMR mutations. Immunohistochemical analysis correctly identified 13 of 16 MMR mutation carriers, corresponding to 81% sensitivity. Ten of 12 patients(83%) with more than 1 SN had MMR mutations. Fifty-two percent of MMR mutation carriers did not meet clinical diagnostic criteria for LS, and 11 of 25 (44%) did not meet the clinical definition of Muir-Torre syndrome. CONCLUSIONS AND RELEVANCE Immunohistochemical screening of SNs is effective in identifying patients with germline MMR mutations and can be used as a first-line test when LSis suspected. Abnormal IHC results, including absence of MSH2, are not diagnostic of LS and should be interpreted cautiously in conjunction with family history and germline genetic testing. Use of family history to select patients for IHC screening has substantial limitations,suggesting that universal IHC screening of SNs merits further study. Clinical genetics evaluation is warranted for patients with abnormal IHC test results, normal IHC test results with personal or family history of other LS-associated neoplasms, and/or multiple SNs.

Illustrative case studies in the return of exome and genome sequencing results

Whole genome and exome sequencing tests are increasingly being ordered in clinical practice, creating a need for research exploring the return of results from these tests. A goal of the Clinical Sequencing and Exploratory Research (CSER) consortium is to gain experience with this process to develop best practice recommendations for offering exome and genome testing and returning results. Genetic counselors in the CSER consortium have an integral role in the return of results from these genomic sequencing tests and have gained valuable insight. We present seven emerging themes related to return of exome and genome sequencing results accompanied by case descriptions illustrating important lessons learned, counseling challenges specific to these tests and considerations for future research and practice.

The clinical phenotype of SDHC-associated hereditary paraganglioma syndrome (PGL3)

CONTEXT

Mutations in the genes encoding subunits of the succinate dehydrogenase complex cause hereditary paraganglioma syndromes. Although the phenotypes associated with the more commonly mutated genes, SDHB and SDHD, are well described, less is known about SDHC-associated paragangliomas.

OBJECTIVE

To describe functionality, penetrance, number of primary tumors, biological behavior, and location of paragangliomas associated with SDHC mutations.

DESIGN

Families with an SDHC mutation were identified through a large cancer genetics registry. A retrospective chart review was conducted with a focus on patient and tumor characteristics. In addition, clinical reports on SDHC-related paragangliomas were identified in the medical literature to further define the phenotype and compare findings.

SETTING

A cancer genetics clinic and registry at a tertiary referral center.

PATIENTS

Eight index patients with SDHC-related paraganglioma were identified.

RESULTS

Three of the eight index patients had mediastinal paraganglioma and four of the eight patients had more than one paraganglioma. Interestingly, the index patients were the only affected individuals in all families. When combining these index cases with reported cases in the medical literature, the mediastinum is the second most common location for SDHC-related paraganglioma (10% of all tumors), occurring in up to 13% of patients.

CONCLUSIONS

Our findings suggest that thoracic paragangliomas are common in patients with SDHC mutations, and imaging of this area should be included in surveillance of mutation carriers. In addition, the absence of paragangliomas among at-risk relatives of SDHC mutation carriers suggests a less penetrant phenotype as compared to SDHB and SDHD mutations.

Adrenocortical carcinoma

Adrenocortical carcinoma (ACC) is a rare endocrine malignancy, often with an unfavorable prognosis. Here we summarize the knowledge about diagnosis, epidemiology, pathophysiology, and therapy of ACC. Over recent years, multidisciplinary clinics have formed and the first international treatment trials have been conducted. This review focuses on evidence gained from recent basic science and clinical research and provides perspectives from the experience of a large multidisciplinary clinic dedicated to the care of patients with ACC.

Traditional roles in a non-traditional setting: genetic counseling in precision oncology

Next generation sequencing technology is increasingly utilized in oncology with the goal of targeting therapeutics to improve response and reduce side effects. Interpretation of tumor mutations requires sequencing of paired germline DNA, raising questions about incidental germline findings. We describe our experiences as part of a research team implementing a protocol for whole genome sequencing (WGS) of tumors and paired germline DNA known as the Michigan Oncology Sequencing project (MI-ONCOSEQ) that includes options for receiving incidental germline findings. Genetic counselors (GCs) discuss options for return of results with patients during the informed consent process and document family histories. GCs also review germline findings and actively participate in the multi-disciplinary Precision Medicine Tumor Board (PMTB), providing clinical context for interpretation of germline results and making recommendations about disclosure of germline findings. GCs have encountered ethical and counseling challenges with participants, described here. Although GCs have not been traditionally involved in molecular testing of tumors, our experiences with MI-ONCOSEQ demonstrate that GCs have important applicable skills to contribute to multi-disciplinary care teams implementing precision oncology. Broader use of WGS in oncology treatment decision making and American College of Medical Genetics and Genomics (ACMG) recommendations for active interrogation of germline tissue in tumor-normal dyads suggests that GCs will have future opportunities in this area outside of research settings.

Adrenocortical carcinoma is a lynch syndrome-associated cancer

PURPOSE

Adrenocortical carcinoma (ACC) is an endocrine malignancy with a poor prognosis. The association of adult-onset ACC with inherited cancer predisposition syndromes is poorly understood. Our study sought to define the prevalence of Lynch syndrome (LS) among patients with ACC.

PATIENTS AND METHODS

One hundred fourteen patients with ACC were evaluated in a specialized endocrine oncology clinic and were prospectively offered genetic counseling and clinical genetics risk assessment (group 1). In addition, families with known mismatch repair (MMR) gene mutations that were recorded in the University of Michigan Cancer Genetics Registry were retrospectively reviewed for the presence of ACC (group 2). ACC tumors from patients with LS were tested for microsatellite instability and immunohistochemistry (IHC) to evaluate for MMR deficiency.

RESULTS

Ninety-four (82.5%) of 114 patients with ACC underwent genetic counseling (group 1). Three individuals (3.2%) had family histories suggestive of LS. All three families were found to have MMR gene mutations. Retrospective review of an additional 135 MMR gene-positive probands identified two with ACC (group 2). Four ACC tumors were available (group 1, 3; group 2, 1). All four tumors were microsatellite stable; three had IHC staining patterns consistent with germline mutation status.

CONCLUSION

The prevalence of LS among patients with ACC is 3.2%, which is comparable to the prevalence of LS in colorectal and endometrial cancer. Patients with ACC and a personal or family history of LS tumors should be strongly considered for genetic risk assessment. IHC screening of all ACC tumors may be an effective strategy for identifying patients with LS.

Familial gastric and pancreatic cancers: Diagnosis and screening

Screening for gastric and pancreatic cancers in asymptomatic individuals is not routinely practiced in the United States. While there is insufficient evidence that general population screening would reduce morbidity and/or mortality associated with these cancers, the utility of screening for individuals at increased risk warrants further study. Clinical challenges include identifying high risk individuals who would be most likely to benefit from screening and determining which screening modalities and intervals would be most effective.

Elevated risk of prostate cancer among men with Lynch syndrome

PURPOSE

Prostate cancer has been described as a component tumor of Lynch syndrome (LS), with tumors obtained from mutation carriers demonstrating the DNA mismatch repair deficiency phenotype. Previous studies quantifying prostate cancer risk in LS have provided conflicting results.

METHODS

We examined cancer histories of probands and their first- through fourth-degree relatives for 198 independent mutation-positive LS families enrolled in two US familial cancer registries. Modified segregation analysis was used to calculate age-specific cumulative risk or penetrance estimates, with accompanying Wald-type CIs. Cumulative lifetime risks and hazard ratio (HR) estimates for prostate cancer were calculated and compared with those of the general population.

RESULTS

Ninety-seven cases of prostate cancer were observed in 4,127 men. Median age at prostate cancer diagnosis was 65 years (range, 38 to 89 years), with 11.53% of affected individuals diagnosed before age 50 years. The cumulative risk of prostate cancer at ages 60 and 80 years was 6.30% (95% CI, 2.47 to 9.96) and 30.0% (95% CI, 16.54 to 41.30), as compared with the population risk of 2.59% and 17.84%, respectively. The overall prostate cancer HR among carriers was 1.99 (95% CI, 1.31 to 3.03).

CONCLUSION

The cumulative lifetime risk of prostate cancer in individuals with LS is two-fold higher than in the general population and is slightly higher in carriers diagnosed before age 60 years (HR, 2.48; 95% CI, 1.34 to 4.59). These estimates are clinically valuable to quantify risk for both patients and providers.

Prevalence of germline TP53 mutations in a prospective series of unselected patients with adrenocortical carcinoma

PURPOSE

Adrenocortical carcinoma (ACC) is a hallmark cancer in families with Li Fraumeni syndrome (LFS) caused by mutations in the TP53 gene. The prevalence of germline TP53 mutations in children diagnosed with ACC ranges from 50-97%. Although existing criteria advocate for TP53 testing in all patients with ACC regardless of age at diagnosis, the overall prevalence of germline mutations in patients diagnosed with ACC has not been well studied.

PATIENTS AND METHODS

A total of 114 patients with confirmed ACC evaluated in the University of Michigan Endocrine Oncology Clinic were prospectively offered genetic counseling and TP53 genetic testing, regardless of age at diagnosis or family history. Ninety-four of the 114 patients met with a genetic counselor (82.5%), with 53 of 94 (56.4%) completing TP53 testing; 9.6% (nine of 94) declined testing. The remainder (32 of 94; 34%) expressed interest in testing but did not pursue it for various reasons.

RESULTS

Four of 53 patients in this prospective, unselected series were found to have a TP53 mutation (7.5%). The prevalence of mutations in those diagnosed over age 18 was 5.8% (three of 52). There were insufficient data to estimate the prevalence in those diagnosed under age 18. None of these patients met clinical diagnostic criteria for classic LFS. Three of the families met criteria for Li Fraumeni-like syndrome; one patient met no existing clinical criteria for LFS or Li Fraumeni-like syndrome. Three of the four patients with mutations were diagnosed with ACC after age 45.

CONCLUSIONS

Genetic counseling and germline testing for TP53 should be offered to all patients with ACC. Restriction on age at diagnosis or strength of the family history would fail to identify mutation carriers.