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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
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Integrating dilution-based sequencing and population genotypes for single individual haplotyping.
Hirotaka Matsumoto1, Hisanori Kiryu
1Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8561, Japan. matsumoto@cb.k.u-tokyo.ac.jp.
BMC Genomics
|August 30, 2014
Summary
A new method effectively detects and removes chimeric fragments, significantly improving single individual haplotyping (SIH) accuracy. This approach integrates statistical phasing to identify artificial recombinant haplotypes, crucial for genetic analyses using advanced sequencing techniques.
Area of Science:
- Genetics
- Bioinformatics
- Computational Biology
Background:
- Haplotype information is crucial for genetic analyses.
- Novel sequencing techniques like dilution-based sequencing enable single individual haplotyping (SIH).
- Chimeric fragments produced by these techniques significantly reduce SIH accuracy.
Purpose of the Study:
- To develop a general method for detecting and removing chimeric fragments.
- To improve the accuracy of single individual haplotyping (SIH).
Main Methods:
- Proposed a novel method to detect chimeric fragments by identifying artificial recombinant haplotypes.
- Integrated statistical phasing, a haplotype inference approach from population genotypes, to detect differences from biological haplotypes.
- Applied the method to two datasets and compared SIH accuracy before and after removing chimeric fragment candidates.
Main Results:
- The proposed method effectively detected chimeric fragments with high AUC values.
- AUC values surpassed those obtained using cluster length and heterozygous calls alone.
- SIH accuracy significantly increased after removing detected chimeric fragment candidates.
Conclusions:
- The developed method is effective for detecting chimeric fragments.
- The method demonstrably improves single individual haplotyping (SIH) accuracy.
- A Ruby script for the method is publicly available.
