Clinical utility of regions of homozygosity (ROH) identified in exome sequencing: when to pursue confirmatory uniparental disomy testing for imprinting disorders?

Xiaoyan Huo; Xinyi Lu; Deyun Lu; Huili Liu; Yi Liu; Qianfeng Zhao; Yu Sun; Weiqian Dai; Wenjuan Qiu; Yongguo Yu; Yanjie Fan

doi:10.1515/cclm-2024-0239

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Article

Clinical utility of regions of homozygosity (ROH) identified in exome sequencing: when to pursue confirmatory uniparental disomy testing for imprinting disorders?

Xiaoyan Huo , Xinyi Lu , Deyun Lu , Huili Liu , Yi Liu , Qianfeng Zhao , Yu Sun , Weiqian Dai , Wenjuan Qiu , Yongguo Yu and Yanjie Fan

Published/Copyright: July 19, 2024

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From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 63 Issue 1

Abstract

Objectives

Regions of homozygosity (ROH) could implicate uniparental disomy (UPD) on specific chromosomes associated with imprinting disorders. Though the algorithms for ROH detection in exome sequencing (ES) have been developed, optimal reporting thresholds and when to pursue confirmatory UPD testing for imprinting disorders remain in ambiguity. This study used a data-driven approach to assess optimal reporting thresholds of ROH in clinical practice.

Methods

ROH analysis was performed using Automap in a retrospective cohort of 8,219 patients and a prospective cohort of 1,964 patients with ES data. Cases with ROH on imprinting-disorders related chromosomes were selected for additional methylation-specific confirmatory testing. The diagnostic yield, the ROH pattern of eventually diagnosed cases and optimal thresholds for confirmatory testing were analyzed.

Results

In the retrospective analysis, 15 true UPD cases of imprinting disorders were confirmed among 51 suspected cases by ROH detection. Pattern of ROH differed between confirmed UPD and non-UPD cases. Maximized yield and minimized false discovery rate of confirmatory UPD testing was achieved at the thresholds of >20 Mb or >25 % chromosomal coverage for interstitial ROH, and >5 Mb for terminal ROH. Current recommendation by ACMG was nearly optimal, though refined thresholds as proposed in this study could reduce the workload by 31 % without losing any true UPD diagnosis. Our refined thresholds remained optimal after independent evaluation in a prospective cohort.

Conclusions

ROH identified in ES could implicate the presence of clinically relevant UPD. This study recommended size and coverage thresholds for confirmatory UPD testing after ROH detection in ES, contributing to the development of evidence-based reporting guidelines.

Keywords: regions of homozygosity (ROH); exome sequencing; uniparental disomy; genetic testing

Corresponding authors: Yongguo Yu and Yanjie Fan, Clinical Genetics Center, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China, E-mail: yongguoyu@shsmu.edu.cn (Y. Yu), fanyanjie@shsmu.edu.cn (Y. Fan)

Funding source: National Key Research and Development Program of China

Award Identifier / Grant number: No.2022YFC2703400

Award Identifier / Grant number: No.2022YFC2703405

Funding source: National Natural Science Foundation of China

Award Identifier / Grant number: No.82171165 and 81873735

Award Identifier / Grant number: No.82271904 and 82070914

Acknowledgments

We would like to acknowledge the affected individuals and their families for the participation in the study.

Research ethics: This study was approved by the Ethics Committee of Xinhua Hospital (Shanghai, China).
Informed consent: Informed consent was obtained from participants or their parents.
Author contributions: XYH, YGY and YJF contributed to the study conception and design. XYH and YJF conducted experiments, analyzed data and wrote the manuscript. QFZ, WQD and YL conducted experiments and analyzed data. HLL, YS, XYL, XYH and YJF analyzed the exome sequencing data. DYL, WJQ and YGY participated in the clinical evaluation of patients and data acquisition. All authors reviewed the manuscript. All authors have accepted responsibility for the entire content of this manuscript and approved its submission.
Competing interests: The authors state no conflict of interest.
Research funding: This work was sponsored by the grants to YF (NSF No. 82171165 & 81873735; 2022YFC2703405), and to YGY the National Key R&D Program of China (No.2022YFC2703400), the National Natural Science Foundation of China (No.82271904 and 82070914).
Data availability: Not applicable.

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Supplementary Material

This article contains supplementary material (https://doi.org/10.1515/cclm-2024-0239).

Received: 2024-02-22

Accepted: 2024-07-07

Published Online: 2024-07-19

Published in Print: 2025-01-29

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Supplementary Material

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Keywords for this article

regions of homozygosity (ROH); exome sequencing; uniparental disomy; genetic testing