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• Discovering the Genetic Basis of Cleft Palate: CIDR

  Cleft palate (CP) is a common craniofacial structural birth defect caused by the incomplete closure of the palate (the structure separating the oral and nasal cavities), resulting in feeding, speech, and hearing problems. CP accounts for 33% of all orofacial clefts (OFCs) or approximately 1 in 1500 babies born worldwide. Although CP is commonly grouped with other types of orofacial clefts (e.g. cleft lip or cleft with cleft palate), CP is embryologically and epidemiologically distinct, suggesting a unique etiology. The risk of CP recurrence in first degree relatives is over 50-fold higher than the population risk, suggesting a strong genetic component. However, there have been a dearth of genetic studies for CP. Three well-powered genome-wide association studies and meta-analysis have revealed only two associated loci, neither of which account for a large portion of the genetic heritability in any population. The goal of this study is to elucidate the genetic architecture of CP by performing whole genome sequencing of case-parent trios in a well-phenotyped, multi-ethnic cohort. 

  Study phs002220

• INCLUDE: Genetic Underpinnings of the Multifactorial Phenotype of Trisomy 21 Patients Unveiled by Multi-Omics Approaches

  The INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) Project is an NIH-wide collaboration that seeks to improve health and quality-of-life for people with Down syndrome. The INCLUDE Project Data Coordinating Center and partners created the INCLUDE Data Hub, a centralized data resource that allows access to large-scale clinical and multi-omics datasets specific to Down syndrome and supports collaborative, cloud-based analysis to accelerate scientific discoveries related to Down syndrome and its co-occurring conditions.Down syndrome (DS) is the most common chromosomal abnormality in livebirths with an incidence of 1 in 700 in the US. To better understand the pathophysiology of DS, this proposal will generate and analyze sequence data on 777 pediatric DS patients from the Children's Hospital of Philadelphia (CHOP), as well as 321 mothers and 148 fathers. We anticipate that the information derived from this deeply-phenotyped cohort will allow for improved understanding of the pathophysiology and molecular mechanisms underlying DS-associated comorbidities, which may inform on new practices for treatment or innovative future therapies.

  Study phs002983

• The Dynamic Landscape of Open Chromatin During Human Cortical Neurogenesis

  Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.

  Study phs001438

• eMERGE Geisinger eGenomic Medicine (GeM) Abdominal Aortic Aneurysm Project (AAAP)

  A large research cohort of Geisinger Abdominal Aortic Aneurysm (AAA) patients was created by enrolling and consenting patients of the Geisinger Department of Vascular Surgery. Consented patients provide blood, serum and DNA samples for research and authorize use of data in their medical record for research. They also complete a data questionnaire that asks information about family history of AAA and other vascular diseases, as well as information on known or suspected AAA risk factors, including smoking history, body mass index, hypertension, type 2 diabetes, and atherosclerotic disease. The AAA cases are 78% male, with a mean age of 74 years; 39% have undergone surgical or endovascular repair; more than 85% or current or past smokers; approximately 20% of cases report a positive family history of AAA. Geisinger AAA patients undergo regular imaging studies, typically every 6 months, to monitor the progression of aneurysm expansion. This allows the growth rates of their aneurysm to be calculated. DNA samples from a total of 910 AAA patients were used for whole genome genotyping; these results are included in the dbGaP.

  Study phs000387

• Kids First: Genomics of Orofacial Clefts in the Philippines

  Orofacial clefts (OFCs) are the most common craniofacial structural birth defect in humans caused by incomplete formation of the upper lip and/or the palate. Over 4,000 children in the Philippines are born with an OFC every year, and the Filipino OFC birth prevalence rate of 1 in 500 live births is one of the highest in the world. Genome-wide association studies support a multifactorial etiology for OFCs, but common variants only account for up to ~25% of the heritable risk in any one population. Sequencing studies in diverse populations is essential to fully understand the genetic architecture of OFCs. The study goals of the Kids First project are to sequence a collection of case-parent trios from the Philippines, in order to identify de novo mutations and inherited rare variants, and understand the population differences in common variant signals in the Philippines versus other populations. Approximately 373 trios from the Philippines were selected for whole genome sequencing (WGS) as part of this Gabriella Miller Kids First project.

  Study phs002595

• Rare germline sequence variants, copy number variations, expression alterations, methylation variations and disease susceptibility in familial melanoma

  Although a number of high-risk melanoma genes have been identified, they account for melanoma risk in less than 40% of melanoma-prone families. The major goals of our research are to identify novel high-penetrance genes for familial melanoma in melanoma-prone families without known mutations and to identify modifier factors, including genetic and epigenetic, in melanoma-prone families with and without known major mutations. We are using whole exome sequencing to identify additional high-risk susceptibility genes and using targeted sequencing to follow up on the top genes in additional family members and in population-based melanoma cases and controls. We are also using RNASeq to investigate genome-wide allele-specific expression and eQTLs in these families to identify genes with expression alteration, which will provide additional information for gene discovery. In addition, we also conducted genome-wide copy number variation (CNV), methylation, and miRNA expression profiling analyses in our melanoma families with the goal of identifying genetic and epigenetic factors as disease modifiers.

  Study phs001177

• Consanguinity and rare mutations outside of MCCC genes underlie non-specific phenotypes of MCC Deficiency

  3-Methylcrotonyl-CoA Carboxylase Deficiency (MCCD) is an autosomal recessive disorder of leucine catabolism, which has a highly variable clinical phenotype, ranging from acute metabolic acidosis to non-specific symptoms such as developmental delay, failure to thrive, hemiparesis, muscular hypotonia, and multiple sclerosis. Implementation of newborn screening for MCCD has resulted in broadening the range of phenotypic expression to include asymptomatic adults. The purpose of this study was to identify factors underlying the varying phenotypes of MCCD. We performed exome sequencing on DNA from 107 healthy controls and 33 cases. We examined these data for associations between either MCC mutational status, genetic ancestry or consanguinity and the absence or presence/specificity of clinical symptoms in MCCD cases. We determined that individuals with non-specific clinical phenotypes are highly inbred compared to cases that are asymptomatic and healthy controls. For five of these individuals we discovered a homozygous damaging mutation in a disease gene that is likely to underlie their non-specific clinical phenotypes previously attributed to MCCD.

  Study phs000776

• Genomic Analysis of Head and Neck Cancers

  These aggregate studies focus on specimens from head and neck squamous cell carcinoma (HNSCC) patients who were treated with standard of care or window of opportunity clinical trial approaches. Specimens were interrogated with exome and RNA-Seq analysis. Patient derived xenografts (PDXs) represent a robust platform for performing co-clinical trial approaches. In the first study we generated a large panel of PDXs and compared genomic profiles between the primary tumor and matched PDX with the patients blood serving as a source of somatic variants. In the second study, we performed a window of opportunity clinical trial in oral cavity squamous cell carcinoma patients using the MEK inhibitor trametinib. In addition, PDX models were generated from these specimens also and analyzed as in the first study. Finally, the third approach used pembrolizumab, an anti-PD1 blocking antibody, in a window of opportunity setting in HNSCC patients. For the latter two studies genomic matched sample analysis was performed to define response and resistance mechanisms. Together, these genomic data will inform several therapeutic approaches for HNSCC patients.

  Study phs001623

• PETAL Repository of Electronic Data COVID-19 Observational Study (RED CORAL)

  To describe characteristics, treatment, and outcomes among patients hospitalized with COVID-19 early in the pandemic, 1480 consecutive adult inpatients with laboratory-confirmed, symptomatic SARS-CoV-2 infection admitted to 57 US hospitals from March 1 to April 1, 2020 were studied.It was found that in a geographically diverse early-pandemic COVID-19 cohort with complete hospital folllow-up, hospital mortality was associated with older age, comorbidity burden, and male sex. Intensive care unit admissions occurred early and were associated with protracted hospital stays. Survivors often required new health care services or respiratory support at discharge.The PETAL Network central institutional review board at Vanderbilt University and the institutional review boards at each participating hospital approved the study or determined that the study was exempt from review. Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002363

• A Pilot Trial of Complement Inhibition Using Eculizumab to Overcome Platelet Transfusion Refractoriness in HLA Allo-Immunized Patients

  Platelet transfusion can be a life-saving procedure in preventing or treating serious bleeding in patients who have low and/or dysfunctional platelets. Heavily transfused patients frequently develop human leukocyte antigen (HLA) allo-immunization resulting in platelet transfusion refractoriness and a high risk for life-threatening thrombocytopenia. Data suggest complement activation leading to the destruction of platelets bound by HLA allo-antibodies may play a pathophysiologic role in platelet refractoriness. We conducted a pilot trial to investigate the use of eculizumab to treat platelet transfusion refractoriness in allo-immunized patients with severe thrombocytopenia. We hypothesized that when we treated patients having platelet refractoriness with eculizumab, platelet counts would increase to higher numbers after platelet transfusions, decreasing the risk of bleeding complications associated with having a low platelet count. The response of the treatment was assessed by the corrected platelet count increment (CCI) 10 - 60 min and 18 - 24 h post transfusion, and any requirement for subsequent platelet transfusions following eculizumab. Reference 1 (PMID: 32086819) contains the main results for this trial.

  Study phs003212