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

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Reference-based phasing using the Haplotype Reference Consortium panel.

Po-Ru Loh^1,2, Petr Danecek³, Pier Francesco Palamara^1,2

¹Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

Nature Genetics

|October 4, 2016

Summary

This summary is machine-generated.

Eagle2 is a new haplotype phasing algorithm that improves accuracy and speed for genetic studies. It leverages large reference panels, enhancing variant discovery across diverse cohort sizes.

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Area of Science:

Genetics
Bioinformatics
Computational Biology

Background:

Haplotype phasing is crucial for medical and population genetics.
Statistical phasing accuracy decreases in smaller cohorts.
Reference-based phasing offers an alternative approach.

Purpose of the Study:

Introduce Eagle2, a novel reference-based phasing algorithm.
Improve phasing accuracy and efficiency across various cohort sizes.
Leverage large external reference panels for enhanced phasing.

Main Methods:

Developed Eagle2, a new phasing algorithm.
Utilized a novel data structure based on the positional Burrows-Wheeler transform.
Integrated information from large external reference panels like the Haplotype Reference Consortium (HRC).

Main Results:

Eagle2 achieves high accuracy across a broad range of cohort sizes.
Demonstrated a ~20x speedup and ~10% increase in accuracy compared to SHAPEIT2.
Achieved >2x accuracy of 1000 Genomes-based phasing on European-ancestry samples using the HRC panel.

Conclusions:

Eagle2 offers a significant advancement in reference-based haplotype phasing.
The algorithm provides a more accurate and efficient solution for genetic studies.
Eagle2 is available open-source via the Sanger Imputation Service and Michigan Imputation Server.