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• Multi-omic dataset of neuroendocrine neoplasm organoids

  This dataset corresponds to one of the first biobanks for the understudied neuroendocrine neoplasms from multiple grades and body sites (lung, pancreas, small intestine). It contains whole-genome sequencing data for original tumors, patient-derived tumor organoids at multiple passages, and matched normal tissue, and RNA-seq data for the original tumor and patient-derived tumor organoids.

  Study EGAS00001005752

• Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer

  Circulating tumor DNA (ctDNA) sequencing provides a minimally-invasive method for tumor molecular stratification. We compared the commercial Guardant360 ctDNA test to an academic sequencing approach for profiling of metastatic prostate cancer. Plasma cell-free DNA (cfDNA) from 24 patients was sequenced with a validated, prostate cancer specific targeted research panel, and sent for simultaneous Guardant360 analysis.

  Study EGAS00001003352

• Role of Genetic Factors in the Pathogenesis of Lung Disease

  Three individuals with lymphangioleiomyomatosis (LAM) underwent evaluation for Tuberous Sclerosis Complex (TSC)-associated mucocutaneous and internal findings. Next-generation sequencing (NGS) of cutaneous findings was used to confirm clinical suspicion for mosaic TSC in individuals with LAM. Mosaic mutations in TSC2 were found in these three individuals.

  Study phs003108

• Genotype variables of the 61 COVID-19 patient cohort used in the main project of data integration

  We selected SNPs with a minor allele frequency (MAF) higher than 10% in the Caucasian population from the Ensembl database. Specifically, we selected ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788) for the present analysis. For more information, please refer to:

  Study EGAS50000000589

• Japanese Alzheimer's disease neuroimaging initiative

  Japanese ADNI aims to establish imaging and biofluid markers that can predict and monitor the progression of changes in the brains of elderly individuals with AD, mild cognitive impairment (MCI) or normal cognition, and eventually be used as a surrogate markers for the clinical trials of DMDs for AD.

  Study JGAS000051

• Microinjection_of_hIPSC_derived_intestinal_organoids_with_Salmonella_Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001253

• WGS-Lung Cancer sample 30 pair

  This study includes 30 paired samples of Korean Lung Cancer paitients. 30 Lung Cancer samples are paired with each normal(Saliva derived for control) 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 EGAS00001001474

• Korean Lung Cancer - 36 pair WES data

  This study includes 36 paired samples of Korean Lung Cancer paitients.36 Lung Cnacer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WES study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002843

• RNA-Seq on OCIAML-22 Fractions

  The donor AML patient (unsorted) that was used to generate OCI-AML22 was expanded for the indicated number of days (Donor: 0 day, 12d: 12 days, 2m: 2 months, 3m: 3 months), then sorted for the indicated fraction (CD34p: CD34+; CD34m: CD34-, CD38m: CD38-, CD38m: CD38-).

  Study EGAS00001006512

• Direct Detection of Early-stage Cancers Using Circulating Tumor DNA

  Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.

  Study EGAS00001002577