Michael S. Noble

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour–normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour–normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

A Landscape of Driver Mutations in Melanoma

Despite recent insights into melanoma genetics, systematic surveys for driver mutations are challenged by an abundance of passenger mutations caused by carcinogenic UV light exposure. We developed a permutation-based framework to address this challenge, employing mutation data from intronic sequences to control for passenger mutational load on a per gene basis. Analysis of large-scale melanoma exome data by this approach discovered six novel melanoma genes (PPP6C, RAC1, SNX31, TACC1, STK19, and ARID2), three of which-RAC1, PPP6C, and STK19-harbored recurrent and potentially targetable mutations. Integration with chromosomal copy number data contextualized the landscape of driver mutations, providing oncogenic insights in BRAF- and NRAS-driven melanoma as well as those without known NRAS/BRAF mutations. The landscape also clarified a mutational basis for RB and p53 pathway deregulation in this malignancy. Finally, the spectrum of driver mutations provided unequivocal genomic evidence for a direct mutagenic role of UV light in melanoma pathogenesis.

Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma

On the basis of multidimensional and comprehensive molecular characterization (including DNA methalylation and copy number, RNA, and protein expression), we classified 894 renal cell carcinomas (RCCs) of various histologic types into nine major genomic subtypes. Site of origin within the nephron was one major determinant in the classification, reflecting differences among clear cell, chromophobe, and papillary RCC. Widespread molecular changes associated with TFE3 gene fusion or chromatin modifier genes were present within a specific subtype and spanned multiple subtypes. Differences in patient survival and in alteration of specific pathways (including hypoxia, metabolism, MAP kinase, NRF2-ARE, Hippo, immune checkpoint, and PI3K/AKT/mTOR) could further distinguish the subtypes. Immune checkpoint markers and molecular signatures of T cell infiltrates were both highest in the subtype associated with aggressive clear cell RCC. Differences between the genomic subtypes suggest that therapeutic strategies could be tailored to each RCC disease subset.

Constraining jet/disc geometry and radiative processes in stellar black holes XTE J1118+480 and GX 339−4

We present results from modelling of quasi-simultaneous broad-band (radio through X-ray) observations of the Galactic stellar black hole (BH) transient X-ray binary (XRB) systems XTE J1118+480 and GX 339−4 using an irradiated disc + compact jet model. In addition to quantifying the physical properties of the jet, we have developed a new irradiated disc model which also constrains the geometry and temperature of the outer accretion disc by assuming a disc heated by viscous energy release and X-ray irradiation from the inner regions. For the source XTE J1118+480, which has better spectral coverage of the two in optical and near-infrared (OIR) wavelengths, we show that the entire broad-band continuum can be well described by an outflow-dominated model + an irradiated disc. The best-fitting radius of the outer edge of the disc is consistent with the Roche lobe geometry of the system, and the temperature of the outer edge of the accretion disc is similar to those found for other XRBs. Irradiation of the disc by the jet is found to be negligible for this source. For GX 339−4, the entire continuum is well described by the jet-dominated model only, with no disc component required. For the two XRBs, which have very different physical and orbital parameters and were in different accretion states during the observations, the sizes of the jet base are similar and both seem to prefer a high fraction of non-thermal electrons in the acceleration/shock region and a magnetically dominated plasma in the jet. These results, along with recent similar results from modelling other galactic XRBs and AGNs, may suggest an inherent unity in diversity in the geometric and radiative properties of compact jets from accreting black holes.

TGCat *: THE CHANDRA TRANSMISSION GRATING DATA CATALOG AND ARCHIVE

The Chandra Transmission Grating Data Archive and Catalog (TGCat) provides easy access to analysis-ready products, specifically, high-resolution X-ray count spectra and their corresponding calibrations. The web interface makes it easy to find observations of a particular object, type of object, or type of observation; to quickly assess the quality and potential usefulness of the spectra from pre-computed summary plots; or to customize a view with an interactive plotter, optionally combining spectra over multiple orders or observations. Data and responses can be downloaded as a package or as individual files, and the query results themselves can be retrieved as ASCII or Virtual Observatory tables. Portable reprocessing scripts used to create the archive and which use the Chandra X-ray Center’s (CXC’s) software and other publicly available software are also available, facilitating standard or customized reprocessing from Level 1 CXC archival data to spectra and responses with minimal user interaction.

Scientific Computation with JavaSpaces

JavaSpaces provides a simple yet expressive mechanism for distributed computing with commodity technology. We discuss the suitability of JavaSpaces for implementing different classes of concurrent computations based on low-level metrics (null messaging and array I/O), and present performance results for several parametric algorithms. We found that although inefficient for communication intensive problems, JavaSpaces yields good speedups for parametric experiments, relative to both sequential Java and C. We also outline a dynamic native compilation technique, which for short, compute-intensive codes further boosts performance without compromising Java portability or extensive algorithm recoding. Discussion and empirical results are presented in the context of our public benchmark suite.

Characterizing genomic alterations in cancer by complementary functional associations

Systematic efforts to sequence the cancer genome have identified large numbers of mutations and copy number alterations in human cancers. However, elucidating the functional consequences of these variants, and their interactions to drive or maintain oncogenic states, remains a challenge in cancer research. We developed REVEALER, a computational method that identifies combinations of mutually exclusive genomic alterations correlated with functional phenotypes, such as the activation or gene dependency of oncogenic pathways or sensitivity to a drug treatment. We used REVEALER to uncover complementary genomic alterations associated with the transcriptional activation of β-catenin and NRF2, MEK-inhibitor sensitivity, and KRAS dependency. REVEALER successfully identified both known and new associations, demonstrating the power of combining functional profiles with extensive characterization of genomic alterations in cancer genomes.

Nozzle: a report generation toolkit for data analysis pipelines

SUMMARY We have developed Nozzle, an R package that provides an Application Programming Interface to generate HTML reports with dynamic user interface elements. Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big datasets. The package can be applied to any project where user-friendly reports need to be created. AVAILABILITY The R package is available on CRAN at http://cran.r-project.org/package=Nozzle.R1. Examples and additional materials are available at http://gdac.broadinstitute.org/nozzle. The source code is also available at http://www.github.com/parklab/Nozzle. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Proteomics, post-translational modifications, and integrative analyses reveal molecular heterogeneity within medulloblastoma subgroups

There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumors, and found post-translational modifications of MYC that are associated with poor outcomes in group 3 tumors. We found kinases associated with subtypes and showed that inhibiting PRKDC sensitizes MYC-driven cells to radiation. Our study shows that proteomics enables a more comprehensive, functional readout, providing a foundation for future therapeutic strategies.

Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Melanoma is an aggressive skin cancer of melanocytic origin characterized by high metastatic potential and mutation rate. Affording a survey of the wide breadth of genomic lesions found in melanoma, we present here an analysis of the somatic mutations discovered in the sequenced exomes of 121 melanoma tumor-normal pairs. We identify frequent genomic alterations both in genes previously implicated in melanoma (BRAF, NRAS, TP53, CDKN2A, PTEN) as well as in several genes whose role in melanoma tumorigenesis has not yet been established and thus are of particular interest. To do so we implement a novel method to increase the identification of genes that are significantly recurrently mutated in melanoma in the setting of its exceptionally high mutation rate. A preponderance of C>T transitions (∼85%) in the observed mutational profile reflects a history of DNA damage due to UV radiation, though the majority of somatic mutations in known melanoma genes are not C>T events. Our study broadens understanding of the genomic lesions involved in melanoma tumorigenesis, and we expect our analysis approach to inform future genomic studies of cancer lineages with similarly high mutation rates. 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 5056. doi:1538-7445.AM2012-5056