Journal article
Detecting copy number alterations in RNA-Seq using SuperFreq
C Flensburg, A Oshlack, IJ Majewski
Bioinformatics | Published : 2021
Abstract
Motivation: Calling copy number alterations (CNAs) from RNA sequencing (RNA-Seq) is challenging, because of the marked variability in coverage across genes and paucity of single nucleotide polymorphisms (SNPs). We have adapted SuperFreq to call absolute and allele sensitive CNAs from RNA-Seq. SuperFreq uses an error-propagation framework to combine and maximize information from read counts and B-allele frequencies. Results: We used datasets from The Cancer Genome Atlas (TCGA) to assess the validity of CNA calls from RNA-Seq. When ploidy estimates were consistent, we found agreement with DNA SNP-arrays for over 98% of the genome for acute myeloid leukaemia (TCGA-AML, n = 116) and 87% for colo..
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Awarded by National Health and Medical Research Council
Funding Acknowledgements
This work was supported by the Australian National Health and Medical Research Council (NHMRC) [Project Grant 1145912 to I.J.M.; Independent Research Institutes Infrastructure Support Scheme grant 9000220], the Cancer Council Victoria [grant-in-aid 1124178 to I.J.M.], a Victorian State Government Operational Infrastructure Support (OIS) grant and a Victorian Cancer Agency fellowship [MCRF15018 to I.J.M.]. We wish to acknowledge the generous support of the Felton Bequest and Mr. Malcolm Broomhead who provided philanthropic support. The funders had no influence over the final content of the manuscript.