BACOM is a statistically principled and unsupervised method that detects copy number deletion types (homozygous versus heterozygous), estimates normal cell fraction, and recovers cancer specific copy number profiles, using allele specific copy number
signals. In a subsequent analysis of TCGA ovarian cancer dataset, the average normal cell fraction estimated by BACOM was found higher than expected. In this letter, we first discuss the advantages of the BACOM in relation to alternative approaches. Then, we show that this elevated estimate of normal cell fraction is the combined result of inaccurate signal modeling and normalization. Lastly, we describe an allele specific signal modeling and normalization scheme that can enhance BACOM applications in many biological contexts. An open source MATLAB program was developed to implement our extended method and it is publically available.
