Journal article

Stable gene expression for normalisation and single-sample scoring

Dharmesh D Bhuva, Joseph Cursons, Melissa J Davis

Nucleic Acids Research | OXFORD UNIV PRESS | Published : 2020

Abstract

Gene expression signatures have been critical in defining the molecular phenotypes of cells, tissues, and patient samples. Their most notable and widespread clinical application is stratification of breast cancer patients into molecular (PAM50) subtypes. The cost and relatively large amounts of fresh starting material required for whole-transcriptome sequencing has limited clinical application of thousands of existing gene signatures captured in repositories such as the Molecular Signature Database. We identified genes with stable expression across a range of abundances, and with a preserved relative ordering across thousands of samples, allowing signature scoring and supporting general data..

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Grants

Awarded by National Health and Medical Research Council


Awarded by Cancer Council Victoria


Awarded by Cure Brain Cancer Foundation


Funding Acknowledgements

National Health and Medical Research Council funding [1128609 to M.J.D., 1147528, 1165208 to J.C.]; Cancer Council Victoria funding [1187825 to M.J.D.]; National Breast Cancer Foundation and Cure Brain Cancer Foundation funding [CBCNBCF-19-009 to M.J.D.]; M.J.D. is the recipient of the Betty Smyth Centenary Fellowship in Bioinformatics; D.D.B. was supported by the Melbourne Research Scholarship (MRS); This study was made possible through Victorian State Government Operational Infrastructure Support and Australian Government NHMRC Independent Research Institute Infrastructure Support scheme. Funding for open access charge: Institutional funding.