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• Rare Disease Susceptibility Alleles in Children with Crohn Disease

  The overall goal of this proposed project is to identify rare genetic variants contributing to childhood onset-Crohn disease. Crohn disease is a chronic inflammatory disorder of the gastrointestinal tract of unclear etiology and no known cure. Affected children suffer from diarrhea, abdominal pain, growth disturbances, and an impaired quality of life. The identified Crohn disease susceptibility alleles have improved our understanding of Crohn disease pathogenesis. However, the identified susceptibility alleles do not account for the observed heritability, nor have disease-causing alleles in many genomic regions been identified. For the proposed studies, we will use 1) existing DNA samples collected from high-risk Crohn kindreds identified using the extensive genealogical records available only in Utah, 2) existing DNA samples obtained from very young children with Crohn disease and their parents, and 3) existing DNA samples obtained from healthy controls that are free of a personal or family history of autoimmune disorders.

  Study phs000926

• Novel Strategies to Eliminate Resistance to B-cell Receptor Inhibitor Therapy in Lymphoid Malignancies

  Ibrutinib and acalabrutinib are BTK inhibitors (BTKi) used as frontline therapies for chronic lymphocytic leukemia (CLL). Clonal evolution during ibrutinib treatment has previously been studied, but limited study of clonal evolution in patients receiving acalabrutinib has been done. Our group analyzed 216 blood samples from 38 CLL patients at multiple time points during their BTKi treatment. Samples were prepared by standard protocols and sequenced using 200x Illumina sequencing. Using the longitudinal data, we reconstructed the clonal evolution of each patient using somatic mutations found within the B-cell populations. Three patterns of clonal evolution were identified: 1) new clone emergence, 2) clonal selection, and 3) clonal replacement. As previously seen in ibrutinib treatment, the evolution of subclones containing CLL-driver mutations was associated with worse clinical outcomes for patients treated with acalabrutinib (Log-rank p=0.04). Understanding clonal evolution during treatment with acalabrutinib can help determine and modify the clinical course of patients with CLL.

  Study phs003042

• Blepharospasm in a Multiplex African-American Pedigree

  Blepharospasm (BSP) is a late-onset focal dystonia characterized by involuntary contractions of the orbicularis oculi muscles. Genetics plays an important role on the pathogenesis of BSP, especially in hereditary BSP families. In this project, a large African-American pedigree with BSP was phenotypically characterized and its relationship with known common dystonia genes was investigated with Sanger sequencing on dystonia genes such as THAP1, TOR1A and GNAL. And whole-exome sequencing (EXOME) of the proband was performed to identify all other dystonia-associated genes for potentially pathogenic SVs. A novel THAP1 SV (c.314T>C, p.L105S) was identified in the family, however, this SV did not co-segregate with blepharospasm in the pedigree. No pathogenic or likely pathogenic SVs in other dystonia-associated genes were identified with whole-exome sequencing. The current study makes available phenotype data and summary genotype data of n=12 family members (mutation absent/heterozygous for THAP1); whole exome sequencing data of one (het) subject are available through public SRA.

  Study phs001206

• Genome-Wide Association Study of Parkinson Disease: Genes and Environment

  This is a gene-environment study of Parkinson's disease. PD is a common, progressive, age-related, movement disorder that affects 1-2% of the people over the age of 65. The NeuroGenetics Research Consortium (NGRC) is the infrastructure of the study. Protocols and methods are standardized across NGRC clinics and labs as much as possible. The 2000 patients and 2000 control subjects selected for this GWAS were recruited at the NGRC-affiliated movement disorder clinics in Oregon, Washington, Georgia and New York. All 4000 subjects were white and all DNA samples were extracted from whole blood and unamplified. Seventy-five percent of subjects have data on cigarette smoking and caffeinated coffee consumption, which are inversely associated with PD risk. This study population represents the norm for clinical genetic studies of PD; i.e., NGRC estimates of risk to relatives, heritability, genotype frequencies, and exposure frequencies (see references) are very close to estimates from meta-analyses.

  Study phs000196

• 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.

  Study phs001730

• Transcriptome study of differential expression in schizophrenia

  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 microarrays on lymphoblastoid cell lines from a total of 413 cases and 446 controls. Regression analysis identified 95 transcripts differentially expressed by affection status at a genome-wide false discovery rate of 0.05, while simultaneously controlling for confounding effects. These transcripts represented 89 genes with functions such as neurotransmission, gene regulation, cell cycle progression, differentiation, apoptosis, and immunity. The observed differential expression of extended major histocompatibility complex region genes converges with the genetic evidence from schizophrenia genome-wide association studies, which find the same region to be the most significant schizophrenia susceptibility locus. Our analysis also provides novel candidate genes for further study to assess their potential contribution to schizophrenia.

  Study phs000775

• Human Liver Cohort (HLC)

  The Human Liver Cohort (HLC) study aimed to characterize the genetic architecture of gene expression in human liver using genotyping, gene expression profiling, and enzyme activity measurements of Cytochrom P450. The HLC was assembled from a total of 780 liver samples screened. DNA samples were genotyped on the Affymetrix 500K SNP and Illumina 650Y SNP genotyping arrays. Only data from those samples which were collected postmortem are accessible through this submission. These 228 samples represent a subset of the 427 samples included in the Human Liver Cohort Publication (Schadt, Molony et al. 2008, PMID: 18462017). RNA samples were profiled on a custom Agilent 44,000 feature microarray composed of 39,280 oligonucleotide probes targeting transcripts representing 34,266 known and predicted genes, including high-confidence, noncoding RNA sequences. Gene Expression data for the samples from which it could be obtained is available in GEO under accession number GSE9588. Results and networks will be made available for download from Sage Bionetworks.

  Study phs000253

• Epigenomics of Patient Outcomes after Aneurysmal SAH

  This project was focused on understanding the pathophysiology following aneurysmal subarachnoid hemorrhage (aSAH). DNA methylation is a key mechanism for regulation of gene expression and function in the adult brain and appears to play an important role in neuroprotection during ischemic events in the brain. Delayed cerebral ischemia (DCI), occurring during the acute phase following aSAH, is a major contributor to the complications that later develop; however, the pathophysiology of DCI and the development of complications is not known. We hypothesize that characterizing the methylome representing the CNS environment post aSAH will clarify the pathophysiology associated with DCI and patient outcomes. The aims of this project focused on the daily genome-wide methylomic changes that occur in DNA representing the CNS for the first 14 days after aSAH, as well as in peripheral blood in a subset of partcipants, and determining if this methylomic data impacts DCI and the development of complications after aSAH.

  Study phs001990

• Sézary Syndrome Originates from Heavily Mutated Hematopoietic Progenitors

  The pathogenesis of cutaneous T cell lymphoma (CTCL) remains unclear. To study the malignant transformation of CTCL, we collected matched hematopoietic stem cell (HSC) extracts from bone marrow, CD4+CD26- malignant T cells, CD4+CD26+ normal T cells, and CD34+ HSCs from apheresis performed on 4 patients. To establish the baseline for calling true mutations without using hematopoietic cells, we also cultured bone marrow fibroblasts from each patient to use as normal controls. Whole exome sequencing (WES) was performed on all samples for somatic mutation calling. We identified >200 mutations in CD34+ HSCs derived from either bone marrow or apheresis. Previously reported key oncodrivers in Sezary Syndrome were identified in autologous HSCs and malignant peripheral cells, but not in progenitor (bone marrow HSCs) cells. Also, we identified specific mutations shared by autologous HSCs and malignant peripheral cells in every patient. WES data of bone marrow HSCs, apheresis HSCs, CD4+CD26- T cells, CD4+CD26+ T cells, and fibroblasts will be available through dbGaP.

  Study phs003158

• Gut Microbiome and Types of Colorectal Polyps

  Colorectal cancer is a heterogeneous disease arising from at least two precursors-the conventional adenoma and the serrated polyp. This dataset was used to test the relationship of the gut microbiota to specific colorectal polyp types. We included samples from two independent study populations based at colonoscopy clinics: the Centers for Disease Control and Prevention (CDC) Study of In-home Tests for Colorectal Cancer (SIT), and the New York University (NYU) Human Microbiome and Colorectal Tumor study. Gut microbiota were assessed in 667 colonoscopy-screened adults by 16S rRNA gene sequencing of stool samples, of which 540 were included in our analysis. Participants were categorized as conventional adenoma cases, serrated polyp cases, or polyp-free controls. CA cases were further classified as proximal or distal and as non-advanced or advanced. Serrated polyp cases were further classified as hyperplastic polyp or sessile serrated adenoma. Our results show associations between gut microbiome composition and presence of conventional adenomas, including reduced diversity and alterations in taxon abundance.

  Study phs001381