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Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, Aoi H, Azuma Y, Itai T, Saida K, Fukuda H, Sekiguchi F, Sakaguchi T, Lei M, Ohori S, Sakamoto M, Kato M, Koike T, Takahashi Y, Tanda K, Hyodo Y, Honjo RS, Bertola DR, Kim CA, Goto M, Okazaki T, Yamada H, Maegaki Y, Osaka H, Ngu LH, Siew CG, Teik KW, Akasaka M, Doi H, Tanaka F, Goto T, Guo L, Ikegawa S, Haginoya K, Haniffa M, Hiraishi N, Hiraki Y, Ikemoto S, Daida A, Hamano SI, Miura M, Ishiyama A, Kawano O, Kondo A, Matsumoto H, Okamoto N, Okanishi T, Oyoshi Y, Takeshita E, Suzuki T, Ogawa Y, Handa H, Miyazono Y, Koshimizu E, Fujita A, Takata A, Miyake N, Mizuguchi T, Matsumoto N. Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses. Hum Mutat 2020; 42:50-65. [PMID: 33131168 DOI: 10.1002/humu.24129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.
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Affiliation(s)
- Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohiro Sakaguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Takayoshi Koike
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Koichi Tanda
- Department of Pediatrics, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Rachel S Honjo
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Debora Romeo Bertola
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Masahide Goto
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Tetsuya Okazaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hiroyuki Yamada
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Yoshihiro Maegaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Lock-Hock Ngu
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Ch'ng G Siew
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Keng W Teik
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Manami Akasaka
- Department of Pediatrics, Iwate Medical University School of Medicine, Morioka, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Muzhirah Haniffa
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Nozomi Hiraishi
- Department of Pediatrics, Yokohama City University Medical Center, Yokohama, Japan
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | - Satoru Ikemoto
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Atsuro Daida
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Shin-Ichiro Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Masaki Miura
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Osamu Kawano
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Akane Kondo
- Clinical Genetics Center, Shikoku Medical Center for Children and Adults, National Hospital Organization, Kagawa, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Tohru Okanishi
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan.,Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Yukimi Oyoshi
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiyuki Ogawa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yayoi Miyazono
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Benquey T, Fockens E, Kouton L, Delmont E, Martini N, Levy N, Attarian S, Bonello-Palot N. A New Point Mutation in the PMP22 Gene in a Family Suffering From Atypical HNPP. J Neuromuscul Dis 2020; 7:505-510. [DOI: 10.3233/jnd-190460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant inherited disorder commonly presenting with acute-onset, non-painful focal sensory and motor mono neuropathy. In 80% of cases, the genetic defect is a 1.5 Mb deletion on chromosome 17p11.2, including PMP22. Only few cases of partial deletion and point mutations in PMP22 are involved in HNPP. We investigated a 62-years-old man with lower limb plexopathy first considered as Garland’s syndrome. A month later, his 29 years old son also consulted for paresthesia on the peroneal nerve. Targeted sequencing of the PMP22 gene identified a c.370delT (p.Trp124Glyfs*31) in both affected patients. We report a new PMP22 point mutation associated with an atypical clinical phenotype of HNPP, a painful plexopathy of the lower limb worsenen by diabetes and a mere paresthesia, but a typical ENMG. This study illustrates the large spectrum of the disease, and emphasizes the importance of a complete ENMG and family history.
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Affiliation(s)
- T. Benquey
- Service de Biochimie et Biologie moléculaire Grand Est, Unité Médicale Pathologies neurologiques et cardiologiques, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Bron, France
| | - E. Fockens
- Referral Centre for ALS and Neuromuscular Diseases, Hospital La Timone 264 rue Saint Pierre, 13005, Marseille, France
| | - L. Kouton
- Referral Centre for ALS and Neuromuscular Diseases, Hospital La Timone 264 rue Saint Pierre, 13005, Marseille, France
| | - E. Delmont
- Referral Centre for ALS and Neuromuscular Diseases, Hospital La Timone 264 rue Saint Pierre, 13005, Marseille, France
| | - N. Martini
- Referral Centre for ALS and Neuromuscular Diseases, Hospital La Timone 264 rue Saint Pierre, 13005, Marseille, France
| | - N. Levy
- Aix Marseille University, INSERM, GMGF, Marseille, France
- Medical Genetics Department, La Timone Teaching hospital, 264, rue Saint-Pierre, 13385 Marseille, France
| | - S. Attarian
- Referral Centre for ALS and Neuromuscular Diseases, Hospital La Timone 264 rue Saint Pierre, 13005, Marseille, France
- Aix Marseille University, INSERM, GMGF, Marseille, France
| | - N. Bonello-Palot
- Aix Marseille University, INSERM, GMGF, Marseille, France
- Medical Genetics Department, La Timone Teaching hospital, 264, rue Saint-Pierre, 13385 Marseille, France
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5
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Fusco C, Spagnoli C, Salerno GG, Pavlidis E, Frattini D, Pisani F. Hereditary neuropathy with liability to pressure palsy (HNPP): report of a family with a new point mutation in PMP22 gene. Ital J Pediatr 2017; 43:97. [PMID: 29078790 PMCID: PMC5658948 DOI: 10.1186/s13052-017-0414-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022] Open
Abstract
Background Hereditary neuropathy with liability to pressure palsy (HNPP) is an autosomal dominant disorder most commonly presenting with acute-onset, non-painful focal sensory and motor mononeuropathy. Approximately 80% of patients carry a 1.5 Mb deletion of chromosome 17p11.2 involving the peripheral myelin protein 22 gene (PMP22), the same duplicated in Charcot-Marie-Tooth 1A patients. In a small proportion of patients the disease is caused by PMP22 point mutations. Case presentation We report on a familial case harbouring a new point mutation in the PMP22 gene. The proband is a 4-years-old girl with acute onset of focal numbness and weakness in her right hand. Electroneurography demonstrated transient sensory and motor radial nerves involvement. In her father, reporting chronic symptoms (cramps and exercise-induced myalgia), we uncovered mild atrophy and areflexia on clinical examination and a mixed (predominantly demyelinating) polyneuropathy with sensory-motor involvement on electrophysiological study. Both carried a nucleotidic substitution c.178 + 2 T > C on intron 3 of the PMP22 gene, involving the splicing donor site, not reported on databases but predicted to be likely pathogenic. Conclusions We described a previously unreported point mutation in PMP22 gene, which led to the development of a HNPP phenotype in a child and her father. In children evaluated for a sensory and motor transient episode, HNPP disorder due to PMP22 mutations should be suspected. Clinical and electrophysiological studies should be extended to all family members even in the absence of previous episodes suggestive for HNPP.
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Affiliation(s)
- Carlo Fusco
- Department of Pediatrics, Child Neurology Unit, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy.,Department of Pediatrics, Pediatric Neurophysiology Laboratory, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Carlotta Spagnoli
- Department of Pediatrics, Child Neurology Unit, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy.
| | - Grazia Gabriella Salerno
- Department of Pediatrics, Child Neurology Unit, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Elena Pavlidis
- Department of Pediatrics, Child Neurology Unit, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Daniele Frattini
- Department of Pediatrics, Child Neurology Unit, Santa Maria Nuova Hospital, IRCCS, viale Risorgimento 80, 42123, Reggio Emilia, Italy
| | - Francesco Pisani
- Child Neuropsychiatry Unit, Medicine & Surgery Department, University of Parma, via Gramsci, 14, 43126, Parma, Italy
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