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Updated: Apr 25, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Probabilistic single-individual haplotyping.

Volodymyr Kuleshov¹

¹Department of Computer Science, Stanford University, Stanford, CA 94305, USA.

Bioinformatics (Oxford, England)

|August 28, 2014

Summary

ProbHap, a new algorithm for genomic haplotyping, leverages long read sequencing to reduce errors by 11% compared to existing methods. This tool provides accurate haplotype phasing with confidence scores for genomic data analysis.

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Accurate genomic haplotyping, determining parental inheritance of genome segments, remains a significant challenge.
Advancements in long-read sequencing technologies are making haplotyping more tractable.
Existing methods for haplotype phasing have limitations in accuracy and confidence scoring.

Purpose of the Study:

To introduce ProbHap, a novel haplotyping algorithm designed for long-read sequencing data.
To develop an accurate and efficient method for genomic haplotyping.
To provide confidence scores for phased genomic positions.

Main Methods:

Development of a new dynamic programming algorithm for probabilistic graphical models.
Optimization of a likelihood function generalizing the minimum error correction objective.

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Application to long-read sequencing data for haplotype phasing.

Main Results:

ProbHap achieves an 11% reduction in errors compared to state-of-the-art haplotyping methods on benchmark datasets.
The algorithm provides confidence scores for phased positions, enabling assessment of accuracy.
Excluding low-confidence positions can further increase accuracy at a minor cost to haplotype completeness.

Conclusions:

ProbHap offers a significant improvement in accuracy for genomic haplotyping using long-read sequencing.
The algorithm's ability to provide confidence scores enhances the reliability of haplotype phasing.
ProbHap represents a valuable tool for genomic research requiring precise haplotyping.