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• Overrepresentation of genetic variation in the AnkyrinG interactome is related to a range of neurological disorders

  Upon the discovery of numerous genes involved in the pathogenesis of neurodevelopmental disorders, several studies showed that a significant proportion of these genes converge on common pathways and protein networks. Here, we used a reversed approach, by screening the well-characterized AnkyrinG protein-protein interaction network, implicated in a variety of neurodevelopmental disorders, for genetic variation in a large cohort of 1009 cases with neurodevelopmental disorder. We identified a significant enrichment of de novo potentially disease-causing variants in this network, confirming that this protein network plays an important role in the emergence of several neurodevelopmental disorders.

  Study EGAS00001004326

• Stockholm-Tartu Atherosclerosis Reverse Network Engineering Task (STARNET)

  STARNET is a genetics of RNA expression study of multiple disease-relevant tissues obtained from living patients with cardiovascular disease. Tissue samples are obtained from blood, atherosclerotic-lesion-free internal mammary artery (MAM) and atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV) during open thorax surgery of 600 coronary artery disease (CAD) patients. All patients gave written informed consent. The inclusion criterion was eligibility for coronary artery by-pass graft (CABG) surgery. Patients with other severe systemic diseases, such as active systemic inflammatory disease or cancer, were excluded. The primary clinical end points were the SYNTAX score based on the extent of coronary atherosclerosis assessed from preoperative angiograms. The STARNET patients are Caucasians (31% females); 32% had diabetes, 75% had hypertension, and 67% had hyperlipidemia; and 33% had an MI before age 60. By New York Heart Association criteria, 45% were class I, 42% class II, 9% class III, and 1% class IV. TYPES AND RNA SEQUENCING: 566 DNA genotype and 3577 RNA-seq profiles from seven tissues from 600 STARNET CABG patients passed quality control (on average 511 RNA-seq profiles/tissue). DNA was genotyped with the OmniExpress Exome array (Illumina, ~900k SNPs) and imputed to a total of 14,098,063 DNA variant calls (6,245,505 with minor allele frequency >5%). The STARNET subjects mainly overlap with Caucasian of Northern European (Finnish) descent. RNA sequencing was performed using the HighSeq2000 platform, poly-A (LIV, SKLM, VAF, SF and blood) and ribo-zero (AOR, MAM) protocols with 50-100 bp read lengths, single end to 15-30 million read depth.

  Study phs001203

• 86 paired-end MiSeq 16S rRNA sequencing samples

  We compared bacterial communities in breast milk from teen (≤19 yr, n = 26) vs. adult (>19 yr, n = 56) mothers, normal weight (BMI 18.5-24.9, n = 63) vs. overweight (BMI ≥ 25, n = 19) mothers, primiparous (parity = 1, n = 41) vs. multiparous (parity > 1, n = 44), early (5-46d postpartum, n = 39) vs. established lactation (4-6 mo postpartum, n = 45), breastfeeding (EBF: PBF, n = 72) vs. mixed feeding (n = 11) and mothers with (Na/K ratio < 0.6, n = 75) and without SCM (Na/K ration ≥ 0.6, n = 10).

  Dataset EGAD00001004160

• Sequencing of pancreatic cancer primary tumors and metastases

  The extent of heterogeneity of driver gene mutations present in naturally occurring metastases is largely unknown, i.e. treatment-naïve metastatic disease. To address this issue, 60x whole genome sequencing of 26 metastases from 4 patients was carried out. We found that the identical driver gene mutations were present in every metastatic lesion of each patient studied. Passenger gene mutations not known or predicted to have functional consequences accounted for all intratumoral heterogeneity. Even with respect to these passenger gene mutations, the genetic similarity among the founding cells of metastases was markedly higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of driver gene mutations among metastases in the same patient has critical, encouraging implications for the success of future targeted therapies in advanced stage disease.

  Study EGAS00001002186

• Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

  Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

  Study EGAS00001005403

• Test Study for EGA using data from 1000 Genomes Project - Phase 3

  The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies...

  Study EGAS00001005042

• RODAM

  The RODAM study assesses the health and wellbeing of Ghanaian residents in Ghana and Europe and follows them up over time. With this unique approach the RODAM study attempts to unravel the causes of cardiovascular disease and its risk factors among African migrants in Europe and non-migrants sub-Saharan Africa. Data are available upon reasonable request. These requests can be made to de RODAM-Pros cohort coordinator (rodamcoordinator@amsterdamumc.nl) or principal investigator, Professor Charles Agyemang (c.o.agyemang@amsterdamumc.nl).

  Dac EGAC50000000474

• Confirmation of a founder effect in a Northern European population (FRL) of a new beta-globin variant: HBB:c.23_26dup (codons 8/9 (+AGAA))

  Beta-thalassemia is a genetic disease caused by a defect in the production of the beta-like globin chain. More than 200 known different variants can lead to the disease and are mainly found in populations that have been exposed to malaria parasites. We recently described a duplication of 4 nucleotides in the first exon of beta-globin gene in several families of patients living in Nord-Pas-de-Calais (France). Using the genotypes at 12 microsatellite markers surrounding the beta-globin gene of four unrelated variant carriers plus an additional one recently discovered, we found that they shared a common haplotype indicating a founder effect that was estimated to have taken place 225 years ago (9 generations). In order to determine whether this variant arose in this region of Northern-Europe or was introduced by migrants from regions of the world where thalassemia is endemic, we genotyped the first 4 unrelated variant carriers and 32 controls from Nord-Pas-de-Calais for 97 European ancestry informative markers (EAIMs). Using these EAIMs and comparing with population reference panels, we demonstrated that the variant carriers were very similar to the controls and were closer to North European populations than to South European or Middle-East populations. Rare beta-thalassemia variants have already been described in patients sampled in non-endemic regions but it is the first proof of a founder effect in Northern Europe. The new genetic panel FRL is under registration in EGA.

  Study EGAS00001000980

• colorectal_epigenome

  Three different types of samples were used: 19 normal adjacent, 17 adenoma and 19 colorectal tumor tissue samples. This included 10 pairs of colorectal cancer and normal samples and 1 pair of adenoma-normal samples of the same patient. Tissue specimens were formalin-fixed paraffin-embedded (FFPE). DNA was isolated using the QIAamp FFPE Tissue kit (Qiagen, Hilden, DE) according to the manufacturer’s instructions. The processed DNA was run on the Illumina Human MethylEPIC® v1.0 BeadChip array.

  Dataset EGAD00010002726

• WGS of cell line MMML-seq / MALY-DE tumor_4167452

  This dataset contains the aligned whole genome sequencing data of cell line 380. This cell was established from the peripheral blood of a 15-year-old boy with acute lymphoblastic leukemia at relapse, showing an immature phenotype and carrying an IGH-MYC (t(8;14)) as well as an IGH-BCL2 (t(14;18)) chromosomal translocation. The sequencing was performed on an Illumina X-ten sequencer.

  Dataset EGAD00001004090