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• International Multiple Sclerosis Genomics Consortium (IMSGC) Genome Wide Association Study of Multiple Sclerosis

  The goal of this study is to perform a comprehensive allelic and genotypic association analysis of the entire human genome in multiple sclerosis. The recent definitive linkage genome screen demonstrated that there is no other MS risk gene with an effect size anywhere near that of the MHC. However, linkage analysis is significantly hampered by reduced power in the face of heterogeneity and requires multiplex families, which also hampers acquiring an appropriate sample size. In contrast, genotyping 500K SNPs allows us to survey a significant amount of the genome (we estimate >70%) directly for allelic or genotypic association. This uses the improved power of association analysis and can also take advantage of the linkage disequilibrium relationships among SNPs to further increase power (e.g. haplotype analysis). Quality control and data analysis are significant challenges. We will initially perform substantial QC checks and analyze the data using both TDT and AFBAC approaches. Multigenic interactions will also be tested using MDR.

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• Comprehensive Omics Analysis of Pediatric Solid Tumors and Establishment of a Repository for Related Biologic Studies (10C0086)

  This study (10-C-0086) collected and analyzed tumor and circulating tumor omics of pediatric and young adult patients with relapsed rhabdomyosarcoma who were co-enrolled in and receiving treatment on the interventional study 17-C-0049. We sought to describe the summary genomic findings of tumors, and report on the detection of circulating tumor DNA (ctDNA) in serial samples. Tumor tissue and blood were collected and analyzed. Tumor samples were subjected to whole exome and/or whole genome sequencing paired with RNA-Seq. Cell free DNA (cfDNA) was extracted from serially collected blood samples and sequenced. Fusion status, mutations, and IGF1R and YES1 expression from tumor samples revealed the presence of a PAX3 fusion in most samples, a number of common mutations, and universal but heterogeneous expression of IGF-1R and YES1. ctDNA was detected above the 3% threshold in a majority of patients and analysis of cfDNA demonstrated an ability to monitor tumor clonal evolution.

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• Vanderbilt Genome-Electronic Records (VGER) Project: QRS Duration

  An important potential enabling resource for Personalized Medicine is the combination of a DNA repository with Electronic Medical Record (EMR) systems sufficiently robust to provide excellence in clinical care and to serve as resources for analysis of disease susceptibility and therapeutic outcomes across patient populations. The Vanderbilt EMR is a state of the art clinical and research tool (that includes >1.7 million records), and is associated with a DNA repository which has been in development for over 3 years; these are the key components of VGER, the Vanderbilt Genome-Electronic Records project, a part of NHGRI's eMERGE network. The VGER model acquires DNA from discarded blood samples collected from routine patient care, and can link these to de-identified data extracted and readily updated from the EMR. The phenotype we analyze here is the QRS duration on the electrocardiogram, since slow conduction (indicated by longer QRS duration) is a marker of arrhythmia susceptibility.

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• Towards a Genomic Understanding of Myeloma

  This project was designed to describe genetic abnormalities in primary samples from patients with multiple myeloma by next generation sequencing. We generated sequence data from multiple myeloma (MM) patients analyzing DNA both from tumor cells (purified from bone marrow using CD138 selection as a marker of plasma cells) and from normal peripheral blood cells (either whole blood or Ficoll-purified mononuclear cells). Using massively parallel sequencing technology (Illumina GA-2 or HiSeq)), we performed whole-genome sequencing (WGS) and/or whole-exome sequencing (WES). The initial set currently deposited contains data from 38 MM patients (23 patients surveyed by WGS and 16 patients by WES, with one patient analyzed by both approaches). Genomes were sampled to high depth, obtaining an average of 33X coverage and 104X coverage for WGS and WES tumors, respectively. The normal samples had similar coverage. Our goal is to help researchers understand the complex genetic landscape of multiple myeloma and provide a resource for the generation of biological hypotheses.

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• Regulatory Genomics of Human Embryonic Development

  We used epigenetic profiling to map active enhancers in the developing human limb and cortex as described in two published studies: Cotney J, Leng J, Yin J, Reilly SK et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 2013;154(1):185-96. Reilly SK, Yin J, Ayoub AE, Emera D et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 2015;347(6226):1155-9. We also used ChIP-seq to map binding sites for the chromatin modifier CHD8 in the developing human brain, as described in one published study: Cotney J, Muhle RA, Sanders SJ, Liu L et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 2015;6:6404. We are also depositing primary human sequence reads related to processed datasets in the Gene Expression Omnibus under the following accession numbers: GSE42413 (Cotney et al. 2013); GSE63649 (Reilly et al. 2015); GSE57369 (Cotney et al. 2015).

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• NHLBI TOPMed: Pediatric Asthma Controller Trial (PACT)

  After a 2-4 week assessment/characterization run-in period, 6-14 year-old children who met NAEPP criteria for mild-moderate persistent asthma specifically based on symptom criteria and methacholine PC20 ≤ 12.5 mg/ml and FEV1 ≥ 80% were randomized to one of the three active treatment arms for 12 months. Randomization was stratified according to clinical center, bronchodilator response (< 12% or ≥ 12%), race (Caucasian or non-Caucasian), and methacholine PC20 (< 2 or ≥ 2 mg/ml). The primary outcome variable was the proportion of asthma-free days during the 12-month treatment period. Secondary outcomes included other measures of asthma control (percentage of rescue-free days, albuterol-free days, and episode-free days; the number of asthma exacerbations requiring prednisone therapy and the time to the first asthma exacerbation), forced oscillation and spirometry, reversibility (FEV1 pre- and post 2 puffs of albuterol MDI), methacholine PC20, exhaled nitric oxide, and asthma-related quality of life.

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• Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

  Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer-associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the polycomb repressive complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1-repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.

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• Deep Sequencing Studies for Cannabis and Stimulant Dependence

  Cannabis and stimulants are among the most widely used illicit drug in the United States, and their use is associated with substantial physical and psychiatric sequelae. Twin studies have shown a substantial genetic component to the etiology of cannabis and stimulant use disorders, but, genome-wide association studies using genotype data obtained from microarrays have yielded few robust results. The advent of increasingly economical whole genome sequencing provides new opportunities to identify trait-associated sequence variations. The present study proposes to identify sequence variants that affect stimulant and cannabis dependence in three cohorts. The three study cohorts were ascertained as part of the Mission Indian Study (PI Cindy Ehlers), the combined Yale-University of Connecticut Addiction Study samples (PI Joel Gelernter) and the San Francisco Family Study (PI Kirk Wilhelmsen). Because three populations with different continental origins were studied, the present study will also ascertain whether the major genetic risk factors for the traits of interest are shared or population-specific.

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• Genetic Control of Expression and Splicing in Developing Human Brain

  Most genetic risk for human diseases lies within non-coding regions of the genome that are predicted to regulate gene expression in a tissue- and stage-specific manner. Given the importance of regulatory pathways during brain development, we characterized the genetic control of the transcriptome in 201 mid-gestational human brains, identifying 7962 eQTL and 4635 sQTL. By integration with GWAS, we characterized the genes and isoforms contributing to specific neuropsychiatric disorders, including SCZ and ASD, as well as other cognition or behavioral-related phenotypes. SCZ and ASD impact distinct developmental gene co-expression modules, yet in both disorders, common and rare genetic variation converge. These analyses demonstrate the highly distinctive effects of transcriptional control, as well as divergent age-related contributions to disease. More broadly, these findings demonstrate the genetic mechanisms by which early developmental events have a striking and widespread influence on adult anatomical and behavioral phenotypes.

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• Rapid Acceleration of Diagnostics - Digital Health Technologies (RADx-DHT): NIH Digital Health Solutions for COVID-19: Team SAE

  The goal of this project is to develop a smartphone-based platform to monitor and support individuals with COVID-19 symptoms (who may need testing) and those who have already tested positive. The app will integrate a Bluetooth-enabled thermometer and pulse oximeter into an approach uniquely designed for low-resource settings and underserved populations. This project will focus on the American Indian/Alaskan Native (AI/AN) underserved population and will determine the feasibility of the digital health solution to collect symptom survey data and vital data including temperature, pulse, and oxygen saturation level. The complete study will include 300 participants 100% medically underserved with at least 51% from the AI/AN community. A combination of hard and soft data will be collected consisting of vital data, medical history and questionnaire data, and participant COVID-19 viral and antibody testing results collected during the study.DOI: https://rapids.ll.mit.edu/10.57895/wv88-by98

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