Training Set (Reference)
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Training Set (Reference). Probe selection based on dosage response. Compute mean intensity across selected probes for PMa and PMb separately. Log transform probe intensity and standardization based on MM probes. Intensity adjustment by

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Training Set (Reference)

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Training set reference

Training Set (Reference)

Probe selection based

on dosage response.

Compute mean intensity

across selected probes for

PMa and PMb separately

Log transform probe intensity and standardization

based on MM probes

Intensity adjustment by

regressing on fragment length and probe GC content

Summarize mean and variance of

PMa and PMb intensity

for each SNP across

sub-groups of individuals

with same genotype

Use training set intensity to

estimate allele-specific

and total CN. Summarize

distribution of total CN of the training set at SNP level

Estimate allele-specific

CN models

at individual SNP level

Test Sample

Intensity adjustment

by regressing on

fragment length and

probe GC content

Intensity adjustment

by regressing on

reference mean

Log transform probe intensity and standardization

based on MM probes

Compute mean

intensity across

selected probes

for PMa and PMb

Compare total CN

with the training set

and derive significance.

Estimate allele-specific

and total CN

Regression tree to

partition the genome

based on total CN.

Average the CN and

significance in each region

Regression tree to

further partition each

region based on

allele-specific CN

  • 100kb kernel smoothing on

  • allele-specific CN

  • total CN

  • total significance


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