Targeted Locus Amplification and Haplotyping

Juliet W. Lefferts; Vera Boersma; Marne C. Hagemeijer; Karima Hajo; Jeffrey M. Beekman; Erik Splinter

doi:10.1007/978-1-0716-2819-5_2

Targeted Locus Amplification and Haplotyping

Juliet W. Lefferts, Vera Boersma, Marne C. Hagemeijer, Karima Hajo, Jeffrey M. Beekman, Erik Splinter^*

^*Corresponding author for this work

Clinical Genetics

Research output: Chapter/Conference proceeding › Chapter › Academic

3 Citations (Scopus)

27 Downloads (Pure)

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.

Original language	English
Title of host publication	Haplotyping
Subtitle of host publication	Methods in Molecular Biology
Pages	31-48
Number of pages	18
ISBN (Electronic)	978-1-0716-2819-5
DOIs	https://doi.org/10.1007/978-1-0716-2819-5_2
Publication status	Published - 2023

Publication series

Series	Methods in Molecular Biology
Volume	2590
ISSN	1064-3745

Bibliographical note

Funding Information: This work was funded by Health Holland grant no. 171114 and the Dutch CF foundation (NCFS) HIT-CF2 program.

Publisher Copyright: © 2023, The Author(s).

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10.1007/978-1-0716-2819-5_2

978-1-0716-2819-5_2Final published version, 635 KBLicence: CC BY

Cite this

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AU - Splinter, Erik

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Targeted Locus Amplification and Haplotyping

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