Rapid Technology to Identify Structural Chromosome Abnormalities I

Through this project, researchers developed a genome-wide technology using single nucleotide polymorphism (SNP) genotyping microarrays and DNA from somatic cell hybrids, termed “hybrid SNPing”. This process allows the rapid, specific and complete characterization of the genome of one species in the context of another species genome, illustrated using two applications on a set of rodent-human somatic cell hybrids retaining one or more human chromosomes and chromosome fragments. First, hybrid SNPing provides a complete human genome molecular karyotype of somatic hybrid cells, to 1-50 kb resolution, as verified by PCR and FISH methodologies. Second, hybrid SNPing provides high-resolution definition of chromosomal rearrangements such as balanced translocations associated with birth defects and other congenital disease.

The average resolution of chromosome fragment and translocation breakpoint mapping from hybrid SNPing using Illumina 300K SNP genotyping arrays was 25.1 kb, with a range of 1.47 kb to 51.3 kb for the nine breakpoints as characterized by this project. Use of Illumina 550K SNP arrays resolved reciprocal balanced translocation breakpoints to 4.2 kb and 4.7 kb. Breakpoints of three balanced translocations [t(15;17), t(14;18, t(3;14)] were directly cloned by PCR and DNA sequencing. With 300K arrays, a maximum of 3 percent of human SNP probes are potentially conserved in rodents, which decreases to 1.5 percent with a more stringent cutoff and phylogenetic sequence analyses.

In conclusion, hybrid SNPing identifies to near nucleotide resolution the DNA content and breakpoints of balanced translocations and chromosome fragments, with envisaged applications in somatic cell genetics to identify oncogenes, tumor suppressor genes, cell senescence genes, stem cell markers, or any functional sequence that can be screened for by cellular phenotypic assays. Other novel applications of the technology include identification of disease-associated SNPs and large DNA fragments in transgenic or gene therapy applications.

Principal Investigator
Robert Nicholls, PhD

Last Update
August 14, 2010
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Last Update
August 14, 2010