AI Article Synopsis
- - Targeted locus amplification (TLA) is a technique that detects all types of genetic variations in a specific genomic region, including structural variations.
- - TLA uses proximity ligation to link genetic variants, enabling researchers to determine allelic relationships and generate haplotypes for a more detailed analysis of genetic variation.
- - The text includes a comprehensive protocol for preparing TLA samples and a bioinformatics pipeline for analyzing the data, demonstrating its effectiveness with the cystic fibrosis transmembrane (CFTR) gene from patient-derived intestinal organoids.
Article Abstract
Targeted locus amplification (TLA) allows for the detection of all genetic variation (including structural variation) in a genomic region of interest. As TLA is based on proximity ligation, variants can be linked to each other, thereby enabling allelic phasing and the generation of haplotypes. This allows for the study of genetic variants in an allele-specific manner. Here, we provide a step-by-step protocol for TLA sample preparation and a complete bioinformatics pipeline for the allelic phasing of TLA data. Additionally, to illustrate the protocol, we show the ability of TLA to re-sequence and haplotype the complete cystic fibrosis transmembrane (CFTR) gene (> 200 kb in size) from patient-derived intestinal organoids.
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| http://dx.doi.org/10.1007/978-1-0716-2819-5_2 | DOI Listing |
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