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Related Experiment Video

Updated: Oct 26, 2025

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

InvertypeR: Bayesian inversion genotyping with Strand-seq data.

Vincent C T Hanlon¹, Carl-Adam Mattsson², Diana C J Spierings³

¹Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada. vhanlon@bccrc.ca.

|August 1, 2021

Summary

This summary is machine-generated.

InvertypeR enhances genomic inversion detection using Strand-seq data by leveraging fixed coordinates and a Bayesian model. This method improves accuracy and reduces manual analysis for studying inversions in disease and variation.

Keywords:

Bayesian genotyping Inversions Strand-seq Structural variation

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Last Updated: Oct 26, 2025

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Single cell Strand-seq is a powerful tool for genomic inversion discovery and phasing.
Conventional Strand-seq methods for inversion detection have limitations, including blindness to known locations and reliance on manual inspection, especially for inversions smaller than 10 Kb.

Purpose of the Study:

To introduce InvertypeR, a novel computational method for accurate genotyping and phasing of genomic inversions using Strand-seq data.
To improve the statistical power and reduce false positives in inversion detection compared to existing methods.

Main Methods:

Development of InvertypeR, a method employing a Bayesian binomial model for genotyping inversions at fixed genomic coordinates.
Validation of InvertypeR by re-genotyping known inversions in three trios and comparing results with existing data.

Main Results:

InvertypeR significantly reduced Mendelian discordance in inversion genotypes from 6.3% to 0.5% in validated trios.
The method successfully genotyped 66 previously unreported inversions in the studied trios by analyzing published coordinates and predicted hotspots.
InvertypeR automates the discovery, genotyping, and phasing of inversions, eliminating the need for manual inspection.

Conclusions:

InvertypeR provides an automated and accurate approach for inversion analysis using Strand-seq data.
The method enhances the utility of Strand-seq for investigating the role of inversions in phenotypic variation, genome instability, and human diseases.
Results are presented in an accessible format, including phased chromosome ideograms linked to genome browser data.