Citations

BACKGROUND Activating, nonamplification ERBB2 mutations ( ERBB2 mut) are not detected by immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH), but are detected by DNA sequencing and may predict clinical responses to human epidermal growth factor receptor (HER2)‐targeted therapy. The authors queried 5605 advanced/metastatic breast cancers (mBC) to uncover the frequency of ERBB2 mut genomic alterations. Clinical responses to anti‐HER2 therapeutics were identified. METHODS DNA was extracted from 40 µm of formalin‐fixed paraffin‐embedded (FFPE) sections. Comprehensive genomic profiling (CGP) was used to evaluate up to 315 genes (592× mean coverage depth). Results were analyzed for base substitutions, short indels, copy number changes, and selected rearrangements. RESULTS Of 5605 cases, 698 (12.5%) featured ERBB2 alterations, including 596 (10.6%) ERBB2 amplifications ( ERBB2 amp) and 138 (2.4%) ERBB2 mut; 38 cases (0.7%) had co‐occurring ERBB2amp and ERBB2mut. ERBB2mut predominantly affected the kinase (124 cases; 90%) or extracellular (15 cases; 11%) domains. Both primary BC (52 cases; 38%) and metastatic site biopsies (86 cases; 62%) were found to harbor ERBB2 mut, which were distributed across carcinoma not otherwise specified (NOS) (69 cases; 50%), invasive ductal carcinoma (IDC) (40 cases; 29%), invasive lobular carcinoma (ILC) (27 cases; 20%), and mucinous mBC (2 cases; 1%). Genes commonly coaltered with ERBB2 were tumor protein 53 ( TP53 ) (49%); phosphatidylinositol 3‐kinase catalytic subunit alpha ( PIK3CA ) (42%); cadherin 1, type 1 ( CDH1 ) (37%); MYC (17%); and cyclin D1 protein ( CCND1 ) (16%). CDH1 mutations were enriched in ERBB2 mut mBC ( P <0.0006) and associated with recurrent mBC. Selected patients with ERBB2 mut, without ERBB2 amp, who responded to anti‐HER2 targeted therapies are presented herein. CONCLUSIONS Within this large series, 1.8% of cases harbored ERBB2 mut, which are undetectable by standard‐of‐care IHC or FISH tests. Metastatic BC driven by ERBB2 mut respond to anti‐HER2 targeted therapies, and expanding clinical trials designed to detect ERBB2 mut by CGP and optimize targeted treatments are warranted. Cancer 2016 . © 2016 American Cancer Society . Cancer 2016;122:2654–2662. © 2016 American Cancer Society.

Abstract Introduction. For patients with non-small cell lung cancer (NSCLC) to benefit from ALK inhibitors, sensitive and specific detection of ALK genomic rearrangements is needed. ALK break-apart fluorescence in situ hybridization (FISH) is the U.S. Food and Drug Administration approved and standard-of-care diagnostic assay, but identification of ALK rearrangements by other methods reported in NSCLC cases that tested negative for ALK rearrangements by FISH suggests a significant false-negative rate. We report here a large series of NSCLC cases assayed by hybrid-capture-based comprehensive genomic profiling (CGP) in the course of clinical care. Materials and Methods. Hybrid-capture-based CGP using next-generation sequencing was performed in the course of clinical care of 1,070 patients with advanced lung cancer. Each tumor sample was evaluated for all classes of genomic alterations, including base-pair substitutions, insertions/deletions, copy number alterations and rearrangements, as well as fusions/rearrangements. Results. A total of 47 patients (4.4%) were found to harbor ALK rearrangements, of whom 41 had an EML4-ALK fusion, and 6 had other fusion partners, including 3 previously unreported rearrangement events: EIF2AK-ALK, PPM1B-ALK, and PRKAR1A-ALK. Of 41 patients harboring ALK rearrangements, 31 had prior FISH testing results available. Of these, 20 were ALK FISH positive, and 11 (35%) were ALK FISH negative. Of the latter 11 patients, 9 received crizotinib based on the CGP results, and 7 achieved a response with median duration of 17 months. Conclusion. Comprehensive genomic profiling detected canonical ALK rearrangements and ALK rearrangements with noncanonical fusion partners in a subset of patients with NSCLC with previously negative ALK FISH results. In this series, such patients had durable responses to ALK inhibitors, comparable to historical response rates for ALK FISH-positive cases.

Abstract Background: Previous failed trials of anti-EGFR therapy (TBCRC001) in breast cancer have not directly assessed EGFR amplification instead relying on pathway activation surrogates. Previous studies have examined EGFR amplification primarily retrospectively for research purposes without being part of a standard diagnostic evaluation. We evaluated 5,606 clincally advanced breast cases for which comprehensive genomic profiling was performed in the course of clinical care to identify EGFR altered mBC cases. Methods: DNA was extracted from 40 microns of FFPE sections from 5,605 mBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 236 or 315 genes to a mean coverage depth of &gt;600X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. Results: 155 (2.7%) of 5,605 mBC featured EGFR alterations. 126 (10.6%) featured EGFR amplification, and 27 (2.2%) featured ERBB2 subs/indels, with no cases harboring both amplification and another GA of EGFR. These patient (pts) had a median age of 55 years (range 30 to 78). For EGFR altered cases, specimens utilized for CGP included 59 (38%) from the patient's primary BC and 93 (60%) from metastatic sites including liver (14%), lymph node (14%), lung (8%), soft tissue (6%), skin (5%) and with information not available for 3 cases. 75 (48%) mBC were submitted as IDC, 69 (45%) as breast carcinoma NOS, 5 (3 %) as metaplastic BC, and 7 (5%) as other mBC. For the 126 EGFR amplified breast patients, quantitative estimation of EGFR copy number ranged from 6 to 380 copies, with a median of 12 copies. A patient with heavily pretreated case and whose TNBC harbored 32 copies of EGFR was begun on erlotinib and has experienced a 20 months ongoing complete response to erlotinib, and will be presented as will other outcomes and biomarker characterization of these cases. Conclusions: Given anecdotal evidence that mBC is responsive to anti-EGFR targeted therapies, prediction of benefit from such therapies may be linked to sensitive and specific detection of EGFR alteration in mBC cases. This study demonstrates a 2.7% EGFR alteration rate of mBC, with a striking median copy number of 12 for the subset of EGFR amplified cases. Given these findings along with anecdotal report of patient benefit, utilization of CGP in the course of clinical care or for clinical trials for mBC may help optimize treatement with targeted therapies for these patients including the direction of anti-EGFR monotherapy to EGFR altered patients. Citation Format: Ali SM, Wang K, Johnson A, Rodriguez AA, Elvin JA, Vergilio J-A, Suh JH, Chumsri S, Morosini D, Yelensky R, Lipson D, Chmielecki J, Miller VA, Ross JS, Chang J, Stephens PJ. EGFR genomic alterations in 5,605 cases of refractory and metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-02.

Abstract Background: Non-amplification ERBB2 alterations (ERBB2 mut) in advanced/metastatic breast cancer (mBC) are not detected by IHC or FISH, but when detected by DNA sequencing assays can lead to clinical responses to anti-HER2 targeted therapy. We queried a database of more than 43,000 clinical cases to uncover the frequency, type and associated genomic alterations (GA) in mBC driven by ERBB2 mut and highlight clinical responses to small molecule drug and antibody-based anti-HER2 therapeutics. Methods: DNA was extracted from 40 microns of FFPE sections from 5,605 mBC. Comprehensive genomic profiling (CGP) was performed using a hybrid-capture, adaptor ligation based next generation sequencing assay of up to 315 genes to a mean coverage depth of &gt;600X. The results were analyzed for base substitutions, short insertions and deletions, selected rearrangements, and copy number changes. Results: 698 (12.5%) of 5,605 mBC featured ERBB2 alterations. 596 (10.6%) featured ERBB2 amplifications and 137 (2.4%) featured ERBB2mut. 35 (0.6%) of total mBC had both ERBB2amp and ERBB2mut, which accounted for 5.0% of all ERBB2 altered mBC. The 137 ERBB2mut mBC cases had a median age of 61 years (range 29 to 93 years) and were sequenced to a mean depth of 600X. Samples utilized for CGP included 52 (38%) from the patient's primary BC and 85 (62%) from metastatic sites including bone/soft tissue/skin (12%), liver (20%), LN (14%), serous cavities (6%), lung (4%) and miscellaneous sites (6%). 71 (52%) mBC were submitted as carcinoma NOS, 44 (32%) as IDC, 22 (16%) as ILC and 1 (1%) as mucinous mBC. Of the 137 ERBB2mut cases, 8 featured more than 1 ERBB2 mut. There were 124 (85%) ERBB2 kinase domain mutations and 15 (10%) extra-cellular domain ERBB2mut. The most common genes co-altered in ERBB2mut mBC were TP53 (49%), PIK3CA (42%), CDH1 (37%), MYC (17%), and CCND1 (16%). The enrichment of ERBB2mut in CDH1 mut mBR was significant (p=0.0006) and associated with relapsed lobular mBC. Multiple case examples of kinase domain and extra-cellular domain ERBB2mut mBC responding to a variety of anti-HER2 targeted therapies will be presented. Conclusions: In this large series of 5,605 mBC, 20% of the total ERBB2 alterations were non-amplification ERBB2mut not detectable by standard of care IHC and FISH slide-based HER2 tests. Given the demonstration of ERBB2mut driven mBC responsive to anti-HER2 targeted therapies in this study, expansion of clinical trials designed to detect these ERBB2mut cases with CGP and optimize the targeted therapies for these patients is strongly recommended. Citation Format: Ross JS, Wang K, Ali SM, Chumsri S, Elvin JA, Vergilio J-A, Suh J, Yelensky R, Lipson D, Chmielecki J, Miller VA, Stephens PJ. Non-amplification ERBB2 genomic alterations in 5,605 cases of refractory and metastatic breast cancer: An emerging opportunity for anti-HER2 targeted therapies. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-05.

Abstract Histiocytic neoplasms are clonal, hematopoietic disorders characterized by an accumulation of abnormal, monocyte-derived dendritic cells or macrophages in Langerhans cell histiocytosis (LCH) and non-Langerhans cell histiocytosis (non-LCH), respectively. The discovery of BRAFV600E mutations in approximately 50% of these patients provided the first molecular therapeutic target in histiocytosis. However, recurrent driving mutations in the majority of patients with BRAFV600E–wild-type non-LCH are unknown, and recurrent cooperating mutations in non-MAP kinase pathways are undefined for the histiocytic neoplasms. Through combined whole-exome and transcriptome sequencing, we identified recurrent kinase fusions involving BRAF, ALK, and NTRK1, as well as recurrent, activating MAP2K1 and ARAF mutations in patients with BRAFV600E–wild-type non-LCH. In addition to MAP kinase pathway lesions, recurrently altered genes involving diverse cellular pathways were identified. Treatment of patients with MAP2K1- and ARAF-mutated non-LCH using MEK and RAF inhibitors, respectively, resulted in clinical efficacy, demonstrating the importance of detecting and targeting diverse kinase alterations in these disorders. Significance: We provide the first description of kinase fusions in systemic histiocytic neoplasms and activating ARAF and MAP2K1 mutations in non-Langerhans histiocytic neoplasms. Refractory patients with MAP2K1- and ARAF-mutant histiocytoses had clinical responses to MEK inhibition and sorafenib, respectively, highlighting the importance of comprehensive genomic analysis of these disorders. Cancer Discov; 6(2); 154–65. ©2015 AACR. This article is highlighted in the In This Issue feature, p. 109

Abstract Purpose: Women with advanced epithelial ovarian cancer are routinely treated with platinum-paclitaxel chemotherapy following cytoreductive surgery, yet only ∼20% achieve long-term disease-free survival. We hypothesized that differences in gene expression before treatment could distinguish patients with short versus long time to recurrence after administration of platinum-paclitaxel combination chemotherapy. Experimental Design: To test this hypothesis, gene expression profiling of 79 primary surgically resected tumors from women with advanced-stage, high-grade epithelial ovarian cancer was done using cDNA microarrays containing 30,721 genes. Supervised learning algorithms were applied in an effort to develop a binary classifier that could discriminate women at risk for early (≤21 months) versus late (&gt;21 months) relapse after initial chemotherapy. Results: A 14-gene predictive model was developed using a set of training samples (n = 51) and subsequently tested using an independent set of test samples (n = 28). This model correctly predicted the outcome of 24 of the 28 test samples (86% accuracy) with 95% positive predictive value for early relapse. Conclusions: Predictive markers for early recurrence can be identified for platinum-paclitaxel combination chemotherapy in primary ovarian carcinoma. The proposed 14-gene model requires further validation.