Cancer TCR Repertoire Datasets

Question

[bioinformatics.cancer]

Hi, Is anyone aware of pubilcly available T Cell Receptor repertoire data sets from immuno-sequencing, particularly from tumor or PBMC in cancer patients or mouse. I am looking for a summarized form repertoire profile dataset that includes clonotype (AA and NT), number and frequency of clones, and V, D, J gene name for each clonotype. Thank you, - Pankaj

Answer 1

[Denise CS]

This paper may help.

Answer 2

[mikhail.shugay]

The paper provided by Denise is about a software for T-cell repertoire post-analysis and thus doesn't contain cancer TCR repertoire datasets (as far as I remember it uses twin repertoire sequencing data from Zvyagin et al PNAS 2014). We have quite a large collection of sequenced repertoires, yet those are mostly from healthy people and people with autoimmune diseases. Regarding cancer datasets you can try to look in these papers:

• http://cancerres.aacrjournals.org/content/early/2012/05/09/0008-5472.CAN-12-0277.full.pdf
• http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666197/
• http://www.nature.com/articles/srep13664

and check out Immunoseq Analyzer page:

http://ww2.adaptivebiotech.com/IMMUNOSEQ-ANALYZER/DEMO

You'll have to register there and try to find cancer patient samples in published samples section (they can be exported as a tabular file with columns that you need)