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Related Experiment Video

Updated: Jul 31, 2025

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

High-throughput Physical Mapping of Chromosomes using Automated in situ Hybridization

Published on: June 28, 2012

Gaps and complex structurally variant loci in phased genome assemblies.

David Porubsky¹, Mitchell R Vollger¹, William T Harvey¹

¹Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.

Genome Research

|May 10, 2023

Summary

This summary is machine-generated.

Human genome assembly still contains over 140 gaps, even with advanced methods. Most gaps and misorientations occur in repetitive DNA, impacting protein-coding genes and highlighting needs for better assembly algorithms.

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Published on: August 21, 2016

Area of Science:

Genomics
Bioinformatics
Human Genetics

Background:

Phased human genome assembly has advanced using long-read data and parental or linked-read information.
Despite progress, current methods like trio-based assembly (e.g., trio-hifiasm) still result in numerous gaps (over 140 per assembly).

Purpose of the Study:

To analyze assembly gaps, breaks, and misorientations in a diverse set of human haploid assemblies.
To compare phasing accuracy using Strand-seq versus parental data.
To identify common locations and types of assembly gaps and assess their impact on protein-coding genes.

Main Methods:

Analysis of 182 haploid assemblies from 77 human samples.
Comparison of chromosome-wide phasing accuracy between trio-based methods and Strand-seq.
Detailed examination of gap locations, focusing on repetitive elements like segmental duplications and satellite DNA.
Estimation of DNA misorientations and identification of large-scale alignment discontinuities (deletions/insertions).

Main Results:

Assembly gaps predominantly cluster in large, identical repeats (35.4% segmental duplications, 22.3% satellite DNA, 27.4% GA/AT-rich regions).
1513 protein-coding genes overlap assembly gaps, with 231 recurrently affected.
6-7 Mbp of DNA are misoriented per haplotype, with 81% corresponding to large inversion polymorphisms.
Significant large-scale deletions (11.9 Mbp) and insertions (161.4 Mbp) per haploid genome identified, primarily in satellite DNA, but also in 230 euchromatic regions impacting 197 protein-coding genes.

Conclusions:

Trio-based methods are the gold standard, but Strand-seq offers comparable chromosome-wide phasing accuracy.
Repetitive regions, particularly segmental duplications and satellite DNA, are major sources of assembly gaps and variations.
Incompletely assembled and variable regions, including those affecting protein-coding genes, are critical targets for improving genome assembly algorithms and pangenome representations.