TranSNiPtomics: Massive Analysis of cDNA Ends (MACE) for simultaneous Gene Expression Profiling and Genotyping in High Throughput

Identification of favorite or adverse alleles for molecular breeding of crops becomes an increasingly busy field. At GenXPro, we developed an allele-finding pipeline based on reduced complexity sequencing coupled with proprietary up- and down-stream techniques and in-house bioinformatics, that is coined MACE (Massive Analysis of cDNA Ends). In MACE, gene expression levels are measured by sequencing and counting a single tag originating from the 3’ end of mRNAs, a region with high density of sequence polymorphisms. By using unique molecule identifiers (TrueQuant technique, GenXPro-GmbH), PCR copies are  eliminated from the dataset to reduce false positive SNPs and biased expression values. When compared to regular RNAseq, the focus onto this 3’-UT region increases the coverage by 10-20 fold and allows to reliably identify SNPs at comparably lower sequencing costs.