Comprehensive validation of a diagnostic strategy for sequencing genes with one or multiple pseudogenes using pseudoxanthoma elasticum as a model |
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| Authors: | Wouter Steyaert Shana Verschuere Paul J Coucke Olivier M Vanakker |
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| Institution: | 1. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium;2. Department of Biomolecular Medicine, Ghent University, Ghent, Belgium;1. Department of Rehabilitation Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China;2. Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;3. Tsinghua-Peking Center for Life Sciences, Beijing 100084, China;4. National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China;1. Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;2. The Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China;3. Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;4. Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan;5. Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou 310058, China;6. MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;1. National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;2. University of the Chinese Academy of Sciences, Beijing 100049, China;3. School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China;1. Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China;2. Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China;3. DIAGenes Precision Medicine, Beijing 102600, China;4. National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China;5. Shanghai Adeptus Biotechnology, Shanghai 200126, China;6. Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China;7. Department of Neurology, Xiangya Hospital, Central South University, Changsha Hunan, 410083, China;8. CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China;9. School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, China;10. CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China;11. State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China |
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| Abstract: | Pseudogenes are frequently encountered noncoding sequences with a high sequence similarity to their protein-coding paralogue. For this reason, their presence is often considered troublesome in molecular diagnostics. In pseudoxanthoma elasticum(PXE), a disease predominantly caused by mutations in ATPbinding cassette family C member 6(ABCC6), the presence of two pseudogenes complicates the analysis of sequence data. With whole-exome sequencing(WES) becoming the standard of care in molecular diagnostics, we wanted to evaluate whether this technique is as reliable as gene-specific targeted enrichment analysis for the analysis of ABCC6. We established a PCR-based targeted enrichment and next-generation sequencing testing approach and demonstrated that the ABCC6-specific enrichment combined with the applied mapping algorithm overcomes the complication of ABCC6 pseudogene aspecificities, contrary to WES. We propose a time-and cost-efficient diagnostic strategy for comprehensive and accurate molecular genetic testing of PXE, which is highly automatable. |
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| Keywords: | Pseudoxanthoma elasticum Pseudogenes Next-generation sequencing Whole-exome sequencing Targeted enrichment |
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