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Chromosomal structural changes in human body known as copy number alteration (CNA) are often associated with diseases, such as various forms of cancer. Therefore, accurate estimation of breakpoints of the CNAs is important to understand the genetic basis of many diseases. The high‐resolution comparative genomic hybridization (HR‐ CGH) and single‐nucleotide polymorphism (SNP) technologies enable cost‐efficient and high‐throughput CNA detection. However, probing provided using these profiles gives data highly contaminated by intensive Gaussian noise having white properties. We observe the probabilistic properties of CNA in HR‐CGH and SNP measurements and show that jitter in the breakpoints can statistically be described with either the discrete skew Laplace distribution when the segmental signal‐to‐noise ratio (SNR) exceeds unity or modified Bessel function‐based approximation when SNR is <1. Based upon these approaches, the confidence masks can be developed and used to enhance the estimates of the CNAs for the given confidence probability by removing some unlikely existing breakpoints.

Enhancing Estimates of Breakpoints in Genome Copy Number Alteration using Confidence Masks