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Xu Y, Zhang Q, Wang Y, Zhou R, Ji X, Meng L, Luo C, Liu A, Jiao J, Chen H, Zeng H, Hu P, Xu Z. Optical Genome Mapping for Chromosomal Aberrations Detection-False-Negative Results and Contributing Factors. Diagnostics (Basel) 2024; 14:165. [PMID: 38248042 PMCID: PMC10814618 DOI: 10.3390/diagnostics14020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
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.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ping Hu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Health Care Hospital, Nanjing 210004, China; (Y.X.); (Q.Z.); (Y.W.); (R.Z.); (X.J.); (L.M.); (C.L.); (A.L.); (J.J.); (H.C.); (H.Z.)
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Women and Children’s Health Care Hospital, Nanjing 210004, China; (Y.X.); (Q.Z.); (Y.W.); (R.Z.); (X.J.); (L.M.); (C.L.); (A.L.); (J.J.); (H.C.); (H.Z.)
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Ciobanu CG, Nucă I, Popescu R, Antoci LM, Caba L, Ivanov AV, Cojocaru KA, Rusu C, Mihai CT, Pânzaru MC. Narrative Review: Update on the Molecular Diagnosis of Fragile X Syndrome. Int J Mol Sci 2023; 24:ijms24119206. [PMID: 37298158 DOI: 10.3390/ijms24119206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/30/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
The diagnosis and management of fragile X syndrome (FXS) have significantly improved in the last three decades, although the current diagnostic techniques are not yet able to precisely identify the number of repeats, methylation status, level of mosaicism, and/or the presence of AGG interruptions. A high number of repeats (>200) in the fragile X messenger ribonucleoprotein 1 gene (FMR1) results in hypermethylation of promoter and gene silencing. The actual molecular diagnosis is performed using a Southern blot, TP-PCR (Triplet-Repeat PCR), MS-PCR (Methylation-Specific PCR), and MS-MLPA (Methylation-Specific MLPA) with some limitations, with multiple assays being necessary to completely characterise a patient with FXS. The actual gold standard diagnosis uses Southern blot; however, it cannot accurately characterise all cases. Optical genome mapping is a new technology that has also been developed to approach the diagnosis of fragile X syndrome. Long-range sequencing represented by PacBio and Oxford Nanopore has the potential to replace the actual diagnosis and offers a complete characterization of molecular profiles in a single test. The new technologies have improved the diagnosis of fragile X syndrome and revealed unknown aberrations, but they are a long way from being used routinely in clinical practice.
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Affiliation(s)
- Cristian-Gabriel Ciobanu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Irina Nucă
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Investigatii Medicale Praxis, St. Moara de Vant No 35, 700376 Iasi, Romania
| | - Roxana Popescu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | - Lucian-Mihai Antoci
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Lavinia Caba
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Anca Viorica Ivanov
- Pediatrics Department, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Karina-Alexandra Cojocaru
- Department of Biochemistry, Faculty of Dental Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
| | - Cristina Rusu
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
| | | | - Monica-Cristina Pânzaru
- Medical Genetics Department, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, University Street No 16, 700115 Iasi, Romania
- Medical Genetics Department, "Saint Mary" Emergency Children's Hospital, St. Vasile Lupu No 62, 700309 Iasi, Romania
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Zhang W, Li D, Pang N, Jiang L, Li B, Ye F, He F, Chen S, Liu F, Peng J, Yin J, Yin F. The second-tier status of fragile X syndrome testing for unexplained intellectual disability/global developmental delay in the era of next-generation sequencing. Front Pediatr 2022; 10:911805. [PMID: 35935362 PMCID: PMC9353215 DOI: 10.3389/fped.2022.911805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Although many unexplained intellectual disability/global developmental delay (ID/GDD) individuals have benefited from the excellent detection yield of copy number variations and next-generation sequencing testing, many individuals still who suffer from ID/GDD of unexplained etiology. In this study, we investigated the applicability of fragile X syndrome (FXS) testing in unexplained ID/GDD individuals with negative or absent genetic testing. METHODS In this study, we used the triplet repeat primed polymerase chain reaction to evaluate the value and application of fragile X testing in unexplained ID/GDD individuals with negative or absent genetic testing (n = 681) from three hospitals. RESULTS Of the 681 ID/GDD individuals with negative or absent genetic testing results detected by FXS testing, 12 men and one woman were positive. This corresponded to a diagnostic yield of 1.9% for FXS testing in our cohort. All FXS individuals had either a family history of ID/GDD or suggestive clinical features. The detection yield of FXS testing in ID/GDD individuals who completed genetic testing (2.70%, 12/438) was significantly higher than in individuals without any genetic testing (0.40%, 1/243). CONCLUSIONS This is the first report of FXS testing in ID/GDD individuals who lacked previous genetic testing, which promotes standardization of the FXS diagnostic process. These results highlight the utility of FXS testing of unexplained ID/GDD individuals with negative results from standard genetic testing. In the era of next-generation sequencing, FXS testing is more suitable as a second-tier choice and provides clinicians and geneticists with auxiliary references for tracing the etiology of ID/GDD.
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Affiliation(s)
- Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Dong Li
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Children's Hospital Affiliated to Chongqing Medical University, Chongqing, China
| | - Baomin Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Jinan, China
| | - Fanghua Ye
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Shimeng Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Fangyun Liu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
| | - Jinghua Yin
- Department of Pathophysiology, Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Pediatrics, Changsha, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Xiangya Hospital, Central South University, Changsha, China
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