Clinico-Genomic Profiling of Conventional and Dedifferentiated Chondrosarcomas Reveals TP53 Mutation to Be Associated with Worse Outcomes

PURPOSE

Chondrosarcomas are the most common primary bone tumor in adults. Isocitrate dehydrogenase 1 (IDH1) and IDH2 mutations are prevalent. We aimed to assess the clinico-genomic properties of IDH mutant versus IDH wild-type (WT) chondrosarcomas as well as alterations in other genes.

EXPERIMENTAL DESIGN

We included 93 patients with conventional and dedifferentiated chondrosarcoma for which there were available clinical next-generation sequencing data. Clinical and genomic data were extracted and compared between IDH mutant and IDH WT chondrosarcomas and between TP53 mutant and TP53 WT chondrosarcomas.

RESULTS

IDH1 and IDH2 mutations are prevalent in chondrosarcoma (50.5%), more common in chondrosarcomas arising in the extremities, associated with higher age at diagnosis, and more common in dedifferentiated chondrosarcomas compared with grades 1-3 conventional chondrosarcoma. There was no difference in survival based on IDH mutation in univariate and multivariate analyses. TP53 mutation was the next most prevalent (41.9%) and is associated with worse overall survival and metastasis-free survival in both univariate and multivariate analyses. TP53 mutation was also associated with higher risk of recurrence following curative-intent surgery and worse survival among patients that presented with de novo metastatic disease.

CONCLUSIONS

IDH mutations are prevalent in chondrosarcoma though were not associated with survival outcomes in this cohort. TP53 mutations were the next most common alteration and were associated with worse outcomes.

Abstract 3432: Ataxia-telangiectasia mutated loss of function displays variant and tissue specific differences across tumor types

Introduction: ATM loss of function (LOF) in cancer may serve as a predictive biomarker of response for antitumor therapies. However, clinical studies of targeted treatments in ATM-aberrant patients have yielded mixed results; thus, identifying the optimal strategy for selecting patients with ATM LOF tumors remains a critical area of unmet need.

Methods: In order to investigate the heterogeneity observed in ATM aberrant tumors, we conducted a pan-cancer genomic and proteomic profiling of ATM LOF, and also performed retrospective review of clinical outcomes for a subset of patients with ATM LOF treated with platinum or ATR inhibition.

Results: We identified 10,609 ATM variants in 8,587 patients with cancer. The prevalence of deleterious (Tier 1) versus variants of unknown significance (VUS)/benign (Tier 2) variants differed by cancer tissue type, as did selective pressure for loss of heterozygosity (LOH). Analysis of ATM protein staining in 471 patient tumors showed tumors with null, inactivating variants were significantly (p<0.005) more likely to display ATM loss of protein (LOP) than tumors with missense or wildtype, but 19% (N=27/140) and 9% (N=13/149) of tumors with ATM-VUS and wildtype showed loss of protein. In addition, concordance between inactivating mutations and loss of protein also differed based on tumor tissue context, with ovarian and breast cancer showing stronger concordance (greater than 80%) than melanoma and lung cancer ( less than 20%). Patients treated with platinum chemotherapy with select tumor types with deleterious variants in ATM and ATM LOP display improved progression free survival (PFS) (HR 0.50, P=0.03). Lastly, patients with tumor types that have stronger ATM variant-to-protein loss concordance display increased benefit from ATR inhibition (HR 0.40, P=0.04).

Conclusions: Our data highlight that there is heterogeneity in ATM LOF in patients due to multiple variables, including notable tissue-specific differences in the type of variants seen and the relationship between ATM variant status and ATM protein. This genomic heterogeneity and tissue-specificity has implications for predictive biomarker development and clinical trial designs.

Citation Format: Patrick G. Pilie, Daniel Mcgrail, Wei-Lien Wang, Natalie Ngoi, Keith Kyewalabye, Khalida Wani, Hung Le, Erick Campbell, Vijaykumar Holla, Kenna R. Shaw, Funda Meric-Bernstam, Alexander J. Lazar, Virginia Giuliani, Timothy Heffernan, Timothy A. Yap. Ataxia-telangiectasia mutated loss of function displays variant and tissue specific differences across tumor types [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 3432.

Integrative Clinical and Genomic Characterization of MTAP-deficient Metastatic Urothelial Cancer

Deficiency of MTAP (MTAPdef) mainly occurs because of homozygous loss of chromosome 9p21, which is the most common copy-number loss in metastatic urothelial cancer (mUC). We characterized the clinical and genomic features of MTAPdef mUC in 193 patients treated at MD Anderson Cancer Center (MDACC) and 298 patients from the phase 2 IMvigor210 trial, which investigated atezolizumab in cisplatin-ineligible and platinum-refractory disease. In the MDACC cohort, visceral metastases were significantly more common for MTAPdef (n = 48) than for MTAP-proficient (MTAPprof; n = 145) patients (75% vs 55.2%; p = 0.02). MTAPdef was associated with poor prognosis (median overall survival [mOS] 12.3 vs 20.2 mo; p = 0.007) with an adjusted hazard ratio of 1.93 (95% confidence interval 1.35-2.98). Similarly, IMvigor210 patients with MTAPlo (n = 29) had a higher incidence of visceral metastases than those with MTAPhi tumors (n = 269; 86.2% vs 72.5%; p = 0.021) and worse prognosis (mOS 8.0 vs 11.3 mo; p = 0.042). Hyperplasia-associated genes were more frequently mutated in MTAPdef tumors (FGFR3: 31% vs 8%; PI3KCA: 31% vs 19%), while alterations in dysplasia-associated genes were less common in MTAPdef tumors (TP53: 41% vs 67%; RB1: 0% vs 16%). Our findings support a distinct biology in MTAPdef mUC that is associated with early visceral disease and worse prognosis. PATIENT SUMMARY: We investigated the outcomes for patients with the most common gene loss (MTAP gene) in metastatic cancer of the urinary tract. We found that this loss correlates with worse prognosis and a higher risk of metastasis in internal organs. There seems to be distinct tumor biology for urinary tract cancer with MTAP gene loss and this could be a potential target for treatment.

Abstract A023: Influence of pre-diagnosis obesity and post-diagnosis aspirin use on survival from stage IV colorectal cancer

Background: The relationship between obesity and colorectal cancer (CRC) outcome is poorly understood in late-stage patients. Increased body mass may negate aspirin use for cancer prevention, but the influence of body mass index (BMI) on post-diagnosis aspirin use is unclear. This study aims to evaluate impacts of pre-diagnosis BMI and post-diagnosis aspirin use on overall survival in late-stage CRC patients on the Assessment of Targeted Therapies Against Colorectal Cancer (ATTACC) clinical protocol. Methods: Patients with metastatic or treatment refractory disease were consented on the ATTACC protocol at MD Anderson Cancer Center and invited to complete a survey on risk factors relevant to CRC etiology. Using survey data, BMI was calculated from the decade prior to initial CRC diagnosis for 656 patients. Survival was measured from stage IV diagnosis until death or last follow-up. Cox Proportional Hazards models were constructed to estimate associations of pre-diagnosis obesity and post-diagnosis aspirin use with overall survival. Results: Controlling for age, sex, race, stage at initial diagnosis, and weight change between pre-diagnosis and survey date, patients with pre-diagnosis obesity had significantly higher likelihood of death (HR 1.45, 95% CI: 1.11, 1.91) compared to those with normal pre-diagnosis BMI. Further, only patients with normal weight pre-diagnosis experienced a survival benefit with post-diagnosis aspirin use (HR 0.59, 95% CI: 0.39, 0.90). Conclusions: Our findings suggest potentially differential tumor development resulting from the long-term physiologic host environment, here obesity. Confirmation and further evaluation are needed to determine whether pre-diagnosis BMI may predict benefit from post-diagnosis aspirin use.

Citation Format: Jennifer S. Davis, Janelle C. Chavez, Melissa Kok, Yazmin San Miguel, Hwa Young Lee, Henry Henderson, Michael J. Overman, Van Karlyle Morris, Bryan Kee, David Fogelman, Shailesh M. Advani, Benny Johnson, Christine Parseghian, John Paul Shen, Arvind Dasari, Kenna R. Shaw, Eduardo Vilar, Kanwal P. Raghav, Imad Shureiqi, Robert A. Wolff, Funda Meric-Bernstam, Dipen Maru, David G. Menter, Scott Kopetz, Shine Chang. Influence of pre-diagnosis obesity and post-diagnosis aspirin use on survival from stage IV colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A023.

Association of Prediagnosis Obesity and Postdiagnosis Aspirin With Survival From Stage IV Colorectal Cancer

IMPORTANCE

The potential relationship between obesity and colorectal cancer (CRC) outcome is poorly understood in patients with late-stage disease. Increased body mass index may negate aspirin use for cancer prevention, but its role as a factor on the effectiveness of postdiagnosis aspirin use is unclear.

OBJECTIVE

To evaluate how prediagnosis obesity and postdiagnosis aspirin use may be associated with overall survival in patients with late-stage colorectal cancer.

DESIGN, SETTING, AND PARTICIPANTS

This cross-sectional study used self-reported data from patients with metastatic or treatment-refractory disease who consented to a clinical protocol at MD Anderson Cancer Center, a large US cancer treatment center. Patients were enrolled between 2010 and 2018 and followed up for mortality through July 2020. Analyses were conducted through March 2022.

EXPOSURES

Body mass index in the decade prior to initial diagnosis and regular aspirin use at survey completion.

MAIN OUTCOMES AND MEASURES

Overall survival was measured from stage IV diagnosis until death or last follow-up. Cox proportional hazards models were constructed to estimate associations of prediagnosis obesity and postdiagnosis aspirin use with overall survival.

RESULTS

Of 656 patients included in this analysis, 280 (42.7%) were women, 135 (20.6%) were diagnosed with CRC before age 45 years, 414 (63.1%) were diagnosed between ages 45 and 65 years, and 107 (16.3%) were diagnosed at 65 years or older; 105 patients (16.0%) were Black or Hispanic, and 501 (76.4%) were non-Hispanic White. Controlling for age, sex, race, stage at initial diagnosis, and weight change between prediagnosis and survey date, patients with obesity in the decade prior to CRC diagnosis had significantly higher likelihood of death (hazard ratio, 1.45; 95% CI, 1.11-1.91) compared with those with normal prediagnosis body mass index. Furthermore, only patients with normal prediagnosis body mass index experienced significant survival benefit with postdiagnosis aspirin use (hazard ratio, 0.59; 95% CI, 0.39-0.90).

CONCLUSIONS AND RELEVANCE

In this cross-sectional study, our findings suggest potentially differential tumor development in the long-term physiologic host environment of obesity. Confirmation and further evaluation are needed to determine whether prediagnosis body mass index may be used to estimate the benefit from postdiagnosis aspirin use.

Repeat large panel genomic sequencing identifies actionable alterations and characterizes the genomic landscape in patients with metastatic solid tumors

3076

Background: The implementation of genomic profiling with next generation sequencing has revolutionized the field of precision oncology. Comprehensive genomic testing of tumors to identify actionable genomic alterations is now commonly performed in the care of patients with advanced/metastatic disease. Although the genomic profile of tumors has been shown to evolve with progression and intervening treatments, the role of repeat genomic testing is not well established. We sought to determine the evolution of actionable genomic alterations in patients undergoing repeat genomic testing on the same comprehensive genomic panel. Methods: We retrospectively examined the molecular profiles and medical records of 262 patients with metastatic solid tumors treated in MD Anderson who underwent genomic testing on the same panel (Oncomine, Thermo Fisher) for the detection of somatic mutations in the coding sequence of 143 cancer-related genes, on at least 2 separate occasions. Genomic alterations were reviewed by a central Precision Oncology Decision Support (PODS) team in order to provide annotations at the alteration level on the functional significance. Results: 262 patients underwent repeat genomic testing using the same genomic panel on samples collected at different time points from July 2010 to Dec 2021 across tumor types. Changes in alterations (gain or loss) were identified on repeat testing in most patients (66%) We then specifically assessed changes in alterations that were categorized as actionable if annotated by the PODS team at the time of reporting. A gain or loss of an actionable alteration was detected in 38% (100/262) patients. New actionable alterations were frequently identified (73%; 73/100), while 41% had loss of an actionable alteration (41/100). 14% had both loss and gain of actionable alteration on repeat testing; 58% had new actionable alteration identified alone; 27% had loss of actionable alteration only. Actionable alterations identified on repeat testing included alterations in PI3K/AKT (27%), EGFR (15%), and MAPK (16%). On repeat testing, changes in ³2 actionable alterations were frequently identified in the same test (43%). Conclusions: Repeat large panel genomic testing identifies both gain and loss of actionable alterations in patients with advanced metastatic cancers. Actionable aberrations frequently co-exist with alterations in a variety of other genes, which highlights the complexities of treating patients with metastatic cancer on progression of disease and suggests that tailored combination strategies may be necessary in these patients.

Clinical implications of tumor-based next-generation sequencing in ovarian cancer

5545

Background: Epithelial ovarian cancer is genetically heterogeneous, both among and within histologic subtypes. Advances in next-generation sequencing have made it feasible to ascertain the somatic genetic signature of each patient, however, critical analysis of population-level sequencing results is required to maximize the potential of this technology. Here, we aimed to assess the clinical relevance of tumor-based next-generation sequencing (tbNGS) in a large cohort of patients with high-grade epithelial ovarian cancer. Methods: Our study population comprised patients with high-grade serous (n = 972), clear cell (n = 33), endometrioid (n = 28), mucinous (n = 4), and mixed (n = 34) or unspecified (n = 21) epithelial ovarian carcinoma diagnosed between April 2013 and September 2021. tbNGS results were identified within the electronic medical record using optical character recognition and natural language processing. Genetic, clinical, and demographic information was collected for patients who had undergone tbNGS. Progression-free survival (PFS) and overall survival (OS) were calculated from date of first treatment to date of first recurrence and date of death, respectively. Data were analyzed using descriptive statistics, univariate and multivariate Cox regression models, and clustering analyses. Results: Of 1092 patients in the described population, 409 (37.5%) had tbNGS results identified. Nearly all (96.1%) revealed one or more genetic aberrations. Most patients (74.6%) had an actionable mutation, defined as relaying eligibility for a targeted treatment or clinical trial. The most frequent alterations were TP53, PIK3CA, and NF1 mutations; and CCNE1 amplification. Ten different targeted institutional and commercial panels were employed, covering a range of 35 to 600+ gene loci. The median time from diagnosis to testing was 14.5 months, likely corresponding to time of recurrence. Though no standalone alterations were significantly related to survival, multivariate and clustering analyses identified several genetic patterns which corresponded to patient outcomes. Mutation of BRAF, PIK3R1, NOTCH3, MET, and/or ATR was correlated with shorter PFS (HR 1.84, p = 0.001); mutation of ATM, RB1, CDKN2A, FGFR1, and/or FGFR2 was associated with improved PFS (HR 0.64, p = 0.04), as was mutation of NBN and/or ATRX (HR 0.54, p < 0.05). MYC, NOTCH3, and/or CREBBP mutations were significantly correlated with worse OS (HR 1.95, p = 0.02). In our population, 40 patients (9.78%) were enrolled in genotypically-relevant clinical trials. Conclusions: tbNGS is prevalent at our institution, and often yields actionable information. We identified several mutational patterns that correlate to patient survival. Detailed analysis of population-level tumor genomics may help to identify therapeutic targets and guide development of clinical decision support tools.

A functional genomic approach to actionable gene fusions for precision oncology

Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown. Here, we develop a functional genomic approach that consists of efficient fusion reconstruction and sensitive cell viability and drug response assays. Applying this approach, we characterize ~100 fusion genes detected in patient samples of The Cancer Genome Atlas, revealing a notable fraction of low-frequency fusions with activating effects on tumor growth. Focusing on those in the RTK-RAS pathway, we identify a number of activating fusions that can markedly affect sensitivity to relevant drugs. Last, we propose an integrated, level-of-evidence classification system to prioritize gene fusions systematically. Our study reiterates the urgent clinical need to incorporate similar functional genomic approaches to characterize gene fusions, thereby maximizing the utility of gene fusions for precision oncology.

Clinical and Molecular Characterization of POLE Mutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers

PURPOSE

DNA polymerase epsilon is critical to DNA proofreading and replication. Mutations in POLE have been associated with hypermutated tumors and antitumor response to immune checkpoint inhibitor (ICI) therapy. We present a clinicopathologic analysis of patients with advanced cancers harboring POLE mutations, the pattern of co-occurring mutations, and their response to ICI therapy within the context of mutation pathogenicity.

METHODS

We conducted a retrospective analysis of next-generation sequencing data at MD Anderson Cancer Center to identify patient tumors with POLE mutations and their co-occurring mutations. The pathogenicity of each mutation was annotated using InterVar and ClinVar. Differences in therapeutic response to ICI, survival, and co-occurring mutations were reported by POLE pathogenicity status.

RESULTS

Four hundred fifty-eight patient tumors with POLE mutations were identified from 14,229 next-generation sequencing reports; 15.0% of POLE mutations were pathogenic, 15.9% benign, and 69.1% variant of unknown significance. Eighty-two patients received either programmed death 1 or programmed death ligand-1 inhibitors as monotherapy or in combination with cytotoxic T-cell lymphocyte-4 inhibitors. Patients with pathogenic POLE mutations had improved clinical benefit rate (82.4% v 30.0%; P = .013), median progression-free survival (15.1 v 2.2 months; P < .001), overall survival (29.5 v 6.8 months; P < .001), and longer treatment duration (median 15.5 v 2.5 months; P < .001) compared to those with benign variants. Progression-free survival and overall survival remained superior when adjusting for number of co-occurring mutations (≥ 10 v < 10) and/or microsatellite instability status (proficient mismatch repair v deficient mismatch repair). The number of comutations was not associated with response to ICI (clinical benefit v progressive disease: median 13 v 11 comutations; P = .18).

CONCLUSION

Pathogenic POLE mutations were associated with clinical benefit to ICI therapy. Further studies are warranted to validate POLE mutation as a predictive biomarker of ICI therapy.

RAC1 Alterations Induce Acquired Dabrafenib Resistance in Association with Anaplastic Transformation in a Papillary Thyroid Cancer Patient

BRAF-activating mutations are the most frequent driver mutations in papillary thyroid cancer (PTC). Targeted inhibitors such as dabrafenib have been used in advanced BRAF-mutated PTC; however, acquired resistance to the drug is common and little is known about other effectors that may play integral roles in this resistance. In addition, the induction of PTC dedifferentiation into highly aggressive KRAS-driven anaplastic thyroid cancer (ATC) has been reported. We detected a novel RAC1 (P34R) mutation acquired during dabrafenib treatment in a progressive metastatic lesion with ATC phenotype. To identify a potential functional link between this novel mutation and tumor dedifferentiation, we developed a cell line derived from the metastatic lesion and compared its behavior to isogenic cell lines and primary tumor samples. Our data demonstrated that RAC1 mutations induce changes in cell morphology, reorganization of F-actin almost exclusively at the cell cortex, and changes in cell adhesion properties. We also established that RAC1 amplification, with or without mutation, is sufficient to drive cell proliferation and resistance to BRAF inhibition. Further, we identified polyploidy of chromosome 7, which harbors RAC1, in both the metastatic lesion and its derived cell line. Copy number amplification and overexpression of other genes located on this chromosome, such as TWIST1, EGFR, and MET were also detected, which might also lead to dabrafenib resistance. Our study suggests that polyploidy leading to increased expression of specific genes, particularly those located on chromosome 7, should be considered when analyzing aggressive thyroid tumor samples and in further treatments.

Abstract 392: Patient-specific, tiered, variant-level actionability correlates with functional effect in growth survival assay

Purpose: There is increasing recognition that variants within an actionable gene may differ in their functional impact and therapeutic implications. The Precision Oncology Decision Support (PODS) team at MD Anderson Cancer Center (MDA) curates a knowledgebase of cancer-associated genomic alterations for their functional impact and therapeutic actionability. However, a substantial number of variants are not characterized within the published literature. In the MDA-PODS classification scheme, these variants are classified as “potentially” actionable, as opposed to “unknown”, if evidence exists that other variants within the same region are oncogenic. To determine the value of this tiered actionability approach, we assessed if a variant with a “potentially” assertion is more likely to have an experimentally validated oncogenic effect within a functional genomics platform (Ng et al., Cancer Cell, 2018). Procedures: Alterations researched within the published literature and found to be of unknown significance were submitted to the functional genomics platform. These variants were tested within two cell line models (Ba/F3 and MCF10A) to assess growth factor-independent survival. Results were returned to PODS indicating whether the variant conferred a change in cell viability compared with the wildtype gene. PODS then compared the functional effect of the variant with the predetermined actionability assertion.

Results: During 2015-2019, PODS received functional genomics results for 485 alterations spanning 38 genes. 115 (24%) of the alterations increased survival and were thus actionable, while 364 (75%) had no effect or suppressed cell viability. Six alterations had conflicting effects in the two cell line models and were not further considered. Of the 479 variants (in 38 genes), 208 variants (43%) in 20 genes were classified as “potentially” actionable prior to functional genomics, while 254 variants (53%) in 35 genes were classified as “unknown”. 17 (4%) were classified as Yes/No for actionability based on other criteria, such as drug response. 78 (38%) of the 208 “potentially” actionable variants were found to be oncogenic in the functional genomics platform as opposed to only 29 (11%) of the 254 variants classified as “unknown” for actionability (p&lt;.01). 70% of the 78 “potentially” actionable, experimentally-validated variants were located within two amino acids of another known oncogenic variant, per our current knowledgebase.

Conclusions: These data display the value of providing a tiered, variant-level actionability scheme that includes a “potentially” actionable assertion, as it is associated with a greater likelihood of being functionally validated. Although genomically-matched therapy is most compelling for patients with known actionable variants and functional testing adds value, tiered actionability predictions can inform therapeutic decisions.

Citation Format: Amber Johnson, Patrick Kwok-Shing Ng, Michael Kahle, Julia Castillo, Bianca Amador, Vijaykumar Holla, Thuy Vu, Le Huang, Fei Su, Sunhee Kim, Jia Zeng, Md Abu Shufean, Tara Conway, Kenna R. Shaw, Timothy A. Yap, Jordi Rodon, Funda Meric-Bernstam. Patient-specific, tiered, variant-level actionability correlates with functional effect in growth survival assay [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 392.

Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer

BACKGROUND

Appendiceal adenocarcinoma (AA) is an orphan disease with unique clinical attributes but often treated as colorectal cancer (CRC). Understanding key molecular differences between AA and CRC is critical.

METHODS

We performed retrospective analyses of AA patients (N = 266) with tumour and/or blood next-generation sequencing (NGS) (2013-2018) with in-depth clinicopathological annotation. Overall survival (OS) was examined. For comparison, CRC cohorts annotated for sidedness, consensus molecular subtypes (CMS) and mutations (N = 3283) were used.

RESULTS

Blood-NGS identified less RAS/GNAS mutations compared to tissue-NGS (4.2% vs. 60.9%, P < 0.0001) and showed poor concordance with tissue for well-/moderately differentiated tumours. RAS (56.2%), GNAS (28.1%) and TP53 (26.9%) were most frequent mutations. Well/moderately differentiated tumours harboured more RAS (69.2%/64.0% vs. 40.5%) and GNAS (48.7%/32.0% vs. 10.1%) while moderate/poorly differentiated tumours had more TP53 (26.0%/27.8% vs. 7.7%) mutations. Appendiceal adenocarcinoma (compared to CRC) harboured significantly fewer APC (9.1% vs. 55.4%) and TP53 (26.9% vs. 67.5%) and more GNAS mutations (28.1% vs. 2.0%) (P < 0.0001). Appendiceal adenocarcinoma mutation profile did not resemble either right-sided CRC or any of the four CMS in CRC. High grade, but no mutation, was independently predictive of survival.

CONCLUSION

Integrated clinico-molecular profiling of AA identified key molecular drivers distinct from CRC. Appendiceal adenocarcinoma has a predominantly grade-driven biology that trumps mutations.

HEREDITARY ENDOCRINE TUMOURS: CURRENT STATE-OF-THE-ART AND RESEARCH OPPORTUNITIES: The state of science in medullary thyroid carcinoma: current challenges and unmet needs

The 16th International Multiple Endocrine Neoplasia Workshop (MEN2019) held in Houston, TX, USA, focused on emerging topics in the pathogenesis and therapy of malignant endocrine tumors associated with MEN syndromes. With MEN-2 syndromes, the most common malignancy is medullary thyroid carcinoma (MTC). In the spirit of the original MEN meeting workshop model, the conference included didactic lectures and interactive working groups of clinicians and researchers focused on the state of science in MTC and ongoing challenges or unmet needs in the understanding of MTC and to develop strategies to address these issues.

Comprehensive assessment of computational algorithms in predicting cancer driver mutations

BACKGROUND

The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient's tumor cells is a central task in the era of precision cancer medicine. Over the decade, many computational algorithms have been developed to predict the effects of missense single-nucleotide variants, and they are frequently employed to prioritize mutation candidates. These algorithms employ diverse molecular features to build predictive models, and while some algorithms are cancer-specific, others are not. However, the relative performance of these algorithms has not been rigorously assessed.

RESULTS

We construct five complementary benchmark datasets: mutation clustering patterns in the protein 3D structures, literature annotation based on OncoKB, TP53 mutations based on their effects on target-gene transactivation, effects of cancer mutations on tumor formation in xenograft experiments, and functional annotation based on in vitro cell viability assays we developed including a new dataset of ~ 200 mutations. We evaluate the performance of 33 algorithms and found that CHASM, CTAT-cancer, DEOGEN2, and PrimateAI show consistently better performance than the other algorithms. Moreover, cancer-specific algorithms show much better performance than those designed for a general purpose.

CONCLUSIONS

Our study is a comprehensive assessment of the performance of different algorithms in predicting cancer driver mutations and provides deep insights into the best practice of computationally prioritizing cancer mutation candidates for end-users and for the future development of new algorithms.

Abstract 3162: Prognostic value of tumor mutational burden using a 409 gene NGS panel in cancer patients with advanced stage recurrent or treatment refractory disease

Tumor Mutational Burden (TMB) is a promising biomarker for prediction of response to immune checkpoint blockade (ICB). It is uncertain whether ICB has prognostic value outside of ICB therapy. The CMS400 next generation sequencing panel (NGS) is a 409 gene, 15,992 amplicon, and 1.745 Mb panel instituted during 2014-2015 and run for 556 cancer patients who had been consented for participation within a prospective molecular pathology biomarker trial (PA14-0099). All patients had advanced or recurrent solid tumor malignancies that were refractory to at least one line of systemic therapy prior to enrollment. Survival time was calculated from time of NGS-tested tissue collection. TMB was calculated by dividing reported mutations (RM) by 1.745Mb, the genetic footprint of the NGS panel. Subtraction of germline single nucleotide polymorphisms was performed for each patient. GraphPad Prism 7.03 software was used to calculate p values and to plot Kaplan-Meier survival curves. One hundred seven patients (19.2%) received ICB. When stratified by reported mutations (RM: 0, 1, 2, 3, 4-5, 6-7, 8-9, 10-18, and &gt;19), a statistically significant decrement of overall survival was seen with increasing TMB in patients not treated with ICB (Table 1, p&lt;0.0001). Also, in patients treated with ICB, significantly increased overall survival was seen on the extreme ends of the TMB spectrum (Table 1, p=0.0249). In contrast, stratification by the top four histologic diagnoses (Colorectal ADCA [n=94] - 34.2 months, breast ductal ADCA [n=44] - 26.6 months, gynecologic high grade serous [n=39] - 45.6 months, and lung ADCA [n=30] - 31.5 months) did not show difference in overall survival (p=0.332). We report here a novel molecular phenomena showing that high TMB in patients with advanced cancers is associated with worse survival. This negative impact of high TMB can be reversed by treatment with ICB. These effects of ICB were seen across a broad spectrum of cancer types.

Median Survival Stratified by Tumor Mutational Burden and ICB Treatment StatusAll PtsAll PtsICB TreatedICB TreatedNo ICBNo ICBReported Mutations# of PtsMedian Survival (Months)# of PtsMedian Survival (Months)# of PtsMedian Survival (Months)p-value (Log-rank)Hazard Ratio of ICB Therapy95% CI of HR of ICB Therapy0 RM7150.71958.85248.50.3190.7050.368 - 1.341 RM8550.91262.07347.40.3390.6840.345 - 1.362 RM9433.91928.07533.90.8650.9510.535 - 1.693 RM8830.51951.26928.90.1890.7040.428 - 1.164-5 RM9330.81141.08230.40.5390.8150.442 - 1.506-7 RM4928.41127.33828.550.6230.8270.401 - 1.718-18 RM5623.95828.84823.10.5491.2520.553 - 2.84&gt;19 RM2041.38102.31224.20.00230.1800.0599 - 0.543Total55635.810747.944933.40.00490.7070.567 - 0.882p-value (Log-rank)&lt;0.00010.0249&lt;0.0001

Citation Format: Richard K. Yang, Peng Wang, Fatima Z. Jelloul, Mark J. Routbort, Scott Kopetz, Kenna R. Shaw, Jack J. Lee, Jiexin Zhang, Hui Chen, Keyur P. Patel, Raja Luthra, Russell R. Broaddus. Prognostic value of tumor mutational burden using a 409 gene NGS panel in cancer patients with advanced stage recurrent or treatment refractory disease [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 3162.

Expanded analysis of secondary germline findings from matched tumor/normal sequencing identifies additional clinically significant mutations

BACKGROUND

Next-generation sequencing (NGS) for tumor molecular profiling can reveal secondary germline pathogenic and likely pathogenic variants (LPV/PV). The American College of Medical Genetics (ACMG) recommends return of secondary results for a subset of 59 genes, but other genes with evidence of clinical utility are emerging. We previously reported that 4.3% of patients who underwent NGS of a targeted panel of 201 genes had LPV/PV based on the ACMG list. Here we report the frequency of additional germline cancer-related gene variants and discuss their clinical utility.

PATIENTS AND METHODS

Matched tumor and germline DNA NGS of a targeted panel of 201 genes was performed in a research laboratory on samples from 1000 patients with advanced or metastatic solid tumors enrolled in a molecular testing protocol (NCT01772771). The frequency of germline LPV/PV in 54 cancer-related genes, beyond the genes in ACMG list, were analyzed.

RESULTS

Among 1000 patients who underwent tumor/normal DNA sequencing, 46 (4.6%) were found to have a germline LPV/PV in the following genes: AR-(5), ATM-(4), BAP1-(1), CDH1-(1), CDKN2A-(1), CHEK1-(2), CHEK2-(10), EGFR-(1), ERCC3-(4), ERCC5-(1), HNF1B-(1), HRAS-(1), MITF-(4), MLL3-(1), NF1-(3), PKHD1-(4), PTCH1-(1), and SMARCA4-(1). Thus, a total 8.7% of patients had an LPV/PV with 2 patients having 2 concomitant germline LPV/PV. Five mutations in high-penetrance hereditary cancer predisposition genes were selected to be returned to patients or their representatives: BAP1, CDH1, CDKN2A, EGFR, and SMARCA4.

CONCLUSIONS

Broader genomic testing is likely to identify additional secondary pathogenic germline alterations, some with potential clinical utility for return to patients and their relatives. The recommended genes for which germline results should be returned are continually changing, warranting continued study.

Molecular Landscape of ERBB2/ERBB3 Mutated Colorectal Cancer

Background

Despite growing therapeutic relevance of ERBB2 amplifications in colorectal cancer (CRC), little is known about ERBB2/ERBB3 mutations. We aimed to characterize these subsets of CRC.

Methods

We performed a retrospective analysis of 419 CRC patients from MD Anderson (MDACC) and 619 patients from the Nurses' Health Study (NHS)/Health Professionals Follow-Up Study (HPFS) with tissue sequencing, clinicopathologic, mutational, and consensus molecular subtype (CMS) profiles of ERBB2/ERBB3 mutant patients. A third cohort of 1623 CRC patients with ctDNA assays characterized the ctDNA profile of ERBB2 mutants. All statistical tests were two-sided.

Results

ERBB2 mutations occurred in 4.1% (95% confidence interval [CI] = 2.4% to 6.4%), 5.8% (95% CI = 4.1% to 8.0%), and 5.1% (95% CI = 4.0% to 6.2%) of MDACC, NHS/HPFS, and ctDNA patients, respectively. ERBB3 mutations occurred in 5.7% (95% CI = 3.7% to 8.4%, 95% CI = 4.0% to 7.8%) of patients in both tissue cohorts. Age, stage, and tumor location were not associated with either mutation. Microsatellite instability (MSI) was associated with ERBB2 (odds ratio [OR] = 5.98, 95% CI = 2.47 to 14.49, P < .001; OR = 5.13, 95% CI = 2.38 to 11.05, P < .001) and ERBB3 mutations (OR = 3.48, 95% CI = 1.51 to 8.02, P = .002; OR = 3.40, 95% CI = 1.05 to 10.96, P = .03) in both tissue cohorts. Neither gene was associated with TP53, APC, KRAS, NRAS, or BRAF mutations in tissue. However, PIK3CA mutations were strongly associated with ERBB2 mutations in all three cohorts (OR = 3.68, 95% CI = 1.83 to 7.41, P = .001; OR = 2.25, 95% CI = 1.11 to 4.58, P = .02; OR = 2.11, 95% CI = 1.25 to 3.58, P = .004) and ERBB3 mutations in the MDACC cohort (OR = 13.26, 95% CI = 5.27 to 33.33, P < .001). ERBB2 (P = 0.08) and ERBB3 (P = .008) mutations were associated with CMS1 subtype. ERBB2 (hazard ratio [HR] = 1.82, 95% CI = 1.23 to 4.03, P = .009), but not ERBB3 (HR = 0.88, 95% CI = 0.45 to 1.73, P = .73), mutations were associated with worse overall survival.

Conclusions

MSI and PIK3CA mutations are associated with ERBB2/ERBB3 mutations. Co-occurring PIK3CA mutations may represent a second hit to oncogenic signaling that needs consideration when targeting ERBB2/ERBB3.

Systematic Functional Annotation of Somatic Mutations in Cancer

The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate >1,000 genomic aberrations, including gene amplifications, point mutations, indels, and gene fusions, potentially doubling the number of driver mutations characterized in clinically actionable genes. Further, the platform is sufficiently sensitive to identify weak drivers. Our data are accessible through a user-friendly, public data portal. Our study will facilitate biomarker discovery, prediction algorithm improvement, and drug development.

Abstract A096: Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer)

Background: Cancer cells deficient in BRCA1/2 are selectively sensitive to the double-stranded DNA breaks induced by poly (ADP-ribose) polymerase (PARP) inhibitors. Multiple ongoing trials are evaluating PARP inhibitors in patients with breast, ovarian, and prostate cancers and germline or somatic BRCA1/2 mutations. There is, however, a great need to determine if the benefit of PARP inhibition can be extended to other tumor types. We sought to assess the efficacy of talazoparib, a potent oral PARP1/2 inhibitor, in patients with germline BRCA mutations in cancer types other than breast and ovarian cancer, and in patients with somatic BRCA alterations or aberrations in other homologous repair genes or PTEN. Methods: This was a single-center, phase II trial in patients with measurable advanced solid tumors. Patients were enrolled on one of four cohorts: 1) somatic alterations of BRCA1/2, 2) mutations/deletions in other BRCA pathway genes, 3) mutations/deletions in PTEN and/or PTEN loss by IHC, and 4) germline BRCA1/2 mutations (not breast/ovarian cancer). Patients were treated with talazoparib at 1 mg PO daily. Response was assessed per RECIST v1.1. Primary end point was clinical benefit rate (CBR; complete response [CR], partial response [PR] or stable disease [SD]&gt;6m). Patients were enrolled based on standard of practice molecular testing. Patients underwent pretreatment biopsies with whole exome sequencing (WES) of tumor and normal DNA. Results: 35 patients (pts) (30 evaluable) were enrolled. Pts had a median of 4 prior lines of treatment. Grade 3-4 treatment-related AEs occurred in 37% of pts, and the most common was thrombocytopenia (23%). The median follow-up was 15.8 mo. CBR was 0%, 44%, 8%, and 29% for cohorts 1-4, respectively. In cohort 1, one patient with a somatic BRCA2 mutation enrolled and did not respond. In cohort 2, two of 9 evaluable pts had a PR: cholangiocarcinoma [CCA] with ATM mutation and bladder cancer with PALB2 mutation, and 2 of 9 pts had prolonged SD (one pt with ovarian cancer and BRIP1 mutation, and one pt with sarcoma and FANCC mutation). Among 13 evaluable pts in the PTEN mutation/loss cohort (cohort 3), one patient with PTEN mutation had prolonged SD. Among 7 evaluable pts with germline BRCA1/2 mutations (cohort 4), one pt with carcinoma of ampulla of Vater had a durable CR, and one pt with CCA had SD for 8 months. WES was performed on 28 evaluable patients. Alterations in two genes, POLQ and PTEN, were significantly associated with progressive disease. PTEN mutations were associated with shorter time to progression (p=0.004) and lower overall survival (p=0.02). Conclusion: Talazoparib demonstrated clinical benefit in selected patients with germline as well as somatic alterations in BRCA pathway genes. Patients with PTEN mutations/loss did not derive significant clinical benefit from PARP inhibition. Further study is needed to confirm these findings and determine implications for patient selection and combination therapy. Clinical trial information: NCT 02286687.

Citation Format: Sarina A. Piha-Paul, Wendy Wen Xiong, Tyler Moss, Rosa M. Mostorino, Shelby Sedelmeier, Kenneth Hess, Siqing Fu, David Hong, Filip Janku, Daniel Karp, Aung Naing, Shubham Pant, Jordi Rodon, Vivek Subbiah, A M. Tsimberidou, Timothy Yap, Milind Javle, Coya Tapia, Kenna R. Shaw, Karina Eterovic, Gordon B. Mills, Funda Meric-Bernstam. Phase II study of the PARP inhibitor talazoparib in advanced cancer patients with somatic alterations in BRCA1/2, mutations/deletions in PTEN or PTEN loss, aberrations in other BRCA pathway genes, and germline mutations in BRCA1/2 (not breast or ovarian cancer) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A096.

Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing

BACKGROUND

Next-generation sequencing of cell-free DNA (cfDNA) has been shown to be a useful noninvasive test for detecting mutations in solid tumors.

METHODS

Targeted gene sequencing was performed with a panel of 263 cancer-related genes for cfDNA and genomic DNA of peripheral blood mononuclear cells (PBMCs) obtained from presurgical specimens of 6 lung cancer patients, and mutation calls in these samples were compared with those of primary tumors and corresponding patient-derived xenografts (PDXs).

RESULTS

Approximately 67% of the mutations detected in the tumor samples (primary tumors and/or PDXs) were also detected in genomic DNA from PBMCs as background mutations. These background mutations consisted of germline polymorphisms and a group of mutations with low allele frequencies, mostly <10%. These variants with a low allele frequency were repeatedly detected in all types of samples from the same patients and at similarly low allele frequency levels in PBMCs from different patients; this indicated that their detection might be derived from common causes, such as homologous sequences in the human genome. Allele frequencies of mutations detected in both primary tumors and cfDNA showed 2 patterns: 1) low allele frequencies (approximately 1%-10%) in cfDNA but high allele frequencies (usually >10% or >3-fold increase) in primary tumors and further enrichment in PDXs and 2) similar allele frequencies across samples.

CONCLUSIONS

Because only a small fraction of total cfDNA might be derived from tumor cells, only mutations with the first allele frequency pattern may be regarded as tumor-specific mutations in cfDNA. Effective filtering of background mutations will be required to improve the accuracy of mutation calls in cfDNA. Cancer 2018;124:1061-9. © 2017 American Cancer Society.

Abstract LB-104: Clinical actionability and clinical trial matching for GENIE patient genotypes using My Cancer Genome, Personalized Cancer Therapy, and OncoKB

AACR Project GENIE is an international data-sharing project with the goal of enhancing precision oncology. On January 5, 2017, data from ~19,000 somatic tumor genotype reports and selected clinical information from patients (http://www.aacr.org/RESEARCH/RESEARCH/PAGES/AACR-PROJECT-GENIE-DATA.ASPX) were released to the public. The eight member institutions contributed patient data, which were then made available on a dedicated cBioPortal website and for download by Sage Bionetworks. As part of the analysis of the first data release, member institutions began work to combine and reconcile their clinical actionability knowledgebases (KBs). In this abstract, we present efforts to combine clinical actionability assertions from My Cancer Genome (MCG; https://www.mycancergenome.org; Vanderbilt-Ingram Cancer Center), Personalized Cancer Therapy (https://pct.mdanderson.org; MD Anderson Cancer Center), and OncoKB (http://oncokb.org; Memorial Sloan Kettering Cancer Center). We also present data on matching GENIE patient genotypes to clinical actionability assertions from these KBs and to biomarker-driven clinical trials to begin defining the landscape of clinical actionability across a large cohort of patients at all stages of disease.The three KBs were combined using a modification of OncoKB’s levels of evidence for clinical actionability. Categories included standard of care therapies (e.g., those with FDA labels and in NCCN guidelines) and investigational therapies with strong clinical data, both on and off the recommended diagnosis indications. Diagnoses were mapped to the OncoTree tumor type hierarchy. Initial efforts to combine the KBs resulted in &gt;500 therapeutic assertions. Using the combined KBs, we matched these assertions to GENIE patient diagnoses and genotypes. In our preliminary results, &gt;33% of patient samples match at least one therapeutic assertion. Of these, ~15% match at the standard of care level, and ~8% match at the level of investigational therapies. The remaining matches were exploratory or matched by biomarker but not diagnosis. Most frequently matching diagnoses at the standard-of-care level were non-small cell lung cancer, breast cancer, and melanoma. Further details will be presented.The MCG team curates diagnosis and biomarker eligibility criteria for all recruiting cancer clinical trials reported in ClinicalTrials.gov. As of January 2017, 5,201 recruiting cancer clinical trials from ClinicalTrials.gov have been reviewed, and 1,884 trials were found to have biomarker eligibility criteria. Of these, 352 trials are testing a targeted therapy and have a known driver mutation as an inclusion criterion. Based on preliminary work, ~16% of patient samples match at least one trial in the limited set. When the trial list is expanded to include all biomarker-driven trials, including those exploring the impact of mutations along an entire cell signaling pathway, ~84% of patient samples match at least one trial; matching biomarkers are often exploratory and patient benefit from the trial intervention is not necessarily expected. For the limited trial set, patients with breast cancer, non-small cell lung cancer, glioma, and melanoma were most likely to match a trial. For the expanded trial set, patients with non-small cell lung cancer, colorectal cancer, breast cancer, and glioma were most likely to match a trial. We will show how genetic testing panel size affects trial matching and present clinical trial matching by disease, gene, alteration type, drug class, and cell signaling pathway.In conclusion, the GENIE project has resulted in more than just the shared data. It has fostered collaborations between institutions to reconcile and improve precision cancer medicine KBs and provided a resource for improving cancer genetic testing and the practice of precision cancer medicine.

[C. M. and D. C. contributed equally to this work.]

Citation Format: Christine M. Micheel, Debayani Chakravarty, Jiaojiong Gao, Ian Maurer, Clinton Miller, Kenna R. Shaw, Mia A. Levy, Nikolaus Schultz, on behalf of the AACR Project GENIE Consortium. Clinical actionability and clinical trial matching for GENIE patient genotypes using My Cancer Genome, Personalized Cancer Therapy, and OncoKB [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 LB-104. doi:10.1158/1538-7445.AM2017-LB-104

Abstract LB-103: Landscape of somatic ERBB2 Mutations: Findings from AACR GENIE and comparison to ongoing ERBB2 mutant basket study

Background: AACR GENIE is an international data-sharing project that aggregates clinical-grade cancer genomic data. As a demonstration of utility, we evaluated the landscape of ERBB2 mutations in the first 18,486 patients included in this registry and compared it to the first 100 patients enrolled in an ongoing international Phase 2 SUMMIT ‘basket’ study of the pan-HER inhibitor neratinib in ERBB2 mutant solid tumors (NCT01953926). Results: ERBB2 mutations were identified in 2.8% (519/18,486) of patients in the GENIE cohort and observed at all participating centers. In total, there were 482 missense, 66 indels, 19 truncating mutations, and 14 structural variants. A total of 263 unique missense mutations were observed including 12 at previously identified hotspots which accounted for 69.2% of all missense mutations. 35 unique cancer types were represented. The tumor types with the highest proportion of ERBB2 mutations were bladder (12.8%, 82/641), breast (3.9%, 87/2230), colorectal (3.3%, 70/2102), and NSCLC (3%, 90/3006). Among patients with copy number data available (91%) 11% had concurrent ERBB2 amplification, most often in breast cancer. The most frequently observed alterations in ERBB2, adjusted for differing exon coverage between panels, was S310F/Y in 0.46% of the GENIE cohort (12.6% of samples with ERBB2 alterations), Y772_A775dup in 0.21% (6.9%), R678Q in 0.17% (4.5%), L755S in 0.16% (5.2%), V777L in 0.12% (3.8%), and V842I in 0.09% (3.1%). The distribution of specific ERBB2 variants differed significantly by tumor type with exon 20 insertions being most common in NSCLC (44.4%, 40/90), L755S (18.9%, 11/92) in breast, S310F/Y (26.9%, 28/104) in bladder, and V842I (13.9%, 10/72) in colorectal cancer. Structural variants included intragenic deletions (n=4) and fusions involving various partners including GRB7 (n=2), and one each of C1orf87, PPIL6, HEXIM2, THRA, ASIC2, BCA3, WIPF2. The frequencies of ERBB2 mutant cancer types observed in the GENIE cohort were generally comparable to those enrolled to the neratinib basket study including NSCLC (17 vs 22%, respectively), breast (16.4 vs 24%), bladder (15.5 vs 14%), colorectal (13.2 vs 17%), and endometrial (4.2 vs 6%). At the variant level, S310F/Y was less prevalent in GENIE compared to the neratinib study (12.6 vs 24%) while all other mutations were generally similar including L755S (5.2 vs 9%), R678Q (4.5 vs 2%), Y772_A775dup (6.9 vs 13%), V777L (3.8 vs 9%), and V842I (3.1 vs 6%). Conclusion: GENIE confirms that a diversity of ERBB2 mutations are prevalent across a variety of tumor types in patients with advanced cancer. The genomic landscape of ERBB2 mutations was largely similar in the population based GENIE cohort and the neratinib SUMMIT study, providing the first direct evidence that basket study enrollment accurately reflects the true landscape of the target alteration.

Citation Format: Alison Schram, Helen H. Won, Fabrice Andre, Monica Arnedos, Funda Meric - Bernstam, Philippe L. Bedard, Kenna R. Shaw, Hugo Horlings, Christine Micheel, Ben Ho Park, Grace Mann, Alshad S. Lalani, Lillian Smyth, David B. Solit, Deborah Schrag, Mia A. Levy, Barrett J. Rollins, Mark Routbort, Charles L. Sawyers, Eva Lepisto, Michael F. Berger, David M. Hyman, on behalf of the AACR Project GENIE Consortium. Landscape of somatic ERBB2 Mutations: Findings from AACR GENIE and comparison to ongoing ERBB2 mutant basket study [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 LB-103. doi:10.1158/1538-7445.AM2017-LB-103

Abstract LB-102: Landscape analysis of the initial data release from AACR Project GENIE

AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is a multi-phase, multi-year, international data-sharing consortium whose goal is to generate an evidence base for precision cancer medicine by integrating and linking clinical-grade cancer genomic data with clinical outcome data for tens of thousands of cancer patients treated at multiple institutions worldwide. The project fulfills an unmet need in oncology by providing the statistical power necessary to identify novel therapeutic targets, to understand genomic determinants of response to therapy, to design new biomarker-driven clinical trials and ultimately, to improve clinical decision-making and the care delivered to patients. Here we describe the goals, structure and data standards of the GENIE consortium and conclusions from a high-level analysis of the first public release of genomic and limited clinical data from approximately 19,000 patients treated at eight cancer centers obtained during this initial phase of the project. We also explore the clinical utility of these genomic data by examining rates of clinical actionability across multiple cancer types and by estimating patient enrollment rates to the NCI MATCH Trial. Based on yearly rates of sequencing at each of the eight founding institutions, together with the planned addition of new members, we estimate the GENIE database could grow to &gt;100,000 samples within five years. Consistent with the goals of the proposed Cancer Moonshot National Cancer Data Ecosystem, GENIE is committed to the principles of generating interoperable, open access data that can be widely shared across the entire scientific community.

Citation Format: Ethan Cerami, Alexander S. Baras, Justin Guinney, Eva Lepisto, Trevor J. Pugh, Nikolaus Schultz, Thomas Stricker, Shawn M. Sweeney, Laura J. van't Veer, Gerrit A. Meijer, Fabrice Andre, Victor E. Velculescu, Kenna R. Shaw, Mia A. Levy, Philippe L. Bedard, Barrett J. Rollins, Charles L. Sawyers, on behalf of the AACR Project GENIE Consortium. Landscape analysis of the initial data release from AACR Project GENIE [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 LB-102. doi:10.1158/1538-7445.AM2017-LB-102

A randomized phase 2 study of MK-2206 versus everolimus in refractory renal cell carcinoma

Background

Activation of the phosphoinisitide-3 kinase (PI3K) pathway through mutation and constitutive upregulation has been described in renal cell carcinoma (RCC), making it an attractive target for therapeutic intervention. We performed a randomized phase II study in vascular endothelial growth factor (VEGF) therapy refractory patients to determine whether MK-2206, an allosteric inhibitor of AKT, was more efficacious than the mammalian target of rapamycin inhibitor everolimus.

Patients and methods

A total of 43 patients were randomized in a 2:1 distribution, with 29 patients assigned to the MK-2206 arm and 14 to the everolimus arm. Progression-free survival (PFS) was the primary endpoint.

Results

The trial was closed at the first futility analysis with an observed PFS of 3.68 months in the MK-2206 arm and 5.98 months in the everolimus arm. Dichotomous response rate profiles were seen in the MK-2206 arm with one complete response and three partial responses in the MK-2206 arm versus none in the everolimus arm. On the other hand, progressive disease was best response in 44.8% of MK2206 versus 14.3% of everolimus-treated patients. MK-2206 induced significantly more rash and pruritis than everolimus, and dose reduction occurred in 37.9% of MK-2206 versus 21.4% of everolimus-treated patients. Genomic analysis revealed that 57.1% of the patients in the PD group had either deleterious TP53 mutations or ATM mutations or deletions. In contrast, none of the patients in the non-PD group had TP53 or ATM defects. No predictive marker for response was observed in this small dataset.

Conclusions

Dichotomous outcomes are observed when VEGF therapy refractory patients are treated with MK-2206, and MK-2206 does not demonstrate superiority to everolimus. Additionally, mutations in DNA repair genes are associated with early disease progression, indicating that dysregulation of DNA repair is associated with a more aggressive tumor phenotype in RCC.

ALK: a tyrosine kinase target for cancer therapy

The anaplastic lymphoma kinase (ALK) gene plays an important physiologic role in the development of the brain and can be oncogenically altered in several malignancies, including non-small-cell lung cancer (NSCLC) and anaplastic large cell lymphomas (ALCL). Most prevalent ALK alterations are chromosomal rearrangements resulting in fusion genes, as seen in ALCL and NSCLC. In other tumors, ALK copy-number gains and activating ALK mutations have been described. Dramatic and often prolonged responses are seen in patients with ALK alterations when treated with ALK inhibitors. Three of these—crizotinib, ceritinib, and alectinib—are now FDA approved for the treatment of metastatic NSCLC positive for ALK fusions. However, the emergence of resistance is universal. Newer ALK inhibitors and other targeting strategies are being developed to counteract the newly emergent mechanism(s) of ALK inhibitor resistance. This review outlines the recent developments in our understanding and treatment of tumors with ALK alterations.

Molecular spectrum of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC somatic gene mutations in Arab patients with colorectal cancer: determination of frequency and distribution pattern

BACKGROUND

The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features.

METHODS

Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed. The mutation rates of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC were recorded, along with clinicopathological features. Other somatic mutation and their rates were also identified. Fisher's exact test was used to determine the association between mutation status and clinical features.

RESULTS

A total of 198 cases were identified; 99 Arab patients and 99 Western patients. Fifty-two point seven percent of Arab patients had stage IV disease at initial presentation, 74.2% had left-sided tumors. Eighty-nine point two percent had tubular adenocarcinoma and 10.8% had mucinous adenocarcinoma. The prevalence rates of KRAS, NRAS, BRAF, PIK3CA, TP53, APC, SMAD, FBXW7 mutations in Arab population were 44.4%, 4%, 4%, 13.1%, 52.5%, 27.3%, 2% and 3% respectively. Compared to 48.4%, 4%, 4%, 12.1%, 47.5%, 24.2%, 11.1% and 0% respectively in matched Western population. Associations between these mutations and patient clinicopathological features were not statistically significant.

CONCLUSIONS

This is the first study to report comprehensive hotspot mutations using NGS in Arab patients with CRC. The frequency of KRAS, NRAS, BRAF, TP53, APC and PIK3CA mutations were similar to reported frequencies in Western population except SMAD4 that had a lower frequency and higher frequency of FBXW7 mutation.

Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set

BACKGROUND

While clinical outcomes following immunotherapy have shown an association with tumor mutation load using whole exome sequencing (WES), its clinical applicability is currently limited by cost and bioinformatics requirements.

METHODS

We developed a method to accurately derive the predicted total mutation load (PTML) within individual tumors from a small set of genes that can be used in clinical next generation sequencing (NGS) panels. PTML was derived from the actual total mutation load (ATML) of 575 distinct melanoma and lung cancer samples and validated using independent melanoma (n = 312) and lung cancer (n = 217) cohorts. The correlation of PTML status with clinical outcome, following distinct immunotherapies, was assessed using the Kaplan-Meier method.

RESULTS

PTML (derived from 170 genes) was highly correlated with ATML in cutaneous melanoma and lung adenocarcinoma validation cohorts (R2 = 0.73 and R2 = 0.82, respectively). PTML was strongly associated with clinical outcome to ipilimumab (anti-CTLA-4, three cohorts) and adoptive T-cell therapy (1 cohort) clinical outcome in melanoma. Clinical benefit from pembrolizumab (anti-PD-1) in lung cancer was also shown to significantly correlate with PTML status (log rank P value < 0.05 in all cohorts).

CONCLUSIONS

The approach of using small NGS gene panels, already applied to guide employment of targeted therapies, may have utility in the personalized use of immunotherapy in cancer.

Abstract A76: Prospective evaluation of two-phase NGS platform coupled to active precision oncology decision support in the therapeutic management of patients with advanced cancers

Background: We initiated a prospective, institution-wide study to determine whether genomic testing with a 409-gene panel in solid tumors can identify new actionable genomic information (beyond that identified by smaller hot-spot panels) and lead to enrollment in genotype matched trials using agents relevant to the alteration(s) identified when coupled with robust decision support tools.

Methods: Eligible patients (pts) had no remaining standard of care therapy anticipated to extend life by more than 3 months, ECOG performance status of ≤ 1, and a willingness to consider clinical trial enrollment. The patients' tumors were initially sequenced using a hotspot panel (predominantly a 50-gene panel, Life Technology, Ion Torrent), and if no actionable alterations were found, then tumor and paired germline were sequenced with a 409-full-length (Ion Proton) gene panel. Actionable genes were defined as those for which a matched genotype selected trial exists in the institution.

Results: 471 pts across more than 30 tumor types were consented and underwent 409-gene testing. Data for each mutation, relevant therapeutic agents and corresponding clinical trials were annotated. Each variant was annotated for the level of evidence that associated a specific alteration in a potentially actionable cancer gene with a potential therapeutic opportunity with appropriate references. Specific mutations, copy number variants and fusions were linked to targeted agents, clinical trials, and functional data. Data were distributed via a publicly accessible website, reports and proactive clinical trial alert notifications. Alterations in a potentially actionable gene were found in 48.0% of patients. Novel alterations in an actionable gene not found on a previous hot-spot panel were found in 36.9% of pts (174 pts). Of the 434 mutations found in actionable genes in these 174 pts, the specific variant in the gene was of known activity based on existing literature in only 17%; for 41% the variant was of unknown significance. Approximately one-quarter of patients with mutations in actionable genes were enrolled on clinical trials using matched-therapies during the period of data review. Reasons for non-enrollment were the treating physician's opinion that there was insufficient evidence for the functional significance of the variant, exclusion criteria or lack of available slots, or other reasons including pt choice.

Conclusions: A significant population of patients with variants in potentially actionable cancer genes not evaluated in a traditional hot-spot cancer gene panel can be identified using a 409-gene targeted gene panel. The high number of variants of unknown significance represents a knowledge gap of clinical importance. While a number of factors contribute to bottlenecks in utilizing the expanded sequencing results, expanded genomic testing combined with robust decision support can facilitate trial enrollment.

Citation Format: Kenna R. Shaw, Scott Kopetz, Vijaykumar Holla, Beate C. Litzenburger, Walter Kinyua, Blessy Sajan, J. Jack Lee, Russell Broaddus. Prospective evaluation of two-phase NGS platform coupled to active precision oncology decision support in the therapeutic management of patients with advanced cancers. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A76.

Abstract 3900: Genomic landscape of human cancer reveals dysregulated TGF-β signaling with prognostic significance

Objective: Genome-wide analysis enables predictive modeling of genetic pathways driving many cancers. While somatic mutations and patterns reflecting key pathways have been identified for many cancers, an integrated analysis of driver mutations identified through mouse/human genetics have yet to be comprehensively defined for hepatocellular cancer (HCC). Previously our group and others have identified that loss of TGF-β signaling leads to spontaneous HCC development, through mouse models and human genetics. Patients with hepatocellular cancer have a poor survival of 9-11 months. Recent clinical studies show that targeting TGF-β improves survival up to 21 months, yet prognostic significances are undefined. The relationships between patterns of mutations and transcriptomic phenotypes for the TGF-β pathway are unclear.

Methods: (1) We analyzed the transcriptome of 488 hepatocellular cancers and screened for mutations in the TGF-β pathway in 202 HCCs from The Cancer Genome Atlas (TCGA). (2) Increased levels of TGF-β-related genes were designated as an “activated” signature that is associated with hepatic fibrosis. Conversely, decreased levels of TGF-β-related genes were defined as an “inactivated” signature, which was associated with the loss of TGF-β tumor suppressor function. (3) We further performed high-fidelity (80x) whole-genome sequence analysis and transcriptome sequencing analysis of eight additional HCCs to define the role of TGF-β in their development and characterize a potential novel “driver mutations” in HCV- and alcohol-associated hepatocellular cancer. (4) We validated the clinical relevance of β2SP alterations in 22 human liver specimens.

Results: (1) Transcriptomic analyses revealed aberrant TGF-β superfamily profiles in 72% of hepatocellular cancers, with mutations in 38% of patients. (2) HCCs characterized by the “inactivated” TGF-β signature were associated with a significantly poorer survival particularly in early stage HCCs, compared to HCCs with the “activated” TGF-β signature (p = 0.0027). (3) We observed the greatest number of functional mutations in the SPTBN1 gene (6%), which encodes a tumor suppressor TGF-β/Smad3 adaptor protein. (4) Furthermore, we found a strong association between DNA damage response genes and the TGF-β pathway at both transcriptomic and genomic levels.

Conclusions: The TGF-β pathway plays a pivotal role in liver tumorigenesis and the molecular signatures we characterize here appear to have prognostic significance. The additional association with the DNA repair pathway supports new approaches to developing biomarkers. Targeting of TGF-β, has the potential for improving survival of liver cancer.

Citation Format: Jian Chen, Jiun-Sheng Chen, Jianping Zhang, Liem Phan, Nina M. Muñoz, Lior H Katz, YoungJin Gi, Vipin Kumar Menon, Ji-Hyun Shin, Yun Seong Jeong, Wilma Jogunoori, Patrizia Farci, Kirti Shetty, Xiaoping Su, Tej K Pandita, Jon White, Bibhuti Mishra, Fausto Zamboni, Xifeng Wu, Asif Rashid, Shulin Li, Milind Javle, Mien-Chie Hung, Franklin Herlong, Marta Davila, John Stroehlein, Kenna R Shaw, Xuemei Wang, Jeffrey S Morris, Rehan Akbani, Lopa Mishra. Genomic landscape of human cancer reveals dysregulated TGF-β signaling with prognostic significance. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3900. doi:10.1158/1538-7445.AM2015-3900

The right drugs at the right time for the right patient: the MD Anderson precision oncology decision support platform

The development of resources for clinical interpretation of cancer-associated genetic alterations has significantly lagged behind the technical developments enabling their detection in a time- and cost-efficient manner. The lack of scientific and informatics decision support for oncologists can lead to no action being taken or suboptimal therapeutic choices being made, which could affect the clinical outcome of a patient as well as convoluting research findings from clinical trials. In this article, we describe the precision oncology decision support (PODS) platform developed within The Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy (IPCT) at MD Anderson Cancer Center; the platform aims to bridge the gap between molecular alteration detection and identification of appropriate treatments.

A decision support framework for genomically informed investigational cancer therapy

Rapidly improving understanding of molecular oncology, emerging novel therapeutics, and increasingly available and affordable next-generation sequencing have created an opportunity for delivering genomically informed personalized cancer therapy. However, to implement genomically informed therapy requires that a clinician interpret the patient's molecular profile, including molecular characterization of the tumor and the patient's germline DNA. In this Commentary, we review existing data and tools for precision oncology and present a framework for reviewing the available biomedical literature on therapeutic implications of genomic alterations. Genomic alterations, including mutations, insertions/deletions, fusions, and copy number changes, need to be curated in terms of the likelihood that they alter the function of a "cancer gene" at the level of a specific variant in order to discriminate so-called "drivers" from "passengers." Alterations that are targetable either directly or indirectly with approved or investigational therapies are potentially "actionable." At this time, evidence linking predictive biomarkers to therapies is strong for only a few genomic markers in the context of specific cancer types. For these genomic alterations in other diseases and for other genomic alterations, the clinical data are either absent or insufficient to support routine clinical implementation of biomarker-based therapy. However, there is great interest in optimally matching patients to early-phase clinical trials. Thus, we need accessible, comprehensive, and frequently updated knowledge bases that describe genomic changes and their clinical implications, as well as continued education of clinicians and patients.

RET fusion as a novel driver of medullary thyroid carcinoma

INTRODUCTION

Oncogenic RET tyrosine kinase gene fusions and activating mutations have recently been identified in lung cancers, prompting initiation of targeted therapy trials in this disease. Although RET point mutation has been identified as a driver of tumorigenesis in medullary thyroid carcinoma (MTC), no fusions have been described to date.

OBJECTIVE

We evaluated the role of RET fusion as an oncogenic driver in MTC.

METHODS

We describe a patient who died from aggressive sporadic MTC < 10 months after diagnosis. Her tumor was evaluated by means of next-generation sequencing, including an intronic capture strategy.

RESULTS

A reciprocal translocation involving RET intron 12 was identified. The fusion was validated using a targeted break apart fluorescence in situ hybridization probe, and RNA sequencing confirmed the existence of an in-frame fusion transcript joining MYH13 exon 35 with RET exon 12. Ectopic expression of fusion product in a murine Ba/F3 cell reporter model established strong oncogenicity. Three tyrosine kinase inhibitors currently used to treat MTC in clinical practice blocked tumorigenic cell growth.

CONCLUSION

This finding represents the report of a novel RET fusion, the first of its kind described in MTC. The finding of this potential novel oncogenic mechanism has clear implications for sporadic MTC, which in the majority of cases has no driver mutation identified. The presence of a RET fusion also provides a plausible target for RET tyrosine kinase inhibitor therapies.

Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer

Molecular annotated patient-derived xenograft (PDX) models are useful for the preclinical investigation of anticancer drugs and individualized anticancer therapy. We established 23 PDXs from 88 surgical specimens of lung cancer patients and determined gene mutations in these PDXs and their paired primary tumors by ultradeep exome sequencing on 202 cancer-related genes. The numbers of primary tumors with deleterious mutations in TP53, KRAS, PI3KCA, ALK, STK11, and EGFR were 43.5%, 21.7%, 17.4%, 17.4%, 13.0%, and 8.7%, respectively. Other genes with deleterious mutations in ≥3 (13.0%) primary tumors were MLL3, SETD2, ATM, ARID1A, CRIPAK, HGF, BAI3, EP300, KDR, PDGRRA and RUNX1. Of 315 mutations detected in the primary tumors, 293 (93%) were also detected in their corresponding PDXs, indicating that PDXs have the capacity to recapitulate the mutations in primary tumors. Nevertheless, a substantial number of mutations had higher allele frequencies in the PDXs than in the primary tumors, or were not detectable in the primary tumor, suggesting the possibility of tumor cell enrichment in PDXs or heterogeneity in the primary tumors. The molecularly annotated PDXs generated from this study could be useful for future translational studies.

Beyond BRAF(V600): clinical mutation panel testing by next-generation sequencing in advanced melanoma

The management of melanoma has evolved due to improved understanding of its molecular drivers. To augment the current understanding of the prevalence, patterns, and associations of mutations in this disease, the results of clinical testing of 699 advanced melanoma patients using a pan-cancer next generation sequencing (NGS) panel of hotspot regions in 46 genes were reviewed. Mutations were identified in 43 of the 46 genes on the panel. The most common mutations were BRAF^V600 (36%), NRAS (21%), TP53 (16%), BRAF^Non-V600 (6%), and KIT (4%). Approximately one-third of melanomas had >1 mutation detected, and the number of mutations per tumor was associated with melanoma subtype. Concurrent TP53 mutations were the most frequent event in tumors with BRAF^V600 and NRAS mutations. Melanomas with BRAF^Non-V600 mutations frequently harbored concurrent NRAS mutations (18%), which were rare in tumors with BRAF^V600 mutations (1.6%). The prevalence of BRAF^V600 and KIT mutations were significantly associated with melanoma subtypes, and BRAF^V600 and TP53 mutations were significantly associated with cutaneous primary tumor location. Multiple potential therapeutic targets were identified in metastatic unknown primary and cutaneous melanomas that lacked BRAF^V600 and NRAS mutations. These results enrich our understanding of the patterns and clinical associations of oncogenic mutations in melanoma.