TCGA CNV/SNP6 Reference Sequence - hg19

Question

[dirigible2012]

Hello all,

The Broad Institute did the CNV analysis for the TCGA samples. The only information I have been able to find about the reference genome* does not give the version of hg19 they are using. I have two questions:

1. Is hg19 exactly the same as Ensembl's GRCh37?
2. It looks from the Ensembl site that the data has had various patches and updates. I have a list of CNV start end co-ordinates and want to extract the genes involved. How much difference will it make if I use a version with the wrong patches?

Thanks,
Stephanie

https://confluence.broadinstitute.org/display/GDAC/FAQ#FAQ-Q Whatreferencegenomebuildareyouusing

Answer 1

[Sean Davis]

For the autosomes and sex chromosomes, hg19 and GRCh37 are the same. For the purposes of start and end coordinates, the patches won't make a difference for the standard chromosomes.