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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing
Audrey Guilmatre1, Gareth Highnam, Christelle Borel
1Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
Human Mutation
|May 23, 2013
Summary
This study introduces a cost-effective method for targeted enrichment and sequencing of simple tandem repeats (STRs), enabling large-scale genotyping. The assay successfully genotyped thousands of STR loci, offering a valuable tool for population genetics research.
Area of Science:
- Genomics
- Population Genetics
- Molecular Biology
Background:
- Simple tandem repeats (STRs) are significant genomic polymorphisms but remain understudied.
- Targeted enrichment strategies are crucial for efficient analysis of specific genomic regions.
Purpose of the Study:
- To develop a cost-effective method for targeted enrichment and high-throughput sequencing of STR regions.
- To enable multiplexed genotyping of thousands of STR loci for large-scale studies.
Main Methods:
- Developed a capture probe strategy targeting flanking sequences of STR loci.
- Utilized high-throughput sequencing (Illumina HiSeq2000) for DNA fragments containing STRs.
- Targeted 6,243 STR loci (<94 bp) and multiplexed eight individuals per lane.
Main Results:
- Achieved genotyping in at least one individual for 67.5% of targeted STRs.
- Observed high genotyping success (>90%) for STRs with moderate G+C content.
- Reported genotyping error rates between 7.6% and 12.4%, primarily single-unit errors at simple repeats.
Conclusions:
- The developed STR capture assay is a cost-effective method for multiplexed genotyping.
- This approach is suitable for large-scale population studies requiring analysis of numerous STR loci.
- Understanding STR variation is crucial for population genetics and has implications for various biological studies.
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