Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication.
An analysis using 2 × mean of normal+2 s.d. as the cutoff to identify highly amplified patients showed statistically not significant separation of the survival curves of amplified vs unamplified patients, but further analysis showed that patients with gene copy changes between ⩾mean of normal+2 s.d. and <2 × mean of normal+2 s.d.
In addition, we also analyzed genes located in diverse chromosomal regions of different gastric cancer TNM-stages or histological subtypes and identified genes with the correlation between gene copy number and expression change based on the above method.
The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression.
No correlation was found between gene copy number and the level of gene expression.
This produces β-value changes and spurious correlations of the β-value to copy number and, consequently, to gene expression, as there is a general correlation between gene copy number and gene expression.
Significant relationship between the gene copy number changes and expressions was found for seven genes: MRPS23, MSN, LSM3, ANXA4, MBNL2, FLJ13291, and MGC14151, for which aberrations were detected in 5 23 tumors.
All gene copy number changes in individual samples are shown in the Additional file 2: Copy number changes detected by aCGH analysis.
To investigate a cohort of patients with gonadal disorders of sex development (DSD) for causative CBX2 gene mutations and or gene copy number changes.
Breast tumors undergo frequent gene copy number changes [ 1, 2].
