Genotyping and Haplotyping Using Thin Flim Biosensor Chips

Yale University, New Haven CT

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Abstract

The overall objective of this proposal is to better understand the genetic diversity among humans by defining the haplotype and linkage disequilibrium parameters at 1,200 single nucleotide polymorphism (SNP) sites in over 2,000 individuals representing 38 different racial/ethnic groups from around the world. This unique sample population, collected by Drs. K.K. and J.R. Kidd, provides the opportunity to not only characterize combinations of genetic variants relevant to disease-gene discovery but to describe the creation, maintenance and distribution of genotypes in the context of population genetic models. Approximately 900 hundred of the SNP sites map uniquely to a 12 Mb region in band 17q21 on human chromosome 17, while the remaining 300 map to twelve 200kb regions dispersed throughout the genome. A total of more than 2 x 10[6] SNP typings will be done with a novel assay platform developed by Dr. Zhong in the PIs laboratory. Allele-discriminating oligonucleotides first are arrayed and covalently attached to a 6x6 mm[2] silicon chip coated with a thin-film optical biosensor. Hybridization of target sequences (e.g. PCR amplicons) is then done in the presence of a mixture of biotinylated, SNP-specific oligomers and a thermostable DNA ligase. Selective ligation of biotinylated probe to the sequence matched (but not mismatched) capture probe is visualized as a color change on the chip surface (gold to blue/purple) after brief incubations with an anti-biotin -horseradish peroxidase (HRP) conjugate and a precipitable HRP substrate. This assay is extremely robust, exhibits high sensitivity and specificity, is flexible (signals detected at low SNIP density without instrumentation or at high SNP density with an automated optical reader) and most importantly very economical. Additional studies will be done to improve the detection sensitivity of the biosensor SNP assay so that global SNP typing can be done with fragmented genomic DNA, thereby markedly increasing the number of SNPs that can be analyzed simultaneously and dramatically reducing the cost/SNP. Finally, we will use multiple displacement amplification (MDA), a novel whole genome DNA amplification procedure, in combination with rnicrodissection of a single metaphase chromosome (or chromosomal segments) to prepare DNA suitable for direct molecular haplotyping on biosensor chips.