Table 1 Notations.

Hom

homozygous

NHet

not heterozygous (is used when we cannot distinguish between two equal nucleotides, i.e. homozygosity, and the loss of one copy)

{Het, Hom}

^*

{ø, Het, Hom}

{Het, NHet, NoCall}

X ^N

true genotypes in normal cells ( ∈ )

X

true genotypes in abnormal cells (X _i ∈ ^*)

Y

genotypes detected by the genotype calling algorithm (Y _i ∈ )

Y ^cn

raw copy number data

copy number events/aberrations

occurrence of copy-neutral LOH (i.e. IBD/UPD event)

IBD/UPD & copy number aberrations

({ = w} = {, = u} for some w, z, u)

cn

all copy number information (both raw data and estimated profile by mBPCR)

p

vector of posterior probabilities to be a breakpoint (for all SNP positions)