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• Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

  Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9125 subjects referred to carrier screening. We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks.

  Study phs001482

• Clonal haematopoiesis in patients with AAA (2019-04-03)

  Recent advances in genomics have demonstrated that clonal haemopoiesis driven by leukaemia associated somatic mutations is a relatively common phenomenon that increases in frequency with advancing age. Whilst individuals with clonal haemopoiesis have an increased risk of developing haematological malignancies, they also have an increased mortality from other causes. Additionally, certain mutations are almost exclusively seen in individuals aged 70 years or older, whilst others are seen in individuals with non-haematological cancers including breast and ovarian. Recently, clonal haemopoiesis was found to be associated with a significantly increased risk of atherosclerotic cardiovascular disease. This association is thought to be causative with clonally-derived macrophages showing elevated expression of several chemokine and cytokine genes that contribute to atherosclerosis. Another vascular pathology, abdominal aortic aneurysm (AAA), increases with age and shares risk factors with atherosclerosis (including smoking, male sex, high cholesterol). However, the impact of these risk factors and the overlap between AAA and atherosclerosis is poorly understood. To investigate a possible link between clonal haemopoiesis and AAA, we will study DNA samples from 300 patients with AAA and up to 200 controls for evidence of clonal haemopoiesis. This will be done using target DNA enrichment with biotinylated RNA baits followed by high throughput sequencing. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004895

• Add Health: Longitudinal Study of a Nationally Representative Sample of Adolescents in Grades 7-12 in the United States during the 1994-95 School Year, Followed into Adulthood with Five Interviews/Surveys in 1995, 1996, 2001-02, 2008, and 2016-18

  The National Longitudinal Study of Adolescent to Adult Health [Add Health] is an ongoing longitudinal study of a nationally representative U.S. cohort of more than 20,000 adolescents in grades 7-12 (aged 12-19 years) in 1994 followed into adulthood with five interviews/surveys in 1995, 1996, 2001-02, 2008, and 2016-18. Add Health was designed to understand how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. Add Health contains unprecedented environmental, behavioral, psychosocial, biological, and genetic data from early adolescence and into adulthood on a large, nationally representative cohort with unprecedented racial, ethnic, socioeconomic, and geographic diversity. Add Health has a large, multidisciplinary user base of over 50,000 researchers around the world who have published over 3,400 research articles. Add Health is housed at the Carolina Population Center of the University of North Carolina at Chapel Hill. Add Health datasets are distributed according to a tiered data disclosure plan designed to protect the data from the risk of direct and indirect disclosure of respondent identity. Add Health's large sample size, population diversity and rich longitudinal database of psychosocial, physical, and contextual data will permit investigation of an exceptionally broad range of phenotypes with known genetic variation. Prospective longitudinal measures are available to document change over time in each of these phenotypes, as well as change in the social environment and life experiences, making the Add Health sample ideal for understanding genetic linkages with health and behavior across the life course. The original design of Add Health included important features for understanding biological processes in health and developmental trajectories across the life course of young people, including an embedded genetic sample with more than 3,000 pairs of adolescents with varying biological resemblance (e.g., twins, full sibs, half sibs, and adolescents who grew up in the same household but have no biological relationship), testing of saliva and urine for sexually transmitted infections and HIV, and biomarkers of cardiovascular health, metabolic processes, immune function, renal function, and inflammation. Add Health therefore has critical objective indicators of health status and disease markers in young adulthood, well before chronic illness or its complications emerge in later adulthood. Because DNA has been collected on the full sample at Wave IV, it is possible to link genetic profiles with social, behavioral, and biological measures over time from adolescence into adulthood. Add Health sampled the multiple environments in which young people live their lives, including the family, peers, school, neighborhood, community, and relationship dyads, and provides independent and direct measurement of these environments over time. Add Health contains extensive longitudinal information on health-related behavior, including life histories of physical activity, involvement in risk behavior, substance use, sexual behavior, civic engagement, education, and multiple indicators of health status based on self-report (e.g., general health, chronic illness), direct measurement (e.g., overweight status and obesity), and biomarkers. No other data resource with this expanse of genotype and phenotype data on a large nationally representative longitudinal sample with race, ethnic, socioeconomic, and geographic diversity exists. A complete reference guide on study design and accomplishments can be found on the Add Health website: https://cdr.lib.unc.edu/concern/articles/6t053j27s.

  Study phs001367

• Somatic mutation burden and copy-number variation analysis in neurofibromatosis type 1-associated plexiform neurofibromas

  Neurofibromatosis type 1 (NF1) is a common tumor-predisposition disorder due to germline mutations in the tumor suppressor gene NF1. A virtually pathognomonic finding of NF1 is the plexiform neurofibroma (PN), a benign, likely congenital tumor that arises from biallelic inactivation of NF1. PN can undergo transformation to a malignant peripheral nerve sheath tumor, an aggressive soft-tissue sarcoma. To better understand the non-NF1 genetic contributions to PN pathogenesis, we performed whole-exome sequencing and genome-wide copy-number determination for 23 low-passage Schwann cell cultures established from surgical PN material with matching germline DNA. All resected tumors were derived from routine debulking surgeries. None of the tumors were considered at risk for malignant transformation at the time, e.g., there was no pain or rapid growth. Deep (~500X) NF1 exon sequencing was also conducted on tumor DNA. Non-NF1 somatic mutation verification was performed using the Ampliseq/IonTorrent platform. We identified 100% of the germline NF1 mutations and found somatic NF1 inactivation in 74% of the PN. One individual with three PNs had different NF1 somatic mutations in each tumor. The median number of somatic mutations per sample, including NF1, was one (range 0 - 8). NF1 was the only gene that was recurrently somatically inactivated in multiple tumors. We found no recurrent non-NF1 locus copy-number variation in PN. This is the first multi-sample whole-exome sequencing study of NF1-associated PN. Taken together with concurrent copy-number data, our comprehensive genetic analysis reveals the primacy of NF1 loss as the driver of PN tumorigenesis.

  Study phs001403

• The Immune Microenvironment, Genome–Wide Copy Number Aberrations and Survival in Mesothelioma

  IntroductionResults of recent clinical studies of immune checkpoint inhibitors in malignant pleural mesothelioma (MPM) have dampened initial enthusiasm. However, the immune environment and targets of these treatments such as program cell death protein 1 (PD-1) and its ligand PD-L1 have not been well characterised in MPM. Using a large cohort of patients, we investigated PD-L1 expression, immune infiltrates and genome-wide copy number status and correlated them to clinicopathological features.Patients and methodsTissue microarrays were constructed and stained with PD-L1(clone E1L3N, CST), CD4, CD8 and FOXP3 antibodies. PD-L1 positivity was defined as ≥5% membranous staining regardless of intensity and PD-L1+hi as ≥50%. Genomic DNA from a representative subset of 113 patients was used for genome-wide copy number analysis. The percent genome alteration (PGA) was computed as a proxy for genomic instability, and statistical analyses were used to relate copy number aberrations (CNA) to other variables.ResultsAmongst 329 patients evaluated, PD-L1+ was detected in 130/311 (41.7%), but PD-L1+hi was only seen in 30/311 (9.6%). PD-L1+ correlated with non–epithelioid histology and increased infiltration with CD4+, CD8+ and FOXP3+ lymphocytes. PD-L1+hi expression correlated with worse prognosis (HR = 2.37; 95%CI= 1.57-3.56; P < 0.001) on univariate analysis, but not in multivariate analysis. Higher PGA was associated with epithelioid histology and poorer survival (HR = 1.59; 95%CI= 1.01-2.5; P = 0.04), but not PD-L1 expression.ConclusionPD-L1 expression was associated with non-epithelioid MPM, poor clinical outcome and increased immunological infiltrates. Increased genomic instability did not correlate with PD-L1 expression, but was associated with poorer survival.

  Study EGAS00001002323

• Coagulation and Fibrinolysis in a Pediatric Insulin Titration Trial

  Summary of the Design and Aims: The Coagulation and Fibrinolysis in a Pediatric Insulin Titration Trial (CAF-PINT) is an ancillary study to the HALF PINT (NCT01565941) randomized, controlled trial that was originally designed to study changes in inflammatory and thrombosis pathways in the setting of an interventional trial. The parent HALF PINT study was designed to study the impact of tight glycemic control (TGC) using an explicit insulin titration algorithm to safely achieve a normal glucose in target range of 80-110 mg/dL versus 150-180mg/dL on clinical outcomes among critically ill hyperglycemic children with Heart and Lung Failure. The CAF PINT study collected blood samples pre randomization and at 2 and 4 days after randomization. Blood samples collected in EDTA tubes were centrifuged at local sites to separate the plasma from cell pellets and frozen prior to shipment. In addition, 0.5 mL of whole blood collected in PAXgene tubes modified for use in pediatrics frozen 24 hours after collection prior to shipment.Population Information: Setting: Twenty-one academic children's hospitals (HALF-PINT) and 1 academic children's hospital (IIT-SBPP). Participants: Critically ill hyperglycemic children requiring mechanical ventilation/vasoactive support (n=293).Interventions and Exposures: Patients in HALF PINT were randomized to achieve a low target glucose (80-110 mg/dL) vs. a higher target (150-180 mg/dL). The primary trial was stopped early due to low likelihood of achieving a statistically significant difference in the primary outcomes. Molecular Technologies Employed: Plasma biomarkers were assayed on thawed plasma using a Luminex panel. RNA was extracted from PAXgene Blood RNA Kits modified for pediatric use. Extracted RNA was sequenced with the Novaseq S4 system (Illumina) to generate 2 x 150 base paired end reads to a target depth of 50 million read-pairs per sample.Principal Findings of the Study: We tested for heterogeneity of treatment effects according to baseline blood inflammatory proteins using logistic regression with individual biomarkers as interaction terms and Cox regression analysis using biomarker-derived latent classes. Children with higher inflammatory proteins including TNFR-1, IL-6, IL-8, and IL-10 had lower mortality when treated with insulin to a target glucose of 80-110 mg/dL as compared to 150-180 mg/dL (interaction p<0.05). Causal forest estimates ranged from a 40% mortality reduction to a 15% mortality increase with TGC, depending on each patient’s individual biomarker profile. Latent class categorization strongly interacted with TGC with respect to mortality (Cox regression interaction p=0.005). Specifically, patients with higher inflammation benefited from TGC (6% mortality with TGC vs. 48% mortality, p=0.004) whereas hypoinflamed patients showed a trend towards harm (14% mortality with TGC vs. 7% mortality, p=0.055).Data available through dbGaP: Transcriptomic (Gene Counts) and phenotype data

  Study phs003016

• Million Veteran Program (MVP) Summary Results from Non-Sensitive Omics Studies

  MVP is an ongoing prospective cohort study and mega‐biobank in the Department of Veterans Affairs Healthcare System designed to study genetic influences on health and disease among veterans. This is the accession to hold publicly available results. Results from sensitive phenotypes or MVP population subsets can be found at accession phs001672 and will require an application for access.

  Study phs002453

• CALGB/SWOG 80405: Genome-Wide Association Study of Patients with Advanced or Metastatic Colorectal Cancer Treated with First-Line Chemotherapy Combined with Cetuximab and/or Bevacizumab

  CALGB/SWOG 80405 (NCT00265850) was a randomized phase III study of bevacizumab, cetuximab, or the combination of these two monoclonal antibodies, in addition to systemic chemotherapy for patients with untreated metastatic adenocarcinoma of the colon or rectum. We prospectively collected germline DNA and conducted genome-wide association studies using clinical outcomes and molecular features.

  Study phs003428

• LuCaP cell line ChIP-seq

  ChIP-seq of 2 LuCaP cell lines with different factors. LuCaP cell line 189.4 was ChIP-sequenced for 6 factors with different conditions as well as the input DNA (n=31 in total). LuCaP 189.4 ChIP-sequence experiments include; 3 H3K27ac/DMSO, 3 H3K27ac/vorinostat, 3 H3K27ac/dexamethasone, 3 H3K27ac/dexamethasone/vorinostat, 3 GR dexamethasone, 3 GR dexamethasone/vorinostat, 3 HDAC3/DMSO, 3 AR, 3 FOXA1, 3 H3K27ac and 1 input sample. LuCaP 35 ChIP-sequence experiments as well as input include (n=10 in total); 3 H3K27ac, 3 AR, 3 FOXA1 and 1 input sample. All 41 samples were sequenced using paired-end reads on Illumina NovaSeq 6000. Each sample has 2 fastq files, one for the forward and reverse read, respectively.

  Dataset EGAD50000001345

• Targeted DNA sequencing and mRNA sequencing data from patients with peritoneal metastasis from colorectal cancer

  Patients with peritoneal metastasis from colorectal cancer (PM-CRC) have inferior prognosis and respond particularly poorly to chemotherapy. This study aims to identify the molecular explanation for the observed clinical behavior and suggest novel treatment strategies in PM-CRC. Tumor samples (230) from a Norwegian national cohort undergoing surgery and hyperthermic intraperitoneal chemotherapy (HIPEC) with mitomycin C (MMC) for PM-CRC were subjected to targeted DNA sequencing, and associations with clinical data were analyzed. mRNA sequencing was conducted on a subset of 30 samples to compare gene expression in tumors harboring BRAF or KRAS mutations and wild-type tumors.

  Dataset EGAD50000000593