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Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9–26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.

Mutations play a fundamental role in the development of cancer, and many create targetable vulnerabilities. There are both public health and basic science benefits from the determination of the proportion of all cancer cases within a population that include a mutant form of a gene. Here, we provide the first such estimates by combining genomic and epidemiological data. We estimate KRAS is mutated in only 11% of all cancers, which is less than PIK3CA (13%) and marginally higher than BRAF (8%). TP53 is the most commonly mutated gene (35%), and KMT2C, KMT2D, and ARID1A are among the ten most commonly mutated driver genes, highlighting the role of epigenetic dysregulation in cancer. Analysis of major cancer subclassifications highlighted varying dependencies upon individual cancer drivers. Overall, we find that cancer genetics is less dominated by high-frequency, high-profile cancer driver genes than studies limited to a subset of cancer types have suggested., Understanding the frequency of gene mutations in cancer could be important for generating targeted therapeutics. Here, the authors use SEER data and cancer genomics data from TCGA to estimate the gene mutation frequencies in the US cancer population.

// Jaeyun Jung 1, * , Cue Hyunkyu Lee 3, * , Hyang Sook Seol 4 , Yeon Sook Choi 4 , Eunji Kim 3, 5 , Eun Ji Lee 1 , Je-Keun Rhee 6 , Shree Ram Singh 7 , Eun Sung Jun 1 , Buhm Han 3 , Seung Mo Hong 8 , Song Cheol Kim 9 , Suhwan Chang 1, 2 1 Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, Korea 2 Department of Physiology, University of Ulsan College of Medicine, Seoul, Korea 3 Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea 4 Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea 5 Department of Chemistry, Seoul National University, Seoul, Korea 6 Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea 7 Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA 8 Department of Pathology, Asan Medical Center, Seoul, Korea 9 Department of Surgery, Asan Medical Center, Seoul, Korea * These authors have contributed equally to this work Correspondence to: Song Cheol Kim, email: drksc@amc.seoul.kr Suhwan Chang, email: suhwan.chang@amc.seoul.kr Keywords: pancreatic cancer, patient-derived xenograft, single nucleotide polymorphism, cancer panel, heterogeneity Received: June 01, 2016 Accepted: August 08, 2016 Published: August 23, 2016 ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is the most challenging type of cancer to treat, with a 5-year survival rate of

Objective To identify in calcifying epithelial odontogenic tumor (CEOT) mutations in oncogenes and tumor suppressor genes. Study Design A panel of 50 genes commonly mutated in cancer was sequenced in CEOT by next-generation sequencing. Sanger sequencing was used to cover the region of the frameshift deletion identified in one sample. Results Missense single nucleotide variants (SNV) with minor allele frequency (MAF) 1%. Conclusions CEOT harbor mutations in the tumor suppressor PTEN and CDKN2A and in the oncogenes JAK3 and MET. As these mutations occurred in only 1 case each, they are probably not driver mutations for these tumors.

Precision Cancer Medicine: Tumors are classified into several molecular subtypes by Genomic Sequencing. Comprehensive targeted-gene panel provides more therapeutic options. CANCERPLEX-JP version 4.0 includes 435 actionable genes, which clinical approaches are available. Utilizing the gene panel platform, we assessed the genes and pathways most frequently altered in Japanese and US cases (Genome Med 2016;8:136). We demonstrate concordance of CANCERPLEX-JP with whole-exome sequencing from the TCGA in identifying hypermutated samples and microsatellite instability in multiple cancer types, such as colorectal and gastric cancer. We introduced our activity for precision medicine at 4th US-Japan Clinical Trials in Oncology Workshop sponsored by Embassy of Japan, at Washington DC, held in June 9, 2016. We highlight the clinical utility of CANCERPLEX-JP (435 genes) in guiding treatment strategies with targeted therapy in solid tumors, thus providing rationale for Comprehensive Genomic Sequencing in actualizing precision medicine. The goal of Precision Medicine is cost effectiveness and realization of genome drug discovery.Super-computing System: This introduction plan is based on the massive medical big data (cancer gene mutation information, genomic data, image data, etc.) possessed by Niigata Prefecture and Niigata University, to construct an integrated analysis system incorporating deep learning, and introduces a high-performance computer system for the development and activation of related industries. Therefore, it is necessary to have an operation system that can connect to the hospital electronic medical record without interference.(Presented at the 1943rd Meeting, July 5, 2017).

Importance Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. Objective To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue (“tumor-normal sequencing”) compared with genetic test results based on current guidelines. Design, Setting, and Participants From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. Exposure Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. Main Outcomes and Measures Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. Results Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing. Conclusions and Relevance In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study. Trial Registration clinicaltrials.gov Identifier: NCT01775072

Background: The epidermal growth factor receptor (EGFR) is a potential therapeutic target for breast cancer treatment; however, its use does not lead to a marked clinical response. Studies of non-small cell lung cancer and colorectal cancer showed that mutations of genes in the PIK3CA/AKT and RAS/RAF/MEK pathways, two major signalling cascades downstream of EGFR, might predict resistance to EGFR-targeted agents. Therefore, we examined the frequencies of mutations in these key EGFR pathway genes in Chinese breast cancer patients. Methods: We used a high-throughput mass-spectrometric based cancer gene mutation profiling platform to detect 22 mutations of the PIK3CA, AKT1, BRAF, EGFR, HRAS, and KRAS genes in 120 Chinese women with breast cancer. Results: Thirteen mutations were detected in 12 (10%) of the samples, all of which were invasive ductal carcinomas (two stage I, six stage II, three stage III, and one stage IV). These included one mutation (0.83%) in the EGFR gene (rs121913445-rs121913432), three (2.50%) in the KRAS gene (rs121913530, rs112445441), and nine (7.50%) in the PIK3CA gene (rs121913273, rs104886003, and rs121913279). No mutations were found in the AKT1, BRAF, and HRAS genes. Six (27.27%) of the 22 genotyping assays called mutations in at least one sample and three (50%) of the six assays queried were found to be mutated more than once. Conclusions: Mutations in the EGFR pathway occurred in a small fraction of Chinese breast cancers. However, therapeutics targeting these potential predictive markers should be investigated in depth, especially in Oriental populations.

Согласно общепризнанной генной теории рака, в течение последних десятилетий рак считали генным заболеванием, возникающим в результате детерминистического последовательного накопления мутаций в небольшой группе раковых генов, происходящего при линейной прогрессии опухоли. Однако в противоположность этому постулату в недавних работах по секвенированию генома и экзома первичных опухолей и их метастазов, а также отдельных участков одной и той же опухоли выявлено огромное количество стохастических генных мутаций в каждой опухоли одного типа и значительную внутриопухолевую генетическую гетерогенность с «разветвленной эволюцией роста опухоли» или «прерывистой клональной эволюцией без прослеживаемых промежуточных разветвлений», или «отсутствие доминантных клонов в опухолевой ткани». Стохастические кариотипические изменения и внутриопухолевая гетерогенность признаны ведущей силой в эволюции опухоли и детерминантой развития терапевтической резистентности и рецидива рака. Эволюция кариотипа/ хромосомной нестабильности и результирующий уровень внутриопухолевой гетерогенности существенно коррелируют с опухолеобразующим потенциалом клеток, прогрессией заболевания от преопухолевого доброкачественного к явно злокачественному и метастазированию, а также с выживаемостью пациентов, чувствительностью к химиотерапии и риском приобретения резистентности. Обсуждается важность эволюционной кариотипической теории в понимании биологии рака и механизмов приобретения стойкости к химиотерапии. Ключевые слова: эволюция опухоли, кариотип, хромосомная нестабильность, внутриопухолевая гетерогенность, раковый ген, химиорезистентность. Згідно із загальновизнаною генною теорією раку, протягом останніх десятиліть рак вважали генним захворюванням, яке виникає в результаті детерміністичного послідовного накопичення мутацій у невеликій групі ракових генів, що відбувається за лінійної прогресії пухлини. Однак на противагу цьому постулату у недавніх роботах із секвенування геному та екзому первинних пухлин і їхніх метастазів, а також окремих ділянок однієї і тієї ж пухлини виявлено величезну кількість стохастичних генних мутацій у кожній пухлині однакового типу та значну внутрішньопухлинну генетичну гетерогенність з «розгалуженою еволюцією росту пухлини» або «переривчастою клональною еволюцією без проміжних розгалужень», або «відсутність домінантних клонів у пухлиннії тканині». Стохастичні каріотипові зміни і внутрішньопухлинну гетерогенність визнано провідною силою в еволюції пухлини і детермінантою розвитку терапевтичної резистентності і рецидиву. Еволюція каріотипу/хромосомної нестабільності і результуючий рівень внутрішньопухлинної гетерогенності суттєво корелюють з пухлиноутворювальним потенціалом клітин, прогресією пухлини від доброякісної до явно злоякісної та метастазування, а також з виживанням пацієнтів, чутливістю до хіміотерапії і ризиком виникнення резистентності. Обговорюється важливість еволюційної каріотипової теорії раку у розумінні біології раку і механізмів набуття стійкості до хіміотерапії. Ключові слова: еволюція пухлини, каріотип, хромосомна нестабільність, внутрішньопухлинна гетерогенність, раковий ген, хіміорезистентність. For decades the conventional gene mutation cancer theory has been postulating that cancer is a genetic disease considered as a result of deterministic sequential accumulation of mutations in the handful of «driver» cancer genes occurring in a continuous linear pattern of cancer progression. However, in contrast to this postulate, recent whole genome and exome sequencing studies of primary tumor bulk and metastases or separate regions withing the same sample have revealed a large number of stochastic gene mutations for each individual with the same cancer type and significant intratumoral genetic heterogeneity with «branched evolutionary tumor growth» or «punctuated clonal evolution without observable intermediate branching» or «no dominant clones in the cancer tissue». Meanwhile, the stochastic karyotypic variation and intratumor heterogeneity are recognized to be the driving force of tumor evolution and major factors in determining relapse with acquired drug resistance. The karyotype evolution/chromosome instability and the resulting magnitude of intratumor heterogeneity significantly correlate with tumorigenic potential of cells, tumor disease progression from precancerous lesions to malignant tumors and metastases, correlate with patient survival, treatment sensitivity, and the risk of acquired resistance. Here, we discuss importance of the evolutionary karyotypic theory in understanding the cancer biology and mechanisms of tumor drug resistance. Keywords: tumor evolution, karyotype, chromosome instability, intratumor heterogeneity, cancer gene, drug resistance.

One way an inherited cancer gene mutation may target specific tissues for cancer is by increasing susceptibility when a tissue is exposed to environmental carcinogens. An example of this may be the increased susceptibility of BRCA1 or BRCA2 mutation carriers to the carcinogen formaldehyde. Formaldehyde is now a proven cause of human myeloid leukemias. Yet millions of tons of formaldehyde are produced every year and it is everywhere. High formaldehyde levels can overwhelm normal enzyme detoxification systems and cause DNA damage. It is known that some types of formaldehyde-associated DNA damage require error-free DNA repairs mediated by pathways containing BRCA1 and BRCA2 proteins. Otherwise some formaldehyde-related DNA damage cannot be properly repaired so mutations may occur. Therefore, carriers of BRCA1 and BRCA2 gene defects should be unduly susceptible to myeloid leukemia. Studies show that inherited biallelic BRCA2 gene defects dramatically increase risks for myeloid leukemia. Heterozygous BRCA1 or BRCA2 mutations also increase risks for myeloid leukemias in 11 of 12 relevant studies. BRCA1/2 mutation carriers may reduce risks for myeloid leukemias by using available precautions to lower their exposure to formaldehyde.

With the rapid decline cost of sequencing, it is now clinically affordable to examine multiple genes in a single disease-targeted test using next generation sequencing. Current targeted sequencing methods require a separate step of targeted capture enrichment during sample preparation before sequencing, and the library preparation process is labor intensive and time consuming. Here, we introduced an amplification-free Single Molecule Targeted Sequencing (SMTS) technology, which combined targeted capture and sequencing in one step. We demonstrated that this technology can detect low-frequency mutations of cancer genes. SMTS has several advantages, namely that it requires little sample preparation and avoids biases and errors introduced by PCR reaction. This technology can be applied in cancer gene mutation detection, inherited condition screening and high-resolution human leukocyte antigen (HLA) typing.

The role of somatic mutation in cancer is well established and several genes have been identified that are frequent targets. This has enabled large-scale screening studies of the spectrum of somatic mutations in cancers of particular organs. Cancer gene mutation databases compile the results of many studies and can provide insight into the importance of specific amino acid sequences and functional domains in cancer, as well as elucidate aspects of the mutation process. Past studies of the spectrum of cancer mutations (in particular genes) have examined overall frequencies of mutation (at specific nucleotides) and of missense, nonsense, and silent substitution (at specific codons) both in the sequence as a whole and in a specific functional domain. Existing methods ignore features of the genetic code that allow some codons to mutate to missense, or stop, codons more readily than others (i.e., by one nucleotide change, vs. two or three). A new codon-based method to estimate the relative rate of substitution (fixation of a somatic mutation in a cancer cell lineage) of nonsense vs. missense mutations in different functional domains and in different tumor tissues is presented. Models that account for several potential influences on rates of somatic mutation and substitution in cancer progenitor cells and allow biases of mutation rates for particular dinucleotide sequences (CGs and dipyrimidines), transition vs. transversion bias, and variable rates of silent substitution across functional domains (useful in detecting investigator sampling bias) are considered. Likelihood-ratio tests are used to choose among models, using cancer gene mutation data. The method is applied to analyze published data on the spectrum of p53 mutations in cancers. A novel finding is that the ratio of the probability of nonsense to missense substitution is much lower in the DNA-binding and transactivation domains (ratios near 1) than in structural domains such as the linker, tetramerization (oligomerization), and proline-rich domains (ratios exceeding 100 in some tissues), implying that the specific amino acid sequence may be less critical in structural domains (e.g., amino acid changes less often lead to cancer). The transition vs. transversion bias and effect of CpG dinucleotides on mutation rates in p53 varied greatly across cancers of different organs, likely reflecting effects of different endogenous and exogenous factors influencing mutation in specific organs.

One of the major breakthroughs in oncogenesis research in recent years is the discovery that, in most patients, oncogenic mutations are concentrated in a few core biological functional pathways. This discovery indicates that oncogenic mechanisms are highly related to the dynamics of biologic regulatory networks, which govern the behaviour of functional pathways. Here, we propose that oncogenic mutations found in different biological functional pathways are closely related to parameter sensitivity of the corresponding networks. To test this hypothesis, we focus on the DNA damage-induced apoptotic pathway—the most important safeguard against oncogenesis. We first built the regulatory network that governs the apoptosis pathway, and then translated the network into dynamics equations. Using sensitivity analysis of the network parameters and comparing the results with cancer gene mutation spectra, we found that parameters that significantly affect the bifurcation point correspond to high-frequency oncogenic mutations. This result shows that the position of the bifurcation point is a better measure of the functionality of a biological network than gene expression levels of certain key proteins. It further demonstrates the suitability of applying systems-level analysis to biological networks as opposed to studying genes or proteins in isolation., Author Summary Among complex genetic diseases affecting humans, cancer is a major cause of death. In 2008, a genome-wide analysis of hundreds of tumour samples showed that oncogenic mutations are concentrated in a few core functional pathways, revealing a new conceptual framework for cancer biology research, where the role of oncogenic mutations and oncogenic mechanisms are addressed from a network perspective. We therefore propose a new way of identifying high-frequency gene mutations in cancer: gene mutations may affect their corresponding proteins' activity in the biological regulatory network and can be considered as perturbations of the dynamical system. Therefore, mutations that induce qualitative changes in biological networks should correspond to high-frequency mutations in cancer. This concept can help us identify and understand the function of genes that play an important role in oncogenesis, thereby allowing targeted and effective design of gene-based therapy in cancer.

The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgrounds, to very specific sites dedicated to individual genes or molecules. A simple search for ‘cancer’ from a typical Web browser search engine yields more than half a million hits; an even more specific search for ‘leukaemia’ (>40 000 hits) or ‘p53’ (>5700 hits) yields far too many hits to allow one to identify particular sites of interest. This review aims to provide a brief guide to some of the resources and databases that can be used as springboards to home in rapidly on information relevant to many fields of cancer research. As such, this article will not focus on a single website but hopes to illustrate some of the ways that postgenomic biology is revolutionizing cancer research. It will cover genomics and proteomics approaches that have been applied to studying global expression patterns in cancers, in addition to providing links ranging from general information about cancer to specific cancer gene mutation databases.

A rare sclerosing variant of rhabdomyosarcoma characterized by prominent hyalinization and pseudovascular pattern has recently been described as a subtype biologically distinct from embryonal, alveolar, and pleomorphic forms. We present cytogenetic and molecular findings as well as experimental studies of an unusual case of sclerosing rhabdomyosarcoma. The primary lesion arose within the plantar subcutaneous tissue of the left foot of an otherwise healthy 23-year-old male who eventually developed pulmonary nodules despite systemic chemotherapy. Two genetic abnormalities identified in surgical and/or autopsy samples of the tumor were introduced into 10T1/2 murine fibroblasts to determine whether these genetic changes cooperatively facilitated transformation and growth. Cytogenetic analysis revealed a complex abnormal hyperdiploid clone, andMDM2gene amplification was confirmed by fluorescence in situ hybridization. Cancer gene mutation screening using a combination of multiplexed PCR and mass spectroscopy revealed aPIK3CAexon 20 H1047R mutation in the primary tumor, lung metastasis, and liver metastasis. However, this mutation was not cooperative withMDM2overexpression in experimental assays for transformation or growth. Nevertheless,MDM2andPIK3CAare genes worthy of further investigation in patients with sclerosing rhabdomyosarcoma and might be considered in the enrollment of these patients into clinical trials of targeted therapeutics.

4108Background: Availability of cancer gene mutation panel-based screening will identify increasing numbers of patients who carry diverse germline mutations. Prevalence of mutations and survival by...

Certain cancer genes contribute to tumorigenesis in a manner of either co-occurring or mutually exclusive (anti-co-occurring) mutations; however, the global picture of when, where and how these functional interactions occur remains unclear. This study presents a systems biology approach for this purpose. After applying this method to cancer gene mutation data generated from large-scale and whole genome sequencing of cancer samples, a network of cancer genes with co-occurring and anti-co-occurring mutations was constructed. Analysis of this network revealed that genes with co-occurring mutations prefer direct signaling transductions and that the interaction relations among cancer genes in the network are related with their functional similarity. It was also revealed that genes with co-occurring mutations tend to have similar mutation frequencies, whereas genes with anti-co-occurring mutations tend to have different mutation frequencies. Moreover, genes with more exons tend to have more co-occurring mutations with other genes, and genes having lower local coherent network structures tend to have higher mutation frequency. The network showed two complementary modules that have distinct functions and have different roles in tumorigenesis. This study presented a framework for the analysis of cancer genome sequencing outputs. The presented data and uncovered patterns are helpful for understanding the contribution of gene mutations to tumorigenesis and valuable in the identification of key biomarkers and drug targets for cancer.

Background: A single genomic event is sufficient to cause CML; Ph translocation and the resulting BCR-ABL fusion. Additional genomic lesions accompany progression, which occurs very rapidly after diagnosis (dx) in a minority. Identification at dx of patients (pts) with poor prognosis remains an important goal and new sequencing technology enhances the prospects of uncovering pathologically relevant lesions for early warning of disease progression. Aim: To determine the somatic genomic landscape at dx, the risk conferred by genomic lesions towards blast crisis (BC), and whether mechanisms that underlie CML progression are shared by other malignancies. Method: Sequencing the whole exome (WES) and transcriptome (RNAseq) of paired tumor-normal samples (bone marrow mesenchymal stromal cells or remission) identified somatic single nucleotide variants, indels and gene fusions. Twenty-eight chronic phase (CP) first line imatinib (IM) treated pts were tested: 14 had BC at a median of 9 mo, r 3-60; and 14 had good response (MMR by 6 mo). Also tested were 4 pts diagnosed in advanced phase (2 accelerated phase [AP]; 2 BC) and 5 historical pts with BC at a median of 64 mo, r 38-100. Results: At dx, a median of 33 somatic variants were detected per pt (r 1-62). The number of variants did not correlate with response, or CP vs AP/BC, but increased with age (r =0.48, P =.007), consistent with accumulation of variants in stem cells with aging and suggesting that many may be "passenger mutations". Non synonymous protein coding variants were present at a median of 7 per pt at dx (r 0-17), again without difference between groups. Most variants had an allele frequency close to 50%, indicating their likely presence in all leukemic cells. However, polyclonality at dx was evident by variants with low allele frequency that either expanded or diminished at BC, Fig A. All 4 pts in AP/BC at dx had mutations in genes implicated in cancer pathogenesis (cancer genes) at dx; CBFB-MYH11 fusion, BCORL1, GATA2 and PTPRT, and SMARCA1. Of the 28 pts with first line IM, 11 had 15 somatic and 1 germline non synonymous variants/fusions at dx of known/potential significance: oncogenic mutations in IDH1 (R132H) and TP53 (germline R248Q); 6 frameshift/stop/splice site mutations in ASXL1, 1 EZH2 stop, 1 SETD1B stop, 1 MLL2 frameshift, 1 CHD1 splice site; and 4 novel fusions. Two of the fusions were generated by inversions of 2-13 MB of chr 22: PPM1F-SPECC1L (truncating the protein phosphatase PPM1F) and MYH9-BCR (truncating MYH9, reported to regulate p53 stability). Of these 11 pts, 9 had BC at a median of 6 mo of IM, r 3-39, and 2 had MMR by 6 mo. The 2 good response pts had ASXL1 mutations (both stop) and 1 also had a fusion involving chr 9 and 22 (TNRC6B-NEK6). The frequency of BC in CP pts with potentially pathogenic variants at dx was significantly higher than pts without such variants; 9/11 (82%) vs 5/17 (29%), P =.02. At BC, 18 pts had WES performed. A median of 6 non synonymous variants were gained (r 0-15) including 1-4 mutations in cancer genes in 15/18 pts, Fig B. Six of 13 first line IM pts also had 11 BCR-ABL KD mutations at BC (8 P loop) and 5/6 were among the pts who acquired mutations in cancer genes. The pt with the germline oncogenic TP53 mutation acquired a novel ANKRD11-UBQLN1 fusion at BC at 5 mo. Interestingly, ANKRD11 is a key regulator of the oncogenic potential of this mutation. In total, 6 genes were recurrently mutated; ASXL1, BCORL1, RUNX1, GATA2, MLL and UBE2A. Mutations occurred in genes that primarily belonged to classes mutated in AML, Fig B. Of the 23 AP/BC samples, 22 had non synonymous variants in genes involved in epigenetic regulation/chromatin modification. Variants were also detected in genes involved in ubiquitination and nuclear export, including an XPO1 variant reported in CLL. Nucleocytoplasmic transport has been implicated in IM resistance. Conclusion: Risk of BC was significantly associated with cancer gene mutation or novel fusions at dx. Some mutated pathways in CML were common to other cancers. Epigenetic regulation/chromatin modification appears to play a central role in CML pathogenesis, and ubiquitination and nuclear export may be of emerging relevance. Notably, most pts with BCR-ABL KD mutations at BC also acquired cancer associated mutations, indicating multiple mechanisms may contribute to progression. Future testing at dx will likely include tumor/normal exome/transcriptome sequencing to aid risk stratification. Figure 1. Figure 1. Disclosures Branford: Novartis: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Ariad: Research Funding; Qiagen: Membership on an entity's Board of Directors or advisory committees. Yeung:Bristol Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hughes:ARIAD: Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria, Research Funding.

G-protein coupled receptors (GPCRs) and G-proteins are critical signal transduction molecules that regulate cell survival, proliferation, motility and differentiation. However, mutations and disruptions in the expression or function of these molecules have been linked to growth, progression and metastasis of various cancers. Recently, major efforts in the area of genome-wide sequencing of tumors have unveiled numerous previously uncharacterized mutations in G-proteins and GPCRs, which could have significant implications to cancer initiation and progression. In particular, mutations in the gene encoding the G-protein G13 (GNA13) and/or its downstream effector, RhoA, have been identified in B cell lymphomas (particularly Burkitt's lymphoma and Diffuse Large B cell Lymphoma), T cell lymphomas, and Head and Neck Squamous Cell Carcinomas (HNSCCs). Our analyses indicate that these mutations are highly statistically significant over background cancer gene mutation rate, and mutations in GNA13 alone occur in ∼10-15% of patients with Burkitt's lymphoma and Diffuse Large B cell Lymphoma. Surprisingly, although G13 and RhoA have previously been linked to cellular transformation and metastatic potential of epithelial cancers, our data suggests that the mutations in GNA13 and/or RHOA in these B cell lymphomas and HNSCC are inhibitory in nature. Furthermore, our results indicate a tumor suppressive function for wild-type GNA13 and RHOA in in vivo cancer models. Overall, our data suggest a novel function tumor suppressive function for the G13/RhoA axis in multiple human malignancies. Citation Format: Morgan O'hayre, Asuka Inoue, Katiuchia Sales, Irina Kufareva, Juan Luis Callejas Valera, Fukun Guo, Constantinos Mikelis, Giovanni DiPasquale, Kira Finkel, Junken Aoki, Yi Zheng, Thomas H. Bugge, J. Silvio Gutkind. Novel roles for GNA13 and RHOA as tumor suppressor genes. [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 2059. doi:10.1158/1538-7445.AM2015-2059

e22050 Background: Multiple primary cancers in a single individual are rare and usually challenging for effective treatments. Identification common cancer gene driver mutations and targets for pati...

G-proteins and their cognate G-protein coupled receptors (GPCRs) are critical signal transduction molecules that regulate cell survival, proliferation, motility and differentiation. The aberrant expression or function of these molecules has been linked to growth, progression and metastasis of various cancers. Recent genome-wide sequencing efforts have unveiled numerous previously uncharacterized mutations in G-proteins and GPCRs, which could have significant implications to cancer initiation and progression. Of interest, recent analyses have demonstrated that there are frequent mutations in GNA13 in Burkitt's lymphoma and Diffuse Large B cell lymphomas (DLBCL) that are highly statistically significant over background cancer gene mutation rate, and occur in ∼10-13% of patients with these lymphomas. Mutations in the downstream target of G13, RhoA, are also present in several Burkitt's lymphoma tumors, highlighting that mutations in this G13-RhoA pathway may be key to the oncogenic potential of these B cell lymphomas. Although G13 activity has previously been linked cellular transformation and metastatic potential of epithelial cancers, our data suggests that the mutations in GNA13 in these B cell lymphomas are mostly inhibitory in nature. Thus, we have functionally characterized several mutations in GNA13 and RHOA found in Burkitt's lymphoma and DLBCL. Citation Format: Morgan L. O'Hayre, Irina Kufareva, Jose P. Vaqué, Miguel A. Piris, J. Silvio Gutkind. Deciphering the effects of GNA13 mutations in B-cell lymphomas. [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 4202. doi:10.1158/1538-7445.AM2014-4202

Background: Advances in sequencing technologies allow for provision of genome-scale data to physicians caring for pediatric cancer patients but current experience with the clinical application of genomic sequencing is limited and the diagnostic yield of these methods is unclear. Methods: The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating tumor and constitutional whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors at Texas Children's Cancer Center (target enrollment n=280). WES of patient blood and frozen tumor samples is being conducted in the CLIA-certified Whole Genome Laboratory at Baylor College of Medicine using the VCRome 2.1 capture reagent and Illumina paired-end sequencing with reports incorporated in the medical record. Results: 120 patients have enrolled to date, including 39 (33%) and 81 (67%) with CNS and non-CNS tumors, respectively. Despite limited diagnostic biopsies in many patients, tumor samples adequate for WES have been obtained from 97 subjects (81%). WES results have been reported for 89 patients. Tumor WES (n=73) revealed 20 of 73 tumors (27%) to contain mutations classified as having proven or potential clinical utility, including recurrent alterations of CTNNB1, BRAF, KIT, and NRAS/KRAS. Notably, less than 50% of somatic mutations would have been detected on an adult-focused cancer panel, BCM Cancer Gene Mutation Panel v.2. Germline WES (n=89) identified diagnostic findings in 11 cases (12%) including 8 patients with pathogenic mutations in dominant cancer susceptibility genes (singletons except for 2 patients with TP53 mutations). Four of these 8 patients had genetic testing recommended clinically. There were 2 patients with mutations providing the genetic cause of non-cancer medical problems and 1 patient with a mutation which explained both liver disease and hepatocellular carcinoma. Downstream testing of at-risk relatives has occurred rapidly in several families and cancer screening recommendations implemented. Seven (8%) medically actionable incidental findings unrelated to phenotype were reported, predominantly in cardiovascular genes and mitochondrial DNA. Conclusions: These data demonstrate the feasibility of routine WES in the pediatric oncology setting. Early results demonstrate that clinically relevant findings are identified by tumor and germline WES in 38% of pediatric solid tumor patients. The yield of clinically relevant somatic and germline alterations would likely increase further by incorporation of complementary genomic methods (e.g. RNA-seq or copy number analysis). Assessment of the clinical utility of the tumor and germline exomes and preferences for reporting of these results to physicians and parents are under study. Supported by NHGRI/NCI 1U01HG006485. Citation Format: Donald W. Parsons, Angshumoy Roy, Federico A. Monzon, Yaping Yang, Dolores H. López-Terrada, Murali M. Chintagumpala, Stacey L. Berg, Susan G. Hilsenbeck, Tao Wang, Robin A. Kerstein, Sarah Scollon, Katie Bergstrom, Richard L. Street, Laurence B. McCullough, Amy L. McGuire, Uma Ramamurthy, Jeff G. Reid, Donna M. Muzny, David A. Wheeler, Christine M. Eng, Richard A. Gibbs, Sharon E. Plon. Diagnostic yield of clinical tumor and germline exome sequencing for newly diagnosed children with solid tumors. [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 5169. doi:10.1158/1538-7445.AM2014-5169

Twelve well-differentiated villoglandular adenocarcinomas (WDVAs) of the uterine cervix were retrospectively analyzed for the presence and specific genotype of human papillomavirus (HPV), tumor suppressor loss (p53, MCC, APC, BRCA1), cancer gene mutation (K-ras-2, exons 1 and 2, p53 exons 5 to 8), and oncogene amplification (c-erbB-2/HER-2/neu, int-2). Tissue for genetic evaluation was obtained by microdissection, using 4-micron-thick histology sections of archival, formalin-fixed, paraffin-embedded specimens. Genotyping involved nucleic acid amplification and DNA sequencing with gene-specific oligonucleotides and L1 region consensus primers for common strains of HPV. Point mutation and HPV strain determination were accomplished by DNA sequence analysis. Tumor suppressor gene loss and oncogene amplification were performed by allelic imbalance analysis in informative subjects based on DNA sequence and microsatellite-length polymorphisms. HPV was present in all tumors and consisted of type 16 (n = 5, 42%) and type 18 (n = 7, 58%) strains, which have been closely associated with cervical neoplasia. K-ras-2 and p53 genes did not manifest point mutational damage. There was no evidence of oncogene amplification or tumor suppressor gene loss. The presence of HPV in all 12 tumors supports the role of HPV infection in the molecular pathogenesis of this uncommon neoplasm. The absence of associated oncogene or tumor suppressor gene damage is consistent with indolent biological behavior and the favorable prognosis of this unusual tumor.

Background Treatment related toxicity complicates outcome in elderly patients with AML (Estey et al. Blood. 2006). Conventionally, 7+3 induction (anthracycline plus cytarabine) results in Complete Remission rate of about 30%. Regimens with less toxicity, such as 10-days (d) schedule of DAC, seem promising with CR rate of 47% (Blum et al. PNAS. 2010). In secondary MDS derived AML, response prediction could be derived from mutation status in epigenetic modifiers (IDH1, IDH2, DNMT3 A, TET2), transcriptional regulators (RUNX1, CBL), and genes in spliceosome machinery, such as SF3B1 and SRSF2 (Husseinzadeh et al. American Society of Hem Meeting. Abstract # 1698. 2012). IDH-1 mutation is known to induce hypermethylator phenotype (fig 1) (Figueroa et al. Cancer Cell. 2010) and might be present in conjunction with SRSF2 mutations, an unique unreported molecular subset, feasible for exploring azanucleoside response prediction. Herein, we report a case of trisomy 8 MDS derived IDH1 and SRSF2 mutated AML who underwent rapid morphological blast differentiation in the context of acute differentiation syndrome while treated with 10 days (d) of hypomethylating dose of DAC. Methods A 61-year-old male with performance status (PS) = 3 presented with leukocytosis of 18.9 K/uL (peripheral blast 90%). He had a history of low-grade MDS diagnosed 2 years before AML transformation. After morphological confirmation of M5 AML, fluorescent in situ hybridation (FISH) revealed 81% nuclei with trisomy 8. Extracted DNA was tested with a custom-designed Leukemia Cancer Gene Mutation Panel using AmpliSeq™ technology and showed IDH1 c.394C>T(p.R132C) mutation (Fig. 2B) and c.284C>T(p.P95L) mutation of SRSF2 gene (Fig. 2C). DAC was initiated at 15 mg/m2 for a total of 10 days every 28 d cycle. Results By day 5 of cycle (C)1 of DAC treatment, brisk and significant rebound leukocytosis of 60 K/uL (Fig. 3) was observed, along with shortness of breath, hypoxemia and radiological evidence of floppy bilateral pulmonary infiltrates suggestive of acute-like differentiation syndrome. In addition to broad-spectrum antimicrobial and antifungal, dexamethasone at 4 mg intravenously (IV) every 8-hour (h) and hydroxyurea at 1 g orally every 8 h resulted in progressive normalization of peripheral blood count and hypoxemia after 48 h. Patient (pt) recovered from C1 and proceeded with C2 of treatment. A similar episode of brisk/robust leukocytosis was observed by day 5 of C2 requiring dexamethasone and hydroxyurea. Progressive morphological differentiation was observed to full mature and morphologically normal monocytes and neutrophil (Fig. 4). Pt expired as result of severe clostridium difficile colitis during C3 of DAC. Conclusions In our case, we observed robust acute differentiation syndrome characterized by rapid increase of WBC, shortness of breath and hypoxemia associated with azanucleoside treatment. Beside a novel association of IDH-1 and SRSF2 mutations, acute differentiation might suggest potential feature for azanucleoside response phenotype. Our case adds body of evidence of connection between epigenetic regulator and spliceosome mutations. Further studies on the impact of dual mutations in epigenetic reprogramming, leukemia transformation, and azanucleoside response will allow improved decision algorithm and therapeutic design. Disclosures: No relevant conflicts of interest to declare.

The Cancer Cell Line Encyclopedia represents a collaborative effort to assemble a comprehensive resource of human cancer models for basic and translational research. The CCLE aims to contain high-density SNP microarray data, gene expression microarray data and selected cancer gene mutation data for approximately 1000 human cancer cell lines spanning many tumor types. In addition, we are assessing sensitivity of some of these cell lines using a series of pharmacological compounds that represent both conventional cytotoxic and targeted agents. Another goal of the CCLE collaboration involves systematic integration of the genomic and pharmacologic datasets in order to identify putative targets of prevalent genetic alterations as well as predictors of pharmacologic sensitivity and resistance. The availability of high-quality data across hundreds of cell lines markedly enhances the statistical power to discover genetic alterations involved in carcinogenesis and molecular predictors of pharmacologic vulnerability. We are assembling systematic algorithms that identify genetic predictors of sensitivity or resistance to particular pharmacological compounds. Toward this end, we integrated a sensitivity dataset for 28 compounds profiled against more than 500 cell lines with all genomic data available in the CCLE. Gene expression, DNA copy-number and loss of heterozygosity values were combined with critical oncogene mutations and genotype information as inputs to multifaceted prediction models for pharmacological sensitivity, the accuracies of which were assessed using cross-validations. Two complementary paths were followed in order to predict for the sensitivity of cancer cell lines to pharmacological compounds. In a categorical classification-based model, we have used the Naïve Bayes algorithm to find the most significant features predictive of the sensitive or resistant status of the cell lines to each of the compounds. A second path that we followed is a regression-based machine learning approach, called the Elastic Net, where the goal is to predict a continuous value representing the sensitivity of each cell line, such as the GI50. For both approaches, we show examples of the results that we get for some compounds in the collection, such as AZD6244 (MEK), PHA-665752 (MET), Nutlin-3 (MDM2). We detail the performances of the prediction models as well as the most significant genetic determinants of sensitivity to these inhibitors. Several previously unappreciated genomic predictors of response or intrinsic resistance to targeted anticancer agents have been identified. Our results suggest that this integrative approach applied to a robust cancer cell line collection such as the CCLE has considerable power to discover novel associations that augment ongoing basic research into cancer biology and drug discovery. Citation Information: Clin Cancer Res 2010;16(14 Suppl):PR4.

The Cancer Cell Line Encyclopedia (CCLE) represents a collaborative effort to assemble a comprehensive resource of human cancer models for basic and translational research. Thus far, the CCLE contains high-density SNP array data, gene expression microarray data and selected cancer gene mutation data for approximately 1,000 human cancer cell lines spanning many tumor types. Additionally, we are assessing the sensitivity of these same cell lines using a series of pharmacological compounds that represent both conventional cytotoxic and targeted agents. Another goal of the CCLE collaboration involves systematic integration of the genomic and pharmacologic datasets in order to identify putative targets of prevalent genetic alterations as well as predictors and modifiers of pharmacologic sensitivity and resistance. The availability of high-quality data generated by uniform criteria across hundreds of cell lines markedly enhances the statistical power to discover genetic alterations involved in carcinogenesis and molecular predictors of pharmacologic vulnerability. As proof of principle, we have carried out systematic nomination of putative targets of genetic alterations using integrative analyses. Here, significant regions of genomic gains and losses have been linked to expression and mutation data to find significant correlations at both single-gene and pathway levels. We have also begun to assemble systematic algorithms that identify genetic predictors of sensitivity or resistance to particular pharmacological compounds, taking advantage of the fact that the CCLE is a comprehensive resource with extensive genomic characterization. Toward this end, we integrated a preliminary sensitivity dataset for 28 compounds accurately profiled against more than 400 cell lines with all genomic data available in the CCLE. To enhance the robustness of our method, we reduced the number of significant genomic features for each cell line to a number that allows properly determined prediction of sensitivity. Expression data was converted to cell line-specific readouts of gene set expression; and DNA gains and losses are reduced to statistically significant regions using the GISTIC algorithm. These values were combined with critical oncogene mutations as inputs to a multifaceted prediction model for pharmacological sensitivity, the accuracy of which was assessed using cross-validation. Our results suggest that this integrative approach applied to a robust cancer cell line collection has considerable power to discover novel associations that augment ongoing basic research into cancer biology and drug discovery. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 105.

We set out to determine the feasibility of using microarray-based resequencing for cancer gene mutation screening by designing GeneChip CustomSeq Resequencing arrays (Affymetrix, Santa Clara, CA, USA) for interrogation of ARAF, BRAF, CDK4, CDK6, CDKN2A, KLF6, HRAS, KRAS, MET, NRAS, PTEN, RAF1, RB1, RET and TP53 (164 exons in total). Arrays also included four intronic bases on either side of the exons to cover splice sites, thus the arrays covered a total of 23,966 bases. Overall performance was very good, with accuracy >99.99% and coverage ~97.5%. Twenty NSCLC samples were analyzed using the arrays, and several well-characterized somatic mutations and germline variants were found. The most significant novel finding was the detection of a transforming MET mutation (T1010I) in a NSCLC patient.