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• Memorial Sloan Kettering (MSKCC) Single Cell Mutational Profiling in Myeloid Malignancies

  Myeloid malignancies have previously been characterized by large scale bulk molecular profiling studies on patient samples. These studies, while clinically informative, are unable to delineate mutation order as well as clonal architecture and complexity. To investigate the clonal framework of myeloid malignancies, the Single Cell Mutational Profiling in Myeloid Malignancies study was designed. This study performed sequencing of 148 samples from 117 adult patients diagnosed with clonal hematopoiesis (n = 21), myeloproliferative neoplasms (MPN; n = 14), and acute myeloid leukemia (AML; n = 82) between 20 and 87 years of age. Sequencing of all samples was performed using the Tapestri single cell DNA sequencing platform from Mission Bio, Inc. The platform utilizes a custom amplicon panel covering 109 amplicons across 31 genes frequently mutated in myeloid malignancies (CH, MPN, AML). Using the single cell DNA sequencing data, we were capable of elucidating clonal architecture and clonal complexity in each sample. In a subset of samples, we also performed simultaneous single cell DNA sequencing and cell surface protein expression analysis using the Tapestri DNA + Protein platform. This study allowed us to determine the expression of 7 cell surface proteins (CD3, CD11b, CD19, CD34, CD38, CD45RA, and CD90) at single cell resolution. We performed DNA+ Protein sequencing on samples from CH patients (n = 7) as well as AML patients (n = 17).

  Study phs002049

• Molecular analysis of post-colonoscopy CRC (PCCRC)

  Background: Post-colonoscopy colorectal cancers (PCCRCs, i.e. CRC diagnosed after a colonoscopy that excluded cancer) pose a challenge in clinical practice. In a retrospective cohort study, we compared clinical and molecular features of PCCRCs and prevalent CRCs. Methods: PCCRCs were defined according to the WEO classification, as cancers occurring within 10 years after a complete index colonoscopy, which excluded CRC. Whole genome chromosomal copy number changes and mutation status of genes commonly affected in CRC (APC, KRAS, BRAF, FBXW7, PIK3CA, NRAS, SMAD4 and TP53) were examined by low-coverage WGS and targeted sequencing, respectively. MSI and CIMP status were also determined. Results: In total, 122 PCCRCs and 98 prevalent CRCs were examined. PCCRCs are more often located proximally in the colon (p<0.001), non-polypoid appearing (p=0.004), early stage (p=0.009), and poorly differentiated (p=0.006) compared to prevalent CRCs. PCCRCs contain less frequently 18q deletions (p<0.001) than prevalent CRCs. MSI (p=0.029) and CIMP (p=0.014) are more frequently observed in PCCRCs. Conclusion: Although no PCCRC specific pathway could be defined, PCCRCs’ molecular features are more associated with MSI and hypermethylation pathways than canonical CIN pathway. The clinical and molecular features observed in PCCRCs support the hypothesis that sessile serrated lesions and non-polypoid CRNs are contributors to the development of these cancers."

  Study EGAS00001004686

• Khoe-San genome Project (KSGP)

  The Khoe-San Genome Project (KSGP) includes whole genome data generated for 190 study participants from Southern Africa (Namibia and South Africa) representing people speaking a Namibian Khoe-San language (n=150, 12 groups) or regional non-Khoe-San groups (n=40), specifically defined here as Namibian Himba (n=10), South African Southern Bantu (n=12 and representing the Ubuntu Genome Project led by the University of Limpopo) or South African Coloured/European (n=18). Deep whole genome data has been generated for the purposes of cataloguing the extent of regional genetic diversity, creating population specific references and evolutionary trajectories, while creating a population-matched panel of normal (PoN) genetic diversity required for disease associated studies across the region.

  Dac EGAC50000000798

• ICR639 CPG NGS Validation series

  The dataset includes sequencing data generated using the TruSight Cancer Panel (TSCP) a targeted NGS assay for analysis of CPGs and orthogonally generated data supporting at least one pathogenic variant in a CPG for a total of 645 pathogenic CPG variants. The set of pathogenic CPG variants includes strong representation of some of the most challenging types of pathogenic variants, with 339 indels, including 16 complex indels and 24 insertions or deletions with length greater than 5bp, and 74 exon CNVs, including 23 single exon CNVs. There are 502 pathogenic variants in BRCA1 or BRCA2, making this an important first-line validation dataset for laboratories performing NGS testing of BRCA1 and BRCA2.

  Dataset EGAD00001004134

• DAC for CancerLocator study

  Dac EGAC00001000602

• Point of contact for Data

  Dac EGAC00001000977

• DAC for CAR-T

  Dac EGAC00001003069

• DAC for PROP1 study

  Dac EGAC00001000312

• DAC for ACC Study

  Dac EGAC00001000376

• Centre for Biocultural History

  Dac EGAC00001000502