Abstract 1149: Genetic analysis of single cells

• Published in: Cancer research (Chicago, Ill.) Ill.), 2010-04, Vol.70 (8_Supplement), p.1149-1149
• Main Authors: Fan, Jian-Bing, Chen, Jing, April, Craig, Klotzle, Brandy, Royce, Thomas, Cann, Gordon, Talasaz, AmirAli H., Islam, Saiful, Kjallquist, Una, Linnarsson, Sten
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM10-1149

We are developing highly sensitive and quantitative genomic technologies for genetic and expression analysis of single cells or trace amount of DNA/RNA materials, using microarray and next-generation sequencing platforms. We have tested various Multiple Displacement Amplification (MDA)-based protocols under a variety of reaction conditions. With our current protocol and a 300K-SNP chip readout, we were able to obtain 88.3% and 93.9% call rate, and 97.4% and 99.9% call accuracy with direct cell lysis from 1 cell and 5 cells, respectively. We are also developing RNA amplification methods for high-throughput expression profiling of single cells. With our current protocol, we were able to generate reproducible expression profiles, R2 = 0.73 and 0.77, using 10 pg and 50 pg total RNA input, respectively. In addition, the profiles correlated well with those obtained with standard 100 ng total RNA input, R2 = 0.61 and 0.77, respectively. Our data show that sequencing of single-cell transcriptomes can clearly distinguish embryonic stem cells from embryonic fibroblasts and tumor cells. We are currently using these technologies to study medical specimens such as circulating tumor cells and cancer stem cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1149.