Efficacy of Nivolumab in Pediatric Cancers with High Mutation Burden and Mismatch Repair Deficiency

PURPOSE

Checkpoint inhibitors have limited efficacy for children with unselected solid and brain tumors. We report the first prospective pediatric trial (NCT02992964) using nivolumab exclusively for refractory nonhematologic cancers harboring tumor mutation burden (TMB) ≥5 mutations/megabase (mut/Mb) and/or mismatch repair deficiency (MMRD).

PATIENTS AND METHODS

Twenty patients were screened, and 10 were ultimately included in the response cohort of whom nine had TMB >10 mut/Mb (three initially eligible based on MMRD) and one patient had TMB between 5 and 10 mut/Mb.

RESULTS

Delayed immune responses contributed to best overall response of 50%, improving on initial objective responses (20%) and leading to 2-year overall survival (OS) of 50% [95% confidence interval (CI), 27-93]. Four children, including three with refractory malignant gliomas are in complete remission at a median follow-up of 37 months (range, 32.4-60), culminating in 2-year OS of 43% (95% CI, 18.2-100). Biomarker analyses confirmed benefit in children with germline MMRD, microsatellite instability, higher activated and lower regulatory circulating T cells. Stochastic mutation accumulation driven by underlying germline MMRD impacted the tumor microenvironment, contributing to delayed responses. No benefit was observed in the single patient with an MMR-proficient tumor and TMB 7.4 mut/Mb.

CONCLUSIONS

Nivolumab resulted in durable responses and prolonged survival for the first time in a pediatric trial of refractory hypermutated cancers including malignant gliomas. Novel biomarkers identified here need to be translated rapidly to clinical care to identify children who can benefit from checkpoint inhibitors, including upfront management of cancer. See related commentary by Mardis, p. 4701.

Distinguishing Gastric/Esophageal Adenocarcinoma from Pancreatic Adenocarcinoma Using Methylation-Based Droplet Digital PCR

The goal of this study was to develop a methylation-based droplet digital PCR to separate 2 cancer classes that do not have sensitive and specific immunohistochemical stains: gastric/esophageal and pancreatic adenocarcinomas. The assay used methylation-independent primers and methylation-dependent probes to assess a single differentially methylated CpG site; analyses of array data from The Cancer Genome Atlas network showed that high methylation at the cg06118999 probe supports the presence of cells originating from the stomach or esophagus (eg, as in gastric metastasis), whereas low methylation suggests that these cells are rare to absent (eg, pancreatic metastasis). On validation using formalin-fixed paraffin-embedded primary and metastatic samples from our institution, methylation-based droplet digital PCR targeting the corresponding CpG dinucleotide generated evaluable data for 60 of the 62 samples (97%) and correctly classified 50 of the 60 evaluable cases (83.3%), mostly adenocarcinomas from the stomach or pancreas. This ddPCR was created to be easy-to-interpret, rapid, inexpensive, and compatible with existing platforms at many clinical laboratories. We suggest that similarly accessible PCRs could be developed for other differentials in pathology that do not have sensitive and specific immunohistochemical stains.

Abstract 6545: Investigating secondary findings in a pediatric cancer cohort: preliminary findings

Purpose: An expected outcome following germline genome sequencing in oncology is the discovery of ‘secondary findings’ (SFs). SFs comprise pathogenic(P)/likely P (LP) germline variants in cancer genes not typically associated with the presenting cancer, in addition to germline variants of uncertain significance (VUS) to the patient’s cancer. Due to the rarity of childhood cancers and a dearth of studies analyzing SFs, many pediatric SFs are categorized as VUS without clinical interpretation. Interpreting SFs poses significant challenges: VUSs and other SFs are frequently not included in clinical molecular reports, and even when reported (often through research), their clinical utility and long-term impact on patient health are unclear. However, we know VUSs can have clinical importance because some VUSs, when investigated thoroughly, have been reclassified as pathogenic predictors of significant health conditions in children. We hypothesize that an in-depth characterization of the landscape of germline SFs/VUSs across a diverse pediatric cancer cohort will reveal new roles of these genes and mutations in pediatric cancers.

Methods: To explore germline SFs in pediatric cancer patients, we analyzed germline whole-genome sequencing (WGS) data for patients with rare, relapsed, refractory, and metastatic childhood cancers enrolled in the SickKids Cancer Sequencing Program (KiCS). We developed a custom analysis pipeline to identify germline single-nucleotide variants and indels deemed SFs, auto-classify their pathogenicity (ex. P, LP, or VUS) using CharGer, filter for PanCanAtlas-indicated cancer predisposition genes, and sort the remaining variants by cancer and non-cancer associations.

Results: The KiCS cohort (n = 511) encompassed over 133 different tumor types; the median age of participants was 14 years (SD = 10.27) and 55% of patients were male. Ongoing work in our lab will catalogue the frequency and distribution of SFs in KiCS and analyze germline variants by subgroup (gene, tumor subtype, stage, demographics, gene function). We will also compare SF prevalence in KiCS to the general population using the gnomAD dataset. Results from preliminary analyses of this cohort will be presented.

Significance: SFs/VUSs are under-utilized in cancer management. This work advances the holistic understanding of germline genomics in pediatric oncology and the roles of SFs in disease. Future studies will evaluate SFs by patient ancestry and validate cancer associations through the evaluation of allelic imbalance/loss of heterozygosity in matched tumor genomes.

Citation Format: Safa Majeed, Stephenie Prokopec, Brianne Laverty, Vallijah Subasri, Michael Taylor, Yvonne Bombard, Trevor Pugh, Adam Shlien, Anita Villani, David Malkin. Investigating secondary findings in a pediatric cancer cohort: preliminary findings. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6545.

Identification of antigenic epitopes recognized by tumor infiltrating lymphocytes in high grade serous ovarian cancer by multi-omics profiling of the auto-antigen repertoire

Immunotherapeutic strategies aimed at enhancing tumor cell killing by tumor-specific T cells hold great potential for reducing tumor burden and prolonging survival of cancer patients. Although many potential tumor antigens have been described, identifying relevant targets when designing anti-cancer vaccines or targeted cell therapies remains a challenge. To identify novel, potentially immunogenic candidate tumor antigens, we performed integrated tumor transcriptomic, seromic, and proteomic analyses of high grade serous ovarian cancer (HGSC) patient tumor samples. We identified tumor neo-antigens and over-expressed antigens using whole exome and RNA sequencing and examined these in relation to patient-matched auto-antibody repertoires. Focusing on MHC class I epitopes recognized by CD8⁺ T cells, HLA-binding epitopes were identified or predicted from the highly expressed, mutated, or auto-antibody target antigen, or MHC-associated peptides (MAPs). Recognition of candidate antigenic peptides was assessed within the tumor-infiltrating T lymphocyte (TIL) population expanded from each patient. Known tumor-associated antigens (TAA) and cancer/testis antigens (CTA) were commonly found in the auto-antibody and MAP repertoires and CD8⁺ TILs recognizing epitopes from these antigens were detected, although neither expression level nor the presence of auto-antibodies correlated with TIL recognition. Auto-antibodies against tumor-mutated antigens were found in most patients, however, no TIL recognition of the highest predicted affinity neo-epitopes was detected. Using high expression level, auto-antibody recognition, and epitope prediction algorithms, we identified epitopes in 5 novel antigens (MOB1A, SOCS3, TUBB, PRKAR1A, CCDC6) recognized by HGSC patient TILs. Furthermore, selection of epitopes from the MAP repertoire identified 5 additional targets commonly recognized by multiple patient TILs. We find that the repertoire of TIL specificities includes recognition of highly expressed and immunogenic self-antigens that are processed and presented by tumors. These results indicate an ongoing autoimmune response against a range of self-antigens targeted by HGSC TILs.

Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases

Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets

Single-cell RNA sequencing (scRNA-seq) clustering and labelling methods are used to determine precise cellular composition of tissue samples. Automated labelling methods rely on either unsupervised, cluster-based approaches or supervised, cell-based approaches to identify cell types. The high complexity of cancer poses a unique challenge, as tumor microenvironments are often composed of diverse cell subpopulations with unique functional effects that may lead to disease progression, metastasis and treatment resistance. Here, we assess 17 cell-based and 9 cluster-based scRNA-seq labelling algorithms using 8 cancer datasets, providing a comprehensive large-scale assessment of such methods in a cancer-specific context. Using several performance metrics, we show that cell-based methods generally achieved higher performance and were faster compared to cluster-based methods. Cluster-based methods more successfully labelled non-malignant cell types, likely because of a lack of gene signatures for relevant malignant cell subpopulations. Larger cell numbers present in some cell types in training data positively impacted prediction scores for cell-based methods. Finally, we examined which methods performed favorably when trained and tested on separate patient cohorts in scenarios similar to clinical applications, and which were able to accurately label particularly small or under-represented cell populations in the given datasets. We conclude that scPred and SVM show the best overall performances with cancer-specific data and provide further suggestions for algorithm selection. Our analysis pipeline for assessing the performance of cell type labelling algorithms is available in https://github.com/shooshtarilab/scRNAseq-Automated-Cell-Type-Labelling.

Genome Reporting for Healthy Populations-Pipeline for Genomic Screening from the GENCOV COVID-19 Study

Genome sequencing holds the promise for great public health benefits. It is currently being used in the context of rare disease diagnosis and novel gene identification, but also has the potential to identify genetic disease risk factors in healthy individuals. Genome sequencing technologies are currently being used to identify genetic factors that may influence variability in symptom severity and immune response among patients infected by SARS-CoV-2. The GENCOV study aims to look at the relationship between genetic, serological, and biochemical factors and variability of SARS-CoV-2 symptom severity, and to evaluate the utility of returning genome screening results to study participants. Study participants select which results they wish to receive with a decision aid. Medically actionable information for diagnosis, disease risk estimation, disease prevention, and patient management are provided in a comprehensive genome report. Using a combination of bioinformatics software and custom tools, this article describes a pipeline for the analysis and reporting of genetic results to individuals with COVID-19, including HLA genotyping, large-scale continental ancestry estimation, and pharmacogenomic analysis to determine metabolizer status and drug response. In addition, this pipeline includes reporting of medically actionable conditions from comprehensive gene panels for Cardiology, Neurology, Metabolism, Hereditary Cancer, and Hereditary Kidney, and carrier screening for reproductive planning. Incorporated into the genome report are polygenic risk scores for six diseases-coronary artery disease; atrial fibrillation; type-2 diabetes; and breast, prostate, and colon cancer-as well as blood group genotyping analysis for ABO and Rh blood types and genotyping for other antigens of clinical relevance. The genome report summarizes the findings of these analyses in a way that extensively communicates clinically relevant results to patients and their physicians. © 2022 Wiley Periodicals LLC. Basic Protocol 1: HLA genotyping and disease association Basic Protocol 2: Large-scale continental ancestry estimation Basic Protocol 3: Dosage recommendations for pharmacogenomic gene variants associated with drug response Support Protocol: System setup.

Characterization of the minimal residual disease state reveals distinct evolutionary trajectories of human glioblastoma

Recurrence of solid tumors renders patients vulnerable to advanced, treatment-refractory disease state with mutational and oncogenic landscape distinctive from initial diagnosis. Improving outcomes for recurrent cancers requires a better understanding of cell populations that expand from the post-therapy, minimal residual disease (MRD) state. We profile barcoded tumor stem cell populations through therapy at tumor initiation, MRD, and recurrence in our therapy-adapted, patient-derived xenograft models of glioblastoma (GBM). Tumors show distinct patterns of recurrence in which clonal populations exhibit either a pre-existing fitness advantage or an equipotency fitness acquired through therapy. Characterization of the MRD state by single-cell and bulk RNA sequencing reveals a tumor-intrinsic immunomodulatory signature with prognostic significance at the transcriptomic level and in proteomic analysis of cerebrospinal fluid (CSF) collected from patients with GBM. Our results provide insight into the innate and therapy-driven dynamics of human GBM and the prognostic value of interrogating the MRD state in solid cancers.

Impacts of the Statewide COVID-19 Lockdown Interventions on Excess Mortality, Unemployment, and Employment Growth

OBJECTIVE

The aim of the study is to determine relationships between lockdowns and excess mortality, unemployment, and employment growth.

METHODS

Each US states' mortality data for 2020 were compared with the prior 3 years to determine excess mortality. Data were compared using measures of lockdowns, or state openness scores and adjusted for age, sex, race/ethnicity, and cardiovascular disease. Comparisons were made with unemployment rates and employment growth rates.

RESULTS

The 2020 excess mortality ranged from -9% to 46%. The average openness score was not significant ( P = 0.20). However, openness was strongly associated with both unemployment ( P = 0.01) and employment growth ( P = 0.0008).

CONCLUSIONS

There was no statistical relationship between excess mortality and openness scores, while there were strong relationships with employment measures. These results suggest that lockdowns are not sufficiently beneficial for future use in this pandemic and raise concerns for use in future pandemics.

Abstract 538: Cell-free whole genome sequencing for the detection of cancer in patients with germline BRCA1/2 mutations

Background: Hereditary breast and ovarian cancer syndrome (HBOC) is caused by a germline likely/pathogenic variant in BRCA1 or BRCA2, leading to increased risk of developing breast, ovarian, prostate, and pancreatic cancers. While HBOC patients often undergo regular surveillance including breast imaging, other cancers have no effective screening or biomarkers. One emerging technology is the analysis of circulating tumor DNA (ctDNA), fragments of DNA that are shed from the tumor into the bloodstream. In sporadic cancer, several studies have demonstrated the advantages and sensitivity of cell-free whole genome sequencing (cfWGS) compared to targeted panel sequencing. However, the use of cfWGS for cancer detection in HBOC has not been explored.

Methods: Matched tumor, germline, and plasma were collected from 5 HBOC patients (3 breast, 2 ovarian) as part of the Canada-wide CHARM consortium (https://charmconsortium.ca). Tumor (40x), germline (20x), and plasma (20x) underwent whole genome sequencing (WGS) and subsequent variant calling pipeline using an ensemble of 6 variant callers. Insertions, deletions, and structural variants were not included in downstream analyses. Plasma tumor fraction prediction and copy number alterations were performed using ichorCNA. Detection of tumor associated mutations in plasma was compared to MRDetect software.

Results: Variant calling identified an average of 11,170 tumor (7,649-16,706) and 1,215 (544-3,205) plasma SNVs per patient. Somatic BRCA1/2 mutations were detected in 0/5; whereas deletion of the intact BRCA1/2 allele was identified in 5/5 patients. An average of 24.6% (8.3%-75.9%) of plasma mutations where shared with SNVs identified in matched tumor. Targeted panel deep-sequencing (20,000X) was only able to detect mutations in TP53 in 3/5 cases (0.8% - 8.6%). Plasma derived copy number alterations correlated well with tumor derived copy number alterations in 3/5 cases and ichorCNA predicted tumor fractions ranged from 0.038 to 0.196.

Conclusions: Traditionally, targeted panel sequencing has been used to identify tumor associated mutations in plasma. While this technique is sensitive, major disadvantages include the narrow breadth of the captured regions and the inability to detect deletion events such as those that occur in BRCA1/2. Here we show that plasma WGS is effective for detecting tumor associated mutations in HBOC and is more sensitive than targeted panel sequencing. We are currently expanding our cohort to an additional 20 matched tumor pairs, including patients with pre-diagnosis plasma timepoints.

Citation Format: Derek Wong, Adriana Aguilar-Mahecha, Josiane Lafleur, Clarissa Chan, Kirsten Farncombe, Maia Norman, Leslie Oldfield, Prabhjit Basra, Stephanie Pederson, Johanna Wellum, Stephenie Prokopec, Mark Basik, Raymond H. Kim, Trevor Pugh. Cell-free whole genome sequencing for the detection of cancer in patients with germline BRCA1/2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 538.

Translational randomized phase II trial of cabozantinib in combination with nivolumab in advanced, recurrent, or metastatic endometrial cancer

BACKGROUND

Combining immunotherapy and antiangiogenic agents is a promising treatment strategy in endometrial cancer. To date, no biomarkers for response have been identified and data on post-immunotherapy progression are lacking. We explored the combination of a checkpoint inhibitor (nivolumab) and an antiangiogenic agent (cabozantinib) in immunotherapy-naïve endometrial cancer and in patients whose disease progressed on previous immunotherapy with baseline biopsy for immune profiling.

PATIENTS AND METHODS

In this phase II trial (ClinicalTrials.gov NCT03367741, registered December 11, 2017), women with recurrent endometrial cancer were randomized 2:1 to nivolumab with cabozantinib (Arm A) or nivolumab alone (Arm B). The primary endpoint was Response Evaluation Criteria in Solid Tumors-defined progression-free survival (PFS). Patients with carcinosarcoma or prior immune checkpoint inhibitor received combination treatment (Arm C). Baseline biopsy and serial peripheral blood mononuclear cell (PBMC) samples were analyzed and associations between patient outcome and immune data from cytometry by time of flight (CyTOF) and PBMCs were explored.

RESULTS

Median PFS was 5.3 (90% CI 3.5 to 9.2) months in Arm A (n=36) and 1.9 (90% CI 1.6 to 3.4) months in Arm B (n=18) (HR=0.59, 90% CI 0.35 to 0.98; log-rank p=0.09, meeting the prespecified statistical significance criteria). The most common treatment-related adverse events in Arm A were diarrhea (50%) and elevated liver enzymes (aspartate aminotransferase 47%, alanine aminotransferase 42%). In-depth baseline CyTOF analysis across treatment arms (n=40) identified 35 immune-cell subsets. Among immunotherapy-pretreated patients in Arm C, non-progressors had significantly higher proportions of activated tissue-resident (CD103+CD69+) ɣδ T cells than progressors (adjusted p=0.009).

CONCLUSIONS

Adding cabozantinib to nivolumab significantly improved outcomes in heavily pretreated endometrial cancer. A subgroup of immunotherapy-pretreated patients identified by baseline immune profile and potentially benefiting from combination with antiangiogenics requires further investigation.

DNA Methylation-Based Classification of Small B-Cell Lymphomas: A Proof-of-Principle Study

Although most small B-cell lymphomas (SBCLs) can be diagnosed using routine methods, challenges exist. For example, marginal zone lymphomas (MZLs) can be difficult to rule-in, in large part because no widely-used, sensitive, and specific biomarker is available for the marginal zone cell of origin. In this study, it was hypothesized that DNA methylation array profiling can assist with the classification of SBCLs, including MZLs. Extramedullary SBCLs, including challenging cases, were reviewed internally for pathology consensus and profiled. By combining the resulting array data set with data sets from other groups, a set of 26 informative probes was selected and used to train machine learning models to classify 4 common SBCLs: chronic lymphocytic leukemia/small lymphocytic lymphoma, follicular lymphoma, mantle cell lymphoma, and MZL. Prediction probability cutoff was used to separate classifiable from unclassifiable cases, and show that the trained model was able to classify 95% of independent test cases (n = 264/279). The concordance between model predictions and pathology diagnoses was 99.6% (n = 262/263) among classifiable test cases. One validation reference test case was reclassified based on model prediction. The model was also used to predict the diagnoses of two challenging SBCLs. Although the differential examined and data on difficult cases are limited, these results support accurate methylation-based classification of SBCLs. Furthermore, high specificities of predictions suggest that methylation signatures can be used to rule-in MZLs.

Abstract 563: cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab

Introduction: Durvalumab immunotherapy has rapidly emerged as standard treatment for stage 3 NSCLC patients following definitive chemoradiotherapy (CRT). Multiple novel immunotherapeutic strategies are in development to enhance the chance of cure in this setting as well. There exists a critical need to identify blood-based biomarkers capable of predicting clinical benefit from adjuvant immunotherapy as well selecting patients at high-risk of relapse for further drug development. Cell-free DNA (cfDNA)-based analysis of both minimal residual disease (MRD) and T-cell receptor (TCR) clonality have immense potential to predict and monitor response to adjuvant immunotherapy. In this study, we have combined innovative cfDNA measures of MRD (CAPPseq), TCR clonality (CapTCR-seq) and methylation (cfMeDIPseq) as potential predictive biomarkers of disease progression in stage 3 NSCLC patients treated with CRT and durvalumab.

Methods: Stage 3 NSCLC patients undergoing CRT and durvalumab were recruited prospectively to undergo serial blood collections at baseline, pre- and post- durvalumab. CAPPseq and cfMeDIPseq were performed as measures of MRD. TCR repertoire analysis (CapTCR-seq) was performed on cfDNA using hybrid-capture TCR sequencing and TCR diversity/clonality was estimated using the Shannon's index. Correlations between MRD, TCR clonality, response and progression-free survival (PFS) were examined using logistic/cox regression.

Results: 79 stage 3 NSCLC patients have been prospectively recruited and undergone serial blood collection. CAPPseq, cfMeDIPseq and capTCR-seq have been completed in 22 patients (5 primary progression on CRT, 17 received durvalumab). Tumor cfDNA was detectable by CAPPseq at baseline in 14 patients. High correlation between tumor cfDNA detected by CAPPseq and cfMeDIPseq was found (R=0.68, p<0.0001). Failure to clear MRD with CRT plus durvalumab was associated with significantly increased risk of recurrence with a median PFS of 5.0 vs 15.0 months (p<0.0001). Lower TCR clonality measured pre-durvalumab trended with lower likelihood of response (OR 0.82, p=0.09) and worse PFS (HR 1.16 P=0.10). Importantly, a decrease in TCR clonality compared to baseline, signaling the lack of clonal expansion on treatment, was significantly associated with a worse PFS (p=0.05). A decrease in TCR clonality of 50% after CRT was associated with a worse PFS (HR 3.5, p=0.14). CAPPseq, cfMeDIPseq and capTCR-seq analyses are ongoing in the full cohort.

Conclusions: Failure to clear MRD and decreasing TCR clonality as assessed by cfDNA was highly correlated with increased risk of recurrence and reduced PFS with consolidation durvalumab. This innovative approach has significant potential to define a new biomarker for the use and development of adjuvant immunotherapy.

Citation Format: Sally CM Lau, Shirin Soleimani, Jinfeng Zou, Justin Burgener, Shelley Kuang, Stephanie WY Wong, Malcolm Ryan, Ben X. Wang, Stephanie Pedersen, Devalben Patel, Penelope A. Bradbury, Geoffrey Liu, Natasha Leighl, Ming S. Tsao, Pamela S. Ohashi, Scott V. Bratman, Trevor Pugh, Frances A. Shepherd, Adrian G. Sacher. cfDNA-based analysis of minimal residual disease and T-cell receptor clonality as predictors of relapse in stage 3 NSCLC treated with chemoradiotherapy and durvalumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 563.

Genomic Landscape of Malignant Peripheral Nerve Sheath Tumor‒Like Melanoma

Malignant peripheral nerve sheath tumor (MPNST)-like melanoma is a rare malignancy with overlapping characteristics of both neural sarcoma and melanoma. Although the genomics of cutaneous melanoma has been extensively studied, those of MPNST-like melanoma have not. To characterize the genomic landscape of MPNST-like melanoma, we performed a single-center, retrospective cohort study at a tertiary academic cancer center. Consecutive patients with a confirmed histologic diagnosis of MPNST-like melanoma were screened, and those whose tissues were locally available were included in this analysis. Archival tissue from six patients (eight samples) was submitted for whole-exome and transcriptome sequencing analysis. We compared these data with available genomic studies of cutaneous melanoma and MPNST. NF1 was altered (mutated, deleted, or amplified) in 67% of patients. Genes related to cell cycle regulation were frequently altered, with frequent deletion of ZNF331, which, to the best of our knowledge, has not been previously described in cutaneous melanoma. The serine protease inhibitor SERPINB4 was deleted in 100% of the patients. We show that MPNST-like melanoma presents overlapping genomic features with cutaneous melanoma and MPNST, but it is unique by the frequency of loss of function of ZNF331 and SERPINB4.

IMMU-18. FAVORABLE OUTCOME IN REPLICATION REPAIR DEFICIENT HYPERMUTANT BRAIN TUMORS TO IMMUNE CHECKPOINT INHIBITION: AN INTERNATIONAL RRD CONSORTIUM REGISTRY STUDY

Pediatric brain tumors with replication repair deficiency (RRD) are hypermutant and may respond to immune checkpoint inhibition (ICI). We performed a consortium registry study of ICI in recurrent RRD cancers. Clinical and companion biomarkers were collected longitudinally on all patients. Biomarkers included tumor mutational burden (TMB), neoantigens and genetic signatures obtained from whole genome and exome sequencing. Immune inference was obtained by RNAseq and T cell rearrangement was collected in the tumor and in blood throughout treatment. Of the 46 tumors on the study, 32 were brain tumors with glioblastoma in 96%. Rapid, objective responses (>50%) were observed in 50% of glioblastomas. Three year overall survival for the whole cohort was 48+/-8% which compares favorably with historical controls. Brain tumors fared worse with OS of 39+/-10% and late recurrences observed even after 2 years of therapy (p=0.02). Tumor size and acute “flare” constitute poor outcome throughout all cancers. While all tumors are hypermutant, TMB and predicted neoantigens correlated with response to ICI (p=0.02). Specific signatures extracted from SNVs and total mutations predicted response to ICI and favorable outcome (p=0.005). RNA inference and TCR reveal that the FLARE phenotype is mostly acute nonspecific immune response and not true progression. Finally, glioblastomas (n=8) which failed single agent ICI had favorable responses to combinational immunotherapies with prolonged survival of 65%+/-8% at one year after failure vs 0 for other patients (p=0.01). RRD glioblastomas exhibit favorable outcome and responses to ICI. Combinational therapies based on tumor and immune signatures of these cancers are necessary.

EPCO-04. GENOMIC AND EPIGENOMIC HALLMARKS OF SCHWANNOMATOSIS SCHWANNOMAS

Schwannomatosis (SWNTS) is a genetic cancer predisposition syndrome that manifests as multiple and often, painful neuronal tumors called schwannomas (SWNs). Very little is known about the epigenomic and genomic alterations in SWNTS related SWNs (SWNTS-SWNs) other than germline mutations in SMARCB1 and LZTR1 plus somatic mutations in NF2 and loss of heterozygosity in chromosome 22q. Herein, we have comprehensively established the specific molecular signatures of SWNTS-SWNs. We found that tumor anatomic location was associated with pain and distinct DNA methylation and transcriptional signatures. DNA sequencing revealed several novel non-22q deletions, specifically in LZTR1-mutant cases. Whole-genome sequencing identified novel recurrent structural rearrangements. Further, chromosomal aberrations in SWNTS-SWNs were accompanied by increased transcription of mismatch repair genes. Our transcriptome analysis detected the SH3PXD2A-HTRA1 gene fusion in SWNTS-SWNs, more commonly in LZTR1-mutant tumors. In addition, we identified the specific genetic, epigenetic, and transcriptional hallmarks of painful SWNs that may be harnessed to develop new treatments for this debilitating syndrome.

Abstract 5724: Revelation of shared transcriptional gradients in glioblastoma tumors and cultured glioma stem cells

The brain tumor Glioblastoma (GBM) is a virtual death sentence for anyone who is diagnosed, with a median survival time of 12-15 months with standard treatments1 and a 5 year survival rate of under 10% 2. There is a strong body of evidence supporting the existence of stem like cells, termed glioma stem cells (GSCs), that can repopulate the tumor after removal and therapy application3-6. Thus, GSCs present a tantalizing target for potential therapies against GBM. However, studies of GSCs have shown heterogeneity at the level of the transcriptome and drug response5,7, suggesting that there is significant biological variation that translates into differential sensitivity to various drugs. A full characterization of biological heterogeneity may aid in the search for targeted therapies.

Here, we profile the transcriptomes of 72 patient derived GSC cultures, and obtain scRNA-seq on 29 cultures from 26 patients (> 69,000 cells) plus 5 GBM tumors (> 14,000 cells). With this data, we find two anticorrelated transcriptional programs in the GSC cultures, one associated with immune or injury response related pathways and the other with neural developmental pathways. We then compare the GSC cultures to patient tumors in the scRNA-seq data, and find that a portion of GBM tumor cells are similar to GSC cultures. We find that a gradient between GSC and astrocyte programs separates cells with stemness properties from those that are not stem-like, and that within stem-like tumor cells and non stem-like tumor cells a gradient between the neural developmental and immune related programs exists as was seen for the cultured GSCs. In GSCs, we also find epigenetic variation in DNA methylation associated with the developmental and immune related programs. Overall these data suggest variation between two biological programs manifests at the level of gene expression and epigenetic regulation in GSCs in tumors.

1. Stupp, R. et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N. Engl. J. Med. 352, 987-996 (2005).

2. Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462-477 (2013).

3. Singh, S. K. et al. Identification of human brain tumour initiating cells. Nature 432, 396-401 (2004).

4. Chen, J. et al. A restricted cell population propagates glioblastoma growth after chemotherapy. Nature 488, 522-526 (2012).

5. Lan, X. et al. Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy. Nature 549, 227-232 (2017).

6. Patel, A. P. et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396-1401 (2014).

7. Meyer, M. et al. Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc. Natl. Acad. Sci. U. S. A. 112, 851-856 (2015).

Citation Format: Owen K. Whitley, Laura M. Richards, Florence Cavalli, Paul Guilhamon, Fiona Coutinho, Michelle Kushida, H. Artee Luchman, Samuel Weiss, Mathieu Lupien, Peter Dirks, Trevor Pugh, Gary Bader. Revelation of shared transcriptional gradients in glioblastoma tumors and cultured glioma stem cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5724.

Abstract IA02: Novel strategies for early cancer detection and prevention: The Li-Fraumeni syndrome story

More than 85% of patients with Li-Fraumeni syndrome harbor germline TP53 mutations. The spectrum of mutations and the heterogeneity of tumor presentation (age of onset and type) within and between families is remarkable and indicates that modifiers must play an important role in defining the phenotype of each patient and each family. We recently reported the feasibility and utility of a clinical surveillance protocol for early detection of tumors in TP53 mutation carriers (Villani et al., Lancet Oncol 2016). Results from deep sequencing of the genome and epigenome of germline and tumor tissues of TP53 mutation carriers provide exciting new insight into the role of modifiers on both the functional activity of p53 in the germline as well as their influence on tumor onset, tumor spectrum, and clinical outcome/response to therapy. Data will be presented to support the creation of molecular algorithms that may be used in a precise manner to predict cancer onset, as well as to better define the molecular landscape of cancers that arise in TP53 mutation carriers. It is anticipated that the combined use of this germline and somatic landscape data can more effectively refine and guide the creation of personalized surveillance and chemoprevention strategies for these patients.

Citation Format: David Malkin, Nicholas Light, Valli Subrasi, Benjamin Brew, Sangeetha Paramathas, Arash Nabbi, Sergei Prykhozhij, Trevor Pugh, Jason Berman, Anna Goldenberg, Adam Shlien. Novel strategies for early cancer detection and prevention: The Li-Fraumeni syndrome story [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA02.

Abstract IA11: Clinical applications of liquid biopsy in multiple myeloma

Multiple myeloma (MM) is characterized by recurrent cytogenetic and molecular abnormalities that have the potential to profoundly impact therapeutic decisions. Conventional karyotyping and/or FISH cytogenetics studies have identified translocations and copy number abnormalities (CNAs) that predict clinical outcomes. More recently, MM whole-exome sequencing studies have uncovered recurrent mutations in genes associated with prognosis and others that are potentially actionable and/or implicated in drug resistance. These observations highlight the need for advanced genomic platforms to inform prognosis and therapeutic decisions.

Currently, molecular profiling of MM is performed on bone marrow (BM) aspirates; however, the genetic information obtained from aspirates is confounded by spatial and temporal intratumor genetic heterogeneity. Genomic studies of MM have confirmed the bias introduced by single-site biopsies, demonstrating that not all mutations are shared between targeted biopsies of extramedullary sites and BM. Further, longitudinal whole-genome sequencing studies have not only uncovered tumor heterogeneity at diagnosis but also subclonal competition with a shifting dominance of tumor clones and accumulation of genetic events during progression that are particularly affected by therapeutic pressures. Thus, information acquired from a single biopsy provides a spatially and temporally limited snapshot of a tumor that likely underestimates the complexity of the tumor genomic landscape.

Analysis of circulating tumor DNA (ctDNA) and in blood plasma has the potential to overcome these barriers, providing access to the genetic landscape of all cancerous lesions and allowing for noninvasive tracking of genomic evolution over time. Circulating biomarkers can provide a “liquid biopsy” alternative to tissue biopsy, providing new opportunities for treatment tailoring based on real-time monitoring from a simple blood test. Here I will discuss the current liquid biopsy technologies under evaluation for genomic characterization of multiple myeloma. I will also describe the potential clinical applications for liquid biopsies to identify patients for targeted therapies, to track genomic changes, and to follow disease burden in patients with multiple myeloma.

Citation Format: Suzanne Trudel, Trevor Pugh. Clinical applications of liquid biopsy in multiple myeloma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA11.

Heterogeneous alteration of the ERBB3-MYC axis associated with MEK inhibitor resistance in a KRAS-mutated low-grade serous ovarian cancer patient

Low-grade serous ovarian cancer (LGSOC) is relatively chemoresistant, and no precision therapy is approved for this indication. Despite promising results in phase II trials, MEK inhibitors have failed to show improved progression-free survival in a phase III trial when compared to physician's choice chemotherapy. We report for the first time temporal changes in the tumor genome assessed in sequential tumor samples of a 48-yr-old patient with a KRAS-mutated LGSOC treated with the MEK inhibitor binimetinib. After an initial long-lasting partial response, rapidly progressive brain metastasis occurred, ultimately leading to patient death. Our study demonstrates that novel genomic alterations accumulated during the course of treatment as a result of therapeutic pressures led to MEK inhibitor resistance and, ultimately, disease evolution with an aggressive behavior observed in this patient. In particular, we describe the presence of ERBB3 amplification and aberrant ERBB3–MYC signaling as a potential mechanism of acquired MEK inhibitor resistance in a patient with LGSOC, which is similar to previous observations in KRAS-mutated colon and lung cancers. Our study highlights the need for an individualized approach to better understand tumor genome evolution and suggests that LGSOC patients may derive improved therapeutic benefit by using a combinatorial strategy used in other cancers in order to overcome emergent resistance to targeted therapies.

OCTANE (Ontario-wide Cancer Targeted Nucleic Acid Evaluation): a platform for intraprovincial, national, and international clinical data-sharing

Cancer is a genetic disease resulting from germline or somatic genetic aberrations. Rapid progress in the field of genomics in recent years is allowing for increased characterization and understanding of the various forms of the disease. The Ontario-wide Cancer Targeted Nucleic Acid Evaluation (octane) clinical trial, open at cancer centres across Ontario, aims to increase access to genomic sequencing of tumours and to facilitate the collection of clinical data related to enrolled patients and their clinical outcomes. The study is designed to assess the clinical utility of next-generation sequencing (ngs) in cancer patient care, including enhancement of treatment options available to patients. A core aim of the study is to encourage collaboration between cancer hospitals within Ontario while also increasing international collaboration in terms of sharing the newly generated data. The single-payer provincial health care system in Ontario provides a unique opportunity to develop a province-wide registry of ngs testing and a repository of genomically characterized, clinically annotated samples. It also provides an important opportunity to use province-wide real-world data to evaluate outcomes and the cost of ngs for patients with advanced cancer. The octane study is attempting to translate knowledge to help deliver precision oncology in a Canadian environment. In this article, we discuss the background to the study and its implementation, current status, and future directions.

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

Study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. Here we use single-cell transcriptomics to study more than 60,000 cells from the developing mouse cerebellum and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. The Sonic Hedgehog medulloblastoma subgroup transcriptionally mirrors the granule cell hierarchy as expected, while group 3 medulloblastoma resembles Nestin+ stem cells, group 4 medulloblastoma resembles unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumours as a disorder of early brain development and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood.

Abstract CT190: A Phase II basket study of hypomethylating agent oral cc-486 and durvalumab in advanced solid tumors (METADUR)

Background

Aberrant DNA methylation contributes to cancer initiation and progression. In preclinical models of solid tumors, chronic low dose administration of DNA hypomethylating agents can induce T-cell mediated immune activation responses by stimulating expression of endogenous retroviral elements, culminating in an IFN-mediated response. The addition of physiological levels of vitamin C may potentiate viral mimicry and increase anti-tumor immune priming. Immunologically ‘cold’ tumors were selected to evaluate whether these strategies can enhance their otherwise poor responses to immune checkpoint blockade.

Methods

PD-L1/PD-1 inhibitor naïve patients (pts) with advanced microsatellite stable colorectal cancer (MSS CRC); platinum resistant ovarian cancer (OC); estrogen receptor positive, HER2 negative breast cancer (ER+HER2- BC) were enrolled in this single institution, multi-cohort, investigator-initiated trial. The initial regimen (regimen A) consisted of oral CC-486 300mg QD Days 1-14 (cycles 1-3 only) in combination with durvalumab 1500mg IV Day 15, in 28 day-cycles. A protocol amendment (regimen B) after 19 patients changed CC-486 to 100 mg QD Days 1-21 (cycles 1-3), added oral vitamin C 500mg QD continuously and kept durvalumab 1500mg IV Day 15, in 28-day cycles. Adverse events (AEs) assessed by CTCAEv4.03 grade (G); tumor response by RECIST 1.1 every 2 cycles; paired tumor biopsies at baseline and cycle 2 days 10-14; and serial peripheral blood mononuclear cells (PBMCs) for immune-profiling (IP) and epigenetic analysis. PD-L1 by IHC was assessed using SP263 assay, positivity defined by TC>25%.

Results

A total of 28 pts with MSS CRC (n=15), OC (n=4), ER+HER2- BC (n=9) were enrolled, 19 pts treated on regimen A, 9 on regimen B. Median age was 56 (range 36-78), ECOG 0:1=7:21, 100% had ≥3 prior lines of therapy, all tumors were PD-L1 negative. Best response was SD (3/28 pts received 3, 3 and 4 cycles respectively) with DCR 7.1%. Median follow-up of 4.7 months, mPFS was 1.9 months (95% CI 1.5-2.3) and mOS was 5 months (95% CI 4.5-10). Three patients (all regimen A) experienced DLTs (2 G4 neutropenia and 1 G3 anemia). Fifteen patients (54%) experienced G1/2 fatigue, 46% experienced G1/2 nausea, vomiting or diarrhea. Toxicity was comparable with addition of vitamin C. Initial analysis of PBMCs by flow cytometry in 3 of 4 OC pts demonstrated an increase in PD-1 and Ki67 expression in CD8 T cells only following administration of durvalumab. EPIC methylation array on 4 pts’ paired tumors and LINE 1 assay on 19 pts’ serial PBMCs (regimen A) demonstrated minimal change in global methylation.

Conclusion

No meaningful clinical responses to CC-486 plus durvalumab were observed. Tumor tissue and PBMCs both demonstrate minimal global DNA demethylation, with or without physiological dose vitamin C. Incremental immune activation beyond PD-L1 blockade was not demonstrated. Clinical trial information: NCT02811497

Citation Format: Kirsty Taylor, Helen Loo Yau, Ben X. Wang, Philippe L. Bedard, Albiruni R. Razak, Aaron R. Hansen, Anna Spreafico, Dave Cescon, Marcus O. Butler, Amit M. Oza, Stephanie Lheureux, Neda Stjepanovic, Lisa Wang, Brendan Van As, Sarah Boross-Harmer, Trevor Pugh, Lillian L. Siu, Daniel D. De Carvalho. A Phase II basket study of hypomethylating agent oral cc-486 and durvalumab in advanced solid tumors (METADUR) [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 CT190.

Early Initiation of Tocilizumab in Clinically Isolated Aortitis

Clinically isolated aortitis can arise from infectious or inflammatory etiologies. Glucocorticoids are the first-line therapy for inflammatory causes of aortitis such as large-vessel vasculitis. However, prolonged steroids use is associated with numerous side effects. We present a case of a 60-year-old woman with clinically isolated aortitis who received early treatment with tocilizumab to avoid prolonged steroid use.

Abstract 2607: The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine

The cBioPortal for Cancer Genomics is an open-access portal (http://cbioportal.org) that enables interactive, exploratory analysis of large-scale cancer genomics data. It integrates genomic and clinical data, and provides a suite of visualization and analysis options, including cohort and patient-level visualization, mutation visualization, survival analysis, enrichment analysis, and network analysis. The user interface is user-friendly, responsive, and makes genomic data easily accessible to translational scientists, biologists, and clinicians.

The cBioPortal is a fully open source platform. All code is available on GitHub (https://github.com/cBioPortal/) under GNU Affero GPL license. The code base is maintained by multiple groups, including Memorial Sloan Kettering Cancer Center, Dana-Farber Cancer Institute, Children’s Hospital of Philadelphia, Princess Margaret Cancer Centre, and The Hyve, an open source bioinformatics company based in the Netherlands. More than 30 academic centers as well as multiple pharmaceutical and biotech companies maintain private instances of the cBioPortal. This includes the recently launched cBioPortal instance at the NCI Genomic Data Commons (https://cbioportal.gdc.nci.nih.gov/), and two large cBioPortal instances hosting genomic and clinical data at MSK and DFCI, supporting the MSK-IMPACT and DFCI Profile projects, two of the largest clinical sequencing efforts in the world.

Our multi-institutional software team has accelerated the progress of evolving the core architectural technologies and developing new features to keep pace with the rapidly advancing fields of cancer genomics and precision cancer medicine. For example, we have integrated multi-platform genomics data with extensive clinical data including patient demographics, treatment history, and survival data. We have also developed a patient-centric view that visualizes both clinical and genomic data with annotation from OncoKB knowledge base. In the next few years, the development team will focus on the following areas:

(1) Implementing major architectural changes to ensure future scalability and performance.

(2) New features to support precision medicine, including (i) improved integration of knowledge base annotation, (ii) enhanced visualization of patient timeline, drug response, and tumor evolution, (iii) new patient similarity metrics, (iv) improved support for immunogenomics and immunotherapy, and (v) new visualization and analysis features for understanding response to therapy.

(3) New analysis and target discovery features for large cohorts, including (i) supporting user-defined virtual cohort by selecting samples from multiple studies, and (ii) comparison of genomic or clinical characteristics of two or more selected cohorts.

(4) Expanding community outreach, user support and training, and documentation.

Citation Format: Jianjiong Gao, Ersin Ciftci, Pichai Raman, Pieter Lukasse, Istemi Bahceci, Adam Abeshouse, Hsiao-Wei Chen, Ino de Bruijn, Benjamin Gross, Zachary Heins, Ritika Kundra, Aaron Lisman, Angelica Ochoa, Robert Sheridan, Onur Sumer, Yichao Sun, Jiaojiao Wang, Manda Wilson, Hongxin Zhang, James Xu, Andy Dufilie, Priti Kumari, James Lindsay, Anthony Cros, Karthik Kalletla, Fedde Schaeffer, Sander Tan, Sjoerd van Hagen, Jorge Reis-Filho, Kees van Bochove, Ugur Dogrusoz, Trevor Pugh, Adam Resnick, Chris Sander, Ethan Cerami, Nikolaus Schultz. The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine [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 2607. doi:10.1158/1538-7445.AM2017-2607

Abstract 2410: Toward mutation analysis of regulatory elements: Epigenetic profiling of primary breast tumors

Non-coding mutations found in regulatory elements can function as driver mutations in breast cancer by changing the binding affinity of transcription factors for DNA, thereby resulting in direct change of expression of genes that promote cancer development. Identifying such additional driver mutations can reveal the molecular mechanisms favorable to breast cancer development and progression, as well as reveal new biomarkers to better tailor personalized/precision cancer medicine. In this study we have collected 20 primary luminal breast tumors and optimized experimental workflow to dissociate solid tumors and map open chromatin using ATAC-seq. In our initial experiments using ATAC-seq profiling of bulk tumor tissues, we were able to call an average of 15x103 peaks. Subsequently, flow cytometry analysis showed the presence of 15-25% of immune cells in our primary tumors. Therefore, we have optimized a workflow to eliminate immune cells and focus mainly on epithelial tumor cells. Primary breast tumors were digested using collagenase and further dissociated with dispase. Cells were sorted into two populations (mammary epithelial and immune cells) using anti-CD45, anti-CD49f and anti-EpCAM antibodies. Sorted mammary epithelial cells were then used for ATAC- and RNA-seq library preparation as well as for generation of patient derived organoids. Our new workflow resulted in an increased number of called peaks (40x103 vs 15x103), as well as a significant increase in the percentage of unique peaks compared to bulk sequencing (45% vs 15%). By refining our workflow to enrich for tumour content, we will continue our ongoing effort to profile these open chromatin regions and contextualize the mutations within in a large cohort of luminal breast cancers using targeted sequencing. These data will be compared with large-scale whole genome data generated by our group and made publicly available by others.

Citation Format: Samah El Ghamrasni, Paul Guilhamon, Rene Quevedo, Cindy Yang, Mathieu Lupien, Trevor Pugh. Toward mutation analysis of regulatory elements: Epigenetic profiling of primary breast tumors [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 2410. doi:10.1158/1538-7445.AM2017-2410

Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies

CONTEXT

- Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes.

OBJECTIVE

- To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics.

DATA SOURCES

- Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified.

CONCLUSIONS

- We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 500×. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non-next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone.