QuantAS: a comprehensive pipeline to study alternative splicing by absolute quantification of splice isoforms

Yu-Chen Song ^1 2, Mo-Xian Chen ^1 2, Kai-Lu Zhang ^1 2, Anireddy S N Reddy ³, Fu-Liang Cao ¹, Fu-Yuan Zhu ^1 2

Abstract

In general, QuantAS provides an accurate quantitative method for isoform quantification, reduces systematic experimental errors, and exhibits high compatibility and specificity. By contrast, other methods such as HiFENS, which is based on fluorescence in situ hybridization (FISH) for the detection of endogenous splicing isoforms, still depend on isoform-specific regions (Shilo et al., [21]).

The method adopts isoform-specific primers to solve the difficulty in isoform identification caused by various alternative splicing (AS) events. It takes functional coding regions as the classification unit of isoform structures to ensure the independence of each isoform (Fig.).