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Li N, Zhang Y, Shen M, Xu Y. A fully integrated SNP genotyping system for hereditary hearing-loss detection. LAB ON A CHIP 2022; 22:697-708. [PMID: 34923580 DOI: 10.1039/d1lc00805f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Hereditary hearing loss is one of the most common human neurosensory disorders, and there is a great need for early intervention methods such as genetically screening newborns. Single nucleotide polymorphisms (SNPs) are the major genetic targets for hearing-loss screening. In this study, a fully integrated SNP genotyping system was constructed to identify hereditary hearing loss-related genetic markers from human whole blood. The entire detection process, including blood cell lysis, nucleic acid extraction, the reaction mixture distribution, the chambers sealing and the two-colour multiplex competitive allele-specific polymerase chain reaction (KASP), can be automatically conducted in a self-contained cassette within 3 hours. To critically evaluate the performance of the system, its specificity, sensitivity and stability were assessed. Then, 13 clinical samples were genotyped with this fluidic cassette system to detect seven hotspot deafness-associated mutations in three genes (MT-RNR1, GJB2 and SLC26A4). The detection results of the cassette system were 100% concordant with those obtained by Sanger sequencing, proving its accuracy in the genetic screening of inherited hearing loss.
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Affiliation(s)
- Nan Li
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Yuanyue Zhang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Minjie Shen
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China.
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Yan D, Xiang G, Chai X, Qing J, Shang H, Zou B, Mittal R, Shen J, Smith RJH, Fan YS, Blanton SH, Tekin M, Morton C, Xing W, Cheng J, Liu XZ. Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach. PLoS One 2017; 12:e0169219. [PMID: 28273078 PMCID: PMC5342170 DOI: 10.1371/journal.pone.0169219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/04/2016] [Indexed: 12/12/2022] Open
Abstract
The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Guangxin Xiang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Xingping Chai
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jie Qing
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Haiqiong Shang
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Bing Zou
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Cambridge, Massachusetts, United States of America
| | - Richard J. H. Smith
- Department of Otolaryngology - Head and Neck Surgery, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Yao-Shan Fan
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Susan H. Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Mustafa Tekin
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Cynthia Morton
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Evolution and Genomic Science, School of Biological Sciences, Manchester Academic Health Science Center, University of Manchester, United Kingdom
| | - Wanli Xing
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- Tsinghua University School of Medicine, Beijing, China
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Tsinghua University School of Medicine, Beijing, China
- Dr. John T. Macdonald Department of Human Genetics and John P.Hussman Institute for Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
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Wang S, Sun Y, Gan W, Liu Y, Xiang G, Wang D, Wang L, Cheng J, Liu P. An automated microfluidic system for single-stranded DNA preparation and magnetic bead-based microarray analysis. BIOMICROFLUIDICS 2015; 9:024102. [PMID: 25825617 PMCID: PMC4352165 DOI: 10.1063/1.4914024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/18/2015] [Indexed: 05/25/2023]
Abstract
We present an integrated microfluidic device capable of performing single-stranded DNA (ssDNA) preparation and magnetic bead-based microarray analysis with a white-light detection for detecting mutations that account for hereditary hearing loss. The entire operation process, which includes loading of streptavidin-coated magnetic beads (MBs) and biotin-labeled polymerase chain reaction products, active dispersion of the MBs with DNA for binding, alkaline denaturation of DNA, dynamic hybridization of the bead-labeled ssDNA to a tag array, and white-light detection, can all be automatically accomplished in a single chamber of the microchip, which was operated on a self-contained instrument with all the necessary components for thermal control, fluidic control, and detection. Two novel mixing valves with embedded polydimethylsiloxane membranes, which can alternately generate a 3-μl pulse flow at a peak rate of around 160 mm/s, were integrated into the chip for thoroughly dispersing magnetic beads in 2 min. The binding efficiency of biotinylated oligonucleotides to beads was measured to be 80.6% of that obtained in a tube with the conventional method. To critically test the performance of this automated microsystem, we employed a commercial microarray-based detection kit for detecting nine mutation loci that account for hereditary hearing loss. The limit of detection of the microsystem was determined as 2.5 ng of input K562 standard genomic DNA using this kit. In addition, four blood samples obtained from persons with mutations were all correctly typed by our system in less than 45 min per run. The fully automated, "amplicon-in-answer-out" operation, together with the white-light detection, makes our system an excellent platform for low-cost, rapid genotyping in clinical diagnosis.
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