RT Journal Article SR Electronic T1 sigQC: A procedural approach for standardising the evaluation of gene signatures JF bioRxiv FD Cold Spring Harbor Laboratory SP 203729 DO 10.1101/203729 A1 Dhawan, Andrew A1 Barberis, Alessandro A1 Cheng, Wei-Chen A1 Domingo, Enric A1 West, Catharine A1 Maughan, Tim A1 Scott, Jacob G. A1 Harris, Adrian L. A1 Buffa, Francesca M. YR 2017 UL http://biorxiv.org/content/early/2017/11/13/203729.abstract AB With the increase in next generation sequencing generating large amounts of genomic data, gene expression signatures are becoming critically important tools, poised to make a large impact on the diagnosis, management and prognosis for a number of diseases. Increasingly, it is becoming necessary to determine whether a gene expression signature may apply to a dataset, but no standard quality control methodology exists. In this work, we introduce the first protocol, implemented in an R package sigQC, enabling a streamlined methodological and standardised approach for the quality control validation of gene signatures on independent data sets. The emphasis in this work is in showing the critical quality control steps involved in the generation of a clinically and biologically useful, transportable gene signature, including ensuring sufficient expression, variability, and autocorrelation of a signature. We demonstrate the application of the protocol in this work, showing how the outputs created from sigQC may be used for the evaluation of gene signatures on large-scale gene expression data in cancer.