No normal files for BTCA-JP


#1

Hi everyone,
I want to download the data(unaligned reads) of BTCA-JP. There are about 20000 FASTQ files from 230 donors. However, I found that the specimen type of all files is Primary tumor - solid tissue, which means there is no sequencing data from matched normal tissue / blood. With only the sequencing data of tumor, I can do nothing…(e.g. identify somatic SNV, somatic CNV,).
So I want to know the reason for lacking data from normal tissue. Does ICGC have these data but I have not found them?

Thanks,
Yang


#2

Hi Yang,

The ICGC has encountered the same issue you are describing. The BTCA-JP project has only made available raw sequencing data at EGA for tumour samples. We are currently following up with the BTCA-JP project to find out the status of their sequencing data for normal samples, so we will get back to you soon. There are indeed a very high number of FASTQ files for each donor, so this is not an error but rather just the way the project sequenced their data. In the meantime, I will let you know as soon as I hear back from the BTCA-JP project about sequencing data for their normal samples.

Regards,
Hardeep


#3

Hi Hardeep,
Thanks for your prompt reply! Looking forward to hear from you soon!

Yang