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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: Jun 21, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Selphi, a tool for improving genotype imputation accuracy.

Adriano De Marino¹, Abdallah Amr Mahmoud¹, Sandra Bohn¹

¹Research & Development, Omics Edge, Miami, FL, USA.

Scientific Reports

|June 19, 2026

Summary

This summary is machine-generated.

Selphi, a novel genotype imputation algorithm, enhances accuracy for rare variants by leveraging whole-chromosome haplotype sharing. This improves genetic studies and polygenic risk score accuracy.

Keywords:

GWAS Genotype imputation Imputation PRS Rare variants

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Published on: June 21, 2018

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Last Updated: Jun 21, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Area of Science:

Genetics
Bioinformatics
Computational Biology

Background:

Genotype imputation is crucial for large-scale genetic studies, inferring missing data.
Existing methods struggle with accurate imputation of rare and infrequent variants.
Current algorithms often rely on limited local haplotype matching.

Purpose of the Study:

Introduce Selphi, a new genotype imputation algorithm.
Improve imputation accuracy, especially for rare variants.
Enhance downstream genetic analyses like GWAS and PRS.

Main Methods:

Selphi combines the Positional Burrows-Wheeler Transform (PBWT) with a multi-stage haplotype selection heuristic.
The method operates across entire chromosomes, capturing extended haplotype sharing patterns.
Evaluated against state-of-the-art methods (Beagle 5.4, IMPUTE5, Minimac4).

Main Results:

Selphi demonstrated higher imputation accuracy than existing methods on 1000 Genomes Project and TOPMed datasets.
Improved accuracy was observed across all super-populations and allele frequencies.
Selphi enhanced concordance with GWAS summary statistics and improved polygenic risk score accuracy on UK Biobank data.

Conclusions:

Selphi offers superior genotype imputation accuracy, particularly for rare variants.
The algorithm facilitates direct integration into downstream genetic analysis pipelines.
Selphi represents a significant advancement in genetic data imputation for large-scale studies.