DAC

Ontario Institute of Cancer Research, Boutros Group Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00001000591 Paul Boutros pboutros [at] mednet [dot] ucla [dot] edu No additional information is available

This DAC controls 23 datasets:

Dataset ID Description Technology Samples
EGAD00001003235 Raw exome sequence data(fastq) for the GATCI project unspecified 172
EGAD00001003236 Raw whole genome sequence data(fastq) for the GATCI project HiSeq X Ten 10
EGAD00001003589 Ultra-Fast Patient-Derived Xenografts Identify Functional and Spatial Tumour Heterogeneities that Drive Therapeutic Resistance - WXS mapped reads 27
EGAD00001003590 Ultra-Fast Patient-Derived Xenografts Identify Functional and Spatial Tumour Heterogeneities that Drive Therapeutic Resistance - WXS unaligned reads Illumina HiSeq 2500 27
EGAD00001004126 Sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found int he bam header. In total, data generated from 174 tumour samples 102 matched blood normal controls was aligned. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers. 264
EGAD00001004127 Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller, to generate germline variant calls across the SureSelect All Exon V5+UTR target region. Variant calls are in VCF format. In total there are samples from 173 donors. 101 donors have calls generated from both normal and tumour samples tumour samples, 94 of which have a matched normal. Details for the call can be found in the vcf headers. 263
EGAD00001004128 Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with SomaticSniper. Somatic variant calls are in VCF format. In total there are 94 tumour samples, each with a matched normal. 178
EGAD00001004129 Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header. 250
EGAD00001005791 Whole exome sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in he bam header. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers. 264
EGAD00001005808 Raw whole exome sequencing data (fastq) for the GATCI project unspecified 264
EGAD00001005810 Raw RNA sequence data (fastq) for the GATCI project unspecified 30
EGAD00001005817 Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with GATK HaplotypeCaller to generate germline variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers 98
EGAD00001005818 Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with SomaticSniper to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers 98
EGAD00001005822 Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM and preprocessed with GATK for indel realignment and base quality score recalibration. Aligned sequence was analyzed with MuTect to generate somatic variant calls. Variant calls are in VCF format. In total, there are 60 tumour samples from 38 patients, all with matched normal. Further details can be found in the vcf headers. 98
EGAD00001005914 Sequence data in fastq format was aligned to the GRCh38 reference genome with BWA-MEM. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found in the bam header 97
EGAD00001005916 Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK Haplotype Caller to generate germline variant calls. Variant calls are in VCF format. Details for the call can be found in the VCF header 263
EGAD00001005917 Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header. 250
EGAD00001005918 Exome sequences were aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/SomaticSniper, to generate somatic variant calls. Somatic variant calls are in VCF format. Details for the mutect call can be found in the vcf header. 178
EGAD00001005926 Raw whole genome sequencing data (fastq) for the GATCI project HiSeq X Ten,unspecified 104
EGAD00010001540 Oncoscan CHP files for the Mesothelemia Project Illumina Oncoscan Array 100
EGAD00010001579 This dataset contains files generated from Affymetrix Oncoscan Arrays. For each sample there are two paired cel files containing the raw data from AT and GT channels. Raw data has been transfromed to OSCHP signal files also within this dataset. Oncoscan Array 157
EGAD00010001626 mpMRI visible prostate tumour samples (PI-RADSv2 5) OncoScan 20
EGAD00010001627 mpMRI invisible prostate tumour samples OncoScan 20