Landscape Of Somatic Alterations Research Articles

The influence of the germline HSD3B1 adrenal-permissive variant (c.1100 C) on somatic alteration landscape, transcriptome, and immune-cell infiltration in prostate cancer.

215 Background: A missense-encoding germline polymorphism in the HSD3B1 gene has been shown to result in adrenal-permissive (c.1100 C, p.367 Thr) or adrenal-restrictive (c.1100 A, p.367 Asn) phenotypes with respect to androgen synthesis from adrenal precursors, and the adrenal-permissive variant is associated with inferior outcomes to hormonal therapies. However, the tumoral characteristics (somatic alteration landscape, transcriptome, immune-cell composition) of prostate cancers that arise in the context of these germline genotypes are unknown. Methods: We utilized the Caris Life Sciences (Phoenix, AZ) database to study the relationship between germline HSD3B1 c.1100 genotypes and somatic tumoral characteristics in 5,421 prostate cancer biopsies. Germline HSD3B1 status was inferred using variant allele frequencies (VAFs) derived from tumor DNA sequencing: c.1100C VAF of 0% defined the AA genotype, VAF of 40-60% defined the AC genotype, and VAF of 100% defined the CC genotype. Each HSD3B1 genotype was interrogated for its associated mutational landscape (by exome sequencing) and tumor transcriptome (by RNA-seq); immune-cell subsets were explored using the quanTIseq deconvolution algorithm. Results: The prevalence of the HSD3B1 c.1100 AA genotype (restrictive–homozygous) was 54.4%, AC (heterozygous) was 34.2%, and CC (permissive–homozygous) was 11.4%. Liver/lung metastases had the highest prevalence of the CC genotype (14.2%), while lymph node metastases had the lowest (10.9%). Among the AR-associated genes, compared to the AA genotype, the CC genotype had greater frequency of TMPRSS2-ERG fusions (35.5% vs 29.7%, P<0.01), AR-V7 (17.2% vs 14.7%, P=0.17), and mRNA expression of AR (median 124 vs 115 TPM, P=0.01), HOXB13 (37 vs 34 TPM, P=0.08) and KLK2 (490 vs 448 TPM, P=0.12); there were no associations with SPOP or FOXA1 mutations or expression. Outside of AR pathways, the MAPK activation signature was higher in the CC relative to the AA genotype (0.27 vs -0.04 MPAS, P=0.01). When examining immune-cell subsets and immunotherapy targets, the CC genotype unexpectedly showed higher CD276 ( B7-H3) expression (30 vs 27 TPM, P<0.01), higher dendritic cells ( P=0.02) and T-regs ( P=0.03), and lower neutrophils ( P=0.10) compared to the AA genotype. Conclusions: The homozygous adrenal-permissive HSD3B1 variant (c.1100 CC) is associated with distinct tumoral features characterized by elevated AR signaling and MAPK activation. It is also associated with a unique immune-cell regulatory landscape, with higher B7-H3 expression, increased intratumoral dendritic cells and decreased immunosuppressive neutrophils. This distinct molecular landscape of HSD3B1 c.1100 CC–associated prostate cancers warrants special therapeutic considerations, including possibly using B7-H3–targeted therapies.

Landscape of somatic alterations in large-scale solid tumors from an Asian population

Extending the benefits of tumor molecular profiling for all cancer patients requires a comprehensive analysis of tumor genomes across distinct patient populations worldwide. In this study, we perform deep next-generation DNA sequencing (NGS) from tumor tissues and matched blood specimens from over 10,000 patients in China by using a 450-gene comprehensive assay, developed and implemented under international clinical regulations. We perform a comprehensive comparison of somatically altered genes, the distribution of tumor mutational burden (TMB), gene fusion patterns, and the spectrum of various somatic alterations between Chinese and American patient populations. Here, we show 64% of cancers from Chinese patients in this study have clinically actionable genomic alterations, which may affect clinical decisions related to targeted therapy or immunotherapy. These findings describe the similarities and differences between tumors from Chinese and American patients, providing valuable information for personalized medicine.

Germline APC (I1307K) mutation and clinical outcomes in prostate cancer.

144 Background: The germline I1307K mutation in the adenomatous polyposis coli (APC) gene is a well known alteration identified in approximately 6% of the Ashkenazi Jewish population. Individuals with this mutation have an increased risk of developing colorectal and other cancers. The implications of the APC (I1307K) mutation in patients with prostate cancer are unknown. We sought to determine the clinical outcomes of patients with prostate cancer and the germline APC (I1307K) mutation. Methods: We retrospectively reviewed records from New York University and Johns Hopkins University to identify patients with the APC (I1307K) mutation. Eligibility criteria included the identification of the mutation either on germline or somatic tissue testing (when germline testing was not available). Aggressive variant prostate cancer (AVPC) was defined using previously established criteria including: presence of small cell histology, presence of exclusively visceral metastases, bulky prostate mass or lymphadenopathy, low PSA with high-volume ( > 20) bone metastases, neuroendocrine marker positivity or short interval ( < 6 months) to castration resistance. Combined somatic alterations in two or more of following genes were assessed: RB1, TP53, PTEN. These somatic alterations have been previously associated with AVPC. Descriptive statistics were used to summarize patient data. Results: From 2016-2021, 13 patients with the germline APC (I1307K) mutation were identified. At the time of analysis 9 (69%) patients were alive. Most patients (7; 54%) had metastatic disease at presentation. Median PSA at diagnosis was 0.4 ng/mL (range: 0.4-20 ng/mL). The median time to castration resistance among those receiving hormonal therapy was 9 months (range: 3-13 months). Presence of small cell histology was found on initial biopsy in 3 patients and on subsequent biopsy in 1 additional patient (31% overall). Bulky prostate mass or lymphadenopathy was found in 3 (23%) patients. There were 2 (15%) patients who had low PSA with high-volume bone metastases. Four (31%) patients had radiographic progression with no concordant PSA increase. Clinically-defined AVPC was found in 7 (54%) patients and in 100% of those patients with metastatic disease. Combined somatic alterations in two or more of RB1, TP53 or PTEN were identified in 3 (23%) patients. Conclusions: Prostate cancers that develop in the presence of the germline APC (I1307K) mutation appear to be enriched for clinically-defined and molecularly-defined AVPC. Several of these patients demonstrated small cell histology and PSA-independent progression, higher than the expected background rate. This raises the hypothesis that the germline APC (I1307K) mutation influences the somatic genomic and/or epigenomic landscape of prostate cancer. Larger studies to validate the increased risk of AVPC in APC (I1307K) carriers, and to elucidate the somatic alteration landscape in these patients, are ongoing.

Somatic mutations in renal cell carcinomas from Chinese patients revealed by whole exome sequencing

BackgroundWhile the somatic mutation profiles of renal cell carcinoma (RCC) have been revealed by several studies worldwide, the overwhelming majority of those were not derived from Chinese patients. The landscape of somatic alterations in RCC from Chinese patients still needs to be elucidated to determine whether discrepancies exist between Chinese patients and sufferers from other countries and regions.MethodsWe collected specimens from 26 Chinese patients with primary RCC, including 15 clear cell renal cell carcinoma (ccRCC) samples, 5 papillary renal cell carcinoma (PRCC) samples and 6 chromophobe renal cell carcinoma (ChRCC) samples. Genomic DNAs were isolated from paired tumor-normal tissues and subjected to whole exome sequencing (WES). Immunohistochemistry analysis was performed to detect the programmed death ligand 1 (PD-L1) expression in tumor tissues.ResultsA total of 1920 nonsynonymous somatic variants in exons and 86 mutations at splice junctions were revealed. The tumor mutation burden of ccRCC was significantly higher than that of ChRCC (P < 0.05). For both ccRCC and PRCC, the most frequent substitution in somatic missense mutations was T:A > A:T, which was different from that recorded in the COSMIC database. Among eight significantly mutated genes in ccRCC in the TCGA database, six genes were verified in our study including VHL (67%), BAP1 (13%), SETD2 (13%), PBRM1 (7%), PTEN (7%) and MTOR (7%). All the mutations detected in those genes had not been reported in ccRCC before, except for alterations in VHL and PBRM1. Regarding the frequently mutated genes in PRCC in our study, DEPDC4 (p.E293A, p.T279A), PNLIP (p.N401Y, p.F342L) and SARDH (p.H554Q, p.M1T) were newly detected gene mutations predicted to be deleterious. As the most recurrently mutated gene in ChRCC in the TCGA dataset, TP53 (p.R81Q) was somatically altered only in one ChRCC case in this study. The HIF-1 signaling pathway was the most affected pathway in ccRCC, while the PI3K-Akt signaling pathway was altered in all of the three RCC types. Membranous PD-L1 expression was positive in tumor cells from 6/26 (23%) RCC specimens. The PD-L1-positive rate was higher in RCC samples with the somatically mutated genes CSPG4, DNAH11, INADL and TMPRSS13 than in specimens without those (P < 0.05).ConclusionsUsing WES, we identified somatic mutations in 26 Chinese patients with RCC, which enriched the racial diversity of the somatic mutation profiles of RCC subjects, and revealed a few discrepancies in molecular characterizations between our study and published datasets. We also identified numerous newly detected somatic mutations, which further supplements the somatic mutation landscape of RCC. Moreover, 4 somatically mutated genes, including CSPG4, DNAH11, INADL and TMPRSS13, might be promising predictive factors of PD-L1-positive expression in RCC tumor cells.

Abstract 5378: Whole exome and RNA sequencing identify novel somatic mutations in gangliogliomas

Abstract Gangliogliomas (GG) are rare, well differentiated, slow growing neuroepithelial tumors, composed of neoplastic mature ganglion cells and neoplastic glial cells. GG comprises 0.4% of all CNS primary tumors, and 70% of GG cases are diagnosed in patients with long-term temporal lobe epilepsy. The molecular pathogenesis of GG is poorly understood. Few groups have described a high frequency of a hotspot BRAF p.V600E mutation. More recently, a co-occurrence of histone H3 p.K27M and BRAF p.V600E mutations was reported in a pediatric midline grade I GG. However, the rarity of these tumors poses challenges to uncovering a more comprehensive landscape of somatic alterations. In this study, we describe the somatic mutational profiles of 12 GG from the University of Sao Paulo Medical School in one of the largest GG case series reported to date. We performed paired germline and somatic whole exome sequencing (WES) and RNA-Seq in all cases: 9 males and 3 females with ages ranging from 1 to 49 years (mean 17 ± 13 years). These tumors were located in the temporal lobe (8), frontal lobe (1), occipital lobe (1), intraventricular region (1), and intramedullary region (1). We used the Nextera Exome Enrichment Kit (Illumina) to perform WES, and the TruSeq Stranded Total RNA (Illumina) to perform RNA-Seq. Sequencing was performed in the Illumina HiSeq 2000. We aligned reads from WES and RNA-Seq libraries to the reference genome (hg19) using BWA and STAR, respectively. We used freebayes to perform variant call from germline WES paired with the respective tumor library (WES or RNA-Seq). We used the vcfcompare tool from vcflib to filter out germline variants and annovar to annotate the final list of variants. We identified mutations in cancer-related genes in 6/12 GGs: hotspot BRAF p.V600E in 4/6 cases, biallelic NF1 mutations (p.Y333X/p.R2258X) co-occurring with hotspot H3F3A (p.K27M) and FGFR1 (p.N546K) mutations in a 13-yo female with intraventricular GG, and, finally, biallelic hotspot TP53 mutations (p.V173M, p.P172T) combined with a hotspot IDH1 (p.R132H) mutation in a 26-yo male with frontal GG. Interestingly, the same combination of mutations observed in one of our patients (FGFR1 p.N546K/H3F3A p.K27M) was recently described in a diffuse leptomeningeal tumor with glial and neuronal markers. In summary, we identified novel mutations in cancer-related genes in 6 GG (50% of our cohort), including cases with mutations in more than one known cancer driver gene. In one of the largest GG case series reported to date, this study expands the spectrum of somatic alterations in GGs to include mutations in genes recurrently altered in higher-grade gliomas, such as IDH1, NF1, and TP53. Citation Format: Suely K. Marie, Sueli M. Oba-Shinjo, Antonio M. Lerario. Whole exome and RNA sequencing identify novel somatic mutations in gangliogliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5378.

Abstract P5-08-01: Reconstructing the evolutionary paths of BIG 1-98

Abstract We are reconstructing the dynamics of tumour growth, treatment response, and origins of resistance of the Breast International Group (BIG) 1-98 study to determine the evolutionary paths of non-responders. We established the somatic alteration landscape of primary tumours collected at surgery from BIG 1-98 patients using targeted DNA sequencing of 287 genes of FFPE samples from 538 patients. Combined analysis of genetic and clinical data indicates increased genomic instability; TP53 mutations and copy number variations of 11q13 and 8p11 are associated with poor prognosis. We developed an in silico simulation framework to investigate if the non-responder outcome is due to (over)-treatment or intrinsic to evolutionary selection prior to diagnosis. To reconstruct the evolutionary history of tumours, we created a computational multitype branching process that tracks the expansion of diverse clonal lineages as they acquire driver and passenger mutations that alter their proliferation and mutation rates. To account for the heterogeneity between patients, we created a fitting procedure based on the Cramer-von Misses statistic to find the likelihood of parameters of our computational model that recreate the mutational landscape and clinicopathological factors observed in each patient. Once the fitting procedure is done, we simulate the course of treatment following the study arm scheme accounting for the cell-cycle action mechanism of Tamoxifen and Letrozole. Using our tool, we are characterising the range of tumour development scenarios covering different degrees of aggressiveness and genomic instability. Our computational model allows simulation of diverse adjuvant-schemes to predict optimised treatment regimes for validation in patient-derived tumour xenograft mouse models. Citation Format: Lara-Gonzalez LL, Loi S, Ferrari D, Papenfuss A, Goode DL. Reconstructing the evolutionary paths of BIG 1-98 [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-08-01.

Abstract 3811: Defining the relevant genome in solid tumors

Abstract Decades of cancer research including comprehensive molecular profiling combined with the development of a broad array of targeted therapies have created the opportunity to transform cancer care by implementing precision oncology based approaches. An important element of this system is the widespread availability of robust and cost-effective multi-variate profiling methods to characterize relevant cancer associated molecular alterations in the future. Current commercially available multi-variate profiling methods vary dramatically with regard to the number of cancer genes that are interrogated. Given that many large scale and detailed molecular profiling studies have been completed, the landscape of somatic alterations in solid tumors is reasonably well-known. Furthermore, the specific gene variants that are relevant to application of targeted therapies are also a matter of record. Therefore, we set out to define the number of relevant cancer genes for precision oncology research based on the currently available empirical evidence. To define recurrent somatic alterations in solid tumors, we created a compendium of variant calls from &amp;gt; 15,000 exomes, defined focal amplifications and deletions from &amp;gt; 30,000 arrays, and defined recurrent fusions from several thousand RNAseq profiles. Statistical approaches were implemented to define genes containing recurrent missense mutations (i.e., hotspots), enriched in truncating mutations or subject to recurrent copy number gain/loss or translocation. This gene set was then used to comprehensively search approved cancer drug labels, clinical practice guidelines, and clinical trials to identify records containing published evidence that specific recurrent somatic gene variants were used as part of the indication statement of an approved targeted therapy, were recommended for testing as part of clinical practice for therapeutic decisions, or were used as enrollment criteria in clinical trials. The relevant cancer genome thus defined consists of &amp;lt; 100 genes. These results suggest that targeted multi-variate profiling approaches may be sufficient to support precision oncology goals in the future. Citation Format: Habib R. Hamidi, Santoshi Bandla, Nick Khazanov, Paul William, Nikki Bonevich, Chris Zurenko, Sarah Anstead, Chris Taylor, Reuban Richmonds, David Galimberti, Ken Kopp, Dinesh Cyanam, Michael Hogan, Vinay Mittal, Seth Sadis. Defining the relevant genome in solid tumors [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 3811. doi:10.1158/1538-7445.AM2017-3811

Abstract 4394: Whole-genome, virome, and immuno-genome of liver cancer indicate its genomic feature associated with virus infection and inflammation

Abstract Liver cancer is prevalent worldwide, mainly associated with virus infection and chronic inflammation, but its underlying molecular mechanism is quite heterogeneous. We performed virome and immuno-genomic analyses, in addition to whole-genome landscape of somatic alterations and transcriptome in 300 liver cancers. Our whole-genome analysis elucidated point mutations in non-coding regions, structural variations, and virus integrations (HBV and AAV), in addition to coding mutations. We discovered novel recurrently mutated coding and non-coding regions, such as NEAT1/MALAT1 lincRNAs, promoters, CTCF-binding sites, and novel regulatory regions, and known cancer genes (CDKN2A, APC, TERT) and novel cancer genes (ASH1L, NCOR1, MACROD2) that were recurrently affected by SVs. For virome analysis, we performed ultra-deep sequencing after capturing HBV sequences from DNAs of 100 liver cancers or adjacent HBV-infected liver tissues, which demonstrated genome-wide HBV-integrations (1794 sites) in liver cancers and infected liver tissues and eliminated pathological mechanism of viral integration. We also generated immuno-genomic profiles of these liver cancers, including HLA genotypes and mutations, neo-antigen presentation, immune signatures, and TCR repertories, which suggested some distinct immunological features and underlying molecular pathways of liver cancer associated with inflammation. These trans-omics data demonstrated comprehensive and distinct immuno-genomic feature of virus-related liver cancer, as well as its distinct whole-genome profiles, and can help to understand the molecular and microenvironment pathways underlying carcinogenesis and treatment response of liver cancer. Citation Format: Hidewaki Nakagawa. Whole-genome, virome, and immuno-genome of liver cancer indicate its genomic feature associated with virus infection and inflammation [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 4394. doi:10.1158/1538-7445.AM2017-4394

Abstract 4397: Deciphering the diversity of somatic alterations and Salmonella infection in gallbladder cancer by whole exome sequencing

Abstract Background: Gallbladder cancer is fifth most common cancers among the gastrointestinal cancers with the majority of patients presented at an advanced state of the disease. In India, gallbladder cancer is a major problem in the northern part of the country with its highest incidence of 22/1,00,000 women and risk factors ranging from gallstones, female gender, ethnicity, Salmonella infections and genetic alterations. Despite its high incidence in our country, there is only few candidate gene based studies and systematic genome-wide studies are far in dismal. Hence there is an unmet need to understand the genomic landscape of Indian gallbladder cancer genome. Materials and methods: We interrogated the coding region of gallbladder cancer genome of 27 samples (10 paired and 7 unpaired tumors) using whole exome sequencing at an average coverage of 100X and above. Further, we validated our findings from whole exome sequencing in an extended cohort of 27 FFPE (Formalin fixed paraffin embedded) samples using other sequencing technologies. In addition we used a computational subtraction tool to identify Salmonella DNA sequences in the whole exome sequencing data. Results: We identified 383 somatic alterations across 17 tumors, which includes an average 112 synonymous, 245 missense, 8 nonsense, 8 indels and 8 splice site changes. The average mutation rate considering the paired tumors is about 14 mutations/Mb. We found recurrent alterations in TP53, CTNNB1, SF3B1, ATM, AKAP11 and other genes by exome sequencing analysis. In addition, we examined our exome sequencing data for identifying Salmonella sequences as well as presence of 143 HPV types using computational subtraction based on HPVDetector. In our analysis we found association of typhoidal Salmonella strains in 11 of 26 gall bladder cancer samples and non-typhoidal Salmonella species in 12 of 26 sample, 6 samples were co-infected with both. Moreover, we observed co-occurrence of TP53 alterations in 4 of 16 Salmonella positive samples while we did not observe TP53 alterations in Salmonella negative samples. Conclusion: Taken together, we present the landscape of somatic alterations in Indian gallbladder cancer genome and identification of non-typhoidal Salmonella species along with co- occurrence of TP53 alterations could aid in the treatment of gallbladder cancer. Note: This abstract was not presented at the meeting. Citation Format: Prajish Sundaram Iyer, Nilesh laxman Gardi, Malika Ranjan, Bikram Sahoo, Pratik Chandrani, Pawan Upadhyay, Mukta R. Ramadwar, Shailesh V. Shrikhande, Amit Dutt. Deciphering the diversity of somatic alterations and Salmonella infection in gallbladder cancer by whole exome sequencing [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 4397. doi:10.1158/1538-7445.AM2017-4397

Abstract A21: Integrative genome and transcriptome sequencing defines the landscape of genetic alterations underlying pediatric rhabdomyosarcoma

Abstract Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. With the development of multimodal chemotherapy regimens, relapse-free survival rates have improved to 70-80% in patients with localized disease albeit with significant toxicity. Despite these gains, survival for those patients with metastatic or recurrent disease remains dismal. Further characterization of the genetic events underlying this tumor type is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. In a collaborative effort between the National Cancer Institute, the Children's Oncology Group, and the Broad Institute, we used a combination of whole-genome, whole-exome and transcriptome sequencing along with high resolution SNP arrays to characterize the landscape of somatic alterations in 147 tumor/normal pairs. Two distinct genotypes are evident in RMS tumors; those characterized by the PAX3 or PAX7 fusion proteins that includes novel fusions with cryptic partners (35% of cases) and those that lack a PAX3/7 fusion but harbor mutations in key signaling pathways (65% of cases). Consistent with other pediatric cancer types, the overall burden of somatic mutations in RMS is relatively low (0.31 somatic protein coding mutations per megabase) especially in tumors that harbor a PAX3/7 gene fusion (0.1 somatic mutations per megabase). In addition to genes previously reported as altered in RMS including NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1 we discovered novel recurrent mutations in FBXW7, and the chromatin remodeling gene BCOR, which provide new potential avenues for therapeutic intervention. Transcriptome analysis showed that 58% of the verified genomic mutations were expressed with a marked enrichment in cell cycle (P=2e-6), protein phoshorylation (P=6.9e-5) and muscle cell differentiation (P=3.3e-4) and many of the tumors appear to accumulate multiple genetic hits within these same pathways. Finally, we identify alteration of the receptor tyrosine kinase/RAS/PIK3CA axis affects 93% of RMS cases which provides a framework for genomics-directed therapies that might improve outcomes for RMS patients. Citation Format: Jack F. Shern, Li Chen, Juliann Chmielecki, Jun Wei, Rajesh Patidar, Young Song, Hongling Liao, Andy Brohl, Daniel Catchpoole, Thomas Badgett, Gad Getz, Jaume Graupera, James Anderson, Stephen X. Skapek, Frederic G. Barr, Douglas S. Hawkins, Javed Khan. Integrative genome and transcriptome sequencing defines the landscape of genetic alterations underlying pediatric rhabdomyosarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A21.

Abstract 5181: Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

Abstract Background: In 2014, it is estimated that there will be over 30,000 new cases of hepatocellular carcinoma (HCC) and an estimated 20,000 subjects will die of this disease in the U.S. alone. Risk factors include chronic HBV/HCV infections, cirrhosis, alcohol abuse, diabetes, and fatty liver disease. However, an important subset of HCC occurs in the absence of any such risk factors. We surveyed the genomic and transcriptomic landscape of this subset of HCC. Methods: We performed whole genome and transcriptome sequencing of 30 matched tumor and non-tumor liver samples from resections performed at Washington University School of Medicine. Somatic variants identified in this discovery set were extended to a set of 89 additional cases by custom capture sequencing for a total of 119 HCCs profiled. All data were processed through The Genome Institute's Genome Modeling System (GMS) to analyze for viral integrations, SNVs, Indels, CNVs, fusions, SVs, expression and differential expression. Results: We report here for the first time the unique landscape of somatic alterations of HCC arising in non-cirrhotic liver. We detected and validated over 3,010 SNVs and indels in coding regions and 2,390 fusion transcripts, as well as extensive copy number and expression changes. We identified a single undiagnosed HBV case with viral integration occurring at the TERT promoter. We also confirmed recent reports of a recurrent TERT promoter mutation (G1295228A) occurring in at least 56% of cases. Additional recurrent mutations were observed in previously reported genes such as CTNNB1, TP53, AXIN1, and ARID1A, along with an increased frequency of RB1 loss, novel recurrent mutations of APOB, fusions in NR1H4, and other alterations. These molecular features were tested for association with clinical variables and outcome. Pathway analysis of recurrently altered genes suggests that, in the absence of external factors, genomic aberrations in basic liver metabolism genes may promote malignant transformation to HCC. Citation Format: Obi L. Griffith, Yiing Lin, Malachi Griffith, Jasreet Hundal, Allison Regier, Robert Fulton, Elizabeth M. Brunt, Richard K. Wilson, William Chapman, Elaine R. Mardis. Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5181. doi:10.1158/1538-7445.AM2014-5181

Abstract 3960: Rapid and efficient large-scale somatic mutation validation approaches for cancer genome sequencing

Abstract The landscape of somatic alterations in cancer is being rapidly uncovered by large-scale cancer genome sequencing projects in individual laboratories as well as consortia such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). The decreasing cost of sequencing has resulted in an increase in the number of cancer genomes that are being sequenced, and thus the numbers of candidate somatic mutations being identified are rapidly expanding. A single cancer genome from a cancer with an average mutation background rate, such as ovarian or breast cancer, will have 3000-6000 mutations. A high mutation rate cancer such as melanoma or colon cancer can have as many as 100,000 mutations/genome. Multiplying these numbers by the dozens of sequenced genomes and hundreds of sequenced exomes across a wide spectrum of tumor types yields a staggering number of candidate mutations. However, approaches for rapidly validating these findings at scale have been lagging behind. Current approaches, such as custom designed hybrid capture arrays followed by sequencing, can take months to complete and cannot begin until the initial sequencing is complete and mutations are called. This can lead to long delays in the interpretation and publication of biological findings. Here we describe the results of several approaches for rapid and efficient validation on large-scale projects, such as TCGA. We will share our approach and results using Fluidigm and PacBio sequencing for validation and sample extension at a small scale with rapid turnaround where we have validated PIK3CA and TP53 mutations in breast cancer samples of varying purity as well as significantly mutated genes in medulloblastoma. Ideally one could validate mutations and gene fusions concurrent with their discovery. To that end, we will also describe our validation results using RNA-Seq data, commonly produced concurrently with genome and exome sequencing, in lung squamous and renal cancer. Finally, we will explore an approach for instant-validation through simultaneous sequencing of barcoded discovery and cross-validation libraries. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3960. doi:1538-7445.AM2012-3960