Evidence map›Paper›PMID 38248042›Full record

ArticleDiagnostics (Basel, Switzerland)2024

Optical Genome Mapping for Chromosomal Aberrations Detection-False-Negative Results and Contributing Factors.

Yiyun Xu, Qinxin Zhang, Yan Wang, Ran Zhou, Xiuqing Ji, Lulu Meng, Chunyu Luo, An Liu, Jiao Jiao, Hao Chen and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Diagnostics (Basel, Switzerland), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Article
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  5. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Yiyun XuDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Qinxin ZhangDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Yan WangDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Ran ZhouDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Xiuqing JiDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Lulu MengDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Chunyu LuoDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
An LiuDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Jiao JiaoDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Hao ChenDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Huasha ZengDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Ping HuDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.
Zhengfeng XuDepartment of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Health Care Hospital, Nanjing 210004, China.

Funding

Jiangsu Province Capability Improvement Project through Science, Technology and Education Jiangsu Provincial Medical Key Discipline ZDXK202211the National Key R&D Program of China 2021YFC1005301the National Key R&D Program of China 2022YFC2703400the National Natural Science Foundation of China 81971398the National Natural Science Foundation of China 82371862
6 · The paper itself

Abstract

Optical genome mapping (OGM) has been known as an all-in-one technology for chromosomal aberration detection. However, there are also aberrations beyond the detection range of OGM. This study aimed to report the aberrations missed by OGM and analyze the contributing factors. OGM was performed by taking both GRCh37 and GRCh38 as reference genomes. The OGM results were analyzed in blinded fashion and compared to standard assays. Quality control (QC) metrics, sample types, reference genome, effective coverage and classes and locations of aberrations were then analyzed. In total, 154 clinically reported variations from 123 samples were investigated. OGM failed to detect 10 (6.5%, 10/154) aberrations with GRCh37 assembly, including five copy number variations (CNVs), two submicroscopic balanced translocations, two pericentric inversion and one isochromosome (mosaicism). All the samples passed pre-analytical and analytical QC. With GRCh38 assembly, the false-negative rate of OGM fell to 4.5% (7/154). The breakpoints of the CNVs, balanced translocations and inversions undetected by OGM were located in segmental duplication (SD) regions or regions with no DLE-1 label. In conclusion, besides variations with centromeric breakpoints, structural variations (SVs) with breakpoints located in large repetitive sequences may also be missed by OGM. GRCh38 is recommended as the reference genome when OGM is performed. Our results highlight the necessity of fully understanding the detection range and limitation of OGM in clinical practice.

Indexed as

copy number variationfalse-negativeoptical genome mappingsegmental duplicationstructural variation

Identifiers

PMID38248042
PMCPMC10814618

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.