Human Karyotyping Using TaqMan Copy Number Assays.

RP-76 Chromosomal or sub-chromosomal changes in genomic copy numbers may lead to various genomic disorders and developmental abnormalities including Down Syndrome etc. In addition, these numerical aberrations, also known as aneuploidy, may also occur in embryos, stem cells, and other cell lines during cell culture. Therefore, karyotyping analysis is crucial for clinical research and diagnosis including prenatal diagnostics, IVF (in vitro fertilization), stem cell and cancer research. Most commonly used technologies for karyotyping analysis are microarray-based comparative genomic hybridization (CGH) and fluorescent in-situ hybridization (FISH). Although they are powerful and have many advantages, their detection of chromosomal gain or loss is not quantitative and may not be reliable. Moreover, the lengthy protocols and cost for sample screening are undesirable. To overcome these problems, we have developed a new method for chromosome karyotyping using TaqMan copy number assays. Since extra or missing chromosomes will cause chromosomal copy number changes, we leverage the existing pre-designed TaqMan Copy Number Assays. We select and validate TaqMan copy number assays that target each of the 24 chromosomes. To cover all the 24 chromosomes on a 384 well plate or a TaqMan Array Card, we select 4 assays per chromosome. We also develop a gene-specific pre-amplification protocol for copy number assays to perform karyotyping analysis using a minute amount of DNA sample. Our preliminary feasibility studies suggest that TaqMan karyotyping assays enable researchers to quantitatively detect chromosome copy number changes for limited quantity of gDNA sample and offer a simple workflow with high sample throughput. As a complementary tool to the existing karyotyping technologies, TaqMan karyotyping is valuable for aneuploidy screening and validating karyotyping results from other platforms.