Application of a target array Comparative Genomic Hybridization to prenatal diagnosis

Ji Hyeon Park,Sung Han Shim,Dong Hyun Cha,Young Min Choi,Song-Ju Yang,Jung Hoon Woo,Kap-Seok Yang

doi:10.1186/1471-2350-11-102

Abstract

BackgroundWhile conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. We have investigated the value of our own designed DNA chip as a prenatal diagnostic tool for detecting submicroscopic deletions/duplications and chromosome aneuploidies.MethodsWe designed a target bacterial artificial chromosome (BAC)-based aCGH platform (MacArray™ M-chip), which specifically targets submicroscopic deletions/duplications for 26 known genetic syndromes of medical significance observed prenatally. To validate the DNA chip, we obtained genomic DNA from 132 reference materials generated from patients with 22 genetic diseases and 94 clinical amniocentesis samples obtained for karyotyping.ResultsIn the 132 reference materials, all known genomic alterations were successfully identified. In the 94 clinical samples that were also subjected to conventional karyotyping, three cases of balanced chromosomal aberrations were not detected by aCGH. However, we identified eight cases of microdeletions in the Yq11.23 chromosomal region that were not found by conventional karyotyping. This region harbors the DAZ gene, and deletions may lead to non-obstructive spermatogenesis.ConclusionsWe have successfully designed and applied a BAC-based aCGH platform for prenatal diagnosis. This platform can be used in conjunction with conventional karyotyping and will provide rapid and accurate diagnoses for the targeted genomic regions while eliminating the need to interpret clinically-uncertain genomic regions.

Highlights

While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis
For clinical purposes, especially prenatal diagnosis, these high-resolution whole-genome array comparative genomic hybridization (aCGH) chips are not adequate because of difficulties of interpretation mainly resulting from benign copy number variations (CNVs), hybridization quality and cost
On the other hand, targeted bacterial artificial chromosome (BAC)-based aCGH methods have been successfully used in prenatal diagnosis [7,10,11,12]

Summary

Introduction

While conventional G-banded karyotyping still remains a gold standard in prenatal genetic diagnoses, the widespread adoption of array Comparative Genomic Hybridization (array CGH) technology for postnatal genetic diagnoses has led to increasing interest in the use of this same technology for prenatal diagnosis. About 10-14 days is required to obtain the result and this may increase the patient's anxiety To overcome these limitations, rapid fluorescent in situ hybridization (FISH), quantitative fluorescent polymerase chain reaction (QF-PCR), and multiplex ligation-dependent probe amplification (MLPA) have been developed and are widely used as adjuncts to conventional methods for. Array comparative genomic hybridization (aCGH) has been used in prenatal as well as postnatal clinical cytogenetics to detect submicroscopic chromosomal imbalances [7,8,9]. This technique gives rapid results and multiplex detection of both numerical and unbalanced structural abnormalities with much higher resolution and wider coverage than conventional karyotyping and other molecular cytogenetic techniques. On the other hand, targeted bacterial artificial chromosome (BAC)-based aCGH methods have been successfully used in prenatal diagnosis [7,10,11,12]

Methods

Results

Discussion

Conclusion