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• Chromatin profiling of baseline and Notch inhibitor treated HCC PDX model

  We generated chromatin accessibility profiles for anti-Notch2 (n=3) and anti-gD (n=3) treated LIV78 tumors. Tumors were isolated, snap frozen in liquid nitrogen and stored at -80C. Tumor tissue was pulverized using a Covaris CP02 CryoPrep Pulverizer. Flash frozen pulverized tumor samples were sent to Active Motif to perform the ATAC-seq assay. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina) to produce FASTQ sequencing files.

  Dataset EGAD50000000735

• Diverse transcriptomic and mutational patterns but limited functional pathway alterations in patient-derived SS cells

  We profile the whole-transcriptome of 7 patient-derived Sézary Syndrome (SS) cells to identify expression patterns, functional programs and expressed gene mutations that may provide clues on new therapeutic options for SS patients. The libraries were sequenced on NextSeq500 (Illumina) with a paired-end read length of 2x75bp.

  Study EGAS50000001151

• The dataset for "ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma”

  The dataset for the study “ctDNA residual disease analyses during perioperative nivolumab or nivolumab plus ipilimumab in resectable diffuse pleural mesothelioma” includes 169 bam files from whole genome sequencing on the Illumina NovaSeq6000 platform. The samples analyzed include tumor (n=28) and normal (n=28) DNA samples, and serial plasma cfDNA (n=113) samples from 28 individuals with resectable diffuse pleural mesothelioma, treated with nivolumab or nivolumab plus ipilimumab on the NCT03918252 trial.

  Dataset EGAD50000001701

• WGS of Five Pancreatic Cancer Patients-Tumor and Normal

  We performed whole genome sequence on tumor-derived and normal cell lines from patients who had terminal pancreatic cancer and consented for rapid autopsy upon their death. The 5 samples are from Dr. Christine Iacobuzio-Donahue's rapid autopsy program as reported in Boland et al. (PLOSOne, 2024, In Press, PMID 38352348).

  Study phs003775

• Genome sequencing of biliary tract cancers

  Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous with poor response to treatments. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed genome sequencing analyses for a large scale samples of BTCs to investigate their somatic and germline driver events and characterize their genomic landscape.

  Study JGAS000109

• Genome sequencing of biliary tract cancers

  Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous with poor response to treatments. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed genome sequencing analyses for a large scale samples of BTCs to investigate their somatic and germline driver events and characterize their genomic landscape.

  Study JGAS000389

• Repeated sampling

  Repeated sampling experiment – sample acquisition A repeated sampling experiment was set up to specifically evaluate the effect of increasing time after death on sample quality. Selected non-tumor and large tumor tissues (with enough material available to collect for this experiment beside routine sampling) were sampled repeatedly at 1.5-hour time intervals during the autopsy.

  Study EGAS50000000224

• Indonesian methylation data

  DNA methylation data were collected to study patterns of functional variation across the broad geography of Indonesia. The region has extremely diverse populations, with very different demographic histories and multiple genetic ancestries. This dataset reports Illumina Epic methylation chip data for individuals from three islands spanning this geographical region: Mentawai, Sumba and West Papua.

  Study EGAS00001003653

• AML_WES

  This 2014_AML_WES study includes 40 paired samples derived from Korean AML paitients. AML Bone Marrow samples were collected and paired with each normal(Saliva or BM derived) sequencing data. The results of this CN study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001001559

• 2017_AML_WGS

  This 2017_AML_WGS study includes 10 paired samples derived from Korean AML paitients. 10 AML Bone Marrow samples were collected and paired with each normal(Saliva or BM derived) sequencing data. The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002388