Somatic Mutations In Human Cancers Research Articles

Abstract 62: COSMIC: Combining the world's knowledge of somatic mutation in human cancer

Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Live since 2004, the 71st release (Nov 2014) describes over 2 million mutations in more than 1 million tumour samples across most human genes. To emphasise depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and clinically relevant patient details. Combination of over 20,000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of populations and new diseases behind known biomarkers. Conversely, our curation of over 15,000 cancer genome studies emphasises knowledge breadth, driving discovery of new unrecognised cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. For example, BRAF is well characterized in skin melanoma, transiently treatable with inhibitors such as Vemurafenib. It is also well known in colorectal cancer, which is largely non-responsive to BRAF inhibitors. COSMIC's unique approach demonstrates the impact of BRAF mutations in much less well-known cancers, for instance, Hairy Cell Leukaemia (89% of samples mutated) and Langerhans Cell Histiocytosis (49%), both of which respond remarkably well to BRAF inhibitors. Converse to skin melanoma, our curations suggest BRAF has a minimal role in Uveal melanoma (6% of Uveal tumors mutated for BRAF), with higher mutation rates in other genes (particularly GNA11, BAP1 and GNAQ), suggesting different mechanisms behind this disease. In addition to describing over two million coding point mutations across cancer, COSMIC also details more than six million non-coding mutations, 10,567 gene fusions, 61,232 genome rearrangements, 702,652 abnormal copy number segments, and more than 6 million abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types. As increasing amounts of genetic data are gathered into COSMIC across human cancer, our annotations are beginning to emphasise events with a higher impact in cancer, highlighting the more functional coding mutations and major amplifications and deletions. This concept of high-impact data is being extended across the entire COSMIC system, much more strongly defining genes and mutations which drive oncogenesis. Citation Format: Simon A. Forbes, Dave Beare, Prasad Gunasekaran, Kenric Leung, Charambulos Boutselakis, Minjie Ding, Mingming Jia, Tisham De, Nidhi Bindal, Chai Yin Kok, Sally Bamford, Sari Ward, Charlotte Cole, Jon Teague, Michael R. Stratton, Peter J. Campbell. COSMIC: Combining the world's knowledge of somatic mutation in human cancer. [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 62. doi:10.1158/1538-7445.AM2015-62

Identifying somatic oncogenic mutations in leukocytes that infiltrate primary breast cancers.

11000 Background: In the past decade, sequencing studies have delineated somatic mutations in human cancers. Given that cancer cells interact with their microenvironment and the presence of somatic...

The genetics of splicing in neuroblastoma.

Regulation of mRNA splicing, a critical and tightly regulated cellular function, underlies the majority of proteomic diversity and is frequently disrupted in disease. Using an integrative genomics approach, we combined both genomic data and exon-level transcriptome data in two somatic tissues (cerebella and peripheral ganglia) from a transgenic mouse model of neuroblastoma, a tumor that arises from the peripheral neural crest. Here, we describe splicing quantitative trait loci associated with differential splicing across the genome that we use to identify genes with previously unknown functions within the splicing pathway and to define de novo intronic splicing motifs that influence splicing from hundreds of bases away. Our results show that these splicing motifs represent sites for functional recurrent mutations and highlight novel candidate genes in human cancers, including childhood neuroblastoma. Somatic mutations with predictable downstream effects are largely relegated to coding regions, which comprise less than 2% of the human genome. Using an unbiased in vivo analysis of a mouse model of neuroblastoma, we have identified intronic splicing motifs that translate into sites for recurrent somatic mutations in human cancers.

Zombies in TCGA.

Next-generation sequencing results obtained to detect somatic mutations in human cancers can also be searched for viruses that contribute to cancer. Recently, human papillomavirus 18 RNA was detected in tumor types not typically associated with HPV infection. Analyses reported in this issue of Journal of Virology demonstrate that the apparent presence of HPV18 RNA in these atypical tumors is due in at least some cases to contamination of samples with HeLa cells, which harbor HPV18.

Identification of Somatic KRAS Mutation in a Korean Baby with Nevus Sebaceus Syndrome

Identification of Somatic <i>KRAS</i> Mutation in a Korean Baby with Nevus Sebaceus Syndrome

COSMIC: exploring the world's knowledge of somatic mutations in human cancer.

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Our latest release (v70; Aug 2014) describes 2 002 811 coding point mutations in over one million tumor samples and across most human genes. To emphasize depth of knowledge on known cancer genes, mutation information is curated manually from the scientific literature, allowing very precise definitions of disease types and patient details. Combination of almost 20 000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers across cancer patient populations. Conversely, our curation of cancer genomes (over 12 000) emphasizes knowledge breadth, driving discovery of unrecognized cancer-driving hotspots and molecular targets. Our high-resolution curation approach is globally unique, giving substantial insight into molecular biomarkers in human oncology. In addition, COSMIC also details more than six million noncoding mutations, 10 534 gene fusions, 61 299 genome rearrangements, 695 504 abnormal copy number segments and 60 119 787 abnormal expression variants. All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.

Abstract 5326: COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer

Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Now running for over 10 years, the 67th release (Oct 2013) describes 1592109 mutations in 947213 tumour samples across 25606 genes. This information is curated manually from the scientific literature, and automatically from genome resequencing consortium data portals. Full curation of the scientific literature provides in-depth understanding of the impact that each gene has in human cancer, and this has been achieved for 127 point-mutated cancer genes, and 185 fusion gene pairs. Curated genes are selected from the Cancer Gene Census (http://cancer.sanger.ac.uk/census), a listing of all genes with substantial evidence implicating them in cancer promotion, currently numbering 513 and updated frequently. The mutations discovered in the re-sequencing of over 8000 tumour genomes are now present in COSMIC (viewable in isolation from the genic curations, http://cancer.sanger.ac.uk/wgs). In addition, the Sanger has now fully exome sequenced 1015 common cancer cell lines, identifying 1146874 coding mutations annotated for functional significance, and this is available exclusively in COSMIC at (http://cancer.sanger.ac.uk/cell_lines). While COSMIC has focused on point mutations and gene fusions, many other mutation mechanisms cause oncogenesis and these are now being integrated. The 67th COSMIC release includes copy number mutations integrated into the database and major web page views. To allow easy graphical examination of this data, copy number information was reduced to ‘gain’ and ‘loss’ annotations for inclusion in histograms and tables, with much more precise detail available with a further click. Copy number data is available in detail for every gene in COSMIC, and also for every tissue. Exploring cancer via COSMIC’s Cancer Browser (http://cancer.sanger.ac.uk/cosmic/browse/tissue), results not just in a plot of the most mutated genes, but now also a circular genome plot summarizing the copy number gains and losses across all the samples from that tumour type, all explorable in more detail via clicks on the pictures. As the genomic data increases in COSMIC, it is becoming more important to qualitatively annotate the information, indicating which is more important or significant to oncogenesis. We are now building systems to better highlight known or putative functional mutations, improving the signal-to-noise ratio of cancer genome resequencing. Citation Format: C Boutselakis, S A. Forbes, P Gunasekaran, M Jia, D Beare, N Bindal, C Y. Kok, K Leung, D Minjie, R Shepherd, S Bamford, S Ward, C Cole, J W. Teague, M Stratton, P Campbell, U McDermott. COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. [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 5326. doi:10.1158/1538-7445.AM2014-5326

When defense turns into attack

The APOBEC3 cytidine deaminases play an important role in innate immunity but have also emerged as mediators of somatic mutations in human cancer. We recently reported a high incidence of APOBEC-mediated driver mutations in human papillomavirus-associated cancer, suggesting a key role for these enzymes in the development of such tumors.

Abstract B179: Targeted next generation sequencing for somatic mutations in human cancer.

Abstract Objective: We have replaced single gene PCR-based methods for the detection of BRAF, KRAS and EGFR variants in routine clinical practice with next generation sequencing assays for the Ion Torrent AmpliSeq Cancer Hotspot Panel v2 (50 genes) and the Illumina TruSeq Amplicon Cancer panel (48 genes). Implementation of these panels requires constant optimization of technical and analytical procedures as reagents and software continue to be developed. In this study we describe somatic mutation findings from our clinical laboratory service. Methods: DNA was extracted from 90 formalin fixed, paraffin embedded tissue specimens that included 50 lung cancer, 24 colon cancer and 16 other cancers. Barcoded libraries were prepared from up to 10ng of extracted DNA and multiplexed on single 318 chips. Data analysis was performed using Golden Helix SVS for the Ion Torrent panel and Variant Studio for the Illumina panel. Variants that remained after the analysis pipeline were individually interrogated using the Integrative Genomics Viewer (IGV). Results: Of the 90 cancer cases sequenced, each panel returned on average 20 variants. Of these, there was 100% concordance between the two panels with respect to the clinically actionable mutations identified. Conclusions: We have implemented next generation sequencing technologies for the detection of somatic mutations in human cancers. Two platforms, the Ion Torrent PGM and the Illumina MiSeq, have been used for the routine analysis of FFPE cancer tissues in a clinical setting with actionable and non-actionable variants reported and archived. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B179. Citation Format: Jason D. Peterson, Francine de Abreu, Torrey L. Gallagher, Paul R. Burchard, Christopher I. Amos, Wendy A. Wells, J. Marc Pipas, Marc S. Ernstoff, Camilo E. Fadul, James R. Rigas, Gregory J. Tsongalis. Targeted next generation sequencing for somatic mutations in human cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B179.

Abstract 3959: COSMIC: Mining the world's knowledge on somatic cancer mutations

Abstract COSMIC, the Catalog Of Somatic Mutations In Cancer (www.sanger.ac.uk/cosmic) is a single resource combining much of the available data on somatic mutations in human cancer. This information is obtained from a number of online sources, including the TCGA and ICGC webportals, the IARC p53 database and the Cancer Genome Project, Sanger Institute, UK; this is then combined with information carefully curated from the scientific literature. Over 20,000 genes have been screened in the search for cancer causing mutations, and details have been curated for all of these, resulting in the annotation of 213,615 mutations across 665,763 tumor samples (COSMIC v56, Nov 2011). The Cancer Gene Census lists all known cancer genes and these are prioritized for curation, generating extensive mutation spectra across 107 point-mutated genes and 111 fusion gene pairs. Increasing whole genome/exome data are also available; currently 559 samples detail 2753 genome rearrangements, 21892 coding and 57396 non-coding point mutations. Most importantly, this information is all rigorously maintained and regularly updated. With new releases every two months, COSMIC is very responsive to the scientific literature, detailing all the latest findings. The data in COSMIC can be examined in a number of different ways. The website has been designed to allow easy graphical browsing of the data, with many mining options to filter desired information. A COSMIC genome browser can be used to visualize COSMIC mutations in a genomic context, and a Biomart is available to download datasets federated with external databases. In addition, the complete data is available for free download for offline analysis. The combination of data from multiple sources in COSMIC allows its use as a discovery tool as well as a reference datasource; substantial mining can be performed between mutant genotypes and clinical phenotypes, searching for novel recurrence patterns between tissues, genes and individual variants. Overall, the top mutated gene reported in human cancer is JAK2, with a published mutation rate of 38% (n=76853), however a phenotype correlation suggests a mutation rate of up to 86% in Polycythaemia Vera, 58% in Myelofibrosis and 55% in Essential Thrombocythaemia. Similarly, KRAS with an overall mutation rate of 23% (n=96055) increases to 69% in Pancreatic ductal carcinomas, and a single report suggests a 70% mutation frequency for MED12 in Uterine Leiomyomas (n=225). In addition to these well characterized cancer genes, new whole-genome screens are beginning to identify many more. For instance the TCGA Ovarian exome screen suggested roles for genes such as CSMD3, HMCN1 and USH2A, and combining multiple whole genome screens suggests roles for further new genes such as BAI3 (13% mutated in lung). As yet, novel recurrent mutations are challenging to identify across studies, but rapidly increasing amounts of whole genome data will make COSMIC a key resource in this search for new therapeutic targets. 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 3959. doi:1538-7445.AM2012-3959

Abstract 46: COSMIC: Enhancing the analysis of whole somatic mutant tumor genomes

Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://www.sanger.ac.uk/cosmic), is a comprehensive web resource for the investigation of somatic mutations in human cancer with data curated and centrally combined from a variety of sources. Currently, point mutation data have been manually curated from the scientific literature on 89 genes, together with full mutation details on a further 57 fusion gene pairs (Release v50, Nov 2010), defined as known cancer genes in the Cancer Gene Census (http://www.sanger.ac.uk/genetics/CGP/Census). Further, in collaboration with the IARC TP53 database, COSMIC now contains the somatic mutation data for the key p53 tumor suppressor gene. Details of many large candidate gene screens, together spanning almost 20,000 genes have also been curated from three sources, the scientific literature, the Cancer Genome Project labs at the Sanger Institute, UK (CGP), and The Cancer Genome Atlas (TCGA) web portal. Finally, COSMIC now presents the results of 48 whole-genome screens, detailing 2689 genomic rearrangements, 1661 coding mutations and 55,440 non-coding mutations. The COSMIC website is designed to allow easy and intuitive browsing of this data, in isolation or various combinations. As the amount and variability of data has increased, the methods of acquiring and interacting with the data have been enhanced. The COSMIC website now provides mining capabilities, with numerous specialization filters, graphically presenting selected data. A more extensive mining tool is the COSMIC Biomart, allowing selection of data using any definitions found in the COSMIC system. With the increasing significance of genomic data in cancer, COSMIC has integrated with the two largest genome browsers, the Ensembl system and the UCSC cancer genomics browser; links are available from and to Ensembl, whilst per-tissue summaries are provided graphically in the UCSC browser. In addition, COSMIC has integrated its own genome browser, a version of ‘Gbrowse’, which provides custom genomic views of the majority of COSMIC data, together with CONAN copy number graphs, within the context of full genome annotations. Looking to the future, much novel global cancer genomics data will soon be made available via the ICGC data coordination centre. COSMIC is well placed to utilize this as a major new source of mutation information, maintaining COSMIC's position as a central resource in human cancer genetics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 46. doi:10.1158/1538-7445.AM2011-46

COSMIC: the catalogue of somatic mutations in cancer

The Catalogue Of Somatic Mutations In Cancer (COSMIC) [1] is one of the largest repositories of information on somatic mutations in human cancer. The project has been running for more than ten years as part of the Cancer Genome Project (CGP) at the Wellcome Trust Sanger Institute in the UK. The data in COSMIC are curated from a variety of sources, primarily the scientific literature and large international consortia. The project includes information from the CGP, along with data from other consortia such as the International Cancer Genome Consortium and The Cancer Genome Atlas. In addition, COSMIC is regularly updated with the genes highlighted in the Cancer Gene Census, which curates the scientific literature for known cancer genes [2]. With the advent of whole exome and genome sequencing technology, the amount of data in COSMIC is increasing rapidly. The recent COSMIC release (version 53; 18 May 2011) contains 608,042 tumor and cell line samples, annotating 176,856 mutations across 19,439 genes, with 352 full exomes, 43 whole genome rearrangement screens and 4 full genomes now available. The data are updated regularly, with new releases scheduled every two months. COSMIC provides a large number of graphical and tabular views for interpreting and mining the large quantity of information, as well as the facility to export the relevant data in various formats. The website can be navigated in many ways to examine mutation patterns on the basis of genes, samples and phenotypes, which are the main entry points to COSMIC. COSMIC also provides various options to browse the data in a genomic context. Integration with the Ensembl genome browser allows the visualization of full genome annotations, together with COSMIC data, on the GRCh37 genome coordinates. COSMIC also contains its own genome browser, which facilitates data analysis by combining genome-wide gene structures and sequences with rearrangement breakpoints, copy number variations and all somatic substitutions, deletions, insertions and complex gene mutations. The main COSMIC website [1] encompasses all of the available data. However, within COSMIC, the Cancer Cell Line Project [3] is a specialized component, which provides details of the genotyping of almost 800 commonly used cancer cell lines, through the set of known cancer genes. Its focus is to identify driver mutations, or those likely to be implicated in the oncogenesis of each tumor. This information forms the basis for integrating COSMIC with the Genomics of Drug Sensitivity in Cancer project [4], which is a joint effort with the Massachusetts General Hospital [5] to screen this panel of cancer cell lines against potential anticancer therapeutic compounds to investigate correlations between somatic mutations and drug sensitivity. Data on somatic mutations in cancer are being produced at a rapidly increasing rate, and the combined analysis of large distributed datasets is becoming ever more difficult. However, COSMIC curates and standardizes this information in a single database, providing user-friendly browsing tools and analytical functions, thus ensuring its role as a key resource in human cancer genetics.

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

COSMIC (http://www.sanger.ac.uk/cosmic) curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136 000 coding mutations in almost 542 000 tumour samples; of the 18 490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs (19 new cancer genes and 30 new fusion pairs this year) and this number is continually increasing. Key amongst these is TP53, now available through a collaboration with the IARC p53 database. In addition to data from the Cancer Genome Project (CGP) at the Sanger Institute, UK, and The Cancer Genome Atlas project (TCGA), large systematic screens are also now curated. Major website upgrades now make these data much more mineable, with many new selection filters and graphics. A Biomart is now available allowing more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus; COSMIC has begun curating full-genome resequencing experiments, developing new web pages, export formats and graphics styles. With all genomic information recently updated to GRCh37, COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

Recent Progress in Phosphoinositide 3-Kinases: Oncogenic Properties and Prognostic and Therapeutic Implications

Phosphatidylinositol 3-kinases (PI3Ks) are a group of lipid kinases that coordinate various fundamental cellular responses including mitogenic signaling, cell survival and proliferation, vesicular trafficking, cytoskeletal rearrangement and metabolism. Overexpression caused by genetic alterations such as the amplification or gain of copy numbers was frequently observed for various PI3Ks in different human cancers. In recent years, the high-frequency somatic mutations of PIK3CA observed in different human cancers further strengthen the notion that PI3Ks are optimal targets for therapeutic intervention. In this review, I summarize current experimental evidence about the transformation capability and oncogenic properties of different PIK3CA mutations identified in human cancers. I also discuss the association of PIK3CA mutations with other genetic markers, as well as the prognostic value of PIK3CA somatic mutations in human cancers. Finally, I discuss the application of PI3Ks as therapeutic targets in human cancers, including targeted and combinational therapies and the potential challenges that confront their clinical applications.

Abstract 93: COSMIC: The catalogue of somatic mutations in cancer receives full genome variant annotations

Abstract COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://www.sanger.ac.uk/cosmic), is one of the most comprehensive web systems describing the impact of somatic mutations in human cancer. The information is sourced directly from the published scientific literature and the Cancer Genome Project's high throughput sequencing laboratories at the Wellcome Trust Sanger Institute UK (CGP), allowing a high data quality to be maintained. The v44 release (Nov. 2009) contained the curation of 8336 papers covering 71 known cancer genes by point mutation and 30 by gene fusion. The mutation data for all these genes is being maintained up-to-date and new genes are regularly added to this list. Additionally, 4871 genes and 2764 samples have been scrutinized by the CGP laboratories. As cancer genetics moves toward the analysis of whole genomes, COSMIC is being updated to handle and display these data and increase the functionality of the website. With the rapid development of sequencing technologies, the quantity of data that can be put into COSMIC is increasing fast. We have extended our curation process to include large exome-wide candidate gene screens, recently including the first such screen from Sjoblom et al (2006), and the first TCGA screen (2008) with other large scale screening datasets being curated. In addition, whole-genome screens are becoming available with many non-coding variations. From the CGP laboratories, we already have two low-coverage genome rearrangement screens in COSMIC and this will rapidly expand, beginning with the imminent release of rearrangement scans in a set of 24 breast tumours. High-coverage genome analyses are also beginning to become available; with full genome coverage, the majority of somatic mutations in a tumour can be identified and COSMIC is being prepared to receive and display this data. With the inclusion of these new data, the COSMIC website has evolved to allow more easy access to required data. New specialization filters are in place to provide methods to search for subsets of COSMIC data in the usual user-friendly web pages. More extensive investigations can be performed using the new COSMIC Biomart, an industry-standard data mining system allowing access through web pages or programmatic interfaces. As the inclusion of new genomic data accelerates and the systems through which it can be accessed evolve, COSMIC is well placed to remain a central resource in human cancer genetics. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. 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 93.

Somatic mutations in human cancer—moving towards large scale resequencing of whole cancer genomes

Somatic mutations in human cancer—moving towards large scale resequencing of whole cancer genomes

Activating ROCK1 somatic mutations in human cancer

Cancer cells acquire characteristics of deregulated growth, survival and increased metastatic potential. Genetic mutations that provide a selective advantage by promoting these characteristics have been termed 'drivers,' whereas mutations that do not contribute to disease initiation/progression are termed 'passengers.' The advent of high-throughput methodologies has facilitated large-scale screening of cancer genomes and the subsequent identification of novel somatic mutations. Although this approach has generated valuable results, the data remain incomplete until the functional consequences of these mutations are determined to differentiate potential drivers from passengers. ROCK1 is an essential effector kinase downstream of Rho GTPases, an important pathway involved in cell migration. The Cancer Genome Project identified three nonsynonymous mutations in the ROCK1 gene. We now show that these somatic ROCK1 mutations lead to elevated kinase activity and drive actin cytoskeleton rearrangements that promote increased motility and decreased adhesion, characteristics of cancer progression. Mapping of the kinase-interacting regions of the carboxy terminus combined with structural modeling provides an insight into how these mutations likely affect the regulation of ROCK1. Consistent with the frequency of ROCK1 mutations in human cancer, these results support the conclusion that there is selective pressure for the ROCK1 gene to acquire 'driver' mutations that result in kinase activation.

Design and analysis issues in genome-wide somatic mutation studies of cancer

The availability of the human genome sequence and progress in sequencing and bioinformatic technologies have enabled genome-wide investigation of somatic mutations in human cancers. This article briefly reviews challenges arising in the statistical analysis of mutational data of this kind. A first challenge is that of designing studies that efficiently allocate sequencing resources. We show that this can be addressed by two-stage designs and demonstrate via simulations that even relatively small studies can produce lists of candidate cancer genes that are highly informative for future research efforts. A second challenge is to distinguish mutated genes that are selected for by cancer (drivers) from mutated genes that have no role in the development of cancer and simply happened to mutate (passengers). We suggest that this question is best approached as a classification problem and discuss some of the difficulties of more traditional testing-based approaches. A third challenge is to identify biologic processes affected by the driver genes. This can be pursued by gene set analyses. These can reliably identify functional groups and pathways that are enriched for mutated genes even when the individual genes involved in those pathways or sets are not mutated at sufficient frequencies to provide conclusive evidence as drivers.

Association of gene variants in the TGF-beta signalling pathways with invasive breast cancer risk

Many studies of normal cells in vitro, of transgenic mouse models and of somatic mutations in human cancers have provided evidence that the cytokine transforming growth factor beta (TGFβ) acts as a suppressor of primary tumour initiation. However, studies of transformed cells in vitro and of mouse models have also implicated TGFβ as a promoter of the later stages of tumour development. A hypothesis that has been proposed to account for this dual action is that TGFβ acts as a tumour suppressor through the ubiquitous ALK5 receptor signalling via SMAD2 and SMAD3 to inhibit proliferation of primary tumour cells, but acts subsequently through the endothelial-specific ALK1 receptor via SMAD1 and SMAD5 to promote angiogenesis, which is required for tumour progression [1]. In a recent meta-analysis we showed that a single nucleotide polymorphism (SNP) generating a leucine to proline substitution in the signal peptide of the TGFB1 protein is associated with an increase in the risk of invasive breast cancer (OR per additional proline allele = 1.08 (95% CI = 1.04 to 1.11), Ptrend = 2.8 × 10-5) [2]. We have also reported that this SNP increases the amount of TGFB1 protein secreted in vitro by threefold [3]. These data suggest that higher levels of TGFB1 may promote the invasive breast tumour phenotype. To determine the effect of host TGFB1 levels in an in vivo model, Tgfb1+/- and Tgfb1+/+ mice have been compared in which the mice carry one or two TGFB1 alleles with the ancestral SNP form encoding proline in the signal peptide. These studies have revealed major effects of TGFB1 in controlling the site of metastatic seeding and the number of metastases that develop. The TGFB1 SNP association with breast cancer suggested that other genes in the TGFβ signalling pathways might be associated with altered risk. We have conducted association studies with SNPs in 16 further genes encoding proteins directly implicated in TGFβ signalling. LTBP1, LTBP2, LTBP4, TGFB1, TGFB2, TGFB3, ALK1, ALK5, TGFBR2, Endoglin, SMAD1, SMAD2, SMAD3, SMAD4, SMAD5, SMAD6 and SMAD7 were analysed. A comprehensive SNP tagging approach was used to select variants for genotyping in a staged study design using up to 6,900 cases and 6,900 controls, all collected from the East Anglia region of the UK (>98% of northwestern European ancestry). From 1,254 common SNPs (minor allele frequency >0.05) in these genes identified from the International HapMap project data, we defined and genotyped 354 tagging SNPs in the East Anglia cases and controls. Statistically significant associations were followed up by genotyping in a Polish set of 2,215 cases and 2,374 controls. Meta-analysis of these results identified associations with cancer susceptibility of a variant in ALK5 (OR per additional rare G allele = 0.88 (95% CI = 0.81 to 0.95), Ptrend = 0.001) and in TGFBR2 (OR per additional rare G allele = 0.96 (95% CI = 0.92 to 1.00), Ptrend = 0.039). Data from two genome-wide studies have been examined to search further for associations in these genes. The haplotype risks and interactions between two or more loci have been investigated and survival analyses have been conducted. From this comprehensive study we have identified tagging SNPs in two TGFβ receptor genes that are significantly associated with risk of invasive breast cancer. Identification of the causative SNPs within the LD blocks tagged by the two SNPs and their effects on signalling via the ALK1 and ALK5 pathways remain to be determined.

The Catalogue of Somatic Mutations in Cancer (COSMIC).

COSMIC is currently the most comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. Almost 4800 genes and 250000 tumors have been examined, resulting in over 50000 mutations available for investigation. This information can be accessed in a number of ways, the most convenient being the Web-based system which allows detailed data mining, presenting the results in easily interpretable formats. This unit describes the graphical system in detail, elaborating an example walkthrough and the many ways that the resulting information can be thoroughly investigated by combining data, respecializing the query, or viewing the results in different ways. Alternate protocols overview the available precompiled data files available for download.