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Related Experiment Video

Updated: Jan 8, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

Challenges in structural variant calling in low-complexity regions.

Qian Qin¹, Heng Li^2,3,4

¹Division of Rheumatology, Inflammation and Immunity, Brigham Women's Hospital, Boston, MA 02115, USA.

|December 12, 2025

Summary

This summary is machine-generated.

Structural variants (SVs) are hard to detect in low-complexity regions (LCRs). These genomic regions contain most confident SVs and cause most errors in variant calling, necessitating specialized analysis.

Keywords:

evaluation low-complexity regions structural variant

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Last Updated: Jan 8, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Structural variants (SVs) are large genomic alterations (≥50 bp) that are difficult to detect.
The challenges in SV detection, particularly in specific genomic regions, are not well understood.

Purpose of the Study:

To quantify the impact of low-complexity regions (LCRs) on structural variant detection.
To identify the role of LCRs in SV detection errors across different long-read sequencing callers.

Main Methods:

Identification and characterization of low-complexity regions (LCRs) in the GRCh38 human genome reference.
Analysis of structural variant calls from long-read sequencing data in sample HG002.
Evaluation of error rates in structural variant callers within LCRs.

Main Results:

Low-complexity regions (LCRs) constitute 1.2% of the GRCh38 genome but harbor 69.1% of confident structural variants (SVs) in sample HG002.
77.3-91.3% of erroneous SV calls occurred within LCRs across multiple long-read SV callers.
SV detection error rates increase with the length of low-complexity regions.

Conclusions:

Structural variants are significantly enriched in low-complexity regions (LCRs).
LCRs present a major challenge for accurate SV detection and analysis using current long-read technologies.
Specialized methods are required for reliable calling and interpretation of SVs within LCRs.