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• VCF file, post sample QC

  This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF.

  Dataset EGAD00001000623

• GabonDiv_SNP_genotyping

  Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study

  Dataset EGAD00010001209

• VCF dataset of Colorectal Cancer Synthetic genomes

  This dataset contains genomic variants data from VCF files of four patients synthetically generated in the EOSC4Cancer project

  Dataset EGAD50000000314

• HIV Viremic Non-Progressors (VNPs) and HIV Progressors Data Access Committee

  Data Access Committe for the project: Analyzing exome sequencing in HIV Viremic Non-Progressors (VNPs) and HIV Progressors

  Dac EGAC50000000062

• Chun Lab DAC

  Data Access Committee (DAC) for datasets produced by the Chun Lab @ Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California.

  Dac EGAC50000000011

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  spatial transcriptomics

  Dataset EGAD00001015262

• Very Low Tumor Mutation Burden Identifies Inflamed Recurrent Glioblastomas Responsive to Cancer Immunotherapy

  A subset of available tumors (with matched blood) from patients enrolled in a phase I clinical trial testing a recombinant poliovirus, published by Desjardins et al. NEJM 2018 (PMID:29943666), were analyzed by whole exome sequencing and RNA-seq. It was discovered that low tumor mutation burden correlated with survival outcome, and also discovered that low tumor mutation burden correlated with higher inflammatory gene signatures by RNA-seq.

  Study phs002270

• RRBS data (cfSort study) from noncancer tissue DNA

  The RRBS libraries of the genomic DNA from the 521 tissue samples were constructed following the standard RRBS protocol. 100-200 ng of intact genomic DNA in the volume of 21.5 µl was used as input material. Restriction digestion was done with 2.5 µl 10xCutSmart buffer and 1 µl MspI (NEB) for 18 h at 37 oC and 20 min at 65 oC. 0.5 µl 10xCutSmart buffer, 0.3 µl dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 µl Klenow (exo-, 5U/µl, NEB) and 2.6 µl RT-PCR water, 0.6 µl 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30 oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 µl 10xThermoFisher HC T4 ligase buffer, 0.4 µl 100 mM ATP (ThermoFisher), 0.2 µl 50 mM DTT, 1 µl ThermoFisher HC T4 DNA ligase (30 Weiss Unit/µl), 30 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 µl RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 µl of universal and index primer each) and 25 µl KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98 oC for 45 s, 9 cycles of 98 oC for 15 s, 60 oC for 30 s and 72 oC for 30 s, followed by a final extension at 72 oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 µl EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.

  Dataset EGAD00001010880

• TIGER-LC High-Throughput Sequencing

  Intrahepatic cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) are clinically disparate primary liver cancers with etiological and biological heterogeneity. We performed sequencing on multiple data levels of Thai CCA and HCC among the Thailand Initiative in Genomics and Expression Research for Liver Cancer (TIGER-LC) cohort using targeted OncoVar platform, whole exome, whole transcriptome, and whole genome metagenomic sequencing.

  Study phs001199

• WGS data of paediatric T-ALL acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one T-ALL patient (ALLK-118), and relapse (from BM and tonsil) and matched remission (control) samples of another T-ALL sample (ALLT-317, tonsil relapse ALLT-3107L). Diagnostic sample of ALLT-317 in the first dataset in this submission. Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit (Cat No. E7645). Both diagnostic/relapse (90x) and remission (30x) samples were sequenced using Illumina Novaseq 6000.

  Dataset EGAD50000002014