Abhishek Bavle

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors.

Importance Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. Objective To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors. Design Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic childrens hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record. Main Outcomes and Measures Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations. Results Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%). Conclusions and Relevance Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney

The X-linked BCL-6 co-repressor (BCOR) gene encodes a key constituent of a variant polycomb repressive complex (PRC) that is mutated or translocated in human cancers. Here we report on the identification of somatic internal tandem duplications (ITDs) clustering in the C terminus of BCOR in 23 of 27 (85%) pediatric clear cell sarcomas of the kidney (CCSK) from two independent cohorts. We profile CCSK tumours using a combination of whole-exome, transcriptome and targeted sequencing. Identical ITD mutations are found in primary and relapsed tumour pairs but not in adjacent normal kidney or blood. Mutant BCOR transcripts and proteins are markedly upregulated in ITD-positive tumours. Transcriptome analysis of ITD-positive CCSKs reveals enrichment for PRC2-regulated genes and similarity to undifferentiated sarcomas harbouring BCOR–CCNB3 fusions. The discovery of recurrent BCOR ITDs defines a major oncogenic event in this childhood sarcoma with significant implications for diagnostic and therapeutic approaches to this tumour.

Multimodality Treatment of Pediatric Esthesioneuroblastoma

Esthesioneuroblastoma (ENB) is a rare cancer of the nasal cavity in children. Radical surgery followed by postoperative radiation is considered the standard of care in adults. A similar approach in children can lead to significant long‐term morbidity.

Integrated tumor and germline whole exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle

The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individuals cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.

Dramatic clinical and radiographic response to BRAF inhibition in a patient with progressive disseminated optic pathway glioma refractory to MEK inhibition

ABSTRACT While clinical and radiographic responses to agents targeting the mitogen-activated protein kinases (MAPK) pathway have been repor-ted in pediatric low-grade gliomas (LGG), early phase trials indicate refractoriness to these medications in some of these patients. We report a patient with disseminated LGG with the BRAFV600E mutation, which was refractory to selumetinib, a MEK inhibitor, but subsequently showed immediate clinical and radiographic response to dabrafenib, a BRAF inhibitor, with sustained effect for 9 months prior to clinical progression. In LGGs, treatment resistance to one agent targeting the MAPK pathway might not imply refractoriness to other agents targeting this pathway.

Abstract IA16: Clinical genomics for children with solid tumors: Current realities and future opportunities

Genome-scale sequencing methods such as whole exome sequencing (WES) have provided significant insight into the pathogenesis of cancer. However, experience with the use of these tests in the clinical care of cancer patients remains limited. Sequencing of tumor and matched normal samples can reveal multiple types of results with implications for clinical practice. The identification of somatic (tumor-specific) mutations has the potential to offer diagnostic and prognostic information and inform selection of therapies. Detection of germline mutations in cancer susceptibility genes may prompt further genetic testing and guide cancer surveillance strategies for both the patient and family members. Germline mutations may also explain non-cancer phenotypes, predict drug responses, or provide reproductive counseling information for parents. The goal of the BASIC3 (Baylor College of Medicine Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating clinical tumor and constitutional WES into the care of children with newly diagnosed solid tumors. This study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors at Texas Children9s Cancer Center for two years after performing CLIA-certified WES of blood and frozen tumor samples. Results are deposited into the electronic health record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record over the two year follow-up period as well as through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Preferences of patient families and oncologists for reporting this complex information are obtained by interviews and audio recording of the WES result disclosure visits. Since the study opened in August 2012, more than 210 subjects have been enrolled (~80% of potentially eligible patients), representing the expected distribution of both CNS and non-CNS tumors. WES results have been reported for 170 subjects, revealing potentially-clinically relevant germline and somatic mutations in cancer genes known to be related to pediatric solid tumors as well as others known to be mutated primarily in adult cancer patients. Data will be presented regarding the diagnostic yield of combined tumor and germline WES for children with newly-diagnosed solid tumors. These results demonstrate the feasibility of routine tumor WES in the pediatric oncology clinic and a significant level of parental interest in receiving WES results and have significant implications for the treatment of children with relapsed and refractory solid tumors and the design of clinical trials using precision oncology approaches for these patients. Further analyses of the clinical utility of the WES data and the preferences of oncologists and parents for reporting of these results are under study. The BASIC3 study is a Clinical Sequencing Exploratory Research (CSER) program project supported by NHGRI/NCI 1U01HG006485. Citation Format: D. William Parsons, Angshumoy Roy, Yaping Yang, Tao Wang, Sarah Scollon, Katie Bergstrom, Robin A. Kerstein, Stephanie Gutierrez, Abhishek Bavle, Frank Y. Lin, Dolores H. Lopez-Terrada, Federico A. Monzon, Jed G. Nuchtern, Uma Ramamurthy, Amy L. McGuire, Susan G. Hilsenbeck, Jeffrey G. Reid, Donna M. Muzny, David A. Wheeler, Stacey L. Berg, Murali M. Chintagumpala, Christine M. Eng, Richard A. Gibbs, Sharon E. Plon. Clinical genomics for children with solid tumors: Current realities and future opportunities. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA16.

Abstract 04: Impact of whole exome sequencing results on clinical decision making for pediatric solid tumor patients in the hypothetical scenario of tumor relapse: A survey of pediatric oncologists

Background: The development of molecularly-targeted agents has made it possible to personalize therapy for patients by targeting the specific mutations in their tumor. Pediatric clinical trials utilizing such strategies are being planned but little is known about the opinions of pediatric oncologists regarding the utility of genomic data for guiding treatment decisions. The goals of this study were to (1) characterize those opinions in the context of children with relapsed/refractory solid tumors and (2) assess the potential impact of clinical whole exome sequencing (WES) data on medical decision-making in that context. Methods: As part of the ongoing BASIC3 clinical sequencing study at Texas Children9s Cancer Center, clinical germline and tumor (if sample available) WES were performed for unselected newly-diagnosed pediatric CNS and non-CNS solid tumor patients. The primary oncologist for each (n=17) received online surveys for each study patient before and after review of WES reports. The pre- and post-WES surveys asked oncologists to rank options for off-study systemic chemotherapy (of any type) for their patient in the hypothetical scenario of tumor relapse. Oncologists were then asked if they would consider using a molecularly-targeted agent in the context of a clinical trial, and if so, which agents (from a representative list), their rank order and the rationale for those choices. Post-WES surveys also included questions regarding perceived utility of the tumor WES results for patient care. Pre-WES surveys were analyzed for baseline oncologist responses regarding these hypothetical treatment decisions. When available, pre- and post-WES surveys were analyzed as pairs as an initial assessment of the influence of the WES results on the oncologist9s choice of therapy. Results: 177/189 (94%) of pre-WES surveys and 111/161 (69%) post-WES surveys were available for analysis. Analysis of pre-exome surveys revealed that oncologists would recommend systemic chemotherapy for 127/177 (72%) patients in the hypothetical event of tumor relapse but would consider a molecularly-targeted agent off-study as their first option in only 8/177 (4%) cases. In contrast, oncologists indicated that they would consider targeted therapies in the context of a clinical trial for 99/177 (56%) patients, most commonly sorafenib (n=21), cixutumumab (n=17), and crizotinib (n=13). There were 26 cases in which somatic mutations were identified in genes categorized as having established or potential clinical relevance, and for which both pre- and post-WES surveys were available. A corresponding targeted agent was ranked for consideration in the hypothetical scenario of relapse on the post-WES survey for 8/26 (31%) of these patients (somatic mutations in MET, JAK2, HRAS, NRAS X 2, ALK, BRAF, KIT), having only been chosen on the pre-WES survey in 2 of those cases. On 8 of 111 (7%) post-WES surveys, the oncologist removed a targeted agent that had been prioritized on the pre-WES survey after no relevant mutation was detected, including the Sonic Hedgehog inhibitor GDC-0449 in 5 cases. Conclusion: Although genomic tests such as WES have the potential to identify molecular targets for therapy in children with relapsed tumors, a survey of pediatric oncologists revealed that most consider such therapies as options only in the context of a clinical trial. These findings support the potential utility of WES in precision oncology approaches as well as the need for clinical trials evaluating the use of integrated genomic testing to guide treatment of children with relapsed solid tumors. Citation Format: Abhishek Bavle, Tao Wang, Frank Y. Lin, Angshumoy Roy, Robin A. Kerstein, Sarah Scollon, Katie Bergstrom, Stephanie Gutierrez, Uma Ramamurthy, Yaping Yang, Christine M. Eng, Richard A. Gibbs, Murali M. Chintagumpala, Susan G. Hilsenbeck, Sharon E. Plon, Stacey L. Berg, D. Williams Parsons. Impact of whole exome sequencing results on clinical decision making for pediatric solid tumor patients in the hypothetical scenario of tumor relapse: A survey of pediatric oncologists. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 04.