CFTR TG-Tract/Poly-T Haplotype

This tool has been developed for the inter-conversion between, genomics sequence,  HGVS nomenclature, and TG-tract/polyT, in CFTR intron 8. It is provided solely for investigational purposes and is not intended to serve as a definitive tool for the identification or accurate resolution of haplotypes from next-generation sequencing or complex diplotypes from Sanger sequencing. Users are hereby cautioned that reliance on its output for clinical, diagnostic, or legally binding determinations is expressly disclaimed.

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The TG-tract poly‑T haplotype caller was originally developed for the extraction of variant HGVS annotations from next‑generation sequencing (NGS) data. Its application to Sanger sequencing, however, is inherently problematic because the superimposition of allelic signals in Sanger traces can lead to misassigned HGVS annotations. Sicko et al. implement an approach that involves quantifying TG repeats and poly‑T tracts directly from NGS FASTQ files, thereby improving enumeration accuracy (1). In contrast, Ding et al. require both forward and reverse Sanger sequencing traces to deconvolute superimposed signals, enabling accurate diplotype calling (2). Both of the aforementioned methods have been validated in a CLIA-certified laboratory setting.

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Since (TG)11(T)7 is the designated reference sequence, a “no call” indicates that the sample conforms to this reference.

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Please submit any Sanger-derived HGVS annotations that were not identified, along with the corresponding diplotype information. This will enhance the tool’s accuracy and benefit other users who are enumerating TG-tract and poly T variations in CFTR.