Detecting copy number alterations in RNA-Seq using SuperFreq.
Christoffer Flensburg, Alicia Oshlack, Ian J Majewski
Bioinformatics | Published : 2021
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..View full abstract