# AgileMultiIdeogram: Rapid Identification and Visualization of Autozygous Regions Using Illumina Short-Read Sequencing Data

## TL;DR

AgileMultiIdeogram helps identify and visualize regions of homozygosity in DNA to detect harmful mutations in individuals with consanguineous parents.

## Contribution

AgileMultiIdeogram is a new tool that identifies autozygous regions using both sequencing and microarray data for diagnostic and research purposes.

## Key findings

- AgileMultiIdeogram successfully identifies autozygous regions from exome and microarray data.
- The tool has been effectively used in both diagnostic and research settings to locate pathogenic mutations.
- Autozygous regions are important for detecting recessive disease mutations in consanguineous individuals.

## Abstract

The incidence of rare recessive disease is significantly increased in children whose parents are related, as both may carry the same deleterious variant inherited from a shared relative. As well as inheriting the same disease mutation, they also inherit the flanking DNA, which can be detected as extended regions of homozygous SNPs. Initially, these regions were detected using microsatellite markers, which were then replaced by microarray genotype data. With the advent of next-generation sequencing, many mutations could be found without identifying these homozygous regions; however, this failed to find the disease mutation in many patients. Consequently, there has been renewed interest in mapping these homozygous regions to help detect a patient’s deleterious mutation. Therefore, we have created AgileMultiIdeogram to identify these regions using both next-generation sequence data as well as microarray genotype data.

Rare autosomal recessive diseases are a major cause of mortality and morbidity. They occur more frequently in individuals with consanguineous parents, in which case the pathogenic variants are often located within regions of genetic identity by descent. A well-established and effective way of identifying these “autozygous” genomic regions has been to search for runs of homozygous genotypes in microarray SNP data. However, with the widespread use of whole-genome and exome sequencing in both diagnostic and research settings, it has become desirable to be able to both map autozygous regions and identify the deleterious variants using a single dataset. We have developed AgileMultiIdeogram, an application that can identify and visualize autozygous regions in inbred individuals using exome data as well as microarray SNP genotype data. This application has been successfully used in both research and diagnostic settings to map pathogenic mutations.