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Nomura F, Shimizu A, Togi S, Ura H, Niida Y. SNP Array Screening and Long Range PCR-Based Targeted Next Generation Sequencing for Autosomal Recessive Disease with Consanguinity: Insight from a Case of Xeroderma Pigmentosum Group C. Genes (Basel) 2023; 14:2079. [PMID: 38003022 PMCID: PMC10671442 DOI: 10.3390/genes14112079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Advances in genetic technologies have made genetic testing more accessible than ever before. However, depending on national, regional, legal, and health insurance circumstances, testing procedures may still need to be streamlined in real-world clinical practice. In cases of autosomal recessive disease with consanguinity, the mutation locus is necessarily isodisomy because both alleles originate from a common ancestral chromosome. Based on this premise, we implemented integrated genetic diagnostic methods using SNP array screening and long range PCR-based targeted NGS in a Japanese patient with xeroderma pigmentosum (XP) under the limitation of the national health insurance system. SNP array results showed isodisomy only in XPC and ERCC4 loci. NGS, with a minimal set of long-range PCR primers, detected a homozygous frameshift mutation in XPC; NM_004628.5:c.218_219insT p.(Lys73AsnfsTer9), confirmed by Sanger sequencing, leading to a rapid diagnosis of XP group C. This shortcut strategy is applicable to all autosomal recessive diseases caused by consanguineous marriages, especially in scenarios with a moderate number of genes to test, a common occurrence in clinical genetic practice.
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Affiliation(s)
- Fumie Nomura
- Department of Dermatology, Kanazawa Medical University, Uchinada 920-0293, Japan (A.S.)
| | - Akira Shimizu
- Department of Dermatology, Kanazawa Medical University, Uchinada 920-0293, Japan (A.S.)
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
| | - Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Uchinada 920-0293, Japan (H.U.)
- Department of Advanced Medicine, Division of Genomic Medicine, Medical Research Institute, Kanazawa Medical University, Uchinada 920-0293, Japan
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Zhou L, Zheng Z, Xu Y, Lv X, Xu C, Xu X. Prenatal diagnosis of 7 cases with uniparental disomy by utilization of single nucleotide polymorphism array. Mol Cytogenet 2021; 14:19. [PMID: 33741026 PMCID: PMC7980353 DOI: 10.1186/s13039-021-00537-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 02/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background The phenotypes of uniparental disomy (UPD) are variable, which may either have no clinical impact, lead to clinical signs and symptoms. Molecular analysis is essential for making a correct diagnosis. This study involved a retrospective analysis of 4512 prenatal diagnosis samples and explored the molecular characteristics and prenatal phenotypes of UPD using a single nucleotide polymorphism (SNP) array. Results Out of the 4512 samples, a total of seven cases of UPD were detected with an overall frequency of 0.16%. Among the seven cases of UPD, two cases are associated with chromosomal aberrations (2/7), four cases (4/7) had abnormal ultrasonographic findings. One case presented with iso-UPD (14), and two case presented with mixed hetero/iso-UPD (15), which were confirmed by Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as maternal UPD (15) associated with Prader-Willi syndrome (PWS). Four cases had iso-UPD for chromosome 1, 3, 14, and 16, respectively; this is consistent with the monosomy rescue mechanism. Another three cases presented with mixed hetero/isodisomy were consistent with a trisomy rescue mechanism. Conclusion The prenatal phenotypes of UPD are variable and molecular analysis is essential for making a correct diagnosis and genetic counselling of UPD. The SNP array is a useful genetic test in prenatal diagnosis cases with UPD.
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Affiliation(s)
- Lili Zhou
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China
| | - Zhaoke Zheng
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China
| | - Yunzhi Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China
| | - Xiaoxiao Lv
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China
| | - Chenyang Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China
| | - Xueqin Xu
- Center of Prenatal Diagnosis, Wenzhou Central Hospital, Wenzhou, 325000, People's Republic of China.
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Pan YW, Chang CW, Jong YJ, Chou YY, Kuo PL. Segmental isodisomy in Prader-Willi syndrome patients: The experience of a single diagnostic center. Pediatr Neonatol 2020; 61:343-345. [PMID: 32192873 DOI: 10.1016/j.pedneo.2020.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/11/2019] [Accepted: 02/15/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Yu-Wen Pan
- Department of Pediatrics, National Cheng-Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Chia-Wei Chang
- Department of Obstetrics and Gynecology, National Cheng-Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Yiin-Jeng Jong
- Genetics Generation Advancement Corp. (GGA Corp.), Taipei, Taiwan
| | - Yen-Yin Chou
- Department of Pediatrics, National Cheng-Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics and Gynecology, National Cheng-Kung University Hospital and College of Medicine, Tainan, Taiwan.
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Ozyilmaz B, Kirbiyik O, Ozdemir TR, Kaya OO, Kutbay YB, Erdogan KM, Guvenc MS, Koc A. The Efficiency of SNP-Based Microarrays in the Detection of Copy-Neutral Events at 15q11.2 and 11p15.5 Loci. J Pediatr Genet 2019; 9:9-18. [PMID: 31976138 DOI: 10.1055/s-0039-1698420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/30/2019] [Indexed: 12/24/2022]
Abstract
Prader-Willi, Angelman, Beckwith-Wiedemann, and Russell-Silver are imprinting syndromes. In this study, we aimed to compare the efficiency of single nucleotide polymorphism (SNP) microarray analysis with methylation-specific Multiplex ligation-dependent probe amplification (MS-MLPA) in the detection of uniparental disomy in these syndromes. The patient samples with regions of loss of heterozygosity (LOH), covering 15q11.2 and 11p15.5 critical loci, were analyzed with MS-MLPA to demonstrate the efficiency of SNP microarray in the detection of uniparental disomy (UPD). In a total of seven patients, LOH covering 15q11.2 and 11p15.5 critical loci was detected. Two (28.6%) of these seven patients showed aberrant methylation (suggesting UPD) in MS-MLPA. SNP microarray is a useful tool in the detection of LOH; however, it should be used with caution, since false-positive or false-negative LOH results can be obtained. Although methylation analysis is recommended as the first tier test in the diagnosis of most of the imprinting disorders, combining methylation analysis with SNP microarray can enhance our evaluation process.
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Affiliation(s)
- Berk Ozyilmaz
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Ozgur Kirbiyik
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Taha R Ozdemir
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Ozge Ozer Kaya
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Yasar B Kutbay
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Kadri M Erdogan
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Merve Saka Guvenc
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
| | - Altug Koc
- Genetic Diagnosis Center, Tepecik Training and Research Hospital, University of Health Sciences, Izmir, Turkey
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CHEN D, QI M. [Research progress on uniparental disomy in cancer]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2019; 48:560-566. [PMID: 31901032 PMCID: PMC8800777 DOI: 10.3785/j.issn.1008-9292.2019.10.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/17/2019] [Indexed: 06/10/2023]
Abstract
Uniparental disomy (UPD) refers to a chromosome defect that an individual's homologous chromosome or segments are inherited from one parent. UPD can cause either aberrant patterns of genomic imprinting or homozygosity of mutations, leading to various diseases, including cancer. The mechanisms of UPD formation are diverse but largely due to the incorrect chromosome separation during cell division. UPD does not alter the number of gene copies, thus is difficult to be detected by conventional cytogenetic techniques effectively. Assisted by the new techniques such as single nucleotide polymorphism arrays, more and more UPD-related cases have been reported recently. UPD events are non-randomly distributed across cancer types, which play important role in the occurrence, development and metastasis of cancer. Here we review the research progress on the formation mechanisms, detection methods, the involved chromosomal regions and genes, and clinical significance of UPD; and also discuss the directions for future studies in this field.
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Affiliation(s)
| | - Ming QI
- 祁鸣(1957-), 男, 博士, 教授, 博士生导师, 主要从事遗传与基因组医学研究; E-mail:
;
https://orcid.org/0000-0002-8421-6727
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Costa RA, Ferreira IR, Cintra HA, Gomes LHF, Guida LDC. Genotype-Phenotype Relationships and Endocrine Findings in Prader-Willi Syndrome. Front Endocrinol (Lausanne) 2019; 10:864. [PMID: 31920975 PMCID: PMC6923197 DOI: 10.3389/fendo.2019.00864] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a complex imprinting disorder related to genomic errors that inactivate paternally-inherited genes on chromosome 15q11-q13 with severe implications on endocrine, cognitive and neurologic systems, metabolism, and behavior. The absence of expression of one or more genes at the PWS critical region contributes to different phenotypes. There are three molecular mechanisms of occurrence: paternal deletion of the 15q11-q13 region; maternal uniparental disomy 15; or imprinting defects. Although there is a clinical diagnostic consensus criteria, DNA methylation status must be confirmed through genetic testing. The endocrine system can be the most affected in PWS, and growth hormone replacement therapy provides improvement in growth, body composition, and behavioral and physical attributes. A key feature of the syndrome is the hypothalamic dysfunction that may be the basis of several endocrine symptoms. Clinical and molecular complexity in PWS enhances the importance of genetic diagnosis in therapeutic definition and genetic counseling. So far, no single gene mutation has been described to contribute to this genetic disorder or related to any exclusive symptoms. Here we proposed to review individually disrupted genes within the PWS critical region and their reported clinical phenotypes related to the syndrome. While genes such as MKRN3, MAGEL2, NDN, or SNORD115 do not address the full spectrum of PWS symptoms and are less likely to have causal implications in PWS major clinical signs, SNORD116 has emerged as a critical, and possibly, a determinant candidate in PWS, in the recent years. Besides that, the understanding of the biology of the PWS SNORD genes is fairly low at the present. These non-coding RNAs exhibit all the hallmarks of RNA methylation guides and can be incorporated into ribonucleoprotein complexes with possible hypothalamic and endocrine functions. Also, DNA conservation between SNORD sequences across placental mammals strongly suggests that they have a functional role as RNA entities on an evolutionary basis. The broad clinical spectrum observed in PWS and the absence of a clear genotype-phenotype specific correlation imply that the numerous genes involved in the syndrome have an additive deleterious effect on different phenotypes when deficiently expressed.
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