Sequencing Analysis of Cutaneous Squamous Cell Carcinoma

The Exome Sequencing Analysis of Cutaneous Squamous Cell Carcinoma (SCC) study is a single-center cohort study. To identify recurrent genomic aberrations that might underlie the development of this malignancy, we performed whole exome sequencing on a series of SCC-normal pairs to distill a list of 336 candidate genes that were subsequently re-sequenced in 100 SCC-normal pairs with an average depth >1200X. This study also included whole-genome copy number analysis on 5 primary SCC with KNSTRN p.Ser24Phe and 5 histologically matched SCC with wild-type KNSTRN.]]>
Fresh surgical specimens as well as archived formalin-fixed, paraffin-embedded (FFPE) samples of SCC and patient-matched normal skin control were verified by histologic review. Samples with heavy neutrophilic infiltrate or widespread necrosis were excluded.]]>
May 2011 - first specimens obtained October 2011 - completion of whole exome sequencing July 2013 - completion of targeted deep sequencing]]>