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Updated: May 19, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Pacific biosciences sequencing technology for genotyping and variation discovery in human data
Mauricio O Carneiro1, Carsten Russ, Michael G Ross
1Broad Institute of MIT and Harvard, Medical and Population Genetics Program, Cambridge, MA 02141, USA. carneiro@broadinstitute.org
BMC Genomics
|August 7, 2012
Summary
Pacific Biosciences sequencing offers longer reads and unique error profiles for medical resequencing. This study confirms its high accuracy for SNP discovery in human amplicon projects.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Pacific Biosciences (PacBio) technology offers novel long-read, single-molecule sequencing with low bias and orthogonal error profiles.
- Addresses limitations of current next-generation sequencing (NGS) platforms for specific applications.
Purpose of the Study:
- Evaluate the utility of the PacBio RS platform for human medical amplicon resequencing.
- Assess its performance for single nucleotide polymorphism (SNP) discovery.
Main Methods:
- Utilized the PacBio RS platform for human medical amplicon resequencing.
- Employed the Genome Analysis Toolkit (GATK) for SNP calling.
- Developed a custom data processing pipeline for PacBio data.
Main Results:
- Achieved high sensitivity and specificity for SNP discovery in targeted amplicons.
- Observed high data quality with predominantly indel errors (~14%) and minimal miscalls (~1%).
- Demonstrated error profiles largely free from context-specific biases common in other platforms.
Conclusions:
- PacBio RS technology shows excellent utility for validation and extension studies in human medical genetics.
- The platform is suitable for SNP discovery and resequencing projects.
- Findings are extendable to other organisms with a reference genome.
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