Objective: We investigated the application of microarray-based comparative genomic hybridization (array CGH) on a fetus showing hemivertebrae and intra-abdominal mass at 15 weeks.

Methods: Conventional karyotyping and high-resolution array CGH techniques using 244K CGH microarray were performed to investigate the possibility of genomic imbalance on the opted chorionic villus sample.

Results: G-banded fetal chromosome analysis showed 46,XY,der(6)t(6;7)(q26;q31.2)pat. Whole genome scan by array CGH fine mapped the origin of the aberrant chromosomes to be a partial single copy gain of 42.5 Mb from chromosome region 7:116266547 --> qter and concurrent partial single copy loss of 8.1 Mb from chromosome region 6:162756975 --> qter. Pathological examination of the abortus showed gastrointestinal malformations, hemivertebrae with scoliosis, clinodactyly and club feet.

Conclusions: Prenatal and perinatal findings of concurrent trisomy 7q and monosomy 6q were unique. This study demonstrated array CGH can interrogate the entire genome at a resolution and rapidity unattainable by conventional cytogenetic techniques and may have wide application in prenatal diagnosis.