Patent ID: 8014953
Filing Date: 2011-09-06
Classification: G16B

Abstract:
1. A method for systematically characterizing putative protein isoforms as apparent targets of nonsense-mediated decay (NMD), the method comprising the following steps, each of which is performed with a suitably programmed computer: identifying a dataset of target putative protein isoform sequences from a curated protein sequence database for characterization; identifying from an mRNA dataset corresponding mRNA sequences representing transcripts encoding the protein isoforms, wherein each of the transcripts comprises a termination codon and a final intron; determining corresponding gene intron-exon structures by mapping the mRNA sequences to corresponding genomic sequences; determining if the transcripts are apparent targets of NMD by comparing the position of the termination codon to the position of the final intron, wherein if the termination codon of the transcript is more than 50 nucleotides upstream of the final intron position, then the transcript is an apparent target of NMD; and outputting from the computer a list of said isoforms that are apparent targets of NMD, wherein the dataset of target putative protein isoform sequences comprises a subset of the isoforms of Table 1: