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Tumor Genomics Committee - EGAC00001000987

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Janne Ravantti
dac-tumorgenomics@helsinki.fi

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This DAC controls 18 datasets

Dataset ID	Description	Technology	Samples
EGAD00001004281	The dataset contains the somatic point mutation data from the exome-targeted region of 36 exome or whole genome sequenced microsatellite unstable colorectal cancers and the somatic point mutation data from 93 additional MiSeq sequenced microsatellite unstable colorectal cancers.		129
EGAD00001004329	Somatic mutations of 256 whole-genome sequenced colorectal tumors. 234 MSS, 19 MSI and 3 POLE mutants. See Katainen R. et al. CTCF/cohesin-binding sites are frequently mutated in cancer, Nature Genetics 2015. doi:10.1038/ng.3335		256
EGAD00001004884	The data consists of 47 exome-sequenced synchronous colorectal cancers from 23 patients. The exomes of corresponding normal samples were used to remove germline variants. All patients are Finnish (white Caucasian). All except one patient (sync_11 who belongs to a LS family) were assumed sporadic. The sequence data was produced with Illumina HiSeq 4000.		47
EGAD00001006572	The dataset contains somatic variants in 344 colorectal cancer samples. Variants are called with Mutect2 (GRCh38). Important: VCF-files include also variants, which have been annotated as "str_contraction" and "panel_of_normals". Please, use only "PASS" variants in studies, which are not microsatellite repeat related. Samples are sequenced with Novaseq 6000, HiSeq 2000, and HiSeq X Ten instruments (average coverage depth ~30+). The dataset consists of 257 MSS, 58 MSI, 25 MSS IBD, and 4 POLE mutant CRCs.		344
EGAD00001010009	Fasq-files from 3 unaffected TET2 mutation carriers, 2 mutation carriers diagnosed with lymphoma and 3 family members without TET2 mutation. Time series data collected from 0, 6 and 12 months after daily dose of 1g vitamin C.	Illumina NovaSeq 6000	24
EGAD00010002410	Average methylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types using nanopolish. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002411	Average hypermethylation on transcription factor binding sites based on nanopolish calls; only positions showing higher methylation than sampleâ€™s average methylation at enhancers were included when defining the average methylation level. Data from 6 individuals at different time points.	Oxford Nanopore	1
EGAD00010002412	Average genome-wide methylation levels per sample at different time points using nanopolish calls. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002413	Average methylation levels based on nanopolish calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002414	Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002415	Average hydroxymethylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002416	Proportion of hyper- and hypomethylated positions at Roadmap annotations. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002417	Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1
EGAD00010002418	CpG hydroxymethylation. Software: minimap2 v.2.16; Megalodon.	Oxford Nanopore	24
EGAD00010002419	Average genome-wide hydroxymethylation levels per sample at different time points using megalodon calls. Data from 8 individuals.	Oxford Nanopore	1
EGAD00010002420	CpG methylation. Software: minimap2 v2.16;Nanopolish.	Oxford Nanopore	24
EGAD00010002421	Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.	Oxford Nanopore	1
EGAD00010002422	Average methylation levels based on nanopolish calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.	Oxford Nanopore	1