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

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

Published on: January 19, 2017

Accurate genome-wide phasing from IBD data.

Keith Noto¹, Luong Ruiz²

¹Ancestry DNA, San Francisco, USA. knoto@ancestry.com.

BMC Bioinformatics

|November 24, 2022

Summary

This summary is machine-generated.

Large genotype databases enable accurate genome-wide phasing by identifying identity by descent (IBD) segments. This method separates parental DNA with high accuracy, even with missing data or errors.

Keywords:

Genotype phasing IBD Long-range phasing

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Area of Science:

Genomics
Population Genetics
Bioinformatics

Background:

Genotype databases are expanding, increasing the number of detectable identity by descent (IBD) segments.
IBD segments represent shared genomic regions inherited from common ancestors.

Purpose of the Study:

To demonstrate that IBD segments can be used for accurate, long-range genome-wide phasing.
To assess the accuracy and robustness of phasing using IBD data.

Main Methods:

Utilizing large genotype databases to identify overlapping IBD segments across entire chromosomes.
Developing a method to separate parental haplotypes based on IBD data.
Testing the method on a dataset of 30,000 individuals.

Main Results:

IBD segments collectively span entire chromosomes, enabling complete genome-wide phasing.
Achieved 98% median accuracy in separating parental DNA across the genome.
Method is robust to genotype errors and missing data, and can impute missing genotypes.

Conclusions:

Genome-wide phasing is achievable using IBD data from large genotype databases.
The proposed method provides accurate long-range phasing without requiring close family genotypes.
The approach is resilient to data imperfections and can improve data quality.