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• miRNA

  miRNA Sequencing of olfactory mucosa (OM) cells derived from cognitively healthy and individuals with AD exposed to traffic-related ultrafine particles (UFPs) for 72h in submerged cultures. The UFPs used for exposures were: A0 and A20. Exposures were compared to the corresponding blank samples.

  Dataset EGAD50000001532

• Dataset for "HPV integration induces gene fusions" (pacBio)

  pacBio whole-genome sequencing data for "HPV integration induces gene fusions" We performed long read whole-genome sequencing on four HPV+ head and neck cancer samples using pacBio HiFi. The sequence reads were submitted in fastq format.

  Dataset EGAD50000001304

• Exome sequencing of an AML treated with BCL2i

  Molecular profiling by exome sequencing of an AML case following treatment with a BCL2 inhibitor

  Dataset EGAD00001007307

• Ultraviolet radiation drives mutations in a subset of mucosal melanomas

  This dataset contains 20 whole genome sequences from 10 tumor-normal pairs from conjunctival melanomas.

  Dataset EGAD00001006568

• Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas: RNAseq variants

  Variants called from RNA-seq data of meningioma tumors.

  Dataset EGAD00001002649

• Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

  Study EGAS00001004660

• Development of molecular targeted therapy for small cell lung cancer by comprehensive genome analysis

  Aims: Identifying new therapeutic targets of small cell lung cancer (SCLC), genome-wide mutation analysis has been performed. Methods: Genomic DNA was extracted from formalin-fixed or methanol-fixed tissue samples. 71 Mb of DNA fragments containing whole coding exons were concentrated using SureSelect Human All Exon V4+UTRs Kit (Agilent Technologies) followed by 100-bp paired end sequencing by HiSeq 2000 (Illumina). Participants/Materials: 51 of 1042 cases of pathologically diagnosed small seen lung cancer that were registered to National Cancer Hospital East Lung Cancer Database in 1992-2012, and which surgically resected or biopsy samples were suitable for DNA extraction for further analyses.

  Study JGAS000037

• Primary Prostate Tumor Tissue DNA Methylation Profiles

  The study cohort includes 525 Caucasian and African American prostate cancer (PCa) patients who underwent radical prostatectomy (RP) as primary therapy for clinically localized adenocarcinoma of the prostate. These patients were previously enrolled in one of two population-based studies: 1) men 40-64 years of age, diagnosed between January 1993 and December 1996; and, 2) men 35-74 years of age, diagnosed between January 2002 and December 2005. Gleason grade and sum, diagnostic PSA, and pathological tumor stage were obtained from the SEER cancer registry. Formalin-fixed paraffin-embedded prostate tumor tissue blocks were obtained from RP specimens and used to make hematoxalin and eosin stained slides, which were reviewed by pathologists to confirm the presence/location of adenocarcinoma. For each patient two 1-mm tumor tissue cores from the dominant lesion that were enriched with >=75% tumor cells were taken for DNA purification. The RecoverAll Total Nucleic Acid Isolation Kit (Ambion/Applied Biosciences, Austin, TX) was used to extract DNA, which was then quantified (PicoGreen), aliquoted onto 96-well plates and shipped to Illumina for DNA methylation profiling using the Infinium® HumanMethylation450 BeadChip.

  Study phs001921

• TREM2+ Cells in Human Basal Cell Carcinomas

  To explore the tumor immune microenvironment heterogeneity in sporadic human basal cell carcinoma tumors, we profiled two individual patient tumors by scRNA-Seq. We identified a population of TREM2+ macrophages, which have been implicated in promoting an immunosuppressive tumor microenvironment. We identify that TREM2+ can promote tumor epithelial proliferation in an immunosuppressive independent manner.

  Study phs003242

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778