Spectrum Of Genomic Alterations Research Articles

Genomic determinants of nested variant urothelial carcinoma.

538 Background: Nested variant urothelial carcinoma (NVUC) is a historically aggressive variant of bladder cancer with management reliant on radical cystectomy given unclear effectiveness of chemotherapy. Given the aggressive behavior of NVUC, the identification of pathogenic and potentially targetable genomic alterations could suggest novel treatment paradigms for this rare histologic variant. Methods: Query of our institutional database identified 81 cases of clinically localized NVUC. Each case was re-reviewed by GU pathologists to confirm the histology. Targeted capture sequencing was performed to define the spectrum of genomic alterations in known and putative cancer genes. Clinical and sequencing data was then compared between the nested variant cases and a prospective cohort of clinically localized high-grade urothelial carcinomas, not otherwise specified (UC NOS). Results: On central re-review, tumors were classified as either classic NVUC (N=53) or high-grade urothelial carcinoma with nested features (N=28). A cohort of UC NOS patients (N=600) was used as a comparator. Median follow-up of the overall cohort was 4.3 years. Classic NVUC was associated with higher risk of cancer specific mortality compared to UC NOS on multivariate analysis (HR 1.76, p=0.04). Tumor mutational burden was lower in classic NVUC tumors versus UC NOS. Evaluation of 136 cancer-associated genes identified differences in mutational frequencies across the 3 cohorts (Table) with RhoA and FOXA1 alterations enriched in NVUC. Conclusions: Patients with NVUC have significantly higher risk of cancer specific mortality than patients with UC NOS. While there was significant overlap between the landscape of genomic alterations in NVUC and UC NOS tumors, NVUC tumors were enriched for RhoA and FOXA1 alterations among others.[Table: see text]

Abstract P4-06-01: Using multi-omic profiling to unravel the complexity of triple-negative breast cancer (TNBC)

Abstract Introduction: TNBCs show marked heterogeneity in their spectrum of genomic alterations, patterns of gene expression, proteomic profiles, and immune microenvironments. Although TNBC heterogeneity has been characterized at each of these levels individually, how variation at one level is associated with differences at other levels is poorly understood. As new targeted and immune-based therapies are developed for TNBC, there is a critical need to better understand this interplay. In this study, we performed “multi-omic” profiling on a cohort of TNBCs in order to determine how various DNA, RNA, protein, and immunologic parameters are correlated. Methods: A cohort of 95 formalin-fixed, paraffin-embedded tumor specimens from primary and metastatic TNBCs was curated. The following parameters in each tumor specimen were quantified: stromal tumor-infiltrating lymphocytes (sTILs) assessed on hematoxylin and eosin stained sections; expression of programmed death-ligand 1 (PD-L1), androgen receptor (AR) and the retinoblastoma tumor suppressor protein (RB) by immunohistochemistry (IHC); and expression of 776 breast cancer-related transcripts (using the nCounter Breast Cancer 360 panel). Targeted tumor DNA sequencing was performed in a subset of cases and tumor mutational burden (TMB) and DNA mismatch repair (MMR) status were determined. Gene expression patterns were analyzed using customized algorithms and we performed descriptive statistics to evaluate associations between DNA, RNA, and protein variables. Results: All 95 TNBC specimens were analyzed for sTILs; IHC for RB, AR, and PD-L1; and transcriptomic profiling. DNA sequencing was performed on 68 cases. The genomic, transcriptomic, and proteomic classification of the cohort is provided in Table 1. AR+ TNBCs (>1% tumor cells on IHC) were more likely to be non-basal (p<0.001), showed higher levels of AR (p<0.001) and FOXA1 (p<0.01) transcripts, were enriched for expression of genes related to mammary differentiation (p<0.001), depleted for expression of genes related to proliferation (p=0.018), “BRCAness” (p<0.001), and homologous recombination deficiency (HRD) (p=0.045), and showed significant upregulation of the immune inhibitory checkpoint molecule TIGIT (p=0.004). RB-positivity (>50% tumor cells on IHC) correlated with higher RB1 transcript levels but not with RB1 deletion/mutation status. RB+ tumors were depleted for expression of genes associated with HRD and BRCAness (p=0.029 and p=0.071). TNBCs showing widespread upregulation of gene expression signatures related to numerous immune processes included those with: (i) higher levels of sTILs, (ii) >1% PD-L1+ stromal mononuclear cells and/or tumor cells, (iii) tumors without RB1 or TP53 alterations. Genomic aberration in the PI3K pathway was associated with increased expression of AR and FOXA1 but not with alterations in immune gene expression. Conclusion: Patterns exist connecting TNBC heterogeneity across the DNA, RNA, and protein levels. Further analyses determining associations between genomic, transcriptomic, and proteomic features in this cohort of TNBC will be presented at the meeting. Genomic, transcriptomic, and proteomic classification of tumors in the entire TNBC cohortTumor site (n=95)Primary64 (67%)Regional nodal4 (4%)Distant nodal or visceral27 (28%)Stromal TILs (n=93)<10%50 (53%)10-49%30 (32%)>50%13 (14%)RB staining (n=95)Positive (>50% tumor cells)52 (55%)AR staining (n=95)Positive (>1% tumor cells)34 (36%)PD-L1 staining (stromal, n=94)Positive (>1% mononuclear cells)34 (37%)PD-L1 staining (tumor, n=94)>1% tumor cells27 (29%)PAM50 subtype (n=90)Basal72 (80%)HER2-enriched15 (17%)Luminal B3 (3%)TNBC subtype (n=91)Basal-like immune activated (BLIA)76 (80%)Basal-like immunosuppressed (BLIS)7 (7%)Mesenchymal (MES)8 (8%)Luminal androgen receptor (LAR)4 (4%)DNA alterations (n=68)TP53 alterations54 (80%)BRCA1/2 mutations14 (21%)RB1 alterations21 (31%)PI3K pathway alterations31 (46%) Citation Format: Shom Goel, Heather Ann Brauer, Yuqi Ren, Kara Gorman, Wafa Osmani, Jessica Pittenger, Chelsea Andrews, Edward T Richardson III, Elizabeth A Mittendorf, MD PhD, Eric P Winer, Stuart Schnitt, Sara M Tolaney. Using multi-omic profiling to unravel the complexity of triple-negative breast cancer (TNBC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-01.

Everolimus (E) plus bevacizumab (B) is effective first-line treatment for patients (pts) with advanced renal cell carcinoma (RCC) with papillary features (PF): Results from a phase II trial.

627 Background: We previously reported on a phase II trial of E+B across various non-clear cell RCC histologies and observed significant activity among pts with papillary or unclassified RCC ( uRCC ) with PF (objective response rate [ORR] 39%, median progression-free survival [PFS] 12.9 months [m]; Voss, JCO, 2016). An expansion cohort limited to these two histologies was conducted to confirm the efficacy of E+B. Methods: E + B was administered at standard doses until progressive disease (PD) or intolerance to therapy. The current analysis included 19 pts with pRCC or uRCC with PF in the initial cohort and 20 pts in the expansion cohort (total n=39). The primary endpoint was 6 month PFS with secondary endpoints of ORR, median PFS, and overall survival (OS). Correlative analyses included next generation sequencing (NGS) from tumor and germline across >341 genes of interest. Results: Of 39 pts, 24 had uRCC with PF, 14 had papillary RCC, and 1 had translocation RCC with PF. Among 37 evaluable pts, the ORR was 35%; 43% for uRCC with PF and 23% for papillary RCC. Six-month PFS for all 39 pts was 78%; 82% for uRCC with PF and 68% for papillary RCC. Median PFS was 13.7m; 13.7m for uRCC with PF and 8.4m for papillary RCC (Table). With median followup of 17.6m, median OS is 33.9m. Toxicity with E+B was similar to previous reports. 33 of 39 pts had NGS performed and partial responses were observed across a wide spectrum of genomic alterations, including several recurrently seen in papillary RCC variants such as mutations in FH, MET, NF2, and ARID1a. Conclusions: The expansion cohort confirms the activity of E+B for pts with advanced papillary RCC or uRCC with PF with superior ORR, PFS, and OS compared to historical results with sunitinib for these histologies. E+B represents a new standard first-line treatment option for these pts. Clinical trial information: NCT01399918. [Table: see text]

Clinical and genomic alterations features of patients with advanced colitis associated cancers (CAC).

e15010 Background: CAC are a catastrophic complication of inflammatory bowel disease. The spectrum of genomic alterations (GA) in CAC is different than that of sporadic colorectal cancer (CRC) (Yaeger et al PMID 27063727). While the prognosis for CAC patients (pts) may be worse than that of sporadic CRC pts, there is little data regarding outcome for metastatic CAC pts treated with standard chemotherapy regimens. We reviewed demographic features and clinical outcome for pts with metastatic CAC in the context of somatic tumor GA. Methods: We identified small and large bowel CAC cases seen at Memorial Sloan Kettering between 2003 and 2015 with tissue available for study. Hybrid capture based next-generation sequencing analysis of over 300 cancer-related genes was used to comprehensively characterize GA. The electronic medical record of each patient was reviewed. Demographic and clinical data was extracted and outcome reviewed in the context of somatic tumor GA. Results: Clinical features for 17 pts with metastatic CAC are shown below. All pts with initial stage III CAC received FOLFOX adjuvant therapy. First-line treatment for metastatic disease included FOLFOX/FOLFIRINOX/FU-LV in 10 previously untreated pts and FOLFIRI after adjuvant therapy. Median duration of survival from time of metastatic disease was 14.8 months, (95% CI 5.7-24.3;range 2-68+ months), substantially less than that expected for pts with Stage IV CRC. Only 4 patients survived for > 24 months. GA were identified in TP53 (87%) and KRAS (33%); potentially targetable alterations were found in 8 pts ( IDH1 (1), EML4-ALK(1), ERBB2 (1); FGFR1/2 (3); BRAF (1); PIK3CA(1). 2 pts received a targeted agent based on GA; 1 partial response to a FGFR inhibitor is ongoing. No patient had a hyper-mutated tumor. Conclusions: Metastatic CAC pts have an exceedingly poor prognosis, with survival well below that expected for sporadic CRC. BRAF mutations associated with poor outcome in sporadic CRC are rare in CAC. 47% of CAC pts had potentially targetable GA. [Table: see text]

Breast ductal carcinoma in situ carry mutational driver events representative of invasive breast cancer

The spectrum of genomic alterations in ductal carcinoma in situ (DCIS) is relatively unexplored, but is likely to provide useful insights into its biology, its progression to invasive carcinoma and the risk of recurrence. DCIS (n=20) with a range of phenotypes was assessed by massively parallel sequencing for mutations and copy number alterations and variants validated by Sanger sequencing. PIK3CA mutations were identified in 11/20 (55%), TP53 mutations in 6/20 (30%), and GATA3 mutations in 9/20 (45%). Screening an additional 91 cases for GATA3 mutations identified a final frequency of 27% (30/111), with a high proportion of missense variants (8/30). TP53 mutations were exclusive to high grade DCIS and more frequent in PR-negative tumors compared with PR-positive tumors (P=0.037). TP53 mutant tumors also had a significantly higher fraction of the genome altered by copy number than wild-type tumors (P=0.005), including a significant positive association with amplification or gain of ERBB2 (P<0.05). The association between TP53 mutation and ERBB2 amplification was confirmed in a wider DCIS cohort using p53 immunohistochemistry as a surrogate marker for TP53 mutations (P=0.03). RUNX1 mutations and MAP2K4 copy number loss were novel findings in DCIS. Frequent copy number alterations included gains on 1q, 8q, 17q, and 20q and losses on 8p, 11q, 16q, and 17p. Patterns of genomic alterations observed in DCIS were similar to those previously reported for invasive breast cancers, with all DCIS having at least one bona fide breast cancer driver event. However, an increase in GATA3 mutations and fewer copy number changes were noted in DCIS compared with invasive carcinomas. The role of such alterations as prognostic and predictive biomarkers in DCIS is an avenue for further investigation.

Abstract PD8-05: Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry

Abstract Objectives: Paucity of data on populations of African Ancestry in clinical trials continues to limit our ability to design and implement innovative solutions to narrow the breast cancer survival gap amongst Africans, African Americans, and European Americans. We have developed a cross-continent research infrastructure to examine the spectrum of genomic alterations in breast tumors from West Africa and subsequently, to compare them to tumors from African American women and women of European Ancestry in The Cancer Genome Atlas (TCGA) database. Methods: Consecutive women with breast cancer presenting for treatment at the University College Hospital, Ibadan and at Lagos State University Teaching Hospital, Lagos, Nigeria gave informed consent and were recruited to the West African Breast Cancer Study (WABCS) between 2013-2016. Tumor-normal pairs were subjected to exome and/or high-depth (90x) genome sequencing. High confidence somatic mutations (substitutions, insertions/deletions and structural variants) were obtained by using multiple variant callers. Furthermore, 1,089 exomic and 80 genomic breast tumor-normal pairs from TCGA were harmonized with WABCS samples, resulting in a cohort of 147 West Africans (147 exome; 40 genome), 154 African Americans (154 exome; 31 genome), and 776 Caucasians (776 exome; 43 genome). Results: Across the exomes, genes commonly altered in breast cancer in TCGA are also altered in women of African ancestry, but the mutational spectrum is quite different, demonstrating overrepresentation of tumors with aggressive phenotypes. Overall, TP53 (65%), ERBB2 (27%), and GATA3 (17%) showed statistically significant higher alteration frequencies in West Africans and African Americans. In contrast, PIK3CA (24%) was less frequently mutated. Of note, GATA3 mutation was statistically significantly more frequent in Nigerians (39%) and African Americans (16.7%) compared to Caucasians (10.5%), in ER-positive cancers. Analysis on Structural Variants (SV), on the other hand, has shown that the genome-wide SV counts among three populations are comparable in ER-negative cancers, while Nigerians have significantly more SV counts compared to African Americans (P=0.0013) or European Americans (P=2.9x10-5) in ER-positive cancers. Similarly, genome-wide substitution patterns in ER+ and ER- cancers varied widely by race/ethnicity. In ER- cases, West Africans carried the highest proportion of canonical APOBEC-associated substitutions, particularly C&amp;gt;T transitions. Conversely, European Americans with ER+ disease showed a higher proportion of C&amp;gt;T than both West Africans (Welch t-test P = 0.044) and African Americans (Welch t-test P = 0.011). Mutation signature analyses highlighted multiple APOBEC signatures, with notable contribution differences across ancestry and ER status. A signature likely corresponding to DNA damage repair correlated with the proportion of genetic ancestry, being most prevalent in European Americans and least common in Nigerians, particularly in ER-negative cancers, with African Americans showing a degree of this signature's contribution in between the two populations (linear model adjusted for age, P=1.0x10-10). Conclusions: Overall, our data suggests mutation spectra differences in across race/ethnicity and geography. Identification of molecular characteristics such as higher rates of HER2 enriched tumors and higher rates of GATA3 mutations in ER positive tumors are beginning to reveal the genomic basis of race-associated phenotypes and outcomes in breast cancer. Population differences in frequency and spectrum of mutations should now inform the design of innovative clinical trials that improve health equity and accelerate Precision Oncology care in diverse populations. Citation Format: Olopade OI, Pitt JJ, Riester M, Odetunde A, Yoshimatsu T, Labrot E, Ademola A, Sanni A, Okedere B, Mahan S, Nwosu I, Leary R, Ajani M, Johnson RS, Sveen E, Zheng Y, Wang S, Fitzgerald DJ, Grundstad J, Tuteja J, Clayton W, Khramtsova G, Oludara M, Omodele F, Benson O, Adeoye A, Morhason-Bello O, Ogundiran T, Babalola C, Popoola A, Morrissey M, Chen L, Huo D, Falusi A, Winckler W, Obafunwa J, Papoutsakis D, Ojengbede O, White KP, Ibrahim N, Oluwasola O, Barretina J. Comparative analysis of the genomic landscape of breast cancers from women of African and European ancestry [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-05.

Spectrum of genomic alterations in FGFR3: current appraisal of the potential role of FGFR3 in advanced urothelial carcinoma.

Molecular analysis has identified subsets of urothelial carcinoma (UC) expressing distinct genetic signatures. Genomic alterations in the oncogenic fibroblast growth factor receptor 3 (FGFR3) pathway are among the most well described in UC and have led to extensive and ongoing investigation of FGFR3-targeted therapies in this disease, although no new drugs have yet been approved. Given the unmet need for effective treatments in advanced and metastatic UC, a better understanding of the known molecular alterations of FGFR3 and of the previous and ongoing clinical investigations of this promising target in UC deserves attention. The objective of the present review is to describe the landscape of alterations and biology of FGFR3 in UC, comprehensively summarize the current state of UC clinical trials of FGFR3 inhibitors, and discuss future therapeutic applications. Using the Pubmed and Clinicaltrials.gov databases, articles describing the spectrum and biological activity of FGFR3 genomic alterations and trials of FGFR3 inhibitors in UC were identified. Search terms included 'FGFR3 genomic alterations' and 'urothelial cancer' or 'bladder cancer'. Genomic alterations, including translocations and activating mutations, are increasingly described in advanced and metastatic UC. The majority of clinical trials have been performed in unselected populations; however, recent studies have reported encouraging preliminary data. We argue that routine use of molecular genomic tumour analysis in UC may inform selection of patients for appropriate trials and we further investigate the potential of FGFR3 as a meaningful clinical target for this difficult disease.

Abstract 4667: The complex genomic landscape of glial tumors reveals distinct subclasses and potential therapeutic targets associated with clinical responses to targeted inhibitors

Abstract The genomic landscape of glial tumors is complex, and the identification of effective targeted treatments has proven challenging. To find potential therapeutic vulnerabilities, we analyzed the spectrum of genomic alterations in over 700 confirmed glial tumors. Extracted DNA was subjected to hybrid capture for 236 cancer-related genes plus 19 genes frequently rearranged in cancer, and sequenced to a median depth of &amp;gt;500x. Resultant sequences were assessed for base substitutions, insertions and deletions, copy number changes, and select rearrangements. Glioblastomas showed frequent alterations in CDKN2A/B (55%), TP53 (40%), PTEN (40%), and EGFR (40%), including EGFRviii (18.6%). Anaplastic astrocytomas harbored frequent alterations in TP53 (65%), IDH1 (55%), and ATRX (51%). Astrocytomas, including both low grade and mixed grade tumors, had a similar genomic landscape to that of anaplastic astrocytomas with frequent alterations in TP53 (53%), IDH1 (45%), and ATRX (36%). In addition to known fusions involving EGFR, FGFR3, and BRAF, we also identified rare, but therapeutically relevant, fusions involving ROS1 and PDGFRA that have been reported exclusively in lung cancer and hypereosinophilic syndrome, respectively. Unsupervised clustering of all glial tumors based on genomic alterations identified six distinct classes each driven by unique combinations of genomic events. Tumors driven by concurrent alterations in IDH1, ATRX, and TP53 were associated with younger age and anaplastic astrocytoma histology (p = 2.2×10−16). The addition of NF1 alterations to IDH1, ATRX, and TP53 mutations was modestly enriched in glioblastoma samples (p = 0.04). Other classes showed distinct drivers (MAPK or PI3K pathway alterations) coupled with unique mechanisms of cell cycle deregulation (CDKN2A/B loss, CDK4/MDM2 amplification, or RB1 alterations). The potential clinical importance of these genomic findings was demonstrated in three patients with surgically confirmed recurrent glioblastoma who received molecularly-matched targeted inhibitors as part of second-line therapy. Patients with activation of EGFR via amplification or mutation (R108K), activation of the mTOR pathway via inactivation of NF1, and constitutive activity of BRAF (V600E) were treated with erlotinib, everolimus, and vemurafenib, respectively, administered in combination with chemotherapy. In all three cases, imaging responses and overall survival were deemed far greater than expected by the treating physician. In conclusion, complex genomic data from glial tumors can be grouped into distinct sub-classes driven by unique combinations of alterations. Anecdotal clinical data suggest that subsets of patients may benefit from molecularly matched targeted therapies; larger studies investigating the efficacy of these agents in selected patients are warranted. Citation Format: Juliann Chmielecki, Michael E. Goldberg, Alex Fichtenholtz, Julia Elvin, Garrett M. Frampton, Siraj M. Ali, Jeffrey S. Ross, Deborah Morosini, Vincent A. Miller, David Piccioni, Santosh Kesari, Philip J. Stephens. The complex genomic landscape of glial tumors reveals distinct subclasses and potential therapeutic targets associated with clinical responses to targeted inhibitors. [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 4667. doi:10.1158/1538-7445.AM2015-4667

Establishing a translational genomics infrastructure in pediatric cancer: the GREAT KIDS experience.

We have recently established a biobanking and sequencing pipeline at the University of Chicago dubbed Genomics for Risk Evaluation and Anticancer Therapy in Kids. We plan to intersect family and personal history of cancer and other diseases with multidimensional genomic profiling in order to: understand how genetics may have contributed to the development of cancer for each child, and investigate the spectrum of genomic alterations within a tumor spatially (e.g., primary site vs distant metastasis) and over time (e.g., diagnosis vs relapse). This review highlights some of the practical considerations involved in creating such a program including the capacity to use our platform for multi-institutional collaborations.

Abstract PD3-5: Whole exome sequencing (WES) of HER2+ metastatic breast cancer (MBC) from patients with or without prior trastuzumab (T): A correlative analysis of TBCRC003

Abstract Background: Although the spectrum of genomic alterations in primary, treatment-naïve breast tumors has been described, the genomic landscape of HER2+ MBC remains underexplored. Furthermore, tumor genomic alterations that arise after progression on anti-HER2 therapy are largely unknown. Methods: We prospectively collected metastatic tumor biopsies from patients (pts) enrolled on TBCRC003 (NCT00470704), a phase II study evaluating the combination of lapatinib (L) and T in pts with HER2+ MBC who had varying degrees of prior T exposure. We performed WES on baseline metastatic biopsies and normal DNA from 57 pts. In 36 pts, we also performed WES on pre-treatment primary tumors. Tumors were analyzed for point mutations, insertions/deletions, and copy number alterations. Results: Total accrual was 116 pts. 87 pts were registered in one of two efficacy cohorts: Cohort 1 included pts w no prior T for MBC. Pts with prior adjuvant T were included if the interval from last T to 1st recurrence &amp;gt; 12 months. Cohort 2 included pts with 1-2 prior lines of T for MBC or recurrence within 12 months of adjuvant T. An additional 29 pts were enrolled in a biomarker cohort (Cohort 3). Per-protocol efficacy analyses for 85 pts deemed evaluable are shown below: Objective Response RateClinical Benefit RateMedian Time to ProgressionCohort 150% (90% CI 33.8-66.2%)57.5% (95% CI 40.9-73.0)7.4 monthsCohort 222.2% (90% CI 11.2-37.1%)42.2% (95% CI 27.7-57.8)5.3 months As we previously reported (Wagle et al, ASCO 2014), across 57 metastatic tumors, significant recurrently mutated genes were TP53 (n=30; 53%) and PIK3CA (n=19; 33%). The frequency of mutant TP53 and PIK3CA was not significantly different from 119 primary, treatment-naïve HER2+ tumors sequenced in the TCGA study (50%, p=0.8 and 27%, p=0.5, respectively). Recurrent copy number alterations were also similar to TCGA data. Comparing the 38 pts who received any prior T with the 19 pts who did not, there was no significant difference in the incidence of mutant TP53 (53% vs 53%, p=1.0) and PIK3CA (37% vs 26%, p=0.6). We identified mutations in the HER2 kinase domain in 4/38 pts who received prior T (11%), as compared to 0/19 T-naïve pts. HER2 kinase domain mutations have been identified in ∼2% of HER2-negative cancers but &amp;lt;1% of primary HER2+ cancers. 3 of the mutations were L755S, which has been shown to be resistant to L and sensitive to irreversible HER2 inhibitors. The 4th mutation was D742N, a novel kinase domain mutation. None of the 4 pts with HER2 kinase domain mutations had an objective response, though 1 pt had stable disease for 29 weeks. An analysis comparing paired archival primary tumors and baseline metastatic biopsies from 36 pts to identify genomic alterations acquired or enriched in the metastatic tumors will be presented. Conclusions: We present an analysis of the genomic landscape of HER2+ MBC, including comparisons between matched primary tumors and metastatic biopsies. Somatic HER2 kinase mutations in pts with HER2+ MBC treated with prior T suggests that these mutations may be involved in resistance to T, and may predict poor response to additional anti-HER2 therapy with combined L and T. Novel therapeutic approaches may be required for these pts. Citation Format: Nikhil Wagle, Nancy U Lin, Andrea L Richardson, Ignaty Leshchiner, Ingrid A Mayer, Andres Forero-Torres, Timothy J Hobday, Elizabeth C Dees, Rita Nanda, Mothaffar F Rimawi, Hao Guo, William T Barry, Ron Bose, Wei Shen, Antonio C Wolff, Stacey B Gabriel, Levi A Garraway, Eric P Winer, Ian E Krop. Whole exome sequencing (WES) of HER2+ metastatic breast cancer (MBC) from patients with or without prior trastuzumab (T): A correlative analysis of TBCRC003 [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD3-5.

GE-07 * THE GENOMIC LANDSCAPE OF DIVERSE BRAIN TUMORS REVEALS KNOWN AND NOVEL ONCOGENIC ALTERATIONS FREQUENTLY ASSOCIATED WITH SENSITIVITY TO TARGETED INHIBITORS

BACKGROUND: Brain tumors are complex cancers that range in behavior from aggressive to indolent. While some oncogenic alterations have been identified in these tumors, the efficacy of molecularly-matched targeted therapies has not been established. We sought to explore the spectrum of genomic alterations in a large unselected clinical collection of brain tumors (n = 282), and to determine the potential therapeutic actionability in these diseases. METHODS: FoundationOne® was used to characterize comprehensively all classes of genomic alterations in 236 cancer-related genes plus 19 genes frequently rearranged in cancer. Captured DNA was sequenced to average median depth of 696x, and resultant sequences were assessed for base substitutions, insertions and deletions, copy number changes, and select rearrangements. RESULTS: This collection consisted of glioblastoma (58.5%), astrocytoma (13.1%), anaplastic astrocytoma (12.4%), oligodendroglioma (9.2%), glioma (6.4%), and gliosarcoma (0.4%). Ninety-six percent (96%) of cases harbored at least one alteration associated with an approved agent or an agent in clinical trials. Activating genomic alterations included rearrangements, amplification, and/or mutations in EGFR, BRAF, PDGFRA, MET, KIT, FGFR3, and KRAS. Recurrent loss of function alterations were identified in TP53, CDKN2A/B, ATRX, NF1, and RB1, among others. Co-occurring alterations in the DNA helicase ATRX and the gene encoding IDH1 were also observed frequently. Interestingly, we identified a FIP1L1-PDGFRA fusion in a glioblastoma, and multiple BRAF fusions in anaplastic astrocytoma. CONCLUSIONS: Genomic alterations associated with an FDA-approved or investigational agents are frequent in brain cancers. Although the efficacy of molecularly-matched therapies has yet to be established in these tumors, converging clinical evidence suggest potential clinical utility. The FIP1L1-PDGFRA fusion identified in a glioblastoma is associated with remarkable sensitivity to imatinib in hypereosinophilic syndrome, and BRAF fusions in other diseases are responsive to combination targeted therapy. These data suggest that comprehensive genomic profiling can identify potential targets for personalized therapies in these tumors.

Whole-exome sequencing (WES) of HER2+ metastatic breast cancer (MBC) from patients (pts) treated with prior trastuzumab (T): A correlative analysis of TBCRC003.

536 Background: Although several large sequencing studies have elucidated the spectrum of genomic alterations in primary, treatment-naive HER2+ cancers, the genomic landscape in metastatic tumors after progression on anti-HER2 therapy remains largely unknown. Methods: We performed WES on baseline metastatic tumor biopsies from 57 pts enrolled on TBCRC003 (NCT00470704), a phase II study evaluating combined lapatinib (L) and T that included pts with varying degrees of prior T exposure. Tumors were analyzed for point mutations, insertions/deletions, and copy number alterations. Results: Across 57 tumors, the median depth of coverage was 99-fold (range 37-160). The median number of coding mutations per sample was 55 (Range: 1-716). Significant recurrently mutated genes were TP53 (n=30; 53%) and PIK3CA (n=19; 33%). The incidence of mutant TP53 and PIK3CA was not significantly different from 104 primary, treatment-naive HER2+ tumors sequenced in the TCGA study (53% and 28%, respectively). Comparing the 40 pts w...

The spectrum of genomic alterations in young adult non-small cell lung cancer (NSCLC).

8077 Background: Identification of targetable genomic alterations in patients (pts) with NSCLC can have a profound impact on treatment and clinical outcomes. Given the complexity and cost of comprehensive genomic testing, clinical characteristics enriching for targetable genomic alterations are of interest. We hypothesized that young adults with NSCLC would have a higher prevalence of targetable genomics alterations compared to the general NSCLC population. Methods: An institutional database of pts with NSCLC was reviewed in an IRB-approved fashion to identify subjects with age &lt; 40 at diagnosis. Clinical characteristics and risk factors were reviewed. Tumor genotyping for alterations in EGFR, KRAS, ALK, BRAF, HER2, and ROS1was pursued as part of an institution-wide genomics protocol. Targeted next-generation sequencing (NGS) of wild-type cases is underway. Results: From 2032 subjects with NSCLC, we identified 70 diagnosed at an age &lt; 40 (3.4%). Pt characteristics: median age 35 (range 20-39); 63% never-smokers, 33% with ≥10 pack-years; 74% adeno, 9% squam, 14% undifferentiated, 3% neuroendocrine; 19% had a family history of lung cancer; 61% stage IV at diagnosis. Median survival from date of advanced disease was 15.8 months. Genotyping was performed on 51 pts with adeno or undifferentiated histology: 14 with EGFR mutations (27%), 5 with KRAS mutations (10%), 8 with ALK rearrangements (16%), 0 with BRAF mutations, 1 with a HER2 insertion (2%), 1 with a ROS1 rearrangement (2%). Compared to a reference prevalence from the Lung Cancer Mutation Consortium (Kris et al, ASCO, 2011), KRAS mutations were less common (p=0.01) and ALK rearrangements were more common (p&lt;0.01). NGS of 2 cases to date has identified one pt with a novel 21 base-pair insertion mutation in FGFR2, not present in germline tissue. Conclusions: 47% (CI: 33%-60%) of pts diagnosed with NSCLC under age 40 harbor a targetable alteration in EGFR, ALK, HER2, or ROS1. These patients may be enriched for targetable genotypes and deserving of a unique treatment approach, and additionally represent an attractive population for genomic discovery.Supported in part by the Bonnie J. Addario Lung Cancer Foundation and the Conquer Cancer Foundation of ASCO.

Cancer gene profile of metastatic breast cancer.

1015 Background: There is great interest in using genomic information to guide therapy selection in cancer patients. The aim of this study was to determine the spectrum of genomic alterations identified in MBC patients, and evaluate the concordance of alterations between primary and recurrent tumors. Methods: We performed comprehensive profiling on formalin-fixed paraffin embedded samples from 42 patients with MBC using a targeted next generation sequencing (NGS) assay in a CLIA laboratory (Foundation Medicine). Genomic libraries were captured for 3,230 exons in 182 cancer related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to an average depth of 390X with 99% of bases covered &gt;100X. In total 30 primary and 37 recurrent tumors were profiled, including 3 separate recurrences in 1 patient and matched primary-recurrences in 22 patients. Point mutations, indels, copy number alterations and rearrangements were assessed. Alterations that are targetable with established or investigational therapeutics were considered “actionable”. Results: At least 1 genomic alteration was identified in all but 2 breast samples (both primary tumors). Point mutations were identified in several cancer-related genes including PIK3CA, TP53, PTEN, CDH1, ARID1A, AKT1, NF1, FBXW7 and FGFR3. Amplification was observed in HER2; 11 of 12 HER2 IHC positive samples were found to have HER2 gains by NGS; in addition, a HER2 gain was identified by NGS in a HER2- (1+ IHC) sample. Amplification of PIK3CA, IGF1R, FGFR2, AKT2, MDM2, and MCL1 plus a CDKN2A homozygous deletion were also identified. While the majority of known driver alterations (85%) were concordant in the matched pairs of primary and recurrent tumors, in 11 of 22 sets there was at least 1 discordant driver alteration, and these included both gains and losses of potential therapeutic targets. Overall 32 of 42 patients (76%) had an actionable genomic alteration. Conclusions: Genomic profiling of breast cancer samples reveals genomic alterations in most metastatic breast cancer patients. Over three quarters of patients have actionable findings, suggesting that genomic profiling may assist in individualized pathway-directed therapy.