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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Jannovar: a java library for exome annotation.

Marten Jäger¹, Kai Wang, Sebastian Bauer

¹Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany.

|March 29, 2014

Summary

This summary is machine-generated.

Jannovar is a Java tool for analyzing whole-exome sequencing data, aiding genetic diagnostics and disease-gene discovery. It efficiently annotates genetic variants and performs pedigree analysis for Mendelian disorders.

Keywords:

bioinformatics exome sequencing genomic annotation interval tree

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Transcript-based annotation and pedigree analysis are crucial for whole-exome sequencing (WES) in genetic diagnostics and disease-gene discovery.
Existing tools may lack comprehensive annotation or efficient pedigree analysis capabilities for complex genetic data.

Purpose of the Study:

To introduce Jannovar, a versatile Java application and library for WES and genome analysis.
To provide efficient transcript annotation and family-based pedigree analysis for genetic variant data.

Main Methods:

Jannovar utilizes an interval tree for rapid identification of transcripts affected by genetic variants.
It generates Human Genome Variation Society (HGVS)-compliant annotations for various genomic regions, including coding sequences, splice junctions, UTRs, and noncoding RNAs.
The tool supports pedigree analysis using Variant Call Format (VCF) files for families with Mendelian disorders.

Main Results:

Jannovar offers stand-alone functionality and can be integrated into larger bioinformatics frameworks.
It provides comprehensive annotations for diverse variant types and genomic elements.
The application performs rapid, seconds-scale annotation of typical exome VCF files on a desktop computer.

Conclusions:

Jannovar is an efficient and versatile tool for computational analysis of exome and genome sequencing data.
It supports critical steps in genetic diagnostics and disease-gene discovery through robust annotation and pedigree analysis.
The software is freely available, promoting wider adoption in the research community.