1
|
Kang JU. Medical Implementation of Microarray Technology. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2020. [DOI: 10.15324/kjcls.2020.52.4.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Ji Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
| |
Collapse
|
2
|
Affiliation(s)
- Ji-Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
| |
Collapse
|
3
|
Chen L, Sun F, Yang X, Jin Y, Shi M, Wang L, Shi Y, Zhan C, Wang Q. Correlation between RNA-Seq and microarrays results using TCGA data. Gene 2017; 628:200-204. [PMID: 28734892 DOI: 10.1016/j.gene.2017.07.056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/20/2017] [Accepted: 07/19/2017] [Indexed: 02/05/2023]
Abstract
RNA sequencing (RNA-Seq) and microarray are two of the most commonly used high-throughput technologies for transcriptome profiling; however, they both have their own inherent strengths and limitations. This research aims to analyze the correlation between microarrays and RNA-Seq detection of transcripts in the same tissue sample to explore the reproducibility between the techniques. Using data of RNA-Seq v2 and three different microarrays provided by The Cancer Genome Atlas, 11,120 genes of 111 lung squamous cell carcinoma samples were simultaneously detected by the four methods. Then we analyzed the Pearson correlation between microarrays and RNA-Seq. Finally, in the six comparison results, 9984 (89.8%) genes, irrespective of which two methods were used, simultaneously showed the existence of correlation, whereas only 83 (0.1%) genes proved to have no significant correlation in either comparison. In addition, the comparisons between 3266 (29.3%) genes showed high correlation (R≥0.8) in all six comparisons, only for 1643 (14.8%) genes correlation were not as high in either comparison. Meanwhile, transcripts with extreme high or low expression levels were more highly discrepant across the methods. In conclusion, we found that, for most transcripts, the results obtained by RNA-Seq and microarrays were highly reproducible.
Collapse
Affiliation(s)
- Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China; Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Fenghao Sun
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| |
Collapse
|
4
|
Kemeny S, Brugnon F, Eymard-Pierre E, Goumy C, Janny L, Tchirkov A, Francannet C, Vago P, Pebrel-Richard C. Characterization by microarray and meiotic segregation study of a der(10)t(10;18) in a patient with infertility and normal phenotype. Asian J Androl 2016; 19:135-137. [PMID: 26975482 PMCID: PMC5227663 DOI: 10.4103/1008-682x.172818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Stephan Kemeny
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Florence Brugnon
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Eléonore Eymard-Pierre
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Carole Goumy
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Laurent Janny
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Andreï Tchirkov
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Christine Francannet
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Philippe Vago
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| | - Céline Pebrel-Richard
- Department of Medical Cytogenetic, Univ Clermont 1, CHU Estaing, Clermont-Ferrand, France EA 4677, ERTICa, Univ Clermont 1, Clermont-Ferrand, France
| |
Collapse
|
5
|
Wen J, Hanna CW, Martell S, Leung PC, Lewis SM, Robinson WP, Stephenson MD, Rajcan-Separovic E. Functional consequences of copy number variants in miscarriage. Mol Cytogenet 2015; 8:6. [PMID: 25674159 PMCID: PMC4324423 DOI: 10.1186/s13039-015-0109-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/09/2015] [Indexed: 02/01/2023] Open
Abstract
Background The presence of unique copy number variations (CNVs) in miscarriages suggests that their integral genes have a role in maintaining early pregnancy. In our previous work, we identified 19 unique CNVs in ~40% of studied euploid miscarriages, which were predominantly familial in origin. In our current work, we assessed their relevance to miscarriage by expression analysis of 14 genes integral to CNVs in available miscarriage chorionic villi. As familial CNVs could cause miscarriage due to imprinting effect, we investigated the allelic expression of one of the genes (TIMP2) previously suggested to be maternally expressed in placenta and involved in placental remodelling and embryo development. Results Six out of fourteen genes had detectable expression in villi and for three genes the RNA and protein expression was altered due to maternal CNVs. These genes were integral to duplication on Xp22.2 (TRAPPC2 and OFD1) or disrupted by a duplication mapping to 17q25.3 (TIMP2). RNA and protein expression was increased for TRAPPC2 and OFD1 and reduced for TIMP2 in carrier miscarriages. The three genes have roles in processes important for pregnancy development such as extracellular matrix homeostasis (TIMP2 and TRAPPC2) and cilia function (OFD1). TIMP2 allelic expression was not affected by the CNV in miscarriages in comparison to control elective terminations. Conclusion We propose that functional studies of CNVs could help determine if and how the miscarriage CNVs affect the expression of integral genes. In case of parental CNVs, assessment of the function of their integral genes in parental reproductive tissues should be also considered in the future, especially if they affect processes relevant for pregnancy development and support. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0109-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jiadi Wen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Courtney W Hanna
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Sally Martell
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| | - Peter Ck Leung
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, V6Z 2 K5 Canada
| | - Suzanne Me Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Wendy P Robinson
- Child & Family Research Institute, Vancouver, V5Z 4H4 Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z3 Canada
| | - Mary D Stephenson
- Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, 60612 USA
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5 Canada.,Child & Family Research Institute, Vancouver, V5Z 4H4 Canada
| |
Collapse
|
6
|
Tao VQ, Chan KYK, Chu YWY, Mok GTK, Tan TY, Yang W, Lee SL, Tang WF, Tso WWY, Lau ET, Kan ASY, Tang MH, Lau YL, Chung BHY. The clinical impact of chromosomal microarray on paediatric care in Hong Kong. PLoS One 2014; 9:e109629. [PMID: 25333781 PMCID: PMC4198120 DOI: 10.1371/journal.pone.0109629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/03/2014] [Indexed: 01/27/2023] Open
Abstract
Objective To evaluate the clinical impact of chromosomal microarray (CMA) on the management of paediatric patients in Hong Kong. Methods We performed NimbleGen 135k oligonucleotide array on 327 children with intellectual disability (ID)/developmental delay (DD), autism spectrum disorders (ASD), and/or multiple congenital anomalies (MCAs) in a university-affiliated paediatric unit from January 2011 to May 2013. The medical records of patients were reviewed in September 2013, focusing on the pathogenic/likely pathogenic CMA findings and their “clinical actionability” based on established criteria. Results Thirty-seven patients were reported to have pathogenic/likely pathogenic results, while 40 had findings of unknown significance. This gives a detection rate of 11% for clinically significant (pathogenic/likely pathogenic) findings. The significant findings have prompted clinical actions in 28 out of 37 patients (75.7%), while the findings with unknown significance have led to further management recommendation in only 1 patient (p<0.001). Nineteen out of the 28 management recommendations are “evidence-based” on either practice guidelines endorsed by a professional society (n = 9, Level 1) or peer-reviewed publications making medical management recommendation (n = 10, Level 2). CMA results impact medical management by precipitating referral to a specialist (n = 24); diagnostic testing (n = 25), surveillance of complications (n = 19), interventional procedure (n = 7), medication (n = 15) or lifestyle modification (n = 12). Conclusion The application of CMA in children with ID/DD, ASD, and/or MCAs in Hong Kong results in a diagnostic yield of ∼11% for pathogenic/likely pathogenic results. Importantly the yield for clinically actionable results is 8.6%. We advocate using diagnostic yield of clinically actionable results to evaluate CMA as it provides information of both clinical validity and clinical utility. Furthermore, it incorporates evidence-based medicine into the practice of genomic medicine. The same framework can be applied to other genomic testing strategies enabled by next-generation sequencing.
Collapse
Affiliation(s)
- Victoria Q. Tao
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kelvin Y. K. Chan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Yoyo W. Y. Chu
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gary T. K. Mok
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Tiong Y. Tan
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Royal Children's Hospital, Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - So Lun Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wing Fai Tang
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Winnie W. Y. Tso
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Elizabeth T. Lau
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Anita S. Y. Kan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Mary H. Tang
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yu-lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Brian H. Y. Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Obstetrics and Gynecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- * E-mail:
| |
Collapse
|