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• The MD Anderson Colorectal Cancer Case Control Study

  Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the US. Driven by common disease common variants hypothesis, genome-wide association studies only identified a number of common susceptibility loci that explained a small portion of CRC heritability. We conducted a case-control study using whole exome sequencing to identify rare genetic variants with intermediate effect size that predispose individuals to colorectal cancer.

  Study phs002691

• A Genome-Wide Association Study for Post-bronchodilator Lung Function in Children with Asthma

  In this study, we conducted a genome-wide association study (GWAS) of post-bronchodilator (BD) FEV1 (forced expiratory volume in 1 second) and FEV1/FVC (forced vital capacity) in Puerto Rican children with asthma. From September 2003 to June 2010, we recruited 618 Puerto Rican children with asthma, which was defined as physician diagnosed asthma and at least one episode of wheezing in the previous year. The recruited children include 267 from public schools in Hartford, Connecticut and 351 from randomly selected households in San Juan, Puerto Rico.

  Study phs001216

• Whole exome sequencing in familial Multiple Sclerosis

  The purpose of the study is to determine whether variants of genes are associated with greater risk of Multiple Sclerosis (MS). We used whole-exome sequencing in 138 individuals from 23 families including at least 2 members with MS. We compare patients with MS, patients with other autoimmune diseases (AID), and unaffected individuals.

  Study EGAS00001004204

• Genomic Profiling of Peripheral T-cell Lymphoma

  Peripheral T-cell lymphomas (PTCLs) are malignant and highly aggressive hematologic tumors arising from mature post-thymic T cells. The diagnosis of PTCL includes diverse lymphoma subgroups, altogether accounting for about 15% of all non-Hodgkin lymphomas. Despite recent advances in uncovering the mutational landscape of PTCLs, the prognoses of most PTCLs remain poor. To overcome the limits of exome sequencing and identify new genomic abnormalities in PTCL, we performed RNAseq and whole genome sequencing. From our analyses, we identified a recurrent in-frame deletion (VAV1 Δ778-786) generated by a focal deletion-driven alternative splicing mechanism as well as novel VAV1 gene fusions (VAV1-THAP4, VAV1-MYO1F, and VAV1-S100A7). These genetic lesions result in increased activation of VAV1 catalytic-dependent (MAPK, JNK) and non-catalytic-dependent (nuclear factor of activated T cells, NFAT) VAV1 effector pathways. These results support an oncogenic role for VAV1 signaling in the pathogenesis of PTCL (Abate et al., 2017). Recently, we have also identified a novel chimeric oncogene, FYN-TRAF3IP2, in the RNA-seq and whole genome sequencing analyses. FYN-TRAF3IP2 leads to aberrant NF-κβ activity downstream of T-cell receptor signaling and induces NF-κβ-driven T-cell transformation when expressed in hematopoietic progenitors in mice. This novel gene fusion supports the oncogenic driver role of NF-κβ signaling in the pathogenesis of PTCL (Kim et al., in review).

  Study phs001962

• Multi-omic analysis of the tumor microenvironment shows clinical correlations in Ph1 study of atezolizumab +/- SoC in MM

  Multiple myeloma (MM) remains incurable, and treatment of relapsed/refractory (R/R) disease is challenging. There is an unmet need for more targeted therapies in this setting; deep cellular and molecular phenotyping of the tumor and microenvironment in MM could help guide such therapies. This phase 1b study (NCT02431208) evaluated the safety and efficacy of the anti-programmed death-ligand 1 monoclonal antibody atezolizumab (Atezo) alone or in combination with the standard of care (SoC) treatments lenalidomide (Len) or pomalidomide (Pom) and/or daratumumab (Dara) in patients with R/R MM. Study endpoints included incidence of adverse events (AEs) and overall response rate (ORR). A novel unsupervised integrative multi-omic analysis was performed using RNA sequencing, mass cytometry immunophenotyping, and proteomic profiling of baseline and on-treatment bone marrow samples from patients receiving Atezo monotherapy or Atezo+Dara. A similarity network fusion (SNF) algorithm was applied to preprocessed data. Eighty-five patients were enrolled. Treatment-emergent deaths occurred in 2 patients; both deaths were considered unrelated to study treatment. ORRs ranged from 11.1% (Atezo+Len cohorts, n=18) to 83.3% (Atezo+Dara+Pom cohort, n=6). High-dimensional multi-omic profiling of the tumor microenvironment and integrative SNF analysis revealed novel correlations between cellular and molecular features of the tumor and immune microenvironment, patient selection criteria, and clinical outcome. Atezo monotherapy and SoC combinations were safe in this patient population and demonstrated some evidence of clinical efficacy. Integrative analysis of high dimensional genomics and immune data identified novel clinical correlations that may inform patient selection criteria and outcome assessment in future immunotherapy studies for myeloma.

  Study EGAS00001007286

• IMCISION RNAseq

  RNA sequencing could be performed on all 32 baseline and 30 on-treatment primary tumor biopsies. Based on gene-set enrichment analysis, the epithelial to mesenchymal transition signature was enriched in baseline tumors of patients without MPR, though its expression was insufficient to predict ICB response. Baseline and on-treatment IFNγ and T-cell signature expression (Z-score) were not significantly higher in patients with an MPR.­­­ Baseline primary tumor hypoxia-associated gene expression in IMCISION did not predict ICB response. However, on-treatment biopsies of MPR tumor samples showed significantly lower hypoxia gene expression when compared to non-MPR samples. Moreover, in a paired analysis of baseline and corresponding on-treatment samples, a significant decrease of hypoxia-related gene expression was observed in MPR biopsies, while this decrease was absent in non-MPR biopsies.

  Study EGAS00001005454

• Myocardial Infarction Genetics Exome Sequencing Consortium: Registre Gironi del Cor

  The Registre Gironi del Cor (REGICOR) study developed a nested case-control cohort from the Girona province in Spain in order to study genetic factors associated with the development of coronary heart disease. All exome sequencing was performed at the Broad Institute of Harvard and MIT; samples sequence capture was performed using Agilent SureSelect Human All Exon Kit v2 and sequencing was performed on an Illumina HiSeq 2000 or 2500.

  Study phs000902

• Allele-specific expression of GATA2 due to epigenetic dysregulation in double mutated CEBPA AML

  Transcriptional deregulation is a central event in the development of acute myeloid leukemia (AML). To identify potential disturbances in gene regulation, we conducted an unbiased screen of allele-specific expression (ASE) in 209 AML cases. The gene encoding GATA binding protein 2 (GATA2) displayed ASE more often than any other myeloid or cancer-related gene. GATA2 ASE was strongly associated with CEBPA double mutations (CEBPA DM), with 95% of cases presenting GATA2 ASE. In CEBPA DM AML with GATA2 mutations, the mutated allele was preferentially expressed. We found that GATA2 ASE is a somatic event lost in complete remission, supporting the notion that it plays a role in CEBPA DM AML. Acquisition of GATA2 ASE involved silencing of one allele via promoter methylation, compensated by overactivation of the other allele, thereby preserving expression levels. Notably, promoter methylation was also lost in remission together with GATA2 ASE. In summary, we propose that GATA2 ASE is acquired by epigenetic mechanisms and is a prerequisite for the development of AML with CEBPA DM. This finding constitutes a novel example of an epigenetic hit cooperating with a genetic hit in the pathogenesis of AML.

  Study EGAS00001004684

• Understanding the Biology of Language Impairment through Whole Genome Sequencing

  This study involves the whole genome sequencing of a cohort of 390 individuals assessed for language ability, IQ, and behavior as schoolchildren. The primary goal of the study is to identify genes, regulatory elements, and pathways which may underlie variation in language ability within an average population. 

  Study phs002255

• Host Genetic Determinants of the Outcome of Staphylococcus Aureus Bacteremia by Whole Exome Sequencing

  In this case-control study, Complicated Staphylococcus aureus (case) is defined as bacteremia plus endocarditis or bone/joint infection, and Uncomplicated Staphylococcus aureus (control) has no such complications and was cured at follow-up. We used whole exome sequencing to examine the cumulative effect of coding variants in each gene on risk of complicated SAB in a discovery sample of 168 SAB cases (84 Complicated SAB and 84 Uncomplicated SAB, frequency matched by age, sex and bacterial clonal complex). Then we evaluated the 334 most significantly associated genes and 8 biological candidate genes in a replication sample of 240 SAB cases (122 complicated and 118 uncomplicated, frequency matched by age, sex and bacterial clonal complex). All participants were white, non-Hispanic of European descent. In the discovery sample, gene-based analysis using SKAT-O identified 334 genes associated with complicated SAB at p<3.5 x 10-3;. Gene-based analysis of the 342 genes in the replication sample using SKATO identified one gene, GLS2 (GeneID: 27165), significantly associated with complicated SAB (p=1.2 x10-4;) after Bonferroni correction. GLS2 is an interesting candidate gene for complicated SAB due to its role in regulating glutamine metabolism, a key factor in white blood cell proliferation and activation.

  Study phs001505