A clinical algorithm for efficient, high-resolution cytogenomic analysis of uncultured perinatal tissue samples; study of more than 700 cases. G. Maire1,2, A. Xuan Tong Yu1,2, E. Kolomietz1,2 1) Mount Sinai Hospital, Toronto, Ontario, Canada; 2) University of Toronto, Laboratory Medicine and Pathobiology.
Genetic testing for chromosomal abnormalities is an indispensible part in perinatal care, reproductive planning and detection of gestational trophoblastic disease. Standard chromosomes analysis by karyotyping is hampered by high culture failure rate, maternal cells overgrowth, culture artifacts and very low resolution. A two steps algorithm based on DNA testing was developed to resolve these problems. Direct extraction of genomic DNA (without culture) was followed by quantitative fluorescence polymerase chain reaction (QF-PCR) to assess i) the fetal origin by genotyping and ii) the common live birth aneuploidies (trisomy 13, 18, 21), sex chromosome aneusomies and triploidy. Subsequently, specimens with normal QF-PCR profile were tested by array-comparative genomic hybridization (array-CGH). Specimens submitted to the laboratory between July 2011 and May 2013 were collected (727). Data on success rate, causes of failure, abnormalities detected and gestation times were collected. DNA extraction performed on products of conception, skin, cartilage or umbilical cord was successful for 93% of the cases. Abnormalities were detected in 32%, of which 60% were detected by QF-PCR alone. Abnormalities of pathogenic clinical significance were found in 30% while only 2 (0.3%) were of unknown clinical significance. Two CNVs were likely benign and 7 were likely pathogenic. In regards to the type of abnormality, autosomal trisomies represented 60%, monosomy X 10% and triploidy 12%. Also, 13% of the abnormalities were copy number variation, of which 57% would have been missed had karyotyping been done instead of array-CGH (based on a theoretical karyotype resolution of 5Mb). In this study we have shown the higher success rate and diagnostic accuracy of the combination of QF-PCR and array-CGH algorithm over the standard karyotyping. Although performed with a high resolution array-CGH platform, only 0.3% showed the problematic variation of unknown clinical significance, while at least 9% of the pathogenic abnormalities would have been missed by G-banding analysis. Overall, the algorithm proved to be an effective and financially viable alternative to conventional karyotype testing for perinatal tissue samples.