China Nagano1, Kandai Nozu2, Naoya Morisada1, Masahiko Yazawa3, Daisuke Ichikawa3, Keita Numasawa4, Hiroyo Kourakata5, Chieko Matsumura6, Satoshi Tazoe7, Ryojiro Tanaka8, Tomohiko Yamamura1, Shogo Minamikawa1, Tomoko Horinouchi1, Keita Nakanishi1, Junya Fujimura1, Nana Sakakibara1, Yoshimi Nozu1, Ming Juan Ye1, Hiroshi Kaito1, Kazumoto Iijima1. 1. Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. 2. Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan. nozu@med.kobe-u.ac.jp. 3. Department of Nephrology and Hypertension, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki-shi, Kanagawa, 216-8511, Japan. 4. Department of Pediatrics, Yokohama City University Hospital, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0041, Japan. 5. Department of Respiratory Medicine, Niigata Saiseikai Sanjo Hospital, 6-18 Oonohata, Sanjyo-shi, Niigata, 955-8511, Japan. 6. Department of Pediatrics, National Hospital Organization Chiba East Hospital, 673 Nitonacho, Chuo-ku, Chiba, Chiba, 260-8712, Japan. 7. Department of Metabolism, Osaka City General Hospital, 2-13-22 Miyakojimahondori, Miyakojima-ku, Osaka, 534-0021, Japan. 8. Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, 1-6-7 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Abstract
BACKGROUND: Comprehensive genetic approaches for diagnosing inherited kidney diseases using next-generation sequencing (NGS) have recently been established. However, even with these approaches, we are still failing to detect gene defects in some patients who appear to suffer from genetic diseases. One of the reasons for this is the difficulty of detecting copy number variations (CNVs) using our current approaches. For such cases, we can apply methods of array-based comparative genomic hybridization (aCGH) or multiplex ligation and probe amplification (MLPA); however, these are expensive and laborious and also often fail to identify CNVs. Here, we report seven cases with CNVs in various inherited kidney diseases screened by NGS pair analysis. METHODS: Targeted sequencing analysis for causative genes was conducted for cases with suspected inherited kidney diseases, for some of which a definitive genetic diagnosis had not been achieved. We conducted pair analysis using NGS data for those cases. When CNVs were detected by pair analysis, they were confirmed by aCGH and/or MLPA. RESULTS: In seven cases, CNVs in various causative genes of inherited kidney diseases were detected by pair analysis. With aCGH and/or MLPA, pathogenic CNV variants were confirmed: COL4A5 or HNF1B in two cases each, and EYA1, CLCNKB, or PAX2 in one each. CONCLUSION: We presented seven cases with CNVs in various genes that were screened by pair analysis. The NGS-based CNV detection method is useful for comprehensive screening of CNVs, and our results revealed that, for a certain proportion of cases, CNV analysis is necessary for accurate genetic diagnosis.
BACKGROUND: Comprehensive genetic approaches for diagnosing inherited kidney diseases using next-generation sequencing (NGS) have recently been established. However, even with these approaches, we are still failing to detect gene defects in some patients who appear to suffer from genetic diseases. One of the reasons for this is the difficulty of detecting copy number variations (CNVs) using our current approaches. For such cases, we can apply methods of array-based comparative genomic hybridization (aCGH) or multiplex ligation and probe amplification (MLPA); however, these are expensive and laborious and also often fail to identify CNVs. Here, we report seven cases with CNVs in various inherited kidney diseases screened by NGS pair analysis. METHODS: Targeted sequencing analysis for causative genes was conducted for cases with suspected inherited kidney diseases, for some of which a definitive genetic diagnosis had not been achieved. We conducted pair analysis using NGS data for those cases. When CNVs were detected by pair analysis, they were confirmed by aCGH and/or MLPA. RESULTS: In seven cases, CNVs in various causative genes of inherited kidney diseases were detected by pair analysis. With aCGH and/or MLPA, pathogenic CNV variants were confirmed: COL4A5 or HNF1B in two cases each, and EYA1, CLCNKB, or PAX2 in one each. CONCLUSION: We presented seven cases with CNVs in various genes that were screened by pair analysis. The NGS-based CNV detection method is useful for comprehensive screening of CNVs, and our results revealed that, for a certain proportion of cases, CNV analysis is necessary for accurate genetic diagnosis.
Authors: Getiria Onsongo; Linda B Baughn; Matthew Bower; Christine Henzler; Matthew Schomaker; Kevin A T Silverstein; Bharat Thyagarajan Journal: J Mol Diagn Date: 2016-09-03 Impact factor: 5.568
Authors: Carolin E Sadowski; Svjetlana Lovric; Shazia Ashraf; Werner L Pabst; Heon Yung Gee; Stefan Kohl; Susanne Engelmann; Virginia Vega-Warner; Humphrey Fang; Jan Halbritter; Michael J Somers; Weizhen Tan; Shirlee Shril; Inès Fessi; Richard P Lifton; Detlef Bockenhauer; Sherif El-Desoky; Jameela A Kari; Martin Zenker; Markus J Kemper; Dominik Mueller; Hanan M Fathy; Neveen A Soliman; Friedhelm Hildebrandt Journal: J Am Soc Nephrol Date: 2014-10-27 Impact factor: 10.121
Authors: Anna Fowler; Shazia Mahamdallie; Elise Ruark; Sheila Seal; Emma Ramsay; Matthew Clarke; Imran Uddin; Harriet Wylie; Ann Strydom; Gerton Lunter; Nazneen Rahman Journal: Wellcome Open Res Date: 2016-11-25