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• Transcriptome of 2-Hydroxypropyl-Beta-Cyclodextrin Treatment in Niemann-Pick Disease Type C1

  Niemann-Pick type C (NPC) disease is a rare and fatal lysosomal storage disorder. Classically, children with NPC demonstrate neurological dysfunction with cerebellar ataxia, dysarthria, seizures, vertical gaze palsy, motor impairment, dysphagia, psychotic episodes, and progressive dementia. In general, adolescent and adult onset forms have a more insidious onset and slower progression. As part of a multi-omics approach to address the genetic architecture of NPC1 disease, we have recently completed a transcriptome analysis using 43 primary NPC1 patient-derived fibroblasts from an NIH-cohort study (NCT00344331) where extensive clinical data has been obtained regarding the natural history of the disease. Initial transcriptome analysis of this dataset demonstrated a set of 485 genes that are significantly upregulated in patient samples and subsequently downregulated in response to 2-hydroxypropyl-beta-cyclodextrin treatment. 

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• National Heart, Lung, and Blood Institute SNP Health Association Asthma Resource Project (SHARP)

  SNP Health Association Resource (SHARe) Asthma Resource project (SHARP) is conducting a genome-wide analysis in adults and children who have participated in National Heart, Lung, and Blood Institute's clinical research trials on asthma. This includes 1041 children with asthma who participated in the Childhood Asthma Management Program (CAMP), 994 children who participated in one or five clinical trials conducted by the Childhood Asthma Research and Education (CARE) network, and 701 adults who participated in one of six clinical trials conducted by the Asthma Clinical Research Network (ACRN). There are three study types. The longitudinal clinical trials can be subsetted for population-based and/or case-control analyses. Each of the childhood asthma studies has a majority of children participating as part of a parent-child trio. The ACRN (adult) studies are probands alone. Control genotypes will be provided for case-control analyses.

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• National Human Genome Research Institute Tumor Sequencing Project (TSP) - Lung Adenocarcinoma

  The Tumor Sequencing Project (TSP) Consortium is a collaboration among participants at the Baylor College of Medicine Human Genome Sequencing Center, the Broad Institute Genome Sequencing Platform, the Dana Farber Cancer Institute, the Memorial Sloan-Kettering Cancer Center, the Genome Sequencing Center and Siteman Cancer Center at Washington University, the M.D. Anderson Cancer Center and the University of Michigan Medical Center. The TSP Part A will pilot approaches to large-scale identification of genomic changes in tumors by sequencing the exonic regions of 623 genes in 188 specimens of adenocarcinoma of the lung, as well as using high density SNP genotyping arrays for high resolution identification of changes in chromosomal copy number. The TSP Part B will pilot approaches to tumor characterization of lung adenocarcinoma samples using next-generation sequencing technologies and benchmark those results against Part A data generated with ABI3730 instruments.

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• Host Response to Respiratory Infections

  In this study, we describe a strategy to identify undiagnosed respiratory viral infections through screening nasopharyngeal (NP) swabs for the chemokine CXCL10, which is highly induced in the nasopharynx as part of the host antiviral response. Using this strategy, we conducted two screens: first, we screened NP swabs collected at Yale New Haven Hospital (YNHH) in January 2017 from patients with undiagnosed respiratory viral infections and identified patients infected with seasonal coronaviruses and the relatively uncommon influenza C virus. Second, we screened samples from the beginning of March 2020 in the weeks before YNHH tested for SARS-CoV-2 and identified four patients that had undiagnosed SARS-CoV-2 infections. Sequences uploaded as part of this study include samples with rhinovirus, human coronavirus NL63, and 8 samples as part of the January 2017 screen for undiagnosed respiratory viral infections.

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• RNAseq Transcriptomic Analyses of European Ancestry Samples in MGS Dataset

  Schizophrenia is a common and severe psychotic disorder. While some common SNPs and rare copy number variants have been identified as being significantly associated with disease risk, the biological mechanisms remain undefined. To identify gene expression abnormalities in schizophrenia, we generated whole-genome gene expression profiles using RNAseq on lymphoblastoid cell lines from schizophrenia cases and controls of European ancestry. Subsets of these data have been used in three studies: (1) gene expression outliers (extreme tails of the distribution of transcript expression values) in 634 cases and 713 controls (PMID: 26022996); (2) baseline differential gene expression by affection status in 529 cases and 660 controls (PMID: 28418402); and (3) baseline versus dopamine stimulated differential gene expression by affection status in 514 cases and 690 controls (PMID: 30115913). Various classes of classes were enriched in the differentially expressed genes, especially brain expressed genes and genes related to immune processes.

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• Nature and Contribution of Noncoding, Regulatory Mutations in Neurodevelopmental Disorders

  This dbGaP study contains variant call files generated from whole-genome sequencing data of families with autism. The variant callers include FreeBayes, GATK, Platypus, and Strelka2. A family-level VCF file, from each caller, is provided for each family in the study. The families included in this study are from the Simons Simplex Collection (SSC), the Study of Autism Genetics Exploration (SAGE), and The Autism Simplex Collection (TASC); sequencing was performed at the New York Genome Center, as part of the Centers for Common Disease Genomics (CCDG) Consortium. The analysis to generate the variant callsets was supported by a K99 Pathway to Independence grant to Dr. Tychele Turner (1K99MH117165-01). *Access to phenotype data at the individual level for Simons Simplex Collection (SSC) subjects can be requested from SFARI Base: https://www.sfari.org/resource/sfari-base/.

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• Emory University African American Vaginal, Oral, and Gut Microbiome in Pregnancy Cohort Study

  The Emory University African American Microbiome in Pregnancy Cohort Study prospectively enrolls African American women between 18-40 years of age without chronic medical conditions into a longitudinal follow-up study that involves completing microbiome sampling and data collection at two time points in pregnancy (8-14 weeks gestation and 24-30 weeks gestation). The study is investigating the role of the oral, vaginal, and gut microbiome on preterm birth and other pregnancy outcomes as well as biobehavioral factors that shape the microbiome among this socio-demographically diverse group of women. Microbiome sampling involves the oral, vaginal, and gut sites. Biobehavioral factors that are being explored for their association with microbiome composition at the three body sites include measures of sociodemographic status as well as diet and nutrition, infectious and stress exposures.

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• Comparative Sequence Analysis Between Primary and Metastatic Colorectal Cancer Lesions

  Molecular profiling for somatic mutations that predict response to anti-EGFR therapy in colorectal cancer (CRC) has become standard practice. However, abundant tissue from metastatic lesions is not always available from patients with metastatic CRC. Concerns involving genetic heterogeneity between primary and metastatic lesions have called into question the suitability of profiling primary tumors in patients with metastatic disease. Further, the identification of discordant mutations between matched primary and metastatic tumors would be of biological interest for the delineation of biomarkers of tumor progression and metastasis. To explore the degree of genetic heterogeneity between matched primary and metastatic tumors in CRC, we performed whole genome sequencing of four patient "trios" comprised of a primary colon tumor, a liver metastasis, and matched normal (non-cancerous) tissue. Somatic mutations and indels were called in each tumor and compared between primary and metastatic lesions.

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• Genetics of Hypertension Associated Treatment (GenHAT) Study, Genomic Background of Blood Pressure Response to Treatment in African Americans

  The GenHAT study is an ancillary pharmacogenomics study to the Antihypertensive and Lipid Lowering Treatment to Prevent Heart Attack Trial (ALLHAT). ALLHAT was a randomized, double-blind, multi-center trial that enrolled 42,418 participants ≥55 years of age with hypertension and at least one additional risk factor for cardiovascular disease (CVD). Participants were randomized to treatment with one of four primary antihypertensive drugs: chlorthalidone (thiazide-like diuretic), amlodipine (CCB), lisinopril (ACE-i), or doxazosin (alpha-adrenergic blocker) in a ratio of 1.7:1:1:1, respectively. Participants were followed for treatment response and CVD outcomes. The original GenHAT study (N=39,114) evaluated the association of candidate hypertensive genetic variants with CVD outcomes for participants consenting to genetic research. The current GWAS study focuses on a subset of African American GenHAT participants (n=6908).  

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• Sex Chromosome Aneuploidy Effects on Human Gene Expression

  Sex chromosome aneuploidy (SCA) syndromes are defined by the presence of a sex chromosome complement other than the typical XX for females and XY for males. SCAs are collectively common and increase risks for diverse immune, metabolic, and neuropsychiatric illnesses. Understanding genome-wide transcriptomic changes in SCAs is critical for clarifying the biological underpinnings of their clinical phenotypes. Assessments of sex chromosome dosage (SCD) effects on gene expression in humans have often been confined to the use of a few SCA subtypes (e.g., XO or XXY) - precluding analysis of the same SCD change in different contexts. Our study used RNA-seq data from lymphoblastoid cell lines in 197 individuals representing diverse SCA karyotypes (49 XX, 24 XXX, 39 XY, 39 XXY, 23 XXYY, 23 XYY) to assess expression changes for 25,075 genes in multiple pairwise SCD group comparisons. The paper reporting our findings has been cited below.

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• Gabriella Miller Kids First Pediatric Research Program in Genetics at the Intersection of Childhood Cancer and Birth Defects

  The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Birth defects and childhood cancer share biological pathways that are important for cell growth and division. We propose that sequencing pediatric patients suffering both conditions will allow us to discover the underlying genes and in turn advance our understanding of the causes of these devastating diseases.

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• The Ultrasound Study of Tamoxifen

  The Ultrasound Study of Tamoxifen is a 12-month longitudinal study to describe volumetric breast density change over time among women with and without tamoxifen exposure. Women were enrolled at the Karmanos Cancer Institute and Henry Ford Health Systems in Detroit, Michigan between 2011-2014. Enrollment included women prescribed tamoxifen for clinical indication (n=82) and a comparison group of women frequency matched on age, race, and menopausal status (n=165). Whole breast ultrasound tomography (UST) scans were used to measure volume averaged sound speed (m/s) as a surrogate of volumetric breast density. Ultrasound tomography (UST) scans were completed at baseline prior to tamoxifen initiation and were repeated at 1-3 months, 4-6 months, and 12 months after tamoxifen initiation. For the comparison group, UST scans were completed at baseline and 12 months. Questionnaires were completed at each scan.

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• CRISPR-Mediated ASD Gene Knockout Reduces Neuronal Activity

  Autism Spectrum Disorder is phenotypically and genetically heterogeneous. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of 10 ASD-relevant genes (AFF2/FMR2, ANOS1, ASTN2, ATRX, CACNA1C, CHD8, DLGAP2, KCNQ2, SCN2A, TENM1). Neurogenin 2 (NGN2)-directed induction of iPSCs allowed production of excitatory neurons, and mutant proteins were not detectable. RNAseq revealed convergence of several neuronal networks. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory post-synaptic current frequencies in AFF2/FMR2-, ASTN2-, ATRX-, KCNQ2- and SCN2A-null neurons. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.

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• Genetic Analysis of Psoriasis and Psoriatic Arthritis: GWAS of Psoriatic Arthritis

  This study is a genome-wide study of genetic associations with psoriatic arthritis (PsA), an inflammatory musculoskeletal condition that develops in up to 30% of people who have chronic psoriasis skin lesions. 1,526 cases affected with psoriatic arthritis and 1,508 unaffected controls were recruited and typed on the Illumina HumanOmni1-Quad BeadChip array. After application of quality control measures to both samples and SNPs, genotypes for 791,217 autosomal SNPs were available for 1,430 PsA cases and 1,417 controls. Imputation using phased haplotypes for the EUR subpopulation of release 3, phase 1 of the 1000 Genomes Project as a reference, resulted in genotypes for 11,532,644 SNPs and 918,976 indels passing our imputation quality threshold (Mach r2 ≥ 0.3) that were available for downstream analysis. Association at a genome-wide threshold of significance was found for five regions (near genes TNIP1, IL12B, HLA-C, TRAF3IP2, and TYK2).

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• OncoArray: Oral and Pharynx Cancer

  Genetic factors play an important role in susceptibility to head and neck cancer and could also explain differences in response to treatment and outcome. The goal of this project is to investigate genetic variation involved in oral and oropharyngeal cancer susceptibility by performing the largest GWAS on these diseases, using a novel genotyping tool specifically designed for cancer studies by the OncoArray Network. This project encompasses data from approximately 6000 oral and pharynx cancer cases and 4000 controls derived from 12 epidemiological studies most of case-control design. The genotyping was centralized at the Center for Inherited Disease Research (CIDR), and the epidemiological data harmonization and analysis were completed at the International Agency for Research on Cancer (IARC). This study was supported by National Institute of Dental and Craniofacial Research (NIDCR) with direct funding to CIDR.

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• Center for Common Disease Genomics (CCDG) - Cardiovascular: Cleveland Clinic Cohort

  The National Human Genome Research Institute (NHGRI) has funded the Centers for Common Disease Genomics (CCDG), a collaborative large-scale genome sequencing effort to comprehensively identify rare risk and protective variants contributing to common disease phenotypes and to better understand the general principles of genomic architecture underlying common, complex inherited diseases. This study contains variant calls derived from the whole genome sequence data of an early-onset coronary artery disease case-control cohort collected by the Cleveland Clinic. Case status was assigned based on the presence of myocardial infarction, coronary artery stenosis greater than 70% in at least one coronary artery, and/or revascularization (coronary angioplasty with or without stent placement or coronary artery bypass grafting) at an early age. For these samples, "early age" is defined as men 60 years of age or younger and women 70 years of age or younger.

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• Modeling Malignant Progression in Glioma

  Gliomas are the most common primary brain tumor in humans. Low-grade gliomas (WHO grade II) invariably progress to high-grade gliomas (WHO grade III or IV). Although malignant progression may take many years, the survival rate after transformation to a high-grade glioma is poor, often only 12-15 months. In this data set, we have identified low-grade gliomas that have progressed to high-grade gliomas or high-grade gliomas that have progressed from low-grade gliomas. Some cases are matched pairs (meaning we have both the original low-grade tumor and the subsequent high-grade tumor). The samples deposited have been analyzed with bulk-RNA sequencing. They are also de-identified but are clinically annotated. When available, genetic information including IDH mutation status, 1p/19q deletion and histological subtype are also included.

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• Circulating Tumor DNA in Intermediate Risk Rhabdomyosarcoma

  In this study, we evaluated circulating tumor DNA (ctDNA) as a biomarker in the serum of 124 patients with newly diagnosed intermediate risk rhabdomyosarcoma (IR RMS) from the Children's Oncology Group (COG) biorepository. In addition to pre-treatment serum, we also analyzed matched tumor tissue and germline in a subset of patients. We profiled samples using ultra-low passage whole genome sequencing (ULP-WGS) and a new custom hybrid-capture sequencing assay, Rhabdo-Seq, to detect copy number alterations, rearrangements, and single nucleotide variants. We found that patients with detectable ctDNA at diagnosis had significantly worse outcomes than those without detectable levels of ctDNA. Our study demonstrates that baseline ctDNA detection is feasible and prognostic in IR RMS. The ULP-WGS and targeted next-generation sequencing (Rhabdo-Seq and TranSS-Seq) data are available in this study.  

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• Functionally-defined Therapeutic Targets in Diffuse Intrinsic Pontine Glioma (DIPG)

  Diffuse Intrinsic Pontine Glioma (DIPG) is a universally fatal childhood cancer. Here, we performed a chemical screen in patient-derived DIPG cell cultures along with RNAseq expression analysis and integrated computational modeling to identify potentially effective therapeutic strategies. Panobinostat, among the more promising agents identified, demonstrated efficacy in pontine orthotopic xenograft models of both H3K27M and histone WT DIPG. These data suggest the potential utility of specific drug combinations and provides evidence of in vivo treatment efficacy of the multi-histone deacetylase inhibitor panobinostat. We are depositing to dbGaP deep sequencing whole exome data for 22 patient tumor samples and 13 matched normals, along with RNAseq data for 12 patient tumor samples and 6 normal pediatric brain tissue samples. In addition, we are depositing 22 RNAseq samples from DIPG cell lines before and after panobinostat treatment.

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• NCI-Maryland Prostate Cancer Case-Control Study

  The study seeks to examine the genetic and ancestral basis of prostate cancer-associated inflammation using a genome-wide association approach. The study population are the participants of the NCI Maryland Prostate Cancer Case-Control study. This study recruited both African American and European American men, and investigated the causes for the excessive burden of prostate cancer among African American men in more general terms. We measured 82 blood-based immune-oncology markers, and genotyped the participants using the HumanOmni5-Quad BeadChip, which provides a significant genome coverage for genetically-admixed and diverse populations, to evaluate the genetic basis and evidence for causality of any immune-inflammation marker that is associated with prostate cancer risk. We want to assess how germline genetics influence the abundance levels of these 82 markers in African American and European American men, which may contribute to differences between them.

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• Genomic Analysis of Peripheral T-Cell Lymphomas

  Peripheral T-cell lymphomas (PTCLs) are a heterogeneous and poorly understood group of non Hodgkin lymphomas. We aim to identify new genetic alterations in PTCL transformation by using a combination of whole exome sequencing of tumor-normal DNA pairs, RNAseq analysis and targeted deep sequencing of candidate genes. Our data identified highly recurrent mutations in epigenetic factors such as TET2, DNMT3A and IDH2 as well as a new highly prevalent mutation in RHOA, the G17V allele that is present in almost 70% of angioimmunoblastic T-cell lymphomas (AITL) and almost 20% of not otherwise specified PTCL (PTCL NOS) samples. In addition, we describe new and recurrent genetic defects including mutations in FYN, ATM, B2M and CD58 implicating SRC signaling, impaired DNA damage response and escape from immune surveillance processes as key players in the pathogenesis of PTCL.

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• Women's Interagency HIV Study (WIHS)

  The Women's Interagency HIV Study (WIHS), a multicenter, prospective study, was established in August 1993 to carry out comprehensive investigations of the impact of HIV infection and its clinical, laboratory, and psychosocial effects in women. The purpose of this study is to collect and evaluate these data from HIV infected and at-risk women to better understand and provide support for women whom are currently HIV infected or who are at risk for HIV infection. Participants will have study visits every 6 months. Questionnaires regarding sexual behavior, health care utilization, medical and obstetric/gynecological history, psychosocial factors, and sociodemographics will be completed by participants. Physical, gynecological, and lipodystrophy examinations will also be conducted at each visit, and current medication regimen will be noted. Blood and other bodily fluid samples will be collected and registered in both local and national repositories of the WIHS in conjunction with NIAID.

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• Molecular Basis of Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2015)

  A subset of advanced prostate cancers can progress from an androgen receptor (AR)-driven state to AR independence, often associated with low or absent AR expression and extensive neuroendocrine differentiation. Once neuroendocrine prostate cancer (NEPC) develops, patients typically demonstrate an aggressive clinical course and poor overall survival. Early diagnosis is important but remains challenging as the clinical and pathologic features associate with AR independence and NEPC are poorly defined. We performed whole exome sequencing of 114 metastatic tumors from 81 patients (35 with morphologic features of NEPC). Serial or synchronous samples were included to characterize heterogeneity and the transition from adenocarcinoma to NEPC. Computational analysis of clonality and allele specific quantification were performed using CLONET. Quantitative mRNA assessment including AR signaling genes and DNA methylation were evaluated in the context of genomic changes.

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• The CHOP Pediatric Genetic Sequencing (PediSeq) Project : Applying Genomic Sequencing in Pediatrics

  The purpose of this research study is to learn more about newer types of genetic testing called whole exome sequencing and whole genome sequencing. Current genetic testing usually examines one gene or a few genes at a time. Exome and genome sequencing allow us to test most of a person's genes at one time with a single test. This testing might identify the reason for a person's unexplained condition or diagnosis. We hope this study will help us identify the best methods for: Educating patients and families about exome and genome sequencing Analyzing exome and genome sequencing data to identify results relevant to patients Giving results to families in a clear, appropriate, and informative manner The current data only includes WES for 159 samples. The WGS samples for 20 samples will be uploaded in the near future.

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• CIDR/NICHD Genetic Basis of Recessive Pediatric Brain Diseases - Group 2

  The purpose of this study is to identify new genetic causes of recessive forms of pediatric neurodevelopmental disorders (NDDs) including Cerebellar hypoplasia (CBH), Lissencephaly (LIS), Microcephaly (MIC), Corpus callosum hypoplasia (CCH), Pontocerebellar hypoplasia (PCH), Pontine tegemental cap dysplasia (PTCD), and Aicardi syndrome among many others. Using whole exome sequencing on one or two affected members per family, we are able to identify many pathogenic genes for these families. Using Human SNP Linkage Scans, which takes advantage of the Illumina HumanCore Array, and parametric linkage analysis software (Genehunter, Allegro, and others), we seek to identify pathogenic loci utilizing 60-70 families per year. Through the combination of parametric linkage analysis with exome sequencing and bioinformatics approaches, we will refine our search for superior sensitivity and accuracy when investigating candidate genes and identifying causative mutations for disease.

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