BioTrove, Inc. today presented SNP genotyping data from a study of human genomic samples using its proprietary high-density nanoliter through-hole array chip for PCR-based genomic assays. SNP genotyping is the company’s first commercial application based on its Living Chip™ nano-fluidics technology platform.
In the pilot study, 90 Coriell CEPH DNA samples were genotyped using 130 TaqMan® Assay-By-Design™ and Assay-On-Demand™ SNP detection assays. The SNP assays were transferred from microplates into the Living Chip using BioTrove's proprietary reformatting technology. A flat block cycler was used to perform PCR and assay results were detected using a slide scanner.
Jesen A. Fagerness, Project Manager, Psychiatry Department at Massachusetts General Hospital, assessed the data quality using several industry metrics. He found an 88.5% assay pass rate with an average genotyping call rate of 96.3%. Further, the results were 99.4% concordant with the genotype calls from the HapMap project. “I am pleased with the pilot’s outcome and impressed with Biotrove’s rapid technical progress,” commented Mr. Fagerness.
“As the demand for more genome-wide experiments increases, one of the challenges is to increase throughput and efficiency,” said Tom Morrison, Ph.D., BioTrove’s Senior Director of Genomics. “The data demonstrate that our SNP genotyping application is capable of conducting thousands of PCRs on a single chip with nanoliter volumes of reagents, combining the best attributes of PCR and micro arrays on one platform.”
BioTrove’s SNP genotyping application enables the analysis of 10s to 1,000s of SNPs at 25nl reaction volumes, providing researchers with flexibility regarding the numbers of SNPs and the number of samples to analyze. The chip is compatible with existing flat bed thermal cyclers, slide scanners and software.
The Living Chip technology enables genetic and genomic analyses on one platform with higher throughput, lower cost and better quantification and sensitivity. The platform is a nano-liter array chip consisting of 300μm through-holes that are differentially coated on the surface and interior, enabling them to function with significantly less volume of valuable and often precious samples. The chip is scalable, with as few as 100 through-holes or as many as 25,000 through-holes, allowing many simultaneous experiments on less sample and great flexibility in experimental design (e.g. 3,000 or 25,000 analysis with one sample or 3,000 or 25,000 samples with one analysis, or a combination of both).
“This successful pilot study is the first step in our commercial strategy of the Living Chip,” noted Patrick T. Carroll, Chief Business Officer of BioTrove. “As researchers are pursuing genome-scale experiments, our nano-fluidics expertise provides them with the technology and tools to conduct such complex experiments in a simple and cost-effective manner.”
BioTrove’s Living Chip commercial strategy is to initially pursue applications in genetics and longer term, the company plans to introduce a family of proprietary products to enable additional high value applications such as transcription analysis.