<p>PDF file - 423KB, Figure S1: Broad copy numbers at the p- and q-arms in the Spanish cohort; Figure S2: Broad copy numbers at the p- and q-arms in the DFCI cohort. (see Figure S1 for an explanation of this plot); Figure S3: These GISTIC output files show the correlation between gene number and frequency of armlevel events in the (a) Spanish cohort and the (b) DFCI cohort; Figure S4: Recurrent copy number gains in the (a) Spanish and (b) DFCI cohort. Figure S5: Recurrent deletions in the (a) Spanish and (b) DFCI cohorts (see Figure S4 for an explanation of this plot); Table S1: Significant (q-value < 0.25) GISTIC broad aberrations and their association with overall survival after start of chemotherapy (Spanish cohort); Table S2: Significant (q-value < 0.25) GISTIC broad aberrations and their association with overall survival after recurrence (DFCI cohort).</p>
Abstract Interpretation of the clinical significance of somatic gene variants in cancer remains a major challenge in cancer diagnosis, prognosis and treatment response prediction. We will report on progress and plans of the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG). The CDWG membership consists of over 150 multi-disciplinary experts in cancer biology, oncology, pathology, genetics, genomics and informatics. The mission of the ClinGen Somatic Cancer CDWG is to facilitate the development of data curation guidelines and standards to determine the clinical significance of somatic alterations in cancer, thereby enhancing the usability, dissemination and implementation of cancer somatic changes in the ClinGen resource and other knowledgebases including CIViC, ClinVar, and the Variant Interpretation for Cancer Consortium (VICC) MetaKB. Our goal is to create high-quality assertions of the clinical significance of specific somatic variants in cancer by leveraging the CIViC curation interface, adapting the germline procedures of ClinGen to somatic variant interpretation, and implementing the interoperability standards of the Global Alliance for Genomics and Health (GA4GH). The ClinGen Somatic effort is overseen by the Somatic CDWG and reports progress to the overall ClinGen consortium. There are Somatic Cancer subdomains focused on particular clinically important domains of cancer variant interpretation including three Task Forces (covering Pediatric Cancer, Hematologic Cancer, and Solid Tumors) and a growing number of Somatic Cancer Variant Curation Expert Panels (SC-VCEPs). To improve quality and consistency of clinical interpretations, each candidate somatic cancer VCEP must complete a four step approval process adapted from ClinGen’s work in Germline disease domains. The Somatic CDWG works to ensure that each group is aware of available training materials and detailed standard operating procedures. Each SC-VCEP also coordinates with the ClinGen Cancer Variant Interpretation Committee (CVI) whose goal is to support development of granular specifications for the AMP/ASCO/CAP guidelines for somatic variant interpretation. New SC-VCEPs are anticipated to focus on specific clinically relevant genes, pathways, disease entities, variant classes or treatment modalities. Currently, three SC-VCEPs have begun to work through the four step process (focused on FGFR mutations, NTRK fusions, and FLT3 mutations respectively), and two more SC-VCEPs are in the planning stage (Histone H3 and Ph-like ALL). To date, ClinGen Somatic groups have contributed 619 evidence lines into CIViC from 353 published papers and 21 assertions of clinical significance. Input from the AACR community is critical for the establishment of new SC-VCEPs that address areas of variant interpretation with the greatest need. Citation Format: Jason Saliba, Gordana Raca, Angshumoy Roy, Ian King, Shamini Selvarajah, Xinjie Xu, Rashmi Kanagal-Shamanna, Laveniya Satgunaseelan, David Meredith, Mark Evans, Alanna Church, Panieh Terraf, Yassmine Akkari, Heather E. Williams, Wan-Hsin Lin, Chimene Kesserwan, Deborah I. Ritter, Kilannin Krysiak, Arpad Danos, Alex Wagner, Marilyn M. Li, Dmitriy Sonkin, Jonathan S. Berg, Sharon E. Plon, Heidi L. Rehm, Shashikant Kulkarni, Ramaswamy Govindan, Obi L. Griffith, Malachi Griffith, on behalf of the ClinGen Somatic CDWG. The Clinical Genome Resource (ClinGen) somatic cancer clinical domain working group [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1192.
Metastatic urothelial carcinoma of the bladder is associated with multiple somatic copy-number alterations (SCNAs). We evaluated SCNAs to identify predictors of poor survival in patients with metastatic urothelial carcinoma treated with platinum-based chemotherapy.We obtained overall survival (OS) and array DNA copy-number data from patients with metastatic urothelial carcinoma in two cohorts. Associations between recurrent SCNAs and OS were determined by a Cox proportional hazard model adjusting for performance status and visceral disease. mRNA expression was evaluated for potential candidate genes by NanoString nCounter to identify transcripts from the region that are associated with copy-number gain. In addition, expression data from an independent cohort were used to identify candidate genes.Multiple areas of recurrent significant gains and losses were identified. Gain of 1q23.3 was independently associated with a shortened OS in both cohorts [adjusted HR, 2.96; 95% confidence interval (CI), 1.35-6.48; P = 0.01 and adjusted HR, 5.03; 95% CI, 1.43-17.73; P < 0.001]. The F11R, PFDN2, PPOX, USP21, and DEDD genes, all located on 1q23.3, were closely associated with poor outcome.1q23.3 copy-number gain displayed association with poor survival in two cohorts of metastatic urothelial carcinoma. The identification of the target of this copy-number gain is ongoing, and exploration of this finding in other disease states may be useful for the early identification of patients with poor-risk urothelial carcinoma. Prospective validation of the survival association is necessary to demonstrate clinical relevance.
198 Background: Docetaxel and androgen receptor (AR) targeted agents have become standard options for mCSPC. CGP data is limited in mCSPC, however has the potential to guide treatment selection. We aimed to establish the feasibility of using CGP to characterize genomic alterations (GAs) in mCSPC. Methods: Patients with mCSPC were prospectively recruited at the Princess Margaret Cancer Centre to the OCTANE trial (NCT02906943), which aims to establish a genomically-characterized and clinically-annotated patient base that can be enrolled into specific research initiatives. Archival tumour specimens (after clinical testing completed) were profiled using next-generation sequencing (NGS) with a custom hybridization capture DNA-based panel (555 genes) or a targeted DNA/RNA amplicon panel (Oncomine Comprehensive Assay v3, 161 driver gene panel). GAs were classified according to the 2017 AMP/ASCO/CAP consensus recommendation. Clinical data were extracted from electronic health records. Results: Since 2016, 17/31 (55%) mCSPC patients who enrolled had sufficient tissue (15 from primary, 1 lymph node, 1 bone) for CGP. All had adenocarcinoma histology, most had high volume (76%) or de novo (71%) mCSPC. Median presenting PSA was 56 µg/L (range 8.4 – 1394). Patients received docetaxel (88%) or abiraterone (12%). Tier I/II GAs consistent with possible benefit from approved or investigational targeted therapies were identified in 14/17 patients (82%). AR pathway GAs (in 29%) were present regardless of prior androgen deprivation therapy or disease volume. DNA damage repair GAs (in 65%) included BRCA2, ATM, PALB2, MLH1/3, CDK12, FANCA, ERCC4, and SPOP. Other GAs involved the cell cycle, mTOR, EGFR, wnt, hedgehog, notch, and epigenetic pathways. Conclusions: In this small cohort, CGP was feasible in the setting of mCSPC for half of the patients. Potentially actionable GAs were identified in over 80% of patients tested. Pending confirmation from larger cohorts, these data support CGP in mCSPC prior to systemic therapy initiation, and highlight its potential role in future biomarker development and trial design in mCSPC.
