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• NIDDK IBD Genetics Consortium Repository Immunochip

  The Immunochip is a custom Illumina Infinium chip comprising 196,524 SNPs and small indels selected primarily based on GWAS analysis of 12 autoimmune and inflammatory diseases. The chip has two purposes: fine mapping of 289 established associations corresponding to 187 distinct loci, and deep replication of suggestive, but not yet proven, associations. Fine-mapping regions were defined as 0.2cM centered on GWAS hit SNPs, and all SNPs and short indels in these regions from the 1000 Genomes Project low coverage pilot CEU samples, as well as variants discovered in resequencing experiments conducted by groups collaborating in the chip design were selected for inclusion. Replication of autoimmune and inflammatory GWAS (including Crohn's disease and ulcerative colitis) contributed the bulk of the remaining SNP lists. Approximately 25,000 SNPs were included as replication of unrelated diseases as part of the WTCCC2 project, which serve as useful null SNPs for these analyses. In total, approximately 240,000 SNPs were selected for inclusion, with an assay design success rate of ~80%. Reprinted from Jostins et al. (2012), with permission from Springer Nature (see https://www.nature.com/reprints/permission-requests.html). Jostins, L., et al. (2012) Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature, 491, 119-24. PMID: 23128233.

  Study phs001721

• Profiling RNA Translation in Pediatric Medulloblastoma

  This study provides RNA-sequencing and ribosome profiling data for patient-derived cell lines and patient tissue samples for children with medulloblastoma. Ribosome profiling is a variant protocol of RNA-sequencing that directly sequences ribosome-bound RNA fragments only. Associated RNA-seq and Ribo-seq data obtained separately for some cancer cell lines can be found on the NCBI SRA as PRJNA957428. Samples were processed for poly-A mRNA sequencing using the Roche Kapa Kit. Ribosome profiling was performed as described in the manuscript referenced below (Hofman et al.) and based on the article by McGlincy et al., Methods (2017). Ribo-seq data were analyzed for sample quality using RiboseQC (Calviello, Nat Struct Mol Biol, 2020). These data were used to quantify P-sites of open reading frames. RNAseq and ribo-seq data were integrated and compared to determine translational efficiency values using TPM (Ribo-seq) over TPM (RNA-seq) as the metric. Ribo-seq data on 14 samples and RNAseq data on 21 samples derived from 16 fresh-frozen surgical samples for medulloblastoma and 5 autopsy samples are available through dbGaP. A second cohort of 4 medulloblastoma samples (RNAseq, Ribo-seq) related to this study can be found on the EGA at EGAS00001007426.

  Study phs003446

• IMCISION DNAseq

  Whole-exome sequencing of 32 primary head and neck squamous cell carcinoma samples prior to treatment with neoadjuvant anti-PD-1 (n=6) or anti-PD-1 + anti-CTLA-4 (n=26) immunotherapy. DNA quantity used: 50ng. Library Preparation Kit: Twist Human Core Exome Plus (Twist Bioscience). Sequencing parameters: NovaSeq 6000, 2x 100 bp. File type: fastQ.

  Dataset EGAD00001008139

• RNA-seq Revision

  The dataset comprises bulk RNA‑seq libraries generated on the Illumina NextSeq 500 platform, including primary human hepatocytes (four donors), colon tissue (four masked replicates), and a comprehensive set of iPSC‑derived samples from the JHU106, ChiPSC18, ChiPSC22, and H9 lines. The collection covers multiple differentiation stages from iPSC to DE to HLC and cultivation protocols (CEL, HAY, SPH) with at least three replicates per condition. All sequencing data are provided as raw FASTQ files, with colon samples delivered as masked FASTQ in accordance with patient consent requirements.

  Dataset EGAD00001008951

• A Somatic Reference Standard for Cancer Genome Sequencing

  In this study, we separately performed PCR-free whole genome sequencing on the paired tumor/normal melanoma COLO-829 and lymphoblastoid COLO-829BL cell lines across three separate institutions (TGen, Illumina, Genome Sciences Centre at the British Columbia Cancer Agency). We performed a meta-analysis of all data, in combination with the originally reported analysis of these cell lines by Pleasance et al., and report a somatic reference standard based on consensus events. This standard can be used as a reference for tumor/normal whole genome analyses.

  Study phs000932

• Resistance to Latent Mycobacterium tuberculosis Infection in Uganda: Immunologic Profiling

  Despite significant exposure to Mycobacterium tuberculosis (Mtb), some humans remain uninfected, as defined by persistently negative immune sensitization tests (tuberculin skin test, TST; interferon gamma release assays, IGRA). To explore mechanisms of natural resistance to Mtb infection, we profiled tissues from highly-exposed Mtb contacts from Uganda. The cohort from this submission were household contacts of pulmonary tuberculosis cases who were followed longitudinally over 8 years and maintained negative TST and IGRA testing on serial evaluations. This cohort is well-described (Stein et al. 2019, PMID: 30165605).

  Study phs002445

• Diversity of the immune microenvironment and response to checkpoint inhibitor immunotherapy in mucosal melanoma

  Mucosal melanoma (MucM) is a rare cancer with a poor prognosis and low response rate to immune checkpoint inhibition (ICI) compared to cutaneous melanoma (CM). To explore the immune microenvironment and potential drivers of MucM’s relative resistance to ICI drugs, we characterized 101 MucM tumors (43 head and neck, 31 female urogenital, 13 male urogenital, 11 anorectal, and 3 other gastro-intestinal) using bulk RNA-sequencing (RNAseq). The original publication is written by JL Vos, JJH Traets, et al. and published in JCI Insight in 2024.

  Study EGAS50000000631

• Nanopore whole-genome sequencing of sample RK067 and variant-call data (SNVs and intermediate-sized deletions) of 174 Japanese samples.

  We performed whole-genome sequencing of a human samples using Oxford Nanopore MinION sequencer, so as to be able to establish methods to detect and identify structural variations in Japanese individuals. Intermediate-sized deletions were identified from 174 Japanese samples��� short-reads whole-genome sequencing data. Variant call information of these intermediate-sized deletions were joined with SNVs identified in a previous study (Fujimoto, A et al., Nat Genet, 2016) to create a reference panel for use in imputation.

  Study JGAS000180

• Whole Genome Sequences of 18th century African descended individuals from Charleston, South Carolina.

  This study presents Whole Genome Sequencing results from the Anson Street African Burial Ground Project, which is a community-based initiative aimed at understanding the histories of 37 Ancestors found during construction in Charleston, South Carolina. Here we report fastq files for all 37 Ancestors. DNA was extracted at the University of Tennessee-Knoxville following Dabney et al. 2013, and dual index libraries prepared using a modified NEBNext Ultra II kit with partial USER enzyme digestion. Libraries were then enriched for human genomic DNA (MyBaits) and sequenced on Illumina Platforms.

  Study EGAS00001006693

• Copy number analysis by SNP array

  Hybridization-based genomic profiling arrays were performed using Genome-Wide Human SNP Array 6.0 or the CytoScan HD array, according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA, USA) now part of Thermo Fisher Scientific (Thermo Fisher Scientific, Inc.) Following the procedures of sample preparation, hybridization, and scanning, the CEL file of Genome-Wide Human SNP Array 6.0 was analyzed as previously described (Magrangeas et al. 2012) and the CEL file of CytoScan HD array was analyzed using the Chromosome Analysis Suite (ChAS) software (Thermo Fisher Scientific, Inc).

  Study EGAS00001005125