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Evolutionary Relationships through Genome Comparisons

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Related Experiment Video

Updated: May 15, 2026

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement
08:06

Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement

Published on: January 19, 2017

A novel method for across-chromosome phasing without relative data.

Emmanuel Sapin1, Kristen M Kelly1, Matthew C Keller1

  • 1Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309, United States.

Bioinformatics (Oxford, England)
|May 13, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces a new method for across-chromosome phasing, improving accuracy for unrelated individuals without needing parental data. The novel approach achieves high accuracy, demonstrating potential for advanced genomic analysis.

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Area of Science:

  • Genomics
  • Population Genetics
  • Bioinformatics

Background:

  • Across-chromosome phasing determines parental haplotype origin across different chromosomes, distinct from within-chromosome phasing.
  • Existing across-chromosome phasing methods struggle with unrelated individuals, limiting their application.
  • This study addresses the need for improved across-chromosome phasing in unrelated individuals.

Purpose of the Study:

  • To develop and evaluate a novel computational method for across-chromosome phasing.
  • To eliminate the requirement for parental or close relative genotype data.
  • To enable accurate haplotype phasing in large, unrelated population cohorts.

Main Methods:

  • A novel window-based SNP-similarity metric was developed for across-chromosome phasing.
  • The method was evaluated using UK Biobank offspring data, with parental genotypes withheld.
  • Implementation utilized parallelization in C within a high-performance computing environment.

Main Results:

  • The novel method achieved a mean across-chromosome phasing accuracy of 95% when within-chromosome phasing had no errors.
  • Accuracy decreased to 83.1% when using data pre-phased by a standard within-chromosomal algorithm.
  • Performance is strongly dependent on the accuracy of the initial within-chromosome phasing.

Conclusions:

  • The developed method offers a significant advancement for across-chromosome phasing in unrelated individuals.
  • Accuracy approaches perfection as within-chromosome phasing accuracy improves.
  • The publicly available code promotes reproducibility and further research in genomic phasing.