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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

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Published on: October 18, 2013

Exome sequencing by targeted enrichment.

Michael James Clark¹, Rui Chen, Michael Snyder

¹Department of Genetics, Stanford University School of Medicine, Palo Alto, California, USA.

Current Protocols in Molecular Biology

|April 3, 2013

Summary

This summary is machine-generated.

This study details methods for human exome sequencing using Agilent SureSelect and Roche Nimblegen platforms. Protocols cover DNA enrichment, sequencing, and data analysis for targeted genomics research.

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Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Targeted exome sequencing is crucial for identifying genetic variations.
Existing platforms offer comprehensive coverage of the human exome.

Purpose of the Study:

To describe optimized protocols for human exome enrichment using Agilent SureSelect and Roche Nimblegen platforms.
To provide guidance on sequencing and data analysis for exome sequencing projects.

Main Methods:

Utilized Agilent SureSelect Human All Exon 50 Mb and Roche Nimblegen SeqCap EZ Exome kits.
Described biochemical procedures for exomic DNA enrichment, including protocol modifications.
Outlined sequencing strategies and an analytical pipeline for data processing.

Main Results:

Established robust protocols for targeted exome enrichment.
Provided recommendations for sequencing depth and data analysis.
Demonstrated the applicability of protocols to human and potentially other organisms.

Conclusions:

The described methods facilitate efficient human exome sequencing.
Optimized protocols and analytical pipelines enhance the study of genetic variations.
These approaches are adaptable for broader targeted enrichment applications.