Journal article

Detecting copy number alterations in RNA-Seq using SuperFreq

Christoffer Flensburg, Alicia Oshlack, Ian J Majewski



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 maximise information from read counts and B-allele frequencies (BAFs). 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% f..

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Awarded by Australian National Health and Medical Research Council (NHMRC)

Awarded by Cancer Council Victoria

Awarded by Victorian Cancer Agency fellowship

Awarded by Australian National Health and Medical Research Council (NHMRC) [Independent Research Institutes Infrastructure Support Scheme]

Awarded by National Health and Medical Research Council of Australia

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.