hpv status for head and neck cancer samples

[Jeffrey E Segall]

Hi,

I really appreciate the aggregation of data that you provide.  I was wondering if you could include HPV status determination in the head and neck cancer samples?

Thanks,

 

Jeffrey E. Segall

Betty and Sheldon Feinberg Senior Faculty Scholar in Cancer Research

Professor, Anatomy and Structural Biology

Professor, Pathology

Price 201

Anatomy and Structural Biology

Albert Einstein College of Medicine

1301 Morris Park Avenue

Bronx, NY 10461

Phone: 718-678-1109

FAX: 718-678-1019

Email:jeffrey...@einstein.yu.edu

http://www.einstein.yu.edu/labs/jeffrey-segall/

 

[Juok Cho]

Hi Jeffery,

The HPV status information of samples are not available in TCGA clinical data. However, they were inspected by researchers in the TCGA HNSC analysis working group and the results based on the awg freeze set are available in the HNSC TCGA marker paper published in nature. The results are also available in HNSC GDAC AWG specific run. Please note that the subtype information available in the awg run is based only on the freeze set. 

Here is the link to the sample information of the HNSC GDAC awg run. 

http://gdac.broadinstitute.org/runs/awg_hnsc__2014_04_12/samples_summary_report/

According to the table in the page, For the 279 total freeze cases, 36 cases are detected as HPV positive and 243 cases were detected as HPV negative.

 Best,

Juok