Comparative Genomic Hybridization–Array Analysis Enhances the Detection of Aneuploidies and Submicroscopic Imbalances in Spontaneous Miscarriages

Abstract

Miscarriage is a condition that affects 10%-15% of all clinically recognized pregnancies, most of which occur in the first trimester. Approximately 50% of first-trimester miscarriages result from fetal chromosome abnormalities. Currently, G-banded chromosome analysis is used to determine if large-scale genetic imbalances are the cause of these pregnancy losses. This technique relies on the culture of cells derived from the fetus, a technique that has many limitations, including a high rate of culture failure, maternal overgrowth of fetal cells, and poor chromosome morphology. Comparative genomic hybridization (CGH)-array analysis is a powerful new molecular cytogenetic technique that allows genomewide analysis of DNA copy number. By hybridizing patient DNA and normal reference DNA to arrays of genomic clones, unbalanced gains or losses of genetic material across the genome can be detected. In this study, 41 product-of-conception (POC) samples, which were previously analyzed by G-banding, were tested using CGH arrays to determine not only if the array could identify all reported abnormalities, but also whether any previously undetected genomic imbalances would be discovered. The array methodology detected all abnormalities as reported by G-banding analysis and revealed new abnormalities in 4/41 (9.8%) cases. Of those, one trisomy 21 POC was also mosaic for trisomy 20, one had a duplication of the 10q telomere region, one had an interstitial deletion of chromosome 9p, and the fourth had an interstitial duplication of the Prader-Willi/Angelman syndrome region on chromosome 15q, which, if maternally inherited, has been implicated in autism. This retrospective study demonstrates that the DNA-based CGH-array technology overcomes many of the limitations of routine cytogenetic analysis of POC samples while enhancing the detection of fetal chromosome aberrations.

Karyotype Versus Microarray Testing for Genetic Abnormalities After Stillbirth

“…20 Microarray analysis, as compared with conventional karyotype analysis, has also increased the detection of genetic abnormalities in pregnancy loss at a gestation of less than 20 weeks. [21][22][23] Two small studies have assessed the usefulness of microarray analysis for the evaluation of stillbirths. A study of 15 stillbirths with abnormalities in two organs and either normal results on karyotype analysis or failed karyotyping identified an instance of trisomy 21 and another instance of an unbalanced translocation.…”

Array-CGH testing in spontaneous abortions with normal karyotypes

“…Schaeffer et al (2004) examined 41 POC samples by a 1 Mb resolution array-CGH, and compared the results with those obtained by G-band analysis. In this study, 37/41 POC cases were in exact concordance with the karyotype results.…”

“…In two cases in which a normal male karyotype (46,XY) had been found, array-CGH revealed the presence of an additional chromosome 7 in one of them and of an additional chromosome 13 in the other. Although the presence of an undetected mosaicism cannot be ruled out, considering that the presence of mosaicism is a rather frequent finding in abortion material (Lebedev et al 2004;Schaeffer et al, 2004;Vorsanova et al 2005), it is also possible that it went undetected by the conventional cytogenetic analysis because of the previously mentioned difficulties usually presented by abortion material. In the third case in which conventional analysis of cells from a long term culture revealed a 46,XX karyotype and the array-CGH analysis showed a male complement with an additional chromosome 18, very likely the analyzed cells were of maternal origin.…”

“…Several of these methods have been used as diagnostic tools, including fluorescent polymerase chain reaction (Diego-Alvarez et al, 2005), interphase-FISH (Horiuchi et al, 1997;Lebedev et al, 2004, Vorsanova et al, 2005, chromosome-CGH (Daniely et al, 1998, Fritz et al, 2001, and multiplex ligation probe amplification (MLPA) (Diego-Alvarez et al, 2006). More recently, array-CGH has been considered as a particularly useful alternative to conventional karyotyping in the field of diagnosis (Schaeffer et al, 2004;Benkhalifa et al, 2005;Shimokawa et al, 2006), as it allows screening gains and losses in thousands of targets simultaneously. Major advantages of the array-based cytogenetic technologies are the high resolution and high throughput (Salman et al, 2004).…”

Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

“…42,43 Identifying segmental copy number changes in genetic diseases Segmental duplications and deletions have been well documented in inherited diseases. 10,48,49 Advances in array-based CGH have greatly facilitated the discovery of such genetic alterations. Megabase interval genomic arrays have been instrumental in delineating regions affected in a variety of genetic diseases.…”