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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Locityper: targeted genotyping of complex polymorphic genes.

Timofey Prodanov^1,2, Elizabeth G Plender^3,4, Guiscard Seebohm⁵

¹Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany.

Biorxiv : the Preprint Server for Biology

|February 24, 2025

Summary

Locityper accurately genotypes challenging disease-associated genes using whole genome sequencing data. This new tool significantly improves variant calling for previously inaccessible genetic loci.

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Area of Science:

Genomics
Bioinformatics
Medical Genetics

Background:

The human genome has many polymorphic loci, including disease-associated genes, that are difficult for accurate variant calling.
Existing variant calling pipelines struggle with these complex genetic regions.

Purpose of the Study:

To introduce Locityper, a novel tool for genotyping challenging genes using short and long-read whole genome sequencing.
To enhance the accurate variant calling of structurally-variable polymorphic loci.

Main Methods:

Locityper recruits and aligns sequencing reads to locus haplotypes, optimizing alignment, insert size, and read depth profiles.
It employs a haplotype-based approach for genotyping complex genetic regions.

Main Results:

Locityper accurately genotypes 194 out of 256 challenging medically relevant loci, a significant improvement over standard methods.
Achieved an 8.8-fold gain in genotyped genes compared to traditional pipelines.
Demonstrated capability for hyperpolymorphic genes like HLA, KIR, MUC, and FCGR.

Conclusions:

Locityper offers a scalable solution for genotyping previously intractable disease-relevant genes.
Its efficiency and accuracy enable association studies in large cohorts.
Facilitates deeper genetic insights into complex diseases.