Question

Download of FF-FFPE pair DNA seq data

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5.5 years ago

dkalfakakou ▴ 10

Hello everybody!

I was wondering if someone knew where I could find some data from Fresh Frozen/FFPE pairs DNA seq. Are there any public resources?

Thank you!

genome sequencing • 1.1k views

ADD COMMENT • link updated 5.5 years ago by Kevin Blighe 87k • written 5.5 years ago by dkalfakakou ▴ 10

score 2 · Answer 1 · 2018-11-01

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5.5 years ago

Kevin Blighe 87k

I found this, after a quick search: Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples (data available at EGA, but may require pre-approval by study author).

You should also note this important study, but I don't know if data is available: Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. They may have links to other studies, though.

I also found this, but it's RNA-seq: - A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples ( data available from NCBI BioPoroject )

ADD COMMENT • link 5.5 years ago by Kevin Blighe 87k

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Thank you very much for taking the time to search and answer! I had already searched for data at BioProject and I couldn't find what I was looking for. I have to admit that I wasn't aware of EGA. I will try to contact the study author. I have already contacted the authors of the 1000G study, but I hadn't had a response. Maybe I will try again.

Thank you once more!

ADD REPLY • link 5.5 years ago by dkalfakakou ▴ 10