MINI REVIEW article
Front. Genet.
Sec. Human and Medical Genomics
This article is part of the Research TopicExploring Genomic Landscapes and Chromosomal Aberrations: Implications in Human Genetic Disorders and Infectious Disease PathogenesisView all 4 articles
Recent advances in the detection technologies for balanced chromosomal rearrangements
Provisionally accepted
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Balanced chromosomal rearrangements (BCRs) refer to a type of chromosomal structural variations without chromosomal gains or losses. BCR carriers may experience fertility issues, including a higher risk of infertility, recurrent miscarriages, or having offspring with chromosomal abnormalities. Since there are no apparent gains or losses of genetic materials in BCR carriers, their detection has long been a focal and challenging issue in the field of chromosomal structural variation analysis. Karyotyping cannot detect submicroscopic rearrangements because of restricted resolution and the application of fluorescence in situ hybridization (FISH) is limited by the necessity of a known loci. Chromosomal microarray analysis and standard short-read sequencing, widely used in clinical practice, cannot detect BCRs. In summary, the clinical detection techniques are unable to accurately identify the breakpoints of BCRs. The improved short-read sequencing such as mate-pair sequencing has been found to detect balanced rearrangements. Emerging advanced technologies such as long-read sequencing, and optical genome mapping, have already shown their potential in detecting BCRs. This review primarily elucidates the principles, applicability, advantages, and limitations of the detection techniques for BCRs, aiming to assist in the early identification and appropriate advice of patients with BCRs in genetic counseling.
Keywords: balanced chromosomal rearrangements, clinicallaboratory techniques, Genome sequencing, Molecular genetic testing, Optical genome mapping
Received: 09 Dec 2025; Accepted: 31 Jan 2026.
Copyright: © 2026 Gao, Ren and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Shanling Liu
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.