PLOS Medicine’s Senior Research Editor, Clare Garvey, recently caught up with Francis Ouellette, the Associate Director of Informatics and Biocomputing at the Ontario Institute for Cancer Research (OICR) to find out about progress in cancer genomics, the issues surrounding the tsunami of data that has been generated by The Cancer Genome Atlas Project (TCGA) and the International Cancer Genome Consortium (ICGC), and how developments may impact clinical care for cancer patients.
This interview accompanies the editorial appearing in this week’s PLOS Medicine.
Francis, can you tell us what the goals of the TCGA and ICGC projects were and how they are overlapping or complementary?
The TCGA pilot was started 2006 and precedes the inaugural ICGC planning working group meeting in 2007 – the ICGC per se started in 2008. Since the beginning, the TCGA has been part of the ICGC. The overall goals of the two projects are similar – to capture the genomic information on tumour types in many different ways: with exome or whole genome sequencing to determine the simple somatic mutations; copy number variations; structural variations and effects on transcriptional regulation that happen in cancer. For this, genomic, mRNA, miRNA, and epigenomic data is collected. The goal of the ICGC has been to capture the genomic, transcriptomic, epigenomic and clinical information on 50 different tumour types and for each of these projects, collect 500 tumours and their matched normal DNA sample (commonly from blood, except for leukemias) for each tumour type and so that’s an ambitious goal of 25,000 donors, i.e. 50,000 genomes (tumour and a ‘normal’ wild type match). Approximately half of the ICGC genomes are from the TCGA projects. If you go to the ICGC data portal you will see a list of all of the cancer genome projects that have submitted data to date.
Since the initial plan to obtain data for 50 tumours, additional projects have been added, taking the number to 85 projects. ICGC Cancer Genome Projects support the characterization of 500 unique cases of one cancer type or subtype. Some of the additional projects focus on rare cancers, such as childhood leukemias, and for these rare tumor types we may only get 100 or 200 donors.