Simultaneous Cycle Sequencing Assessment of (TG)m and Tn Tract Length in CFTR Gene

Abstract

The lengths of the dinucleotide (TG)m and mononucleotide Tn repeats, both located at the intron 8/exon 9 splice acceptor site of the cystic fibrosis transmembrane conductance regulator (CFTR) gene whose mutations cause cystic fibrosis (CF), have been shown to influence the skipping of exon 9 in CFTR mRNA. This exon 9-skipped mRNA encodes a nonfunctional protein and is associated with various clinical manifestations in CF. As a result of growing interest in these repeats, several assessment methods have been developed, most of which are, however, cumbersome, multi-step, and time consuming. Here, we describe a rapid method for the simultaneous assessment of the lengths of both (TG)m and Tn repeats, based on a nonradioactive cycle sequencing procedure that can be performed even without DNA extraction. This method determines the lengths of the (TG)m and Tn tracts of both alleles, which in our samples ranged from TG8 to TG12 in the presence of T5, T7, and T9 alleles, and also fully assesses the aplotypes. In addition, the repeats in the majority of these samples can be assessed by single-strand sequencing, with no need to sequence the other strand, thereby saving a considerable amount of time and effort.