251
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Whole‐exome sequencing as a diagnostic tool for distal renal tubular acidosis. JORNAL DE PEDIATRIA (VERSÃO EM PORTUGUÊS) 2015. [DOI: 10.1016/j.jpedp.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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252
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Reddy B, Kelawala DN, Shah T, Patel AB, Patil DB, Parikh PV, Patel N, Parmar N, Mohapatra AB, Singh KM, Menon R, Pandya D, Jakhesara SJ, Koringa PG, Rao MV, Joshi CG. Identification of putative SNPs in progressive retinal atrophy affected Canis lupus familiaris using exome sequencing. Mamm Genome 2015; 26:638-49. [PMID: 26515695 DOI: 10.1007/s00335-015-9607-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/08/2015] [Indexed: 11/30/2022]
Abstract
Progressive retinal atrophy (PRA) is one of the major causes of retinal photoreceptor cell degeneration in canines. The inheritance pattern of PRA is autosomal recessive and genetically heterogeneous. Here, using targeted sequencing technology, we have performed exome sequencing of 10 PRA-affected (Spitz=7, Cocker Spaniel=1, Lhasa Aphso=1 and Spitz-Labrador cross breed=1) and 6 normal (Spitz=5, Cocker Spaniel=1) dogs. The high-throughput sequencing using 454-Roche Titanium sequencer generated about 2.16 Giga bases of raw data. Initially, we have successfully identified 25,619 single nucleotide polymorphisms (SNPs) that passed the stringent SNP calling parameters. Further, we performed association study on the cohort, and the highly significant (0.001) associations were short-listed and investigated in-depth. Out of the 171 significant SNPs, 113 were previously unreported. Interestingly, six among them were non-synonymous coding (NSC) SNPs, which includes CPPED1 A>G (p.M307V), PITRM1 T>G (p.S715A), APP G>A (p.T266M), RNF213 A>G (p.V1482A), C>A (p.V1456L), and SLC46A3 G>A (p.R168Q). On the other hand, 35 out of 113 unreported SNPs were falling in regulatory regions such as 3'-UTR, 5'-UTR, etc. In-depth bioinformatics analysis revealed that majority of NSC SNPs have damaging effect and alter protein stability. This study highlighted the genetic markers associated with PRA, which will help to develop genetic assay-based screening in effective breeding.
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Affiliation(s)
- Bhaskar Reddy
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.,Department of Zoology, Genetic Diagnostic Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Divyesh N Kelawala
- Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Tejas Shah
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Anand B Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Deepak B Patil
- Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Pinesh V Parikh
- Department of Veterinary Surgery & Radiology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Namrata Patel
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Nidhi Parmar
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Amit B Mohapatra
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Krishna M Singh
- Datar Genetics Ltd, F-8, D Road, Ambad, Nasik, Maharashtra, 422010, India
| | - Ramesh Menon
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Dipal Pandya
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Subhash J Jakhesara
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Prakash G Koringa
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India
| | - Mandava V Rao
- Department of Zoology, Genetic Diagnostic Centre, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Chaitanya G Joshi
- Ome Research Facility, Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, 388001, India.
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253
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Exome Capture with Heterologous Enrichment in Pig (Sus scrofa). PLoS One 2015; 10:e0139328. [PMID: 26431395 PMCID: PMC4592256 DOI: 10.1371/journal.pone.0139328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/11/2015] [Indexed: 12/26/2022] Open
Abstract
The discovery of new protein-coding DNA variants related to carcass traits is very important for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer the opportunity to focus on the regions of DNA potentially related to the gene and protein expression. In this research a human commercial target enrichment kit was used to evaluate its performances for pig exome capture and for the identification of DNA variants suitable for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa (ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and 35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a total of 232,530 single nucleotide variants (SNVs) of which 20.6% mapped in exonic regions and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom MassARRAY® system confirms that this “human-on-pig” approach offers new potentiality for the identification of DNA variants in protein-coding genes.
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254
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Palagano E, Blair HC, Pangrazio A, Tourkova I, Strina D, Angius A, Cuccuru G, Oppo M, Uva P, Van Hul W, Boudin E, Superti-Furga A, Faletra F, Nocerino A, Ferrari MC, Grappiolo G, Monari M, Montanelli A, Vezzoni P, Villa A, Sobacchi C. Buried in the Middle but Guilty: Intronic Mutations in the TCIRG1 Gene Cause Human Autosomal Recessive Osteopetrosis. J Bone Miner Res 2015; 30:1814-21. [PMID: 25829125 DOI: 10.1002/jbmr.2517] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/16/2015] [Accepted: 03/22/2015] [Indexed: 11/10/2022]
Abstract
Autosomal recessive osteopetrosis (ARO) is a rare genetic bone disease with genotypic and phenotypic heterogeneity, sometimes translating into delayed diagnosis and treatment. In particular, cases of intermediate severity often constitute a diagnostic challenge and represent good candidates for exome sequencing. Here, we describe the tortuous path to identification of the molecular defect in two siblings, in which osteopetrosis diagnosed in early childhood followed a milder course, allowing them to reach the adult age in relatively good conditions with no specific therapy. No clearly pathogenic mutation was identified either with standard amplification and resequencing protocols or with exome sequencing analysis. While evaluating the possible impact of a 3'UTR variant on the TCIRG1 expression, we found a novel single nucleotide change buried in the middle of intron 15 of the TCIRG1 gene, about 150 nucleotides away from the closest canonical splice site. By sequencing a number of independent cDNA clones covering exons 14 to 17, we demonstrated that this mutation reduced splicing efficiency but did not completely abrogate the production of the normal transcript. Prompted by this finding, we sequenced the same genomic region in 33 patients from our unresolved ARO cohort and found three additional novel single nucleotide changes in a similar location and with a predicted disruptive effect on splicing, further confirmed in one of them at the transcript level. Overall, we identified an intronic region in TCIRG1 that seems to be particularly prone to splicing mutations, allowing the production of a small amount of protein sufficient to reduce the severity of the phenotype usually associated with TCIRG1 defects. On this basis, we would recommend including TCIRG1 not only in the molecular work-up of severe infantile osteopetrosis but also in intermediate cases and carefully evaluating the possible effects of intronic changes.
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Affiliation(s)
- Eleonora Palagano
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Harry C Blair
- Veteran's Affairs Medical Center and Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alessandra Pangrazio
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Irina Tourkova
- Veteran's Affairs Medical Center and Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dario Strina
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Andrea Angius
- CRS4, Science and Technology Park Polaris, Piscina Manna, Pula, Italy.,Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Monserrato, Italy
| | - Gianmauro Cuccuru
- CRS4, Science and Technology Park Polaris, Piscina Manna, Pula, Italy
| | - Manuela Oppo
- CRS4, Science and Technology Park Polaris, Piscina Manna, Pula, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Piscina Manna, Pula, Italy
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Andrea Superti-Furga
- Department of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Flavio Faletra
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Agostino Nocerino
- Clinica Pediatrica, Azienda Ospedaliero-Universitaria "S Maria della Misericordia", Udine, Italy
| | - Matteo C Ferrari
- Hip and Prosthetic Replacement Unit, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Guido Grappiolo
- Hip and Prosthetic Replacement Unit, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Marta Monari
- Clinical Investigation Laboratory, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Alessandro Montanelli
- Clinical Investigation Laboratory, Humanitas Clinical and Research Center, Rozzano, Italy
| | - Paolo Vezzoni
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Anna Villa
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
| | - Cristina Sobacchi
- UOS/IRGB, Milan Unit, National Research Council (CNR), Milan, Italy.,Humanitas Clinical and Research Center, Rozzano, Italy
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255
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Sokolenko AP, Suspitsin EN, Kuligina ES, Bizin IV, Frishman D, Imyanitov EN. Identification of novel hereditary cancer genes by whole exome sequencing. Cancer Lett 2015; 369:274-88. [PMID: 26427841 DOI: 10.1016/j.canlet.2015.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 02/09/2023]
Abstract
Whole exome sequencing (WES) provides a powerful tool for medical genetic research. Several dozens of WES studies involving patients with hereditary cancer syndromes have already been reported. WES led to breakthrough in understanding of the genetic basis of some exceptionally rare syndromes; for example, identification of germ-line SMARCA4 mutations in patients with ovarian hypercalcemic small cell carcinomas indeed explains a noticeable share of familial aggregation of this disease. However, studies on common cancer types turned out to be more difficult. In particular, there is almost a dozen of reports describing WES analysis of breast cancer patients, but none of them yet succeeded to reveal a gene responsible for the significant share of missing heritability. Virtually all components of WES studies require substantial improvement, e.g. technical performance of WES, interpretation of WES results, mode of patient selection, etc. Most of contemporary investigations focus on genes with autosomal dominant mechanism of inheritance; however, recessive and oligogenic models of transmission of cancer susceptibility also need to be considered. It is expected that the list of medically relevant tumor-predisposing genes will be rapidly expanding in the next few years.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Ilya V Bizin
- Laboratory of Bioinformatics, RASA Research Center, St.-Petersburg State Polytechnical University, St.-Petersburg 195251, Russia
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen, Freising 85354, Germany; Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg 85764, Germany
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia; Department of Oncology, St.-Petersburg State University, St.-Petersburg 199034, Russia.
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256
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Wang C, Duan S, Lv G, Lai X, Chen R, Lin H, Qiu S, Tang J, Kuang W, Xu C. Using whole exome sequencing and bioformatics in the molecular autopsy of a sudden unexplained death syndrome (SUDS) case. Forensic Sci Int 2015; 257:e20-e25. [PMID: 26385840 DOI: 10.1016/j.forsciint.2015.08.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/27/2015] [Accepted: 08/28/2015] [Indexed: 01/09/2023]
Abstract
Whole exome sequencing (WES) and bioinformatics analysis were used to investigate potential disease-causing gene mutations in a sudden unexplained death syndrome (SUDS) case after autopsy and pathology tests failed to suggest an obvious disease mechanism. Following whole exome sequencing, a 3-step bioinformatics filtering procedure was carried out to identify possible pathogenic genomic features. Single nucleotide variations (SNVs) were analyzed and ranked by likely mutation impact using various open online tools. After screening, we identified G643S as a putative causative heterozygous mutation in the KCNQ1 gene. This mutation has been reported in abnormalities consistent with SUDS, such as IKs in cardiac myocytes, a condition that predisposes for arrhythmias. Our work demonstrates the application of sequencing technology at the whole exome level for determining potential causes of an otherwise unexplained death.
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Affiliation(s)
- Chun Wang
- Chengdu Sport University, Chengdu, Sichuan 610041, PR China
| | - Shan Duan
- Shenzhen Research Institute of Population and Family Planning, Shenzhen, Guangdong 518040, PR China
| | - Guoli Lv
- Guangzhou institute of Forensic Science, Guangzhou, Guangdong 510030, PR China
| | - Xiaoping Lai
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Rui Chen
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Hanguang Lin
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Shengyuan Qiu
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Jianpin Tang
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Wenjian Kuang
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China
| | - Chuanchao Xu
- Guangdong Medical College, Dongguan, Guangdong 523808, PR China.
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257
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Sénécal K, Vears DF, Bertier G, Knoppers BM, Borry P. Genome-based newborn screening: a conceptual analysis of the best interests of the child standard. Per Med 2015; 12:439-441. [PMID: 29749887 DOI: 10.2217/pme.15.28] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Karine Sénécal
- Centre of Genomics & Policy, McGill University, Montreal, Canada
| | - Danya F Vears
- Centre for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
| | | | | | - Pascal Borry
- Centre for Biomedical Ethics & Law, Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
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258
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Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
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Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
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259
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Sebastian A, Herdegen M, Migalska M, Radwan J. amplisas: a web server for multilocus genotyping using next-generation amplicon sequencing data. Mol Ecol Resour 2015; 16:498-510. [DOI: 10.1111/1755-0998.12453] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/16/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Alvaro Sebastian
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Magdalena Herdegen
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Magdalena Migalska
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
| | - Jacek Radwan
- Evolutionary Biology Group; Faculty of Biology; Adam Mickiewicz University; ul. Umultowska 89 61-614 Poznan Poland
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260
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Chiang J(PW, Lamey T, McLaren T, Thompson JA, Montgomery H, De Roach J. Progress and prospects of next-generation sequencing testing for inherited retinal dystrophy. Expert Rev Mol Diagn 2015; 15:1269-75. [PMID: 26394700 PMCID: PMC4659341 DOI: 10.1586/14737159.2015.1081057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Next-generation sequencing, also known as massively paralleled sequencing, offers an unprecedented opportunity to study disease mechanisms of inherited retinal dystrophies: a dramatic change from a few years ago. The specific involvement of the retina and the manageable number of genes to sequence make inherited retinal dystrophies an attractive model to study genotype-phenotype correlations. Costs are reducing rapidly and the current overall mutation detection rate of approximately 60% offers real potential for personalized medicine and treatments. This report addresses the challenges ahead, which include: better understanding of the mutation mechanisms of syndromic genes in apparent non-syndromic patients; finding mutations in patients who have tested negative or inconclusive; better variant calling, especially for intronic and synonymous variants; more precise genotype-phenotype correlations and making genetic testing more broadly accessible.
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Affiliation(s)
- John (Pei-Wen) Chiang
- Casey Eye Institute Molecular Diagnostic Laboratory, Oregon Health Science University, Portland, OR, USA
| | - Tina Lamey
- Australian Inherited Retinal Disease Register and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - Terri McLaren
- Australian Inherited Retinal Disease Register and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Register and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - Hannah Montgomery
- Australian Inherited Retinal Disease Register and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - John De Roach
- Australian Inherited Retinal Disease Register and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
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261
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Fogel BL, Lee H, Strom SP, Deignan JL, Nelson SF. Clinical exome sequencing in neurogenetic and neuropsychiatric disorders. Ann N Y Acad Sci 2015; 1366:49-60. [PMID: 26250888 DOI: 10.1111/nyas.12850] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Exome sequencing has recently been elevated to the standard of care for genetic diagnostic testing, particularly for genetically diverse and clinically heterogeneous disorders. This review provides a clinically oriented discussion of the next-generation sequencing technology that makes exome sequencing possible and how such technology is applied to the diagnosis of Mendelian disease, including clinically significant de novo variation, interpretation of variants of uncertain clinical significance, the future potential for genetic assessments of disease risk, and the substantial benefits in diagnostic efficiency. Important caveats are also discussed, including the implications of incidental or secondary findings detected during exome sequencing and the relationship of exome sequencing to other methods of clinical genomic testing, such as chromosomal microarray and genome sequencing. Overall, the widespread adoption and use of exome sequencing in routine clinical practice is expected to improve diagnosis rates and reduce test costs, while leading to improvements in patient outcomes and a renewed emphasis on disease management.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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262
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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263
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Shimizu K, Oishi A, Oishi M, Ogino K, Morooka S, Sugahara M, Gotoh N, Yoshimura N. Next-Generation Sequencing-Based Molecular Diagnosis of Choroideremia. Case Rep Ophthalmol 2015; 6:246-50. [PMID: 26327910 PMCID: PMC4553918 DOI: 10.1159/000437348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We screened patients with choroideremia using next-generation sequencing (NGS) and identified a novel mutation and a known mutation in the CHM gene. One patient presented an atypical fundus appearance for choroideremia. Another patient presented macular hole retinal detachment in the left eye. The present case series shows the utility of NGS-based screening in patients with choroideremia. In addition, the presence of macular hole in 1 of the 2 patients, together with a previous report, indicated the susceptibility of patients with choroideremia to macular hole.
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Affiliation(s)
- Kayo Shimizu
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Maho Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Ogino
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Satoshi Morooka
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masako Sugahara
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimoto Gotoh
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
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264
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Nyegaard M, Rendtorff ND, Nielsen MS, Corydon TJ, Demontis D, Starnawska A, Hedemand A, Buniello A, Niola F, Overgaard MT, Leal SM, Ahmad W, Wikman FP, Petersen KB, Crüger DG, Oostrik J, Kremer H, Tommerup N, Frödin M, Steel KP, Tranebjærg L, Børglum AD. A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment. PLoS Genet 2015. [PMID: 26197441 PMCID: PMC4510537 DOI: 10.1371/journal.pgen.1005386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nonsyndromic hearing impairment (NSHI) is a highly heterogeneous condition with more than eighty known causative genes. However, in the clinical setting, a large number of NSHI families have unexplained etiology, suggesting that there are many more genes to be identified. In this study we used SNP-based linkage analysis and follow up microsatellite markers to identify a novel locus (DFNA66) on chromosome 6q15-21 (LOD 5.1) in a large Danish family with dominantly inherited NSHI. By locus specific capture and next-generation sequencing, we identified a c.574C>T heterozygous nonsense mutation (p.R192*) in CD164. This gene encodes a 197 amino acid transmembrane sialomucin (known as endolyn, MUC-24 or CD164), which is widely expressed and involved in cell adhesion and migration. The mutation segregated with the phenotype and was absent in 1200 Danish control individuals and in databases with whole-genome and exome sequence data. The predicted effect of the mutation was a truncation of the last six C-terminal residues of the cytoplasmic tail of CD164, including a highly conserved canonical sorting motif (YXXФ). In whole blood from an affected individual, we found by RT-PCR both the wild-type and the mutated transcript suggesting that the mutant transcript escapes nonsense mediated decay. Functional studies in HEK cells demonstrated that the truncated protein was almost completely retained on the plasma cell membrane in contrast to the wild-type protein, which targeted primarily to the endo-lysosomal compartments, implicating failed endocytosis as a possible disease mechanism. In the mouse ear, we found CD164 expressed in the inner and outer hair cells of the organ of Corti, as well as in other locations in the cochlear duct. In conclusion, we have identified a new DFNA locus located on chromosome 6q15-21 and implicated CD164 as a novel gene for hearing impairment.
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Affiliation(s)
- Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
- * E-mail:
| | - Nanna D. Rendtorff
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark
- Clinical Genetic Clinic, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | | | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Anne Hedemand
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Francesco Niola
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Friedrik P. Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | | | | | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten Frödin
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Lisbeth Tranebjærg
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark
- Clinical Genetic Clinic, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Anders D. Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
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265
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Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Prakash A, Chen W, Sood R, Ledin J, Burgess SM. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res 2015; 25:1030-42. [PMID: 26048245 PMCID: PMC4484386 DOI: 10.1101/gr.186379.114] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 04/22/2015] [Indexed: 02/07/2023]
Abstract
The use of CRISPR/Cas9 as a genome-editing tool in various model organisms has radically changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the genome and large-scale phenotyping efforts. We describe a cloning-free single-guide RNA (sgRNA) synthesis, coupled with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish genome, in which we obtained a 99% success rate for generating mutations and an average germline transmission rate of 28%. We verified 678 unique alleles from 58 genes by high-throughput sequencing. We demonstrate that our method can be used for efficient multiplexed gene targeting. We also demonstrate that phenotyping can be done in the F1 generation by inbreeding two injected founder fish, significantly reducing animal husbandry and time. This study compares germline transmission data from CRISPR/Cas9 with those of TALENs and ZFNs and shows that efficiency of CRISPR/Cas9 is sixfold more efficient than other techniques. We show that the majority of published "rules" for efficient sgRNA design do not effectively predict germline transmission rates in zebrafish, with the exception of a GG or GA dinucleotide genomic match at the 5' end of the sgRNA. Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies.
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Affiliation(s)
- Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Matthew C LaFave
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer Idol
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Viviana Gallardo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Blake Carrington
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin Bishop
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - MaryPat Jones
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mingyu Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Ursula Harper
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sunny C Huang
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anupam Prakash
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Raman Sood
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Johan Ledin
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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266
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Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS One 2015; 10:e0131166. [PMID: 26115441 PMCID: PMC4483235 DOI: 10.1371/journal.pone.0131166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/29/2015] [Indexed: 12/19/2022] Open
Abstract
Next Generation Sequencing (NGS) methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS information needs. This study sought to investigate (1) how and where sequencing data is generated and analyzed, (2) research objectives and goals for NGS, (3) workforce capacity and unmet needs, (4) storage capacity and unmet needs, (5) available and anticipated funding resources, and (6) future challenges. As a precursor to informed decision making at our institution, we undertook a systematic needs assessment of investigators using survey methods. We recruited 331 investigators from over 60 departments and divisions at the University of Pittsburgh Schools of Health Sciences and had 140 respondents, or a 42% response rate. Results suggest that both sequencing and analysis bottlenecks currently exist. Significant educational needs were identified, including both investigator-focused needs, such as selection of NGS methods suitable for specific research objectives, and program-focused needs, such as support for training an analytic workforce. The absence of centralized infrastructure was identified as an important institutional gap. Key principles for organizations managing this change were formulated based on the survey responses. This needs assessment provides an in-depth case study which may be useful to other academic medical centers as they identify and plan for future needs.
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Affiliation(s)
- Albert Geskin
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth Legowski
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Anish Chakka
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Uma R Chandran
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - M. Michael Barmada
- Institute for Personalized Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - William A. LaFramboise
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Jeremy Berg
- Institute for Personalized Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Rebecca S. Jacobson
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
- Institute for Personalized Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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267
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Nakamura Y, Kikugawa S, Seki S, Takahata M, Iwasaki N, Terai H, Matsubara M, Fujioka F, Inagaki H, Kobayashi T, Kimura T, Kurahashi H, Kato H. PCSK5 mutation in a patient with the VACTERL association. BMC Res Notes 2015; 8:228. [PMID: 26055999 PMCID: PMC4467638 DOI: 10.1186/s13104-015-1166-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/12/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The VACTERL association is a typically sporadic, non-random collection of congenital anomalies that includes vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula with esophageal atresia, renal anomalies, and limb abnormalities. Although several chromosomal aberrations and gene mutations have been reported as disease-causative, these findings have been sparsely replicated to date. CASE PRESENTATION In the present study, whole exome sequencing of a case with the VACTERL association uncovered a novel frameshift mutation in the PCSK5 gene, which has been reported as one of the causative genes for the VACTERL association. Although this mutation appears potentially pathogenic in its functional aspects, it was also carried by the healthy father. Furthermore, a database survey revealed several other deleterious variants in the PCSK5 gene in the general population. CONCLUSIONS Further studies are necessary to clarify the etiological role of the PCSK5 mutation in the VACTERL association.
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Affiliation(s)
- Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
| | | | - Shoji Seki
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Masahiko Takahata
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Norimasa Iwasaki
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Hidetomi Terai
- Department of Orthopaedic Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.
| | - Mitsuhiro Matsubara
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Fumio Fujioka
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Tatsuya Kobayashi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Tomoatsu Kimura
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Hiroyuki Kato
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
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268
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Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, Carrington B, Bishop K, Jones M, Li M, Harper U, Huang SC, Prakash A, Chen W, Sood R, Ledin J, Burgess SM. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res 2015. [PMID: 26048245 DOI: 10.1101/gr.186379.114.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of CRISPR/Cas9 as a genome-editing tool in various model organisms has radically changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the genome and large-scale phenotyping efforts. We describe a cloning-free single-guide RNA (sgRNA) synthesis, coupled with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish genome, in which we obtained a 99% success rate for generating mutations and an average germline transmission rate of 28%. We verified 678 unique alleles from 58 genes by high-throughput sequencing. We demonstrate that our method can be used for efficient multiplexed gene targeting. We also demonstrate that phenotyping can be done in the F1 generation by inbreeding two injected founder fish, significantly reducing animal husbandry and time. This study compares germline transmission data from CRISPR/Cas9 with those of TALENs and ZFNs and shows that efficiency of CRISPR/Cas9 is sixfold more efficient than other techniques. We show that the majority of published "rules" for efficient sgRNA design do not effectively predict germline transmission rates in zebrafish, with the exception of a GG or GA dinucleotide genomic match at the 5' end of the sgRNA. Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies.
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Affiliation(s)
- Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Matthew C LaFave
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jennifer Idol
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Viviana Gallardo
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Blake Carrington
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin Bishop
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - MaryPat Jones
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mingyu Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Ursula Harper
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sunny C Huang
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Anupam Prakash
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Raman Sood
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Johan Ledin
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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269
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Zhu Q, Hu Q, Shepherd L, Wang J, Wei L, Morrison CD, Conroy JM, Glenn ST, Davis W, Kwan ML, Ergas IJ, Roh JM, Kushi LH, Ambrosone CB, Liu S, Yao S. The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology. Cancer Epidemiol Biomarkers Prev 2015; 24:1207-13. [PMID: 25990554 DOI: 10.1158/1055-9965.epi-15-0205] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/13/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) has recently emerged as an appealing approach to systematically study coding variants. However, the requirement for a large amount of high-quality DNA poses a barrier that may limit its application in large cancer epidemiologic studies. We evaluated the performance of WES with low input amount and saliva DNA as an alternative source material. METHODS Five breast cancer patients were randomly selected from the Pathways Study. From each patient, four samples, including 3 μg, 1 μg, and 0.2 μg blood DNA and 1 μg saliva DNA, were aliquoted for library preparation using the Agilent SureSelect Kit and sequencing using Illumina HiSeq2500. Quality metrics of sequencing and variant calling, as well as concordance of variant calls from the whole exome and 21 known breast cancer genes, were assessed by input amount and DNA source. RESULTS There was little difference by input amount or DNA source on the quality of sequencing and variant calling. The concordance rate was about 98% for single-nucleotide variant calls and 83% to 86% for short insertion/deletion calls. For the 21 known breast cancer genes, WES based on low input amount and saliva DNA identified the same set variants in samples from a same patient. CONCLUSIONS Low DNA input amount, as well as saliva DNA, can be used to generate WES data of satisfactory quality. IMPACT Our findings support the expansion of WES applications in cancer epidemiologic studies where only low DNA amount or saliva samples are available.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York.
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Lori Shepherd
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Carl D Morrison
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Jeffrey M Conroy
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York
| | - Sean T Glenn
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Marilyn L Kwan
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Isaac J Ergas
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Janise M Roh
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York.
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270
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Tetreault M, Bareke E, Nadaf J, Alirezaie N, Majewski J. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities. Expert Rev Mol Diagn 2015; 15:749-60. [PMID: 25959410 DOI: 10.1586/14737159.2015.1039516] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Whole-exome sequencing (WES) represents a significant breakthrough in the field of human genetics. This technology has largely contributed to the identification of new disease-causing genes and is now entering clinical laboratories. WES represents a powerful tool for diagnosis and could reduce the 'diagnostic odyssey' for many patients. In this review, we present a technical overview of WES analysis, variants annotation and interpretation in a clinical setting. We evaluate the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases. Finally, we discuss the efficacy of WES as a diagnostic tool and the impact on patient management.
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Affiliation(s)
- Martine Tetreault
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
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271
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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272
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O'Brien TD, Jia P, Xia J, Saxena U, Jin H, Vuong H, Kim P, Wang Q, Aryee MJ, Mino-Kenudson M, Engelman JA, Le LP, Iafrate AJ, Heist RS, Pao W, Zhao Z. Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer. Methods 2015; 83:118-27. [PMID: 25913717 DOI: 10.1016/j.ymeth.2015.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/16/2015] [Accepted: 04/16/2015] [Indexed: 01/01/2023] Open
Abstract
Whole exome sequencing (WES) and RNA sequencing (RNA-Seq) are two main platforms used for next-generation sequencing (NGS). While WES is primarily for DNA variant discovery and RNA-Seq is mainly for measurement of gene expression, both can be used for detection of genetic variants, especially single nucleotide variants (SNVs). How consistently variants can be detected from WES and RNA-Seq has not been systematically evaluated. In this study, we examined the technical and biological inconsistencies in SNV detection using WES and RNA-Seq data from 27 pairs of tumor and matched normal samples. We analyzed SNVs in three categories: WES unique - those only detected in WES, RNA-Seq unique - those only detected in RNA-Seq, and shared - those detected in both. We found a small overlap (average ∼14%) between the SNVs called in WES and RNA-Seq. The WES unique SNVs were mainly due to low coverage, low expression, or their location on the non-transcribed strand in RNA-Seq data, while the RNA-Seq unique SNVs were primarily due to their location out of the WES-capture boundary regions (accounting ∼71%), as well as low coverage of the regions, low coverage of the mutant alleles or RNA-editing. The shared SNVs had high locus-specific coverage in both WES and RNA-Seq and high gene expression levels. Additionally, WES unique and RNA-Seq unique SNVs showed different nucleotide substitution patterns, e.g., ∼55% of RNA-Seq unique variants were A:T→G:C, a hallmark of RNA editing. This study provides an important evaluation on the inconsistencies of somatic SNVs called in WES and RNA-Seq data.
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Affiliation(s)
- Timothy D O'Brien
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Junfeng Xia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Uma Saxena
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - Hailing Jin
- Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States.
| | - Huy Vuong
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Pora Kim
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Qingguo Wang
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States.
| | - Martin J Aryee
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - Jeffrey A Engelman
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - Rebecca S Heist
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA 02114, United States.
| | - William Pao
- Department of Medicine/Division of Hematology-Oncology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States.
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, United States; Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, United States; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, United States.
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273
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Talukder AK, Ravishankar S, Sasmal K, Gandham S, Prabhukumar J, Achutharao PH, Barh D, Blasi F. XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine. PLoS One 2015; 10:e0123569. [PMID: 25905921 PMCID: PMC4408095 DOI: 10.1371/journal.pone.0123569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/20/2015] [Indexed: 12/14/2022] Open
Abstract
In translational cancer medicine, implicated pathways and the relevant master genes are of focus. Exome's specificity, processing-time, and cost advantage makes it a compelling tool for this purpose. However, analysis of exome lacks reliable combinatory analysis tools and techniques. In this paper we present XomAnnotate – a meta- and functional-analysis software for exome. We compared UnifiedGenotyper, Freebayes, Delly, and Lumpy algorithms that were designed for whole-genome and combined their strengths in XomAnnotate for exome data through meta-analysis to identify comprehensive mutation profile (SNPs/SNVs, short inserts/deletes, and SVs) of patients. The mutation profile is annotated followed by functional analysis through pathway enrichment and network analysis to identify most critical genes and pathways implicated in the disease genesis. The efficacy of the software is verified through MDS and clustering and tested with available 11 familial non-BRCA1/BRCA2 breast cancer exome data. The results showed that the most significantly affected pathways across all samples are cell communication and antigen processing and presentation. ESCO1, HYAL1, RAF1 and PRKCA emerged as the key genes. Network analysis further showed the purine and propanotate metabolism pathways along with RAF1 and PRKCA genes to be master regulators in these patients. Therefore, XomAnnotate is able to use exome data to identify entire mutation landscape, pathways, and the master genes accurately with wide concordance from earlier microarray and whole-genome studies -- making it a suitable biomedical software for using exome in next-generation translational medicine.
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Affiliation(s)
- Asoke K. Talukder
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
- * E-mail:
| | - Shashidhar Ravishankar
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Krittika Sasmal
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Santhosh Gandham
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Jyothsna Prabhukumar
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Prahalad H. Achutharao
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
| | - Debmalya Barh
- InterpretOmics India Pvt Ltd, #329, 7 Main, HAL 2 Stage, Indiranagar, Bangalore, 560 008, Karnataka, India
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, 721172, India
| | - Francesco Blasi
- Laboratory of Transcriptional Regulation in Development and Cancer, IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milano, Italy
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274
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Ye Z, Kadolph C, Strenn R, Wall D, McPherson E, Lin S. WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data. Comput Biol Med 2015; 68:165-9. [PMID: 25890833 DOI: 10.1016/j.compbiomed.2015.03.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Identification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data. METHODS The Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation. RESULTS An open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE CONCLUSIONS: The WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF׳s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs.
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Affiliation(s)
- Zhan Ye
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Christopher Kadolph
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Robert Strenn
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Daniel Wall
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Elizabeth McPherson
- Department of Medical Genetics Services, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
| | - Simon Lin
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
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275
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Autistic spectrum disorders: A review of clinical features, theories and diagnosis. Int J Dev Neurosci 2015; 43:70-7. [PMID: 25862937 DOI: 10.1016/j.ijdevneu.2015.04.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/03/2015] [Accepted: 04/06/2015] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is a set of neurodevelopmental disorders that is among the most severe in terms of prevalence, morbidity and impact to the society. It is characterized by complex behavioral phenotype and deficits in both social and cognitive functions. Although the exact cause of ASD is still not known, the main findings emphasize the role of genetic and environmental factors in the development of autistic behavior. Environmental factors are also likely to interact with the genetic profile and cause aberrant changes in brain growth, neuronal development, and functional connectivity. The past few years have seen an increase in the prevalence of ASD, as a result of enhanced clinical tests and diagnostic tools. Despite growing evidence for the involvement of endogenous biomarkers in the pathophysiology of ASD, early detection of this disorder remains a big challenge. This paper describes the main behavioral and cognitive features of ASD, as well as the symptoms that differentiate autism from other developmental disorders. An attempt will be made to integrate all the available evidence which point to reduced brain connectivity, mirror neurons deficits, and inhibition-excitation imbalance in individuals with ASD. Finally, this review discusses the main factors involved in the pathophysiology of ASD, and illustrates some of the most important markers used for the diagnosis of this debilitating disorder.
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276
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Mele C, Lemaire M, Iatropoulos P, Piras R, Bresin E, Bettoni S, Bick D, Helbling D, Veith R, Valoti E, Donadelli R, Murer L, Neunhäuserer M, Breno M, Frémeaux-Bacchi V, Lifton R, Remuzzi G, Noris M. Characterization of a New DGKE Intronic Mutation in Genetically Unsolved Cases of Familial Atypical Hemolytic Uremic Syndrome. Clin J Am Soc Nephrol 2015; 10:1011-9. [PMID: 25854283 DOI: 10.2215/cjn.08520814] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/09/2015] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Genetic and acquired abnormalities causing dysregulation of the complement alternative pathway contribute to atypical hemolytic uremic syndrome (aHUS), a rare disorder characterized by thrombocytopenia, nonimmune microangiopathic hemolytic anemia, and acute kidney failure. However, in a substantial proportion of patients the disease-associated alterations are still unknown. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS Whole-exome and whole-genome sequencing were performed in two unrelated families with infantile recessive aHUS. Sequencing of cDNA from affected individuals was used to test for the presence of aberrant mRNA species. Expression of mutant diacylglycerol kinase epsilon (DGKE) protein was evaluated with western blotting. RESULTS Whole-exome sequencing analysis with conventional variant filtering parameters did not reveal any obvious candidate mutation in the first family. The report of aHUS-associated mutations in DGKE, encoding DGKE, led to re-examination of the noncoding DGKE variants obtained from next-generation sequencing, allowing identification of a novel intronic DGKE mutation (c.888+40A>G) that segregated with disease. Sequencing of cDNA from affected individuals revealed aberrant forms of DGKE mRNA predicted to cause profound abnormalities in the protein catalytic site. By whole-genome sequencing, the same mutation was found in compound heterozygosity with a second nonsense DGKE mutation in all affected siblings of another unrelated family. Homozygous and compound heterozygous patients presented similar clinical features, including aHUS presentation in the first year of life, multiple relapsing episodes, and proteinuria, which are prototypical of DGKE-associated aHUS. CONCLUSIONS This is the first report of a mutation located beyond the exon-intron boundaries in aHUS. Intronic mutations such as these are underreported because conventional filtering parameters used to process next-generation sequencing data routinely exclude these regions from downstream analyses in both research and clinical settings. The results suggest that analysis of noncoding regions of aHUS-associated genes coupled with mRNA sequencing might provide a tool to explain genetically unsolved aHUS cases.
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Affiliation(s)
- Caterina Mele
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Mathieu Lemaire
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Paraskevas Iatropoulos
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Rossella Piras
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Elena Bresin
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Serena Bettoni
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - David Bick
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Daniel Helbling
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Regan Veith
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Elisabetta Valoti
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Roberta Donadelli
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Luisa Murer
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Maria Neunhäuserer
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Matteo Breno
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Véronique Frémeaux-Bacchi
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Richard Lifton
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
| | - Giuseppe Remuzzi
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material.
| | - Marina Noris
- Due to the number of contributing authors,the affiliations are provided in the Supplemental Material
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277
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Abstract
Next-generation sequencing (NGS) technologies have played a central role in the genetic revolution. These technologies, especially whole-exome sequencing, have become the primary tool of geneticists to identify the causative DNA variants in Mendelian disorders, including hereditary deafness. Current research estimates that 1% of all human genes have a function in hearing. To date, mutations in over 80 genes have been reported to cause nonsyndromic hearing loss (NSHL). Strikingly, more than a quarter of all known genes related to NSHL were discovered in the past 5 years via NGS technologies. In this article, we review recent developments in the usage of NGS for hereditary deafness, with an emphasis on whole-exome sequencing.
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278
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Meienberg J, Zerjavic K, Keller I, Okoniewski M, Patrignani A, Ludin K, Xu Z, Steinmann B, Carrel T, Röthlisberger B, Schlapbach R, Bruggmann R, Matyas G. New insights into the performance of human whole-exome capture platforms. Nucleic Acids Res 2015; 43:e76. [PMID: 25820422 PMCID: PMC4477645 DOI: 10.1093/nar/gkv216] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/03/2015] [Indexed: 11/18/2022] Open
Abstract
Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.
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Affiliation(s)
- Janine Meienberg
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich CH-8952, Switzerland
| | - Katja Zerjavic
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich CH-8952, Switzerland
| | - Irene Keller
- Department of Clinical Research, University of Berne, Berne CH-3010, Switzerland
| | - Michal Okoniewski
- Functional Genomics Center Zurich, Zurich CH-8057, Switzerland Division of Scientific IT Services, ETH Zurich, Zurich CH-8092, Switzerland
| | | | - Katja Ludin
- Division of Medical Genetics, Center for Laboratory Medicine, Aarau CH-5001, Switzerland
| | - Zhenyu Xu
- Sophia Genetics SA, Lausanne CH-1015, Switzerland
| | - Beat Steinmann
- Division of Metabolism, University Children's Hospital, Zurich CH-8032, Switzerland
| | - Thierry Carrel
- Department of Cardiovascular Surgery, University Hospital, Berne CH-3010, Switzerland
| | - Benno Röthlisberger
- Division of Medical Genetics, Center for Laboratory Medicine, Aarau CH-5001, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Berne, Berne CH-3012, Switzerland
| | - Gabor Matyas
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich CH-8952, Switzerland Department of Cardiovascular Surgery, University Hospital, Berne CH-3010, Switzerland Zurich Center for Integrative Human Physiology, University of Zurich, Zurich CH-8057, Switzerland
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279
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Proxy molecular diagnosis from whole-exome sequencing reveals Papillon-Lefevre syndrome caused by a missense mutation in CTSC. PLoS One 2015; 10:e0121351. [PMID: 25799584 PMCID: PMC4370501 DOI: 10.1371/journal.pone.0121351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/30/2015] [Indexed: 01/10/2023] Open
Abstract
Papillon-Lefevre syndrome (PLS) is an autosomal recessive disorder characterised by severe early onset periodontitis and palmoplantar hyperkeratosis. A previously reported missense mutation in the CTSC gene (NM_001814.4:c.899G>A:p.(G300D)) was identified in a homozygous state in two siblings diagnosed with PLS in a consanguineous family of Arabic ancestry. The variant was initially identified in a heterozygous state in a PLS unaffected sibling whose whole exome had been sequenced as part of a previous Primary ciliary dyskinesia study. Using this information, a proxy molecular diagnosis was made on the PLS affected siblings after consent was given to study this second disorder found to be segregating within the family. The prevalence of the mutation was then assayed in the local population using a representative sample of 256 unrelated individuals. The variant was absent in all subjects indicating that the variant is rare in Saudi Arabia. This family study illustrates how whole-exome sequencing can generate findings and inferences beyond its primary goal.
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280
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Yadav SS, Li J, Lavery HJ, Yadav KK, Tewari AK. Next-generation sequencing technology in prostate cancer diagnosis, prognosis, and personalized treatment. Urol Oncol 2015; 33:267.e1-13. [PMID: 25791755 DOI: 10.1016/j.urolonc.2015.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing (NGS) of the genetic information of cancer cells has revolutionized the field of cancer biology, including prostate cancer (PCa). New recurrent alterations have been identified in PCa (e.g., TMPRSS2-ERG translocation, SPOP and CHD1 mutations, and chromoplexy), and many previous ones in well-established pathways have been validated (e.g., androgen receptor overexpression and mutations; PTEN, RB1, and TP53 loss/mutations). With its highly heterogeneous nature, PCa continues to pose a tremendous challenge in terms of diagnosis and prognosis. Combining the information gained through NGS studies with clinicopathological and radiological data will help diagnose the aggressiveness of the cancer with greater accuracy. Furthermore, understanding the heterogeneity of tumor through single-cell or single-molecule sequencing technology will also strengthen the prognosis and provide better, patient-specific drug identification. As this research becomes more prominent, it is important that urologic oncologists become familiar with the various NGS technologies and the results generated using them. We highlight the commonly used NGS tools and summarize recent discoveries relevant to PCa.
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Affiliation(s)
- Shalini S Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY
| | - Jinyi Li
- Department of Urology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY
| | - Hugh J Lavery
- Department of Urology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY
| | - Kamlesh K Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY.
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY.
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281
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Zebisch A, Schulz E, Grosso M, Lombardo B, Acierno G, Sill H, Iolascon A. Identification of a novel variant of epsilon-gamma-delta-beta thalassemia highlights limitations of next generation sequencing. Am J Hematol 2015; 90:E52-4. [PMID: 25488195 DOI: 10.1002/ajh.23913] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Armin Zebisch
- Division of Hematology; Medical University of Graz; Graz Austria
| | - Eduard Schulz
- Division of Hematology; Medical University of Graz; Graz Austria
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology; University Federico II of Naples; Naples Italy
- CEINGE-Advanced Biotechnologies; Naples Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology; University Federico II of Naples; Naples Italy
- CEINGE-Advanced Biotechnologies; Naples Italy
| | - Giovanni Acierno
- Department of Molecular Medicine and Medical Biotechnology; University Federico II of Naples; Naples Italy
- CEINGE-Advanced Biotechnologies; Naples Italy
| | - Heinz Sill
- Division of Hematology; Medical University of Graz; Graz Austria
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology; University Federico II of Naples; Naples Italy
- CEINGE-Advanced Biotechnologies; Naples Italy
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282
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Abstract
PRACTICAL RELEVANCE The health of the cat is a complex interaction between its environment (nurture) and its genetics (nature). Over 70 genetic mutations (variants) have been defined in the cat, many involving diseases, structural abnormalities and clinically relevant health concerns. As more of the cat's genome is deciphered, less commonly will the term 'idiopathic' be used regarding the diagnosis of diseases and unique health conditions. State-of-the-art health care will include DNA profiling of the individual cat, and perhaps its tumor, to establish the best treatment approaches. Genetic testing and eventually whole genome sequencing should become routine diagnostics for feline health care. GLOBAL IMPORTANCE Cat breeds have disseminated around the world. Thus, practitioners should be aware of the breeds common to their region and the mutations found in those regional populations. Specific random-bred populations can also have defined genetic characteristics and mutations. AUDIENCE This review of 'the good, the bad and the ugly' DNA variants provides the current state of knowledge for genetic testing and genetic health management for cats. It is aimed at feline and general practitioners wanting to update and review the basics of genetics, what tests are available for cats and sources for genetic testing. The tables are intended to be used as references in the clinic. Practitioners with a high proportion of cat breeder clientele will especially benefit from the review. EVIDENCE BASE The data presented is extracted from peer-reviewed publications pertaining to mutation identification, and relevant articles concerning the heritable trait and/or disease. The author also draws upon personal experience and expertise in feline genetics.
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Affiliation(s)
- Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, Columbia, MO 65201, USA
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283
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Kim HS, Kim YH. Recent progress in atomistic simulation of electrical current DNA sequencing. Biosens Bioelectron 2015; 69:186-98. [PMID: 25744599 DOI: 10.1016/j.bios.2015.02.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 10/24/2022]
Abstract
We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices.
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Affiliation(s)
- Han Seul Kim
- School of Energy, Environment, Water, and Sustaibability, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Yong-Hoon Kim
- School of Energy, Environment, Water, and Sustaibability, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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284
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Bhatnagar B, Garzon R. The use of molecular genetics to refine prognosis in acute myeloid leukemia. Curr Hematol Malig Rep 2015; 9:148-57. [PMID: 24659319 DOI: 10.1007/s11899-014-0208-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The discovery and application of advanced molecular techniques, such as gene and microRNA expression profiling, whole genome and exome sequencing, proteomic analysis and methylation assays, have allowed for the identification of recurrent molecular abnormalities in acute myeloid leukemia (AML) that have revolutionized our understanding of the genetic landscape of the disease. These modalities have emerged as valuable tools that permit a more comprehensive and detailed molecular characterization of AML. Many of these molecular abnormalities have been shown to predict prognosis, particularly within the context of cytogenetically normal AML. This review will discuss the major techniques and platforms that have been used to identify novel recurrent gene mutations in AML and briefly describe how these discoveries have impacted on outcome prediction.
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285
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Abstract
Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine.
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Affiliation(s)
- David G. Peters
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213
| | - Svetlana A. Yatsenko
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213
| | - Urvashi Surti
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
| | - Aleksandar Rajkovic
- Department of Obstetrics, Gynecology, and Reproductive Sciences,
University of Pittsburgh, Pittsburgh, PA 15213,Department of Pathology, University of Pittsburgh, Pittsburgh, PA
15213,Magee-Womens Research Institute, University of Pittsburgh,
Pittsburgh, PA 15213,Department of Human Genetics, University of Pittsburgh, Pittsburgh,
PA 15213
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286
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Shi L, Li B, Huang Y, Ling X, Liu T, Lyon GJ, Xu A, Wang K. "Genotype-first" approaches on a curious case of idiopathic progressive cognitive decline. BMC Med Genomics 2014; 7:66. [PMID: 25466957 PMCID: PMC4267425 DOI: 10.1186/s12920-014-0066-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In developing countries, many cases with rare neurological diseases remain undiagnosed due to limited diagnostic experience. We encountered a case in China where two siblings both began to develop idiopathic progressive cognitive decline starting from age six, and were suspected to have an undiagnosed neurological disease. METHODS Initial clinical assessments included review of medical history, comprehensive physical examination, genetic testing for metabolic diseases, blood tests and brain imaging. We performed exome sequencing with Agilent SureSelect exon capture and Illumina HiSeq2000 platform, followed by variant annotation and selection of rare, shared mutations that fit a recessive model of inheritance. To assess functional impacts of candidate variants, we performed extensive biochemical tests in blood and urine, and examined their possible roles by protein structure modeling. RESULTS Exome sequencing identified NAGLU as the most likely candidate gene with compound heterozygous mutations (chr17:40695717C > T and chr17:40693129A > G in hg19 coordinate), which were documented to be pathogenic. Sanger sequencing confirmed the recessive patterns of inheritance, leading to a genetic diagnosis of Sanfilippo syndrome (mucopolysaccharidosis IIIB). Biochemical tests confirmed the complete loss of activity of alpha-N-acetylglucosaminidase (encoded by NAGLU) in blood, as well as significantly elevated dermatan sulfate and heparan sulfate in urine. Structure modeling revealed the mechanism on how the two variants affect protein structural stability. CONCLUSIONS Successful diagnosis of a rare genetic disorder with an atypical phenotypic presentation confirmed that such "genotype-first" approaches can particularly succeed in areas of the world with insufficient medical genetics expertise and with cost-prohibitive in-depth phenotyping.
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Affiliation(s)
- Lingling Shi
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, 510623, China. .,Guangdong Medical Key Laboratory of Brain Function and Diseases, Jinan University, Guangzhou, Guangdong, 510623, China. .,GHM Collaboration and Innovation Center for Tissue Regeneration and Repair, Jinan University, Guangzhou, Guangdong, 510623, China.
| | - Bingxiao Li
- Neonatal Intensive Care Unit, The 1st Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510623, China.
| | - Yonglan Huang
- Department of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, 510623, China.
| | - Xueying Ling
- Medical Imaging Center, The 1st Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510623, China.
| | - Tianyun Liu
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11797, USA.
| | - Anding Xu
- Department of Neurology, The 1st Affiliated Hospital, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, 90089, USA. .,Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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287
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Eyal O, Oren A, Jüppner H, Somech R, De Bellis A, Mannstadt M, Szalat A, Bleiberg M, Weisman Y, Weintrob N. Hypoparathyroidism and central diabetes insipidus: in search of the link. Eur J Pediatr 2014; 173:1731-4. [PMID: 25367057 PMCID: PMC5103624 DOI: 10.1007/s00431-014-2448-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/13/2014] [Accepted: 10/20/2014] [Indexed: 11/24/2022]
Abstract
UNLABELLED Two siblings (a 15-year-old boy and an 11-year-old girl) who presented with hypocalcemic seizure at the age of 2 years and 2 months (boy) and 2 years and 4 months (girl) were diagnosed with hypoparathyroidism. At the age of 3 years, the girl developed central diabetes insipidus with good response to desmopressin acetate treatment. The family history was unremarkable, and there was no consanguinity between the parents. The father is of Iraqi/Egyptian Jewish origin and the mother is of Iranian/Romanian Jewish origin. Sequence analysis of the candidate genes for isolated hypoparathyroidism encoding calcium-sensing receptor, parathyroid hormone, and glial cells missing homolog B did not reveal any mutations. Whole-exome sequencing identified a homozygous mutation in the autoimmune regulatory gene (AIRE), c.374A>G;p.Y85C, characteristic for Jewish Iranians with autoimmune polyendocrine syndrome type 1 (APS1), which was confirmed by the Sanger sequencing. Antibodies against the adrenal, pancreatic islet cell, ovary, thyroid, pituitary, celiac, and parietal cell were negative in both siblings, while anti-diuretic hormone antibodies were positive only in the girl. No other symptoms or signs of APS1 developed during all the years of follow-up. CONCLUSION APS1 should be part of the differential diagnosis in children presenting with isolated hypoparathyroidism or hypoparathyroidism with central diabetes insipidus (CDI). These cases show that the AIRE mutation characteristic of Iranian Jews can also be found in non-Iranian Jews.
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Affiliation(s)
- Ori Eyal
- Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children Hospital, Tel Aviv Sourasky Medical Center, 6 Weizmann St., 6423906 Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Oren
- Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children Hospital, Tel Aviv Sourasky Medical Center, 6 Weizmann St., 6423906 Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Harald Jüppner
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Pediatric Department, Pediatric Immunology Service, Jeffery Modell Foundation (JMF) Center, Edmond and Lily Safra Children’s Hospital, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Annamaria De Bellis
- Department of Cardiothoracic and Respiratory Sciences, Section of Endocrinology, Faculty of Medicine and Surgery, Second University of Naples, Naples, Italy
| | - Michael Mannstadt
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Auryan Szalat
- Internal Medicine Department, Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Margalit Bleiberg
- Clinical Immunology Laboratory, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Yosef Weisman
- Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children Hospital, Tel Aviv Sourasky Medical Center, 6 Weizmann St., 6423906 Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naomi Weintrob
- Pediatric Endocrinology and Diabetes Unit, Dana-Dwek Children Hospital, Tel Aviv Sourasky Medical Center, 6 Weizmann St., 6423906 Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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288
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Wei Q, Zhu H, Qian X, Chen Z, Yao J, Lu Y, Cao X, Xing G. Targeted genomic capture and massively parallel sequencing to identify novel variants causing Chinese hereditary hearing loss. J Transl Med 2014; 12:311. [PMID: 25388789 PMCID: PMC4234825 DOI: 10.1186/s12967-014-0311-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/23/2014] [Indexed: 11/15/2022] Open
Abstract
Background Hereditary hearing loss is genetically heterogeneous, and hundreds of mutations in than 60 genes are involved in this disease. Therefore, it is difficult to identify the causative gene mutations involved. In this study, we combined targeted genomic capture and massively parallel sequencing (MPS) to address this issue. Methods Using targeted genomic capture and MPS, 104 genes and three microRNA regions were selected and simultaneously sequenced in 23 unrelated probands of Chinese families with nonsyndromic hearing loss. The results were validated by Sanger sequencing for all available members of the probands’ families. To analyze the possible pathogenic functional effects of the variants, three types of prediction programs (Mutation Taster, PROVEAN and SIFT) were used. A total of 195 healthy Chinese Han individuals were compared as controls to verify the novel causative mutations. Results Of the 23 probands, six had mutations in DFNA genes [WFS1 (n = 2), COCH, ACTG1, TMC1, and POU4F3] known to cause autosomal dominant nonsyndromic hearing loss. These included one novel in-frame indel mutation, three novel missense mutations and two reported missense mutations. Furthermore, one proband from a family with recessive DFNB carried two monoallelic mutations in the GJB2 and USH2A genes. All of these mutations co-segregated with the hearing loss phenotype in 36 affected individuals from 7 families and were predicted to be pathogenic. Conclusions Mutations in uncommon deafness genes contribute to a portion of nonsyndromic deafness cases. In the future, critical gene mutations may be accurately and quickly identified in families with hereditary hearing loss by targeted genomic capture and MPS. Electronic supplementary material The online version of this article (doi:10.1186/s12967-014-0311-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qinjun Wei
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China.
| | - Hongmei Zhu
- Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Xuli Qian
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China.
| | - Zhibin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Jun Yao
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China.
| | - Yajie Lu
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China.
| | - Xin Cao
- Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University, Nanjing, 210029, PR China.
| | - Guangqian Xing
- Department of Otolaryngology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
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289
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Abstract
Chronic pancreatitis is a progressive inflammatory disease in which pancreatic secretory parenchyma is destroyed and replaced by fibrous tissue, eventually leading to malnutrition and diabetes. Alcohol is the leading cause in Western countries, but genetic factors are also implicated. Since the identification of mutations in the cationic trypsinogen (PRSS1) gene as a cause of hereditary pancreatitis in 1996, we have seen great progress in our understanding of the genetics of pancreatitis. It has been established that mutations in the genes related to the activation and inactivation of trypsin(ogen) such as PRSS1, serine protease inhibitor Kazal type 1 (SPINK1) and chymotrypsin C (CTRC) genes are associated with pancreatitis. In 2013, carboxypeptidase A1 (CPA1) was identified as a novel pancreatitis susceptibility gene. Endoplasmic reticulum stress in pancreatic acinar cells resulting from the mis-folding of mutated pancreatic enzymes has been shown to act as a novel mechanism underlying the susceptibility to pancreatitis. In Japan, the nationwide survey revealed 171 patients (96 males and 75 females) with hereditary pancreatitis in 59 families based on the European Registry of Hereditary Pancreatitis and Familial Pancreatic Cancer criteria. Because about 30% of families with hereditary pancreatitis do not carry mutations in any of the known pancreatitis susceptibility genes, other yet unidentified genes might be involved. Next generation sequencers can perform billions of sequencing reactions with a read length of 150-250 nucleotides. Comprehensive analysis using next generation sequencers will be a promising strategy to identify novel pancreatitis-associated genes and further clarify the pathogenesis of pancreatitis.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine
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290
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Haus T, Prinz K, Pauling B, Roos C. Genotyping of non-human primate models: perspectives and challenges for the implementation of the "three R's". Primate Biol 2014. [DOI: 10.5194/pb-1-1-2014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Although non-human primates (NHPs) represent only a minor fraction of all animals used in biomedical research, there is a continuous effort to further reduce, refine and replace research with NHPs in accordance with the principles of the three R's. Most of the NHP model species are genetically highly diverse, and significant variation occurs among populations of different geographic origins, particularly in macaques. Since such differences can considerably affect the outcome of biomedical experiments, genotyping represents a promising tool to refine research approaches and to reduce the number of NHPs in biomedical research. Accordingly, the European Primate Network (EUPRIM-Net) developed an anonymous online survey to evaluate possibilities and potential hindrances for the application of genotyping in NHP research. On the one hand, our results point to the importance of genetic variation in NHPs and the need to consider the genetic background for future research approaches. On the other hand, our survey identified several hindrances and limiting factors for the application of genotyping and its incorporation in research, primate husbandry and breeding. We provide some fundamental recommendations on how to meet these challenges and how genotyping can be efficiently used to refine NHP research and to reduce the number of NHPs in biomedical research in the long term.
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291
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Requena T, Cabrera S, Martín-Sierra C, Price SD, Lysakowski A, Lopez-Escamez JA. Identification of two novel mutations in FAM136A and DTNA genes in autosomal-dominant familial Meniere's disease. Hum Mol Genet 2014; 24:1119-26. [PMID: 25305078 DOI: 10.1093/hmg/ddu524] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Meniere's disease (MD) is a chronic disorder of the inner ear defined by sensorineural hearing loss, tinnitus and episodic vertigo, and familial MD is observed in 5-15% of sporadic cases. Although its pathophysiology is largely unknown, studies in human temporal bones have found an accumulation of endolymph in the scala media of the cochlea. By whole-exome sequencing, we have identified two novel heterozygous single-nucleotide variants in FAM136A and DTNA genes, both in a Spanish family with three affected cases in consecutive generations, highly suggestive of autosomal-dominant inheritance. The nonsense mutation in the FAM136A gene leads to a stop codon that disrupts the FAM136A protein product. Sequencing revealed two mRNA transcripts of FAM136A in lymphoblasts from patients, which were confirmed by immunoblotting. Carriers of the FAM136A mutation showed a significant decrease in the expression level of both transcripts in lymphoblastoid cell lines. The missense mutation in the DTNA gene produces a novel splice site which skips exon 21 and leads to a shorter alternative transcript. We also demonstrated that FAM136A and DTNA proteins are expressed in the neurosensorial epithelium of the crista ampullaris of the rat by immunohistochemistry. While FAM136A encodes a mitochondrial protein with unknown function, DTNA encodes a cytoskeleton-interacting membrane protein involved in the formation and stability of synapses with a crucial role in the permeability of the blood-brain barrier. Neither of these genes has been described in patients with hearing loss, FAM136A and DTNA being candidate gene for familiar MD.
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Affiliation(s)
- Teresa Requena
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada 18016, Spain
| | - Sonia Cabrera
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada 18016, Spain
| | - Carmen Martín-Sierra
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada 18016, Spain
| | - Steven D Price
- Department of Anatomy and Cell Biology, University of Illinois, Chicago, IL 60612, USA and
| | - Anna Lysakowski
- Department of Anatomy and Cell Biology, University of Illinois, Chicago, IL 60612, USA and
| | - José A Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer/University of Granada/Junta de Andalucía, PTS, Granada 18016, Spain, Department of Otolaryngology, Hospital de Poniente, El Ejido, Almería 04700, Spain
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292
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A diagnostic approach for cerebral palsy in the genomic era. Neuromolecular Med 2014; 16:821-44. [PMID: 25280894 DOI: 10.1007/s12017-014-8331-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
An ongoing challenge in children presenting with motor delay/impairment early in life is to identify neurogenetic disorders with a clinical phenotype, which can be misdiagnosed as cerebral palsy (CP). To help distinguish patients in these two groups, conventional magnetic resonance imaging of the brain has been of great benefit in "unmasking" many of these genetic etiologies and has provided important clues to differential diagnosis in others. Recent advances in molecular genetics such as chromosomal microarray and next-generation sequencing have further revolutionized the understanding of etiology by more precisely classifying these disorders with a molecular cause. In this paper, we present a review of neurogenetic disorders masquerading as cerebral palsy evaluated at one institution. We have included representative case examples children presenting with dyskinetic, spastic, and ataxic phenotypes, with the intent to highlight the time-honored approach of using clinical tools of history and examination to focus the subsequent etiologic search with advanced neuroimaging modalities and molecular genetic tools. A precise diagnosis of these masqueraders and their differentiation from CP is important in terms of therapy, prognosis, and family counseling. In summary, this review serves as a continued call to remain vigilant for current and other to-be-discovered neurogenetic masqueraders of cerebral palsy, thereby optimizing care for patients and their families.
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293
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Bao R, Huang L, Andrade J, Tan W, Kibbe WA, Jiang H, Feng G. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform 2014; 13:67-82. [PMID: 25288881 PMCID: PMC4179624 DOI: 10.4137/cin.s13779] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 12/21/2022] Open
Abstract
The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.
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Affiliation(s)
- Riyue Bao
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Wei Tan
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, USA
| | - Warren A Kibbe
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
| | - Hongmei Jiang
- Department of Statistics, Northwestern University, Evanston, IL, USA
| | - Gang Feng
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
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294
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Paz-Filho G, Boguszewski MCS, Mastronardi CA, Patel HR, Johar AS, Chuah A, Huttley GA, Boguszewski CL, Wong ML, Arcos-Burgos M, Licinio J. Whole exome sequencing of extreme morbid obesity patients: translational implications for obesity and related disorders. Genes (Basel) 2014; 5:709-25. [PMID: 25158045 PMCID: PMC4198926 DOI: 10.3390/genes5030709] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/23/2014] [Accepted: 08/14/2014] [Indexed: 12/11/2022] Open
Abstract
Whole-exome sequencing (WES) is a new tool that allows the rapid, inexpensive and accurate exploration of Mendelian and complex diseases, such as obesity. To identify sequence variants associated with obesity, we performed WES of family trios of one male teenager and one female child with severe early-onset obesity. Additionally, the teenager patient had hypopituitarism and hyperprolactinaemia. A comprehensive bioinformatics analysis found de novo and compound heterozygote sequence variants with a damaging effect on genes previously associated with obesity in mice (LRP2) and humans (UCP2), among other intriguing mutations affecting ciliary function (DNAAF1). A gene ontology and pathway analysis of genes harbouring mutations resulted in the significant identification of overrepresented pathways related to ATP/ITP (adenosine/inosine triphosphate) metabolism and, in general, to the regulation of lipid metabolism. We discuss the clinical and physiological consequences of these mutations and the importance of these findings for either the clinical assessment or eventual treatment of morbid obesity.
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Affiliation(s)
- Gilberto Paz-Filho
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Margaret C S Boguszewski
- Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil.
| | - Claudio A Mastronardi
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Hardip R Patel
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Angad S Johar
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Aaron Chuah
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Gavin A Huttley
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Cesar L Boguszewski
- Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil.
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, and Department of Psychiatry, School of Medicine, Flinders University, PO Box 11060 Adelaide SA 5001, Adelaide, Australia.
| | - Mauricio Arcos-Burgos
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Julio Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, and Department of Psychiatry, School of Medicine, Flinders University, PO Box 11060 Adelaide SA 5001, Adelaide, Australia.
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295
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Fogel BL, Clark MC, Geschwind DH. The neurogenetics of atypical parkinsonian disorders. Semin Neurol 2014; 34:217-24. [PMID: 24963681 DOI: 10.1055/s-0034-1381738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although classic Parkinson disease is the disorder most commonly associated with the clinical feature of parkinsonism, there is in fact a broader spectrum of disease represented by a collection of phenotypically similar neurodegenerative conditions that mimic many of its core features. These atypical parkinsonian disorders most commonly include progressive supranuclear palsy and corticobasal degeneration, disorders both associated with frontotemporal dementia, as well as multiple system atrophy and dementia with Lewy bodies. Although the clinical distinction of these disorders still remains a challenge to physicians, recent advances in genetics are poised to tease apart the differences. Insights into the molecular etiologies underlying these conditions will improve diagnosis, yield a better understanding of the underlying disease pathology, and ultimately lend stimulation to the development of potential treatments. At the same time, the wide range of phenotypes observed from mutations in a single gene warrants broad testing facilitated by advances in DNA sequencing. These expanding genomic approaches, ranging from the use of next-generation sequencing to identify causative or risk-associated gene variations to the study of epigenetic modification linking human genetics to environmental factors, are poised to lead the field into a new age of discovery.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Mary C Clark
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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296
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Genome typing of nonhuman primate models: implications for biomedical research. Trends Genet 2014; 30:482-7. [PMID: 24954183 DOI: 10.1016/j.tig.2014.05.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 12/18/2022]
Abstract
The success of personalized medicine rests on understanding the genetic variation between individuals. Thus, as medical practice evolves and variation among individuals becomes a fundamental aspect of clinical medicine, a thorough consideration of the genetic and genomic information concerning the animals used as models in biomedical research also becomes critical. In particular, nonhuman primates (NHPs) offer great promise as models for many aspects of human health and disease. These are outbred species exhibiting substantial levels of genetic variation; however, understanding of the contribution of this variation to phenotypes is lagging behind in NHP species. Thus, there is a pivotal need to address this gap and define strategies for characterizing both genomic content and variability within primate models of human disease. Here, we discuss the current state of genomics of NHP models and offer guidelines for future work to ensure continued improvement and utility of this line of biomedical research.
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297
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Longoni M, Marangi G, Zollino M. Utility and Challenges of Next Generation Sequencing in Pediatric Disorders. CURRENT PEDIATRICS REPORTS 2014. [DOI: 10.1007/s40124-014-0039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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298
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Jurkiewicz D, Gliwicz D, Ciara E, Gerfen J, Pelc M, Piekutowska-Abramczuk D, Kugaudo M, Chrzanowska K, Spinner NB, Krajewska-Walasek M. Spectrum of JAG1 gene mutations in Polish patients with Alagille syndrome. J Appl Genet 2014; 55:329-36. [PMID: 24748328 PMCID: PMC4102774 DOI: 10.1007/s13353-014-0212-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/19/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Abstract
Alagille syndrome (ALGS) is an autosomal dominant disorder characterized by developmental abnormalities in several organs including the liver, heart, eyes, vertebrae, kidneys, and face. The majority (90-94 %) of ALGS cases are caused by mutations in the JAG1 (JAGGED1) gene, and in a small percent of patients (∼1 %) mutations in the NOTCH2 gene have been described. Both genes are involved in the Notch signaling pathway. To date, over 440 different JAG1 gene mutations and ten NOTCH2 mutations have been identified in ALGS patients. The present study was conducted on a group of 35 Polish ALGS patients and revealed JAG1 gene mutations in 26 of them. Twenty-three different mutations were detected including 13 novel point mutations and six large deletions affecting the JAG1 gene. Review of all mutations identified to date in individuals from Poland allowed us to propose an effective diagnostic strategy based on the mutations identified in the reported patients of Polish descent. However, the distribution of mutations seen in this cohort was not substantively different than the mutation distribution in other reported populations.
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Affiliation(s)
- Dorota Jurkiewicz
- Department of Medical Genetics, The Children's Memorial Health Institute, Al. Dzieci Polskich 20, 04-730, Warsaw, Poland,
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299
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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