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. 2023:2590:31-48.
doi: 10.1007/978-1-0716-2819-5_2.

Targeted Locus Amplification and Haplotyping

Juliet W Lefferts #  1   2 , Vera Boersma #  3 , Marne C Hagemeijer  1   2   4 , Karima Hajo  3 , Jeffrey M Beekman  1   2 , Erik Splinter  5
Affiliations

Targeted Locus Amplification and Haplotyping

Juliet W Lefferts et al. Methods Mol Biol. 2023.

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.

Keywords: Cystic fibrosis; Genetic variation; Haplotyping; Next generation sequencing; Organoids; Phasing; Proximity ligation; Targeted Locus Amplification (TLA).

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References

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