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Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants

Published on: February 21, 2015

Copy number variations in 119 Chinese children with idiopathic short stature identified by the custom genome-wide

Guorui Hu¹, Yanjie Fan¹, Lili Wang¹

¹Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092 China.

Molecular Cytogenetics

|February 18, 2016

Abstract

Background:

Idiopathic short stature (ISS) refers to short stature with no evident etiologies. The custom genome-wide microarray specifically designed to cover height-related genes may be helpful to detect copy number variations (CNVs) in ISS patients, which may be missed by the general microarray. The aim of the study was to validate the applicability of the custom microarray and to analyze CNVs in Chinese ISS children.

Results:

Sixty non-polymorphic CNVs were identified in 119 ISS patients. There were 13 small CNVs with a size below 50 kb, accounting for 21.7 % of all the CNVs (13/60). Five pathogenic or possibly pathogenic CNVs were detected in five patients, including deletions at 22q11.21, duplications at 4q11-q13.1, 4q12 and Yp11.32-p11.2. Taking only the pathogenic variants into account, the diagnostic yield was 2.5 % (3/119). The TMEM165, POLR2B and PDGFRA genes were analyzed as candidate genes. A 15 kb deletion in the RASA2 gene was of interest for further investigation.

Conclusions:

This study showed that the custom microarray is applicable to detect CNVs in patients with short stature. Candidate genes and CNVs detected in ISS patients may be helpful for CNV analysis of short stature, especially in East Asian population.

Keywords:

Copy number variation Custom chromosomal microarray East Asian population Idiopathic short stature

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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