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

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seqr: A web-based analysis and collaboration tool for rare disease genomics.

Lynn S Pais^1,2, Hana Snow¹, Ben Weisburd¹

¹Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

|March 10, 2022

Summary

Seqr is an open-source tool that aids in diagnosing rare genetic diseases by analyzing exome and genome sequencing data. It supports collaborative research, enabling faster diagnosis and novel gene discovery for rare inherited disorders.

Keywords:

data sharing genomic analysis novel gene discovery rare disease diagnosis research collaboration variant filtration

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In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

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Area of Science:

Genomics
Rare Disease Research
Bioinformatics

Background:

Exome and genome sequencing generate vast data for rare disease diagnosis.
Efficient tools are needed for variant filtering and decision support in genomic datasets.
Current methods require robust platforms for collaborative analysis.

Purpose of the Study:

To introduce seqr, an open-source, web-based tool for family-based monogenic disease analysis.
To provide a framework for genomic analysis in rare diseases leveraging seqr's capabilities.
To facilitate variant filtration, annotation, and causal variant identification.

Main Methods:

Development of seqr, a collaborative, web-based platform for genomic data analysis.
Utilizing seqr for variant filtration, annotation, and causal variant identification.
Implementing a framework for rare disease genomic analysis and data sharing.

Main Results:

Seqr has been used in multiple research pipelines and a clinical diagnostic lab.
Analyses of over 10,000 families supported diagnosis for >3,800 individuals.
Discovery of over 300 novel disease genes has been facilitated by seqr.

Conclusions:

Seqr enables efficient, collaborative analysis of genomic data for rare disease diagnosis.
The open-source platform lowers the cost of participation in rare disease research.
Seqr supports a community effort for rare disease diagnosis and novel gene discovery.