W448 High Resolution TranSNiPtomics : Gene Expression and SNP Detection in High Throughput and High Resolution by "Massive Analysis of cDNA Ends" (MACE)

Date: Saturday, January 14, 2012
Time: 10:20 AM
Room: Pacific Salon 1
Bjorn Rotter , GenXPro-GmbH, Frankfurt am Main, Germany
MACE (Massive Analysis of cDNA Ends) a variant of “3Seq”, “PAS-seq” or “3’UTR-seq”, is the ideal deep sequencing method for high-resolution gene expression analysis of any biological material. Deep coverage, excellent quantification and highly reliable SNP detection at low cost are the hallmarks that distinguish this transcription profiling technology from conventional approaches such as RNA-seq. In MACE, each transcript is represented by only one single, highly specific cDNA fragment. In consequence, hundreds of millions of transcript molecules are analyzed simultaneously on a single Illumina HiSeq sequencing lane, providing the required resolution even after multiplexing up to 12 samples. In RNA Seq, each transcript is represented by 10-30 fragments, and hence 10-30 x more sequencing is required to obtain a similar resolution. By applying "TrueQuant", a propriatary technique to identify PCR-introduced bias, MACE data provide reliabel quantification of transcript-tags, even after PCR was applied. The analyzed 3’ends of transcripts are mostly consisting of 3’ untranslated regions (3’-UTRs) which are under lower evolutionary pressure. As a consequence, these regions contain many sequence polymorphisms such as SNPs or Indels. Since these are located in genes, they represent highly valuable genomic markers, often directly linked to specific traits. Since MACE focuses only on the 3’ ends of each transcript, the required coverage to define an SNP, even in low-abundant transcripts is achieved.