1
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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2
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Juárez OE, Arreola-Meraz L, Sánchez-Castrejón E, Avila-Poveda OH, López-Galindo LL, Rosas C, Galindo-Sánchez CE. Oviducal gland transcriptomics of Octopus maya through physiological stages and the negative effects of temperature on fertilization. PeerJ 2022; 10:e12895. [PMID: 35378931 PMCID: PMC8976471 DOI: 10.7717/peerj.12895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/16/2022] [Indexed: 01/11/2023] Open
Abstract
Background Elevated temperatures reduce fertilization and egg-laying rates in the octopus species. However, the molecular mechanisms that control the onset of fertilization and egg-laying in the octopus' oviducal gland are still unclear; and the effect of temperature on the expression of key reproductive genes is unknown. This study aims to better understand the molecular bases of octopus fertilization and egg-laying, and how they are affected by elevated temperatures. Method RNA-seq of oviducal glands was performed for samples before, during, and after fertilization and their transcriptomic profiles were compared. Also, at the fertilization stage, the optimal and thermal-stress conditions were contrasted. Expression levels of key reproductive genes were validated via RT-qPCR. Results In mated females before egg-laying, genes required for the synthesis of spermine, spermidine, which may prevent premature fertilization, and the myomodulin neuropeptide were upregulated. Among the genes with higher expression at the fertilization stage, we found those encoding the receptors of serotonin, dopamine, and progesterone; genes involved in the assembly and motility of the sperm flagellum; genes that participate in the interaction between male and female gametes; and genes associated with the synthesis of eggshell mucoproteins. At temperatures above the optimal range for reproduction, mated females reduced the fertilization rate. This response coincided with the upregulation of myomodulin and APGW-amide neuropeptides. Also, genes associated with fertilization like LGALS3, VWC2, and Pcsk1 were downregulated at elevated temperatures. Similarly, in senescent females, genes involved in fertilization were downregulated but those involved in the metabolism of steroid hormones like SRD5A1 were highly expressed.
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Affiliation(s)
- Oscar E. Juárez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, Ensenada, Baja California, México
| | - Lousiana Arreola-Meraz
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, Ensenada, Baja California, México
| | - Edna Sánchez-Castrejón
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, Ensenada, Baja California, México
| | - Omar Hernando Avila-Poveda
- Facultad de Ciencias del Mar, Universidad Autónoma de Sinaloa, Mazatlán, Sinaloa, México,Programa Investigadoras e Investigadores por México, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Laura L. López-Galindo
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Baja California, México
| | - Carlos Rosas
- Unidad Multidisciplinaria de Docencia e Investigación - Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Clara E. Galindo-Sánchez
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, Ensenada, Baja California, México
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3
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Cho EH, Ki CS, Yun SA, Kim SY, Jhun BW, Koh WJ, Huh HJ, Lee NY. Genetic Analysis of Korean Adult Patients with Nontuberculous Mycobacteria Suspected of Primary Ciliary Dyskinesia Using Whole Exome Sequencing. Yonsei Med J 2021; 62:224-230. [PMID: 33635012 PMCID: PMC7934102 DOI: 10.3349/ymj.2021.62.3.224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Nontuberculous mycobacteria (NTM) is ubiquitous in the environment, but NTM lung disease (NTM-LD) is uncommon. Since exposure to NTM is inevitable, patients who develop NTM-LD are likely to have specific susceptibility factors, such as primary ciliary dyskinesia (PCD). PCD is a genetically heterogeneous disorder of motile cilia and is characterized by chronic respiratory tract infection, organ laterality defect, and infertility. In this study, we performed whole exome sequencing (WES) and investigated the genetic characteristics of adult NTM patients with suspected PCD. MATERIALS AND METHODS WES was performed in 13 NTM-LD patients who were suspected of having PCD by clinical symptoms and/or ultrastructural ciliary defect observed by transmission electron microscopy. A total of 45 PCD-causing genes, 23 PCD-candidate genes, and 990 ciliome genes were analyzed. RESULTS Four patients were found to have biallelic loss-of-function (LoF) variants in the following PCD-causing genes: CCDC114, DNAH5, HYDIN, and NME5. In four other patients, only one LoF variant was identified, while the remaining five patients did not have any LoF variants. CONCLUSION At least 30.8% of NTM-LD patients who were suspected of having PCD had biallelic LoF variants, and an additional 30.8% of patients had one LoF variant. Therefore, PCD should be considered in patients with NTM-LD with symptoms or signs suspicious of PCD.
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Affiliation(s)
- Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Su Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Lee SY, Hwang H, Kang YM, Kim H, Kim DG, Jeong JE, Kim JY, Yoo JS. SAAVpedia: Identification, Functional Annotation, and Retrieval of Single Amino Acid Variants for Proteogenomic Interpretation. J Proteome Res 2019; 18:4133-4142. [PMID: 31612721 DOI: 10.1021/acs.jproteome.9b00366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Next-generation genome sequencing has enabled the discovery of numerous disease- or drug-response-associated nonsynonymous single nucleotide variants (nsSNVs) that alter the amino acid sequences of a protein. Although several studies have attempted to characterize pathogenic nsSNVs, few have been confirmed as single amino acid variants (SAAVs) at the protein level. Here we developed the SAAVpedia platform to identify, annotate, and retrieve pathogenic SAAV candidates from proteomic and genomic data. The platform consists of four modules: SAAVidentifier, SAAVannotator, SNV/SAAVretriever, and SAAVvisualizer. The SAAVidentifier provides a reference database containing 18 206 090 SAAVs and performs the identification and quality assessment of SAAVs. The SAAVannotator provides functional annotation with biological, clinical, and pharmacological information for the interpretation of condition-specific SAAVs. The SNV/SAAVretriever module enables bidirectional navigation between relevant SAAVs and nsSNVs with diverse genomic and proteomic data. SAAVvisualizer provides various statistical plots based on functional annotations of detected SAAVs. To demonstrate the utility of SAAVpedia, the proteogenomic pipeline with protein-protein interaction network analysis was applied to proteomic data from breast cancer and glioblastoma patients. We identified 1326 and 12 breast-cancer- and glioblastoma-related genes that contained one or more SAAVs, including BRCA2 and FAM49B, respectively. SAAVpedia is a suitable platform for confirming whether a genomic variant is maintained in an amino acid sequence. Furthermore, as a result of the SAAV discovery of these positive controls, the SAAVpedia could play a key role in the protein functional study for the Human Proteome Project (HPP).
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Affiliation(s)
- Soo Youn Lee
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Young-Mook Kang
- Drug Information Platform Center , Korea Research Institute of Chemical Technology , 141 Gajeong-ro , Daejeon 34114 , Korea
| | - Hyejin Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Dong Geun Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Ji Eun Jeong
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea
| | - Jong Shin Yoo
- Research Center for Bioconvergence Analysis , Korea Basic Science Institute , 162 Yeongudaji-ro , Cheongju 28119 , Korea.,Graduate School of Analytical Science and Technology , Chungnam National University , 99 Daehak-ro , Daejeon 34134 , Korea
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Abstract
RATIONALE Cystic fibrosis, like primary ciliary dyskinesia, is an autosomal recessive disorder characterized by abnormal mucociliary clearance and obstructive lung disease. We hypothesized that genes underlying the development or function of cilia may modify lung disease severity in persons with cystic fibrosis. OBJECTIVES To test this hypothesis, we compared variants in 93 candidate genes in both upper and lower tertiles of lung function in a large cohort of children and adults with cystic fibrosis with those of a population control dataset. METHODS Variants within candidate genes were tested for association using the SKAT-O test, comparing cystic fibrosis cases defined by poor (n = 127) or preserved (n = 127) lung function with population controls (n = 3,269 or 3,148, respectively). Associated variants were then tested for association with related phenotypes in independent datasets. RESULTS Variants in DNAH14 and DNAAF3 were associated with poor lung function in cystic fibrosis, whereas variants in DNAH14 and DNAH6 were associated with preserved lung function in cystic fibrosis. Associations between DNAH14 and lung function were replicated in disease-related phenotypes characterized by obstructive lung disease in adults. CONCLUSIONS Genetic variants within DNAH6, DNAH14, and DNAAF3 are associated with variation in lung function among persons with cystic fibrosis.
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Development of an evidence-based algorithm that optimizes sensitivity and specificity in ES-based diagnostics of a clinically heterogeneous patient population. Genet Med 2018; 21:53-61. [PMID: 30100613 PMCID: PMC6752300 DOI: 10.1038/s41436-018-0016-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 11/29/2022] Open
Abstract
Purpose Next-generation sequencing (NGS) is rapidly replacing Sanger sequencing in genetic diagnostics. Sensitivity and specificity of NGS approaches are not well-defined, but can be estimated from applying NGS and Sanger sequencing in parallel. Utilizing this strategy, we aimed at optimizing exome sequencing (ES)–based diagnostics of a clinically diverse patient population. Methods Consecutive DNA samples from unrelated patients with suspected genetic disease were exome-sequenced; comparatively nonstringent criteria were applied in variant calling. One thousand forty-eight variants in genes compatible with the clinical diagnosis were followed up by Sanger sequencing. Based on a set of variant-specific features, predictors for true positives and true negatives were developed. Results Sanger sequencing confirmed 81.9% of ES-derived variants. Calls from the lower end of stringency accounted for the majority of the false positives, but also contained ~5% of the true positives. A predictor incorporating three variant-specific features classified 91.7% of variants with 100% specificity and 99.75% sensitivity. Confirmation status of the remaining variants (8.3%) was not predictable. Conclusions Criteria for variant calling in ES-based diagnostics impact on specificity and sensitivity. Confirmatory sequencing for a proportion of variants, therefore, remains a necessity. Our study exemplifies how these variants can be defined on an empirical basis.
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7
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Knoppers BM, Nguyen MT, Sénécal K, Tassé AM, Zawati MH. Next-Generation Sequencing and the Return of Results. Cold Spring Harb Perspect Med 2016; 6:a026724. [PMID: 27599532 PMCID: PMC5046689 DOI: 10.1101/cshperspect.a026724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The impact of next-generation sequencing (NGS) on the issue of return of results is defying clear policy guidance and creating international confusion. Limiting ourselves to the return of results revealed by NGS (including incidental findings) in adults, children, family members of deceased individuals, and population studies, we describe and contrast emerging policy positions in Europe, Canada, and the United States. Until there are clear, scientific, and professional standards and practical policy, both researchers and clinicians cannot be faulted for being either hesitant or pressured to return NGS results.
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Affiliation(s)
| | - Minh Thu Nguyen
- Centre of Genomics and Policy, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Karine Sénécal
- Centre of Genomics and Policy, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Anne Marie Tassé
- Public Population Project in Genomics and Society (PG), Montreal, Quebec H3A 0G1, Canada
| | - Ma'n H Zawati
- Centre of Genomics and Policy, McGill University, Montreal, Quebec H3A 0G1, Canada
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8
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Pediatric otolaryngology, molecular diagnosis of hereditary hearing loss: next-generation sequencing approach. Curr Opin Otolaryngol Head Neck Surg 2016; 23:480-4. [PMID: 26488533 DOI: 10.1097/moo.0000000000000208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Sensorineural hearing loss (SNHL) is the most common sensory birth defect. The purpose of this article is to review the advances in next-generation sequencing (NGS) and molecular diagnosis of hereditary hearing loss. RECENT FINDINGS Early diagnosis and detection of SNHL is critical for the development of appropriate speech and language, as neuroplasticity peaks in the first few years of life. There has been increased accuracy of NGS genetic testing, which has helped created a paradigm shift in the diagnosis of hearing loss. The diagnostic yield of genetic testing now approaches that of radiographic imaging; however, there remains a difference in cost and time delay. With the introduction of comprehensive genetic panels, 23-129 genes can be sequenced from the same blood sample. SUMMARY Diagnostic genetic testing of SNHL in the past has been confined to a few genes through Sanger sequencing. The advent of NGS allows for development of comprehensive genetic panels, which test for up to 129 genes while improving the accuracy and efficiency of testing. This type of testing may become more common as the costs decrease and more genes are discovered.
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Bertier G, Hétu M, Joly Y. Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views. BMC Med Genomics 2016; 9:52. [PMID: 27514372 PMCID: PMC4982236 DOI: 10.1186/s12920-016-0213-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature. METHODS In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users. RESULTS Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles. CONCLUSIONS WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
- UMR 1027, Inserm, University of Toulouse III - Paul Sabatier, 37 allées Jules Guesde, F-31000 Toulouse, France
| | - Martin Hétu
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
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Shapiro AJ, Zariwala MA, Ferkol T, Davis SD, Sagel SD, Dell SD, Rosenfeld M, Olivier KN, Milla C, Daniel SJ, Kimple AJ, Manion M, Knowles MR, Leigh MW. Diagnosis, monitoring, and treatment of primary ciliary dyskinesia: PCD foundation consensus recommendations based on state of the art review. Pediatr Pulmonol 2016; 51:115-32. [PMID: 26418604 PMCID: PMC4912005 DOI: 10.1002/ppul.23304] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/30/2015] [Accepted: 08/21/2015] [Indexed: 01/10/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, rare lung disease resulting in chronic oto-sino-pulmonary disease in both children and adults. Many physicians incorrectly diagnose PCD or eliminate PCD from their differential diagnosis due to inexperience with diagnostic testing methods. Thus far, all therapies used for PCD are unproven through large clinical trials. This review article outlines consensus recommendations from PCD physicians in North America who have been engaged in a PCD centered research consortium for the last 10 years. These recommendations have been adopted by the governing board of the PCD Foundation to provide guidance for PCD clinical centers for diagnostic testing, monitoring, and appropriate short and long-term therapeutics in PCD patients.
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Affiliation(s)
- Adam J Shapiro
- Department of Pediatrics, Montreal Children's Hospital, McGill University, Quebec, Canada
| | - Maimoona A Zariwala
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Marsico Lung Institute, Chapel Hill, North Carolina
| | - Thomas Ferkol
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Stephanie D Davis
- Department of Pediatrics, Riley Hospital for Children, Indiana University, Indianapolis, Indiana
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado
| | - Sharon D Dell
- Department of Pediatrics, The Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Margaret Rosenfeld
- Department of Pediatrics, Seattle Children's Hospital and University of Washington, Seattle, Washington
| | | | - Carlos Milla
- Department of Pediatrics, Stanford University, Palo Alto, California
| | - Sam J Daniel
- Department of Otolaryngology, Montreal Children's Hospital, McGill University, Montreal, Quebec, Canada
| | - Adam J Kimple
- Department of Otolaryngology-Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | | | - Michael R Knowles
- Department of Medicine, University of North Carolina, Marsico Lung Institute, Chapel Hill, North Carolina
| | - Margaret W Leigh
- Department of Pediatrics, University of North Carolina, Marsico Lung Institute, Chapel Hill, North Carolina
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Plasma metabolomic profiles enhance precision medicine for volunteers of normal health. Proc Natl Acad Sci U S A 2015; 112:E4901-10. [PMID: 26283345 DOI: 10.1073/pnas.1508425112] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Precision medicine, taking account of human individuality in genes, environment, and lifestyle for early disease diagnosis and individualized therapy, has shown great promise to transform medical care. Nontargeted metabolomics, with the ability to detect broad classes of biochemicals, can provide a comprehensive functional phenotype integrating clinical phenotypes with genetic and nongenetic factors. To test the application of metabolomics in individual diagnosis, we conducted a metabolomics analysis on plasma samples collected from 80 volunteers of normal health with complete medical records and three-generation pedigrees. Using a broad-spectrum metabolomics platform consisting of liquid chromatography and GC coupled with MS, we profiled nearly 600 metabolites covering 72 biochemical pathways in all major branches of biosynthesis, catabolism, gut microbiome activities, and xenobiotics. Statistical analysis revealed a considerable range of variation and potential metabolic abnormalities across the individuals in this cohort. Examination of the convergence of metabolomics profiles with whole-exon sequences (WESs) provided an effective approach to assess and interpret clinical significance of genetic mutations, as shown in a number of cases, including fructose intolerance, xanthinuria, and carnitine deficiency. Metabolic abnormalities consistent with early indications of diabetes, liver dysfunction, and disruption of gut microbiome homeostasis were identified in several volunteers. Additionally, diverse metabolic responses to medications among the volunteers may assist to identify therapeutic effects and sensitivity to toxicity. The results of this study demonstrate that metabolomics could be an effective approach to complement next generation sequencing (NGS) for disease risk analysis, disease monitoring, and drug management in our goal toward precision care.
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12
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Whole-Exome Sequencing and Targeted Copy Number Analysis in Primary Ciliary Dyskinesia. G3-GENES GENOMES GENETICS 2015; 5:1775-81. [PMID: 26139845 PMCID: PMC4528333 DOI: 10.1534/g3.115.019851] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Primary ciliary dyskinesia (PCD) is an autosomal-recessive disorder resulting from loss of normal ciliary function. Symptoms include neonatal respiratory distress, chronic sinusitis, bronchiectasis, situs inversus, and infertility. Clinical features may be subtle and highly variable, making the diagnosis of PCD challenging. The diagnosis can be confirmed with ciliary ultrastructure analysis and/or molecular genetic testing of 32 PCD-associated genes. However, because of this genetic heterogeneity, comprehensive molecular genetic testing is not considered the standard of care, and the most efficient molecular approach has yet to be elucidated. Here, we propose a cost-effective and time-efficient molecular genetic algorithm to solve cases of PCD. We conducted targeted copy number variation (CNV) analysis and/or whole-exome sequencing on 20 families (22 patients) from a subset of 45 families (52 patients) with a clinical diagnosis of PCD who did not have a molecular genetic diagnosis after Sanger sequencing of 12 PCD-associated genes. This combined molecular genetic approach led to the identification of 4 of 20 (20%) families with clinically significant CNVs and 7 of 20 (35%) families with biallelic pathogenic mutations in recently identified PCD genes, resulting in an increased molecular genetic diagnostic rate of 55% (11/20). In patients with a clinical diagnosis of PCD, whole-exome sequencing followed by targeted CNV analysis results in an overall molecular genetic yield of 76% (34/45).
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13
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Ghemlas I, Li H, Zlateska B, Klaassen R, Fernandez CV, Yanofsky RA, Wu J, Pastore Y, Silva M, Lipton JH, Brossard J, Michon B, Abish S, Steele M, Sinha R, Belletrutti M, Breakey VR, Jardine L, Goodyear L, Sung L, Dhanraj S, Reble E, Wagner A, Beyene J, Ray P, Meyn S, Cada M, Dror Y. Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes. J Med Genet 2015; 52:575-84. [PMID: 26136524 DOI: 10.1136/jmedgenet-2015-103270] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Phenotypic overlap among the inherited bone marrow failure syndromes (IBMFSs) frequently limits the ability to establish a diagnosis based solely on clinical features. >70 IBMFS genes have been identified, which often renders genetic testing prolonged and costly. Since correct diagnosis, treatment and cancer surveillance often depend on identifying the mutated gene, strategies that enable timely genotyping are essential. METHODS To overcome these challenges, we developed a next-generation sequencing assay to analyse a panel of 72 known IBMFS genes. Cases fulfilling the clinical diagnostic criteria of an IBMFS but without identified causal genotypes were included. RESULTS The assay was validated by detecting 52 variants previously found by Sanger sequencing. A total of 158 patients with unknown mutations were studied. Of 75 patients with known IBMFS categories (eg, Fanconi anaemia), 59% had causal mutations. Among 83 patients with unclassified IBMFSs, we found causal mutations and established the diagnosis in 18% of the patients. The assay detected mutant genes that had not previously been reported to be associated with the patient phenotypes. In other cases, the assay led to amendments of diagnoses. In 20% of genotype cases, the results indicated a cancer surveillance programme. CONCLUSIONS The novel assay is efficient, accurate and has a major impact on patient care.
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Affiliation(s)
- Ibrahim Ghemlas
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hongbing Li
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Bozana Zlateska
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Robert Klaassen
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | | | - John Wu
- British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | | | | | - Jeff H Lipton
- Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Josee Brossard
- Centre hospitalier universitaire, Sherbrooke, Quebec, Canada
| | - Bruno Michon
- Centre Hospital University Quebec-Pav CHUL, Sainte-Foy, Quebec, Canada
| | - Sharon Abish
- Montreal Children's Hospital, Montreal, Québec, Canada
| | | | - Roona Sinha
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Mark Belletrutti
- Stollery Children's Hospital, University of Alberta, Edmonton, Alberta, Canada
| | - Vicky R Breakey
- McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Lawrence Jardine
- Children's Hospital at London Health Sciences Centre, London, Ontario, Canada
| | - Lisa Goodyear
- Janeway Child Health Centre, St. John's, Newfoundland, Canada
| | - Lillian Sung
- Population Health Sciences, Research Institute, The Hospital For Sick Children, Toronto, Ontario, Canada
| | - Santhosh Dhanraj
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Amanda Wagner
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Beyene
- Program in Population Genomics, Department of Clinical Epidemiology & Biostatistics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ray
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Molecular Genetic Laboratory, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen Meyn
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Michaela Cada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yigal Dror
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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14
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Wooderchak-Donahue W, VanSant-Webb C, Tvrdik T, Plant P, Lewis T, Stocks J, Raney JA, Meyers L, Berg A, Rope AF, Yetman AT, Bleyl SB, Mesley R, Bull DA, Collins RT, Ojeda MM, Roberts A, Lacro R, Woerner A, Stoler J, Bayrak-Toydemir P. Clinical utility of a next generation sequencing panel assay for Marfan and Marfan-like syndromes featuring aortopathy. Am J Med Genet A 2015; 167A:1747-57. [PMID: 25944730 DOI: 10.1002/ajmg.a.37085] [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: 12/08/2014] [Accepted: 03/15/2015] [Indexed: 12/28/2022]
Abstract
Aortopathy can be defined as aortic dilation, aneurysm, dissection, and tortuosity. Familial aortopathy may occur secondary to fibrillin-1 (FBN1) mutations in the setting of Marfan syndrome, or may occur as a result of other genetic defects with different, but occasionally overlapping, phenotypes. Because of the phenotypic overlap and genetic heterogeneity of disorders featuring aortopathy, we developed a next generation sequencing (NGS) assay and comparative genomic hybridization (CGH) array to detect mutations in 10 genes that cause thoracic aortic aneurysms (TAAs). Here, we report on the clinical and molecular findings in 175 individuals submitted for aortopathy panel testing at ARUP laboratories. Ten genes associated with heritable aortopathies were targeted using hybridization capture prior to sequencing. NGS results were analyzed, and variants were confirmed using Sanger sequencing. Array CGH was used to detect copy-number variation. Of 175 individuals, 18 had a pathogenic mutation and 32 had a variant of uncertain significance (VUS). Most pathogenic mutations (72%) were identified in FBN1. A novel large SMAD3 duplication and FBN1 deletion were identified. Over half who had TAAs or other aortic involvement tested negative for a mutation, suggesting that additional aortopathy genes exist. We anticipate that the clinical sensitivity of at least 10.3% will rise with VUS reclassification and as additional genes are identified and included in the panel. The aortopathy NGS panel aids in the timely molecular diagnosis of individuals with disorders featuring aortopathy and guides proper treatment.
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Affiliation(s)
- Whitney Wooderchak-Donahue
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Chad VanSant-Webb
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Tatiana Tvrdik
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Parker Plant
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Tracey Lewis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Jennifer Stocks
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Joshua A Raney
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Lindsay Meyers
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Alizabeth Berg
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah
| | - Alan F Rope
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Anji T Yetman
- Department of Pediatrics, Division of Cardiology, University of Utah, Salt Lake City, Utah
| | - Steven B Bleyl
- Department of Pediatrics, Division of Cardiology, University of Utah, Salt Lake City, Utah.,Clinical Genetics Institute, Intermountain Healthcare, Salt Lake City, Utah
| | - Rebecca Mesley
- Department of Surgery, Division of Cardiothoracic Surgery, University of Utah, Salt Lake City, Utah
| | - David A Bull
- Department of Surgery, Division of Cardiothoracic Surgery, University of Utah, Salt Lake City, Utah
| | - R Thomas Collins
- Department of Pediatrics and Internal Medicine, Cardiology Division, Arkansas Children's Hospital, Little Rock, Arkansas
| | | | - Amy Roberts
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts
| | - Ronald Lacro
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts
| | - Audrey Woerner
- Division of Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Joan Stoler
- Division of Genetics, Boston Children's Hospital, Boston, Massachusetts
| | - Pinar Bayrak-Toydemir
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
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15
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Pereira R, Oliveira J, Ferraz L, Barros A, Santos R, Sousa M. Mutation analysis in patients with total sperm immotility. J Assist Reprod Genet 2015; 32:893-902. [PMID: 25877373 DOI: 10.1007/s10815-015-0474-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/01/2015] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Perform the genetic characterization of five patients with total sperm immotility using Sanger sequencing and Whole Exome Sequencing (WES), in order to increase the knowledge on the genetics of sperm immotility and, ultimately, allow the identification of potential genetic markers for infertility. METHODS Prospective study at a University Medical school. We analysed five men with total sperm immotility, four with dysplasia of the fibrous sheath (DFS), associated with disruption of several axonemal structures, and one patient with situs inversus totalis, which showed absence of dynein arms (DA) and nexin bridges. We screened 7 genes by Sanger sequencing, involved in sperm motility and associated to ultrastructural defects found in these patients (CCDC39, CCDC40, DNAH5, DNAI1, RSPH1, AKAP3 and AKAP4). Additionally, we performed WES analysis in the patient with situs inversus. RESULTS We identified nine new DNA sequence variants by WES. Two of these variants were considered particularly relevant: a homozygous missense change in CCDC103 gene (c.104G > C, p.R35P) probably related with absence of dynein arms; the other in the INSL6 gene (c.262_263delCC) is thought to be also involved in sperm immotility. CONCLUSIONS Our work suggests that WES is an effective strategy, especially as compared with conventional sequencing, to study highly heterogenic genetic diseases, such as sperm immotility. For future work we expect to expand the analysis of WES to the other four patients and complement findings with expression analysis or functional studies to determine the impact of the novel variants.
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Affiliation(s)
- Rute Pereira
- Laboratory of Cell Biology, Department of Microscopy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto (UP), Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
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16
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Li J, Huang Q, Ge L, Xu J, Shi X, Xie W, Liu X, Liu X. Identification of genetic variations of a Chinese family with paramyotonia congenita via whole exome sequencing. GENOMICS DATA 2015; 4:65-8. [PMID: 26484179 PMCID: PMC4535863 DOI: 10.1016/j.gdata.2015.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 11/09/2022]
Abstract
Paramyotonia congenita (PC) is a rare autosomal dominant neuromuscular disorder characterized by juvenile onset and development of cold-induced myotonia after repeated activities. The disease is mostly caused by genetic mutations of the sodium channel, voltage-gated, type IV, alpha subunit (SCN4A) gene. This study intended to systematically identify the causative genetic variations of a Chinese Han PC family. Seven members of this PC family, including four patients and three healthy controls, were selected for whole exome sequencing (WES) using the Illumina HiSeq platform. Sequence variations were identified using the SoftGenetics program. The mutation R1448C of SCN4A was found to be the only causative mutation. This study applied WES technology to sequence multiple members of a large PC family and was the first to systematically confirm that the genetic change in SCN4A is the only causative variation in this PC family and the SCN4A mutation is sufficient to lead to PC.
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Affiliation(s)
- Jinxin Li
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Qinghai Huang
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Liang Ge
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Jing Xu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Wei Xie
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Xiang Liu
- Hainan Medical University, Hainan 571199, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing 210096, China
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17
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Standardizing nasal nitric oxide measurement as a test for primary ciliary dyskinesia. Ann Am Thorac Soc 2014; 10:574-81. [PMID: 24024753 DOI: 10.1513/annalsats.201305-110oc] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RATIONALE Several studies suggest that nasal nitric oxide (nNO) measurement could be a test for primary ciliary dyskinesia (PCD), but the procedure and interpretation have not been standardized. OBJECTIVES To use a standard protocol for measuring nNO to establish a disease-specific cutoff value at one site, and then validate at six other sites. METHODS At the lead site, nNO was prospectively measured in individuals later confirmed to have PCD by ciliary ultrastructural defects (n = 143) or DNAH11 mutations (n = 6); and in 78 healthy and 146 disease control subjects, including individuals with asthma (n = 37), cystic fibrosis (n = 77), and chronic obstructive pulmonary disease (n = 32). A disease-specific cutoff value was determined, using generalized estimating equations (GEEs). Six other sites prospectively measured nNO in 155 consecutive individuals enrolled for evaluation for possible PCD. MEASUREMENTS AND MAIN RESULTS At the lead site, nNO values in PCD (mean ± standard deviation, 20.7 ± 24.1 nl/min; range, 1.5-207.3 nl/min) only rarely overlapped with the nNO values of healthy control subjects (304.6 ± 118.8; 125.5-867.0 nl/min), asthma (267.8 ± 103.2; 125.0-589.7 nl/min), or chronic obstructive pulmonary disease (223.7 ± 87.1; 109.7-449.1 nl/min); however, there was overlap with cystic fibrosis (134.0 ± 73.5; 15.6-386.1 nl/min). The disease-specific nNO cutoff value was defined at 77 nl/minute (sensitivity, 0.98; specificity, >0.999). At six other sites, this cutoff identified 70 of the 71 (98.6%) participants with confirmed PCD. CONCLUSIONS Using a standardized protocol in multicenter studies, nNO measurement accurately identifies individuals with PCD, and supports its usefulness as a test to support the clinical diagnosis of PCD.
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18
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Popatia R, Haver K, Casey A. Primary Ciliary Dyskinesia: An Update on New Diagnostic Modalities and Review of the Literature. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2014; 27:51-59. [PMID: 24963453 DOI: 10.1089/ped.2013.0314] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/14/2014] [Indexed: 12/19/2022]
Abstract
Primary ciliary dyskinesia (PCD) is a genetic condition affecting approximately 1 in 15,000-20,000 individuals, and the majority of cases exhibit an autosomal recessive inheritance pattern. However, genetic heterogenicity is seen in PCD and reflects the complexity of ciliary structure and biogenesis. There have been many recent advances in the diagnosis and management of PCD in the last few years, including advanced genetic sequencing, nasal nitric oxide assay, and ciliary motility tests. This article focuses on the ultrastructure and pathophysiology of ciliary dyskinesias, along with a review of clinical features, screening, and diagnostic tests. It also reflects upon the diagnostic challenge caused by the diverse clinical presentation, which will be of great value to pediatricians for considering PCD in their differential list, henceforth leading to early recognition and management, along with awareness of the recent advances in the field of genetics and other techniques for diagnosis of this condition.
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Affiliation(s)
- Rizwana Popatia
- Division of Pulmonary Medicine, Boston Children's Hospital , Boston, Massachusetts
| | - Kenan Haver
- Division of Pulmonary Medicine, Boston Children's Hospital , Boston, Massachusetts
| | - Alicia Casey
- Division of Pulmonary Medicine, Boston Children's Hospital , Boston, Massachusetts
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19
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Gao R, Liu Y, Gjesing AP, Hollensted M, Wan X, He S, Pedersen O, Yi X, Wang J, Hansen T. Evaluation of a target region capture sequencing platform using monogenic diabetes as a study-model. BMC Genet 2014; 15:13. [PMID: 24476040 PMCID: PMC3943834 DOI: 10.1186/1471-2156-15-13] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 12/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Monogenic diabetes is a genetic disease often caused by mutations in genes involved in beta-cell function. Correct sub-categorization of the disease is a prerequisite for appropriate treatment and genetic counseling. Target-region capture sequencing is a combination of genomic region enrichment and next generation sequencing which might be used as an efficient way to diagnose various genetic disorders. We aimed to develop a target-region capture sequencing platform to screen 117 selected candidate genes involved in metabolism for mutations and to evaluate its performance using monogenic diabetes as a study-model. RESULTS The performance of the assay was evaluated in 70 patients carrying known disease causing mutations previously identified in HNF4A, GCK, HNF1A, HNF1B, INS, or KCNJ11. Target regions with a less than 20-fold sequencing depth were either introns or UTRs. When only considering translated regions, the coverage was 100% with a 50-fold minimum depth. Among the 70 analyzed samples, 63 small size single nucleotide polymorphisms and indels as well as 7 large deletions and duplications were identified as being the pathogenic variants. The mutations identified by the present technique were identical with those previously identified through Sanger sequencing and Multiplex Ligation-dependent Probe Amplification. CONCLUSIONS We hereby demonstrated that the established platform as an accurate and high-throughput gene testing method which might be useful in the clinical diagnosis of monogenic diabetes.
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Affiliation(s)
| | | | | | | | | | | | | | - Xin Yi
- BGI-Shenzhen, Shenzhen, China.
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20
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Cottrell CE, Al-Kateb H, Bredemeyer AJ, Duncavage EJ, Spencer DH, Abel HJ, Lockwood CM, Hagemann IS, O'Guin SM, Burcea LC, Sawyer CS, Oschwald DM, Stratman JL, Sher DA, Johnson MR, Brown JT, Cliften PF, George B, McIntosh LD, Shrivastava S, Nguyen TT, Payton JE, Watson MA, Crosby SD, Head RD, Mitra RD, Nagarajan R, Kulkarni S, Seibert K, Virgin HW, Milbrandt J, Pfeifer JD. Validation of a next-generation sequencing assay for clinical molecular oncology. J Mol Diagn 2013; 16:89-105. [PMID: 24211365 DOI: 10.1016/j.jmoldx.2013.10.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 08/23/2013] [Accepted: 10/01/2013] [Indexed: 11/29/2022] Open
Abstract
Currently, oncology testing includes molecular studies and cytogenetic analysis to detect genetic aberrations of clinical significance. Next-generation sequencing (NGS) allows rapid analysis of multiple genes for clinically actionable somatic variants. The WUCaMP assay uses targeted capture for NGS analysis of 25 cancer-associated genes to detect mutations at actionable loci. We present clinical validation of the assay and a detailed framework for design and validation of similar clinical assays. Deep sequencing of 78 tumor specimens (≥ 1000× average unique coverage across the capture region) achieved high sensitivity for detecting somatic variants at low allele fraction (AF). Validation revealed sensitivities and specificities of 100% for detection of single-nucleotide variants (SNVs) within coding regions, compared with SNP array sequence data (95% CI = 83.4-100.0 for sensitivity and 94.2-100.0 for specificity) or whole-genome sequencing (95% CI = 89.1-100.0 for sensitivity and 99.9-100.0 for specificity) of HapMap samples. Sensitivity for detecting variants at an observed 10% AF was 100% (95% CI = 93.2-100.0) in HapMap mixes. Analysis of 15 masked specimens harboring clinically reported variants yielded concordant calls for 13/13 variants at AF of ≥ 15%. The WUCaMP assay is a robust and sensitive method to detect somatic variants of clinical significance in molecular oncology laboratories, with reduced time and cost of genetic analysis allowing for strategic patient management.
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Affiliation(s)
- Catherine E Cottrell
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Hussam Al-Kateb
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri.
| | - Andrew J Bredemeyer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Eric J Duncavage
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - David H Spencer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Haley J Abel
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Christina M Lockwood
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Ian S Hagemann
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Stephanie M O'Guin
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Lauren C Burcea
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher S Sawyer
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Dayna M Oschwald
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jennifer L Stratman
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Dorie A Sher
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Mark R Johnson
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Justin T Brown
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Paul F Cliften
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Bijoy George
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Leslie D McIntosh
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Savita Shrivastava
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Tudung T Nguyen
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Mark A Watson
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Seth D Crosby
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Richard D Head
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Robi D Mitra
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Rakesh Nagarajan
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Shashikant Kulkarni
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri; Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Karen Seibert
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Herbert W Virgin
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - Jeffrey Milbrandt
- Department of Genetics, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
| | - John D Pfeifer
- Department of Pathology and Immunology, Genomics and Pathology Services, Washington University School of Medicine, St. Louis, Missouri
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21
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Dorn C, Grunert M, Sperling SR. Application of high-throughput sequencing for studying genomic variations in congenital heart disease. Brief Funct Genomics 2013; 13:51-65. [PMID: 24095982 DOI: 10.1093/bfgp/elt040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Congenital heart diseases (CHD) represent the most common birth defect in human. The majority of cases are caused by a combination of complex genetic alterations and environmental influences. In the past, many disease-causing mutations have been identified; however, there is still a large proportion of cardiac malformations with unknown precise origin. High-throughput sequencing technologies established during the last years offer novel opportunities to further study the genetic background underlying the disease. In this review, we provide a roadmap for designing and analyzing high-throughput sequencing studies focused on CHD, but also with general applicability to other complex diseases. The three main next-generation sequencing (NGS) platforms including their particular advantages and disadvantages are presented. To identify potentially disease-related genomic variations and genes, different filtering steps and gene prioritization strategies are discussed. In addition, available control datasets based on NGS are summarized. Finally, we provide an overview of current studies already using NGS technologies and showing that these techniques will help to further unravel the complex genetics underlying CHD.
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Affiliation(s)
- Cornelia Dorn
- Department of Cardiovascular Genetics, Experimental and Clinical Research Center (ECRC), Charité-University Medicine Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany. Department of Biochemistry, Free University Berlin, Berlin, Germany. Tel.: +49-(0)30-450540123; Fax: +49-(0)30-84131699;
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22
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Abstract
Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.
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23
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Srebniak MI, Mout L, Van Opstal D, Galjaard RJH. 0.5 Mb array as a first-line prenatal cytogenetic test in cases without ultrasound abnormalities and its implementation in clinical practice. Hum Mutat 2013; 34:1298-303. [PMID: 23674485 DOI: 10.1002/humu.22355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/02/2013] [Indexed: 01/08/2023]
Abstract
Using whole-genome array testing instead of karyotyping in prenatal diagnosis for all indications may be desirable because of the higher diagnostic yield and shorter reporting time. The goal of this research was finding the optimal array resolution that could replace routine prenatal karyotyping in cases without ultrasound abnormalities, for example, referred for advanced maternal age or abnormal first trimester screening. As variants of unknown clinical significance (VOUS), if reported, might complicate decision-making about continuation of pregnancy, such an optimal array resolution should have a high abnormality detection rate and reveal a minimal amount of VOUS. The array data of 465 fetuses were retrospectively evaluated with several resolution levels, and the Decipher microdeletion/microduplication syndrome list was reviewed to assess what could be theoretically missed with a lower resolution. A 0.5-Mb resolution showed a high diagnostic yield potential and significantly minimized the number of VOUS. Based on our experience, we recommend genomic SNP array as a first-tier test in prenatal diagnosis. The resolution should be chosen based on the indication. In cases of fetal ultrasound abnormalities or intrauterine fetal death (IUFD), high-resolution analysis should be done. In other cases, we advise replacing karyotyping by SNP array analysis with 0.5 Mb resolution.
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24
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Teves ME, Zhang Z, Costanzo RM, Henderson SC, Corwin FD, Zweit J, Sundaresan G, Subler M, Salloum FN, Rubin BK, Strauss JF. Sperm-associated antigen-17 gene is essential for motile cilia function and neonatal survival. Am J Respir Cell Mol Biol 2013; 48:765-72. [PMID: 23418344 PMCID: PMC3727877 DOI: 10.1165/rcmb.2012-0362oc] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 01/16/2013] [Indexed: 11/24/2022] Open
Abstract
Primary ciliary dyskinesia (PCD), resulting from defects in cilia assembly or motility, is caused by mutations in a number of genes encoding axonemal proteins. PCD phenotypes are variable, and include recurrent respiratory tract infections, bronchiectasis, hydrocephaly, situs inversus, and male infertility. We generated knockout mice for the sperm-associated antigen-17 (Spag17) gene, which encodes a central pair (CP) protein present in the axonemes of cells with "9 + 2" motile cilia or flagella. The targeting of Spag17 resulted in a severe phenotype characterized by immotile nasal and tracheal cilia, reduced clearance of nasal mucus, profound respiratory distress associated with lung fluid accumulation and disruption of the alveolar epithelium, cerebral ventricular expansion consistent with emerging hydrocephalus, failure to suckle, and neonatal demise within 12 hours of birth. Ultrastructural analysis revealed the loss of one CP microtubule in approximately one quarter of tracheal cilia axonemes, an absence of a C1 microtubule projection, and other less frequent CP structural abnormalities. SPAG6 and SPAG16 (CP proteins that interact with SPAG17) were increased in tracheal tissue from SPAG17-deficient mice. We conclude that Spag17 plays a critical role in the function and structure of motile cilia, and that neonatal lethality is likely explained by impaired airway mucociliary clearance.
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Affiliation(s)
| | - Zhibing Zhang
- Department of Obstetrics and Gynecology
- Department of Biochemistry and Molecular Biology
| | | | | | | | - Jamal Zweit
- Department of Biochemistry and Molecular Biology
- Department of Radiology
| | | | | | - Fadi N. Salloum
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, and
| | - Bruce K. Rubin
- Department of Physiology and Biophysics
- Department of Pediatrics, Virginia Commonwealth University, Richmond, Virginia
| | - Jerome F. Strauss
- Department of Obstetrics and Gynecology
- Department of Biochemistry and Molecular Biology
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Sivakumaran TA, Husami A, Kissell D, Zhang W, Keddache M, Black AP, Tinkle BT, Greinwald JH, Zhang K. Performance evaluation of the next-generation sequencing approach for molecular diagnosis of hereditary hearing loss. Otolaryngol Head Neck Surg 2013; 148:1007-16. [PMID: 23525850 DOI: 10.1177/0194599813482294] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To evaluate the performance of a next-generation sequencing (NGS)-based targeted resequencing genetic test, OtoSeq, to identify the sequence variants in the genes causing sensorineural hearing loss (SNHL). STUDY DESIGN Retrospective study. SETTING Tertiary children's hospital. SUBJECTS AND METHODS A total of 8 individuals presenting with prelingual hearing loss were used in this study. The coding and flanking intronic regions of 24 well-studied SNHL genes were enriched using microdroplet polymerase chain reaction and sequenced on an Illumina HiSeq 2000 sequencer. The filtered high-quality sequence reads were mapped to reference sequence, and variants were detected using NextGENe software. RESULTS A total of 1148 sequence variants were detected in 8 samples in 24 genes. Using in-house developed NGS data analysis criteria, we classified 810 (~71%) of these variants as potential true variants that include previously detected pathogenic mutations in 5 patients. To validate our strategy, we Sanger sequenced the target regions of 5 of the 24 genes, accounting for about 29.2% of all target sequence. Our results showed >99.99% concordance between NGS and Sanger sequencing in these 5 genes, resulting in an analytical sensitivity and specificity of 100% and 99.997%, respectively. We were able to successfully detect single base substitutions, small deletions, and insertions of up to 22 nucleotides. CONCLUSION This study demonstrated that our NGS-based mutation screening strategy is highly sensitive and specific in detecting sequence variants in the SNHL genes. Therefore, we propose that this NGS-based targeted sequencing method would be an alternative to current technologies for identifying the multiple genetic causes of SNHL.
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Affiliation(s)
- Theru A Sivakumaran
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.
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Targeted Sequence Capture and High-Throughput Sequencing in the Molecular Diagnosis of Ichthyosis and Other Skin Diseases. J Invest Dermatol 2013; 133:573-6. [DOI: 10.1038/jid.2012.332] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Svobodová T, Djakow J, Zemková D, Cipra A, Pohunek P, Lebl J. Impaired Growth during Childhood in Patients with Primary Ciliary Dyskinesia. Int J Endocrinol 2013; 2013:731423. [PMID: 24454367 PMCID: PMC3876717 DOI: 10.1155/2013/731423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/19/2013] [Indexed: 11/23/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) leads to recurrent/chronic respiratory infections, resulting in chronic inflammation and potentially in chronic pulmonary disease with bronchiectasis. We analyzed longitudinal data on body length/height and body mass index (BMI) for 29 children and young adults with PCD aging 1.5-24 years (median, 14.5) who had been diagnosed at the age of 0.5-17 years (median, 8). Of these, 10 carried pathogenic mutations in either DNAH5 or DNAI1. In children with PCD, body length/height progressively decreased from +0.40 ± 0.24 SDS (the 1st birthday), +0.16 ± 0.23 SDS (3 years old), and -0.13 ± 0.21 SDS (5 years old) to -0.54 ± 0.19 SDS (7 years old; P = 0.01 versus 0), -0.67 ± 0.21 SDS (9 years old; P = 0.005 versus 0), -0.52 ± 0.24 SDS (11 years old; P = 0.04 versus 0), and -0.53 ± 0.23 SDS (13 years old; P = 0.03 versus 0). These results reflect low growth rates during the childhood growth period. Thereafter, heights stabilized up to the age of 17 years. The growth deterioration was not dependent on sex or disease severity but was more pronounced in DNAH5 or DNAI1 mutation carriers. BMI did not differ from population standards, which suggests that nutritional deficits are not the cause of growth delay. We conclude that PCD leads to chronic deprivation with significant growth deterioration during childhood.
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Affiliation(s)
- Tamara Svobodová
- Department of Pediatrics, 2nd Faculty of Medicine, University Hospital Motol, Charles University, 150 06 Prague, Czech Republic
| | - Jana Djakow
- Department of Pediatrics, 2nd Faculty of Medicine, University Hospital Motol, Charles University, 150 06 Prague, Czech Republic
| | - Daniela Zemková
- Department of Pediatrics, 2nd Faculty of Medicine, University Hospital Motol, Charles University, 150 06 Prague, Czech Republic
| | - Adam Cipra
- Department of Pediatrics, Masaryk's Hospital, 400 11 Usti nad Labem, Czech Republic
| | - Petr Pohunek
- Department of Pediatrics, 2nd Faculty of Medicine, University Hospital Motol, Charles University, 150 06 Prague, Czech Republic
| | - Jan Lebl
- Department of Pediatrics, 2nd Faculty of Medicine, University Hospital Motol, Charles University, 150 06 Prague, Czech Republic
- *Jan Lebl:
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Wooderchak-Donahue WL, O'Fallon B, Furtado LV, Durtschi JD, Plant P, Ridge PG, Rope AF, Yetman AT, Bayrak-Toydemir P. A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective. BMC Med Genomics 2012; 5:50. [PMID: 23148498 PMCID: PMC3534588 DOI: 10.1186/1755-8794-5-50] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/09/2012] [Indexed: 12/13/2022] Open
Abstract
Background Aortopathies are a group of disorders characterized by aneurysms, dilation, and tortuosity of the aorta. Because of the phenotypic overlap and genetic heterogeneity of diseases featuring aortopathy, molecular testing is often required for timely and correct diagnosis of affected individuals. In this setting next generation sequencing (NGS) offers several advantages over traditional molecular techniques. Methods The purpose of our study was to compare NGS enrichment methods for a clinical assay targeting the nine genes known to be associated with aortopathy. RainDance emulsion PCR and SureSelect RNA-bait hybridization capture enrichment methods were directly compared by enriching DNA from eight samples. Enriched samples were barcoded, pooled, and sequenced on the Illumina HiSeq2000 platform. Depth of coverage, consistency of coverage across samples, and the overlap of variants identified were assessed. This data was also compared to whole-exome sequencing data from ten individuals. Results Read depth was greater and less variable among samples that had been enriched using the RNA-bait hybridization capture enrichment method. In addition, samples enriched by hybridization capture had fewer exons with mean coverage less than 10, reducing the need for followup Sanger sequencing. Variants sets produced were 77% concordant, with both techniques yielding similar numbers of discordant variants. Conclusions When comparing the design flexibility, performance, and cost of the targeted enrichment methods to whole-exome sequencing, the RNA-bait hybridization capture enrichment gene panel offers the better solution for interrogating the aortopathy genes in a clinical laboratory setting.
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Wei X, Sun Y, Xie J, Shi Q, Qu N, Yang G, Cai J, Yang Y, Liang Y, Wang W, Yi X. Next-generation sequencing identifies a novel compound heterozygous mutation in MYO7A in a Chinese patient with Usher Syndrome 1B. Clin Chim Acta 2012; 413:1866-71. [PMID: 22898263 DOI: 10.1016/j.cca.2012.07.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 07/27/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Targeted enrichment and next-generation sequencing (NGS) have been employed for detection of genetic diseases. The purpose of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection of hereditary hearing loss, and identify inherited mutations involved in human deafness accurately and economically. METHODS To make genetic diagnosis of hereditary hearing loss simple and timesaving, we designed a 0.60 MB array-based chip containing 69 nuclear genes and mitochondrial genome responsible for human deafness and conducted NGS toward ten patients with five known mutations and a Chinese family with hearing loss (never genetically investigated). RESULTS Ten patients with five known mutations were sequenced using next-generation sequencing to validate the sensitivity of the method. We identified four known mutations in two nuclear deafness causing genes (GJB2 and SLC26A4), one in mitochondrial DNA. We then performed this method to analyze the variants in a Chinese family with hearing loss and identified compound heterozygosity for two novel mutations in gene MYO7A. CONCLUSIONS The compound heterozygosity identified in gene MYO7A causes Usher Syndrome 1B with severe phenotypes. The results support that the combination of enrichment of targeted genes and next-generation sequencing is a valuable molecular diagnostic tool for hereditary deafness and suitable for clinical application.
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Ghosh S, Krux F, Binder V, Gombert M, Niehues T, Feyen O, Laws HJ, Borkhardt A. Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies. Scand J Immunol 2012; 75:350-4. [PMID: 22017423 DOI: 10.1111/j.1365-3083.2011.02658.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Primary immunodeficiencies are genetic disorders in which components of immunological pathways are either missing or dysregulated. With the advent of next-generation sequencing, testing for genes in conditions with a heterogeneous genetic background seems more promising. We designed a custom microarray with 385K probe capacity to capture exons of 395 human genes, known or predicted to be associated with primary immunodeficiency and immune regulation. Enriched target DNA was sequenced using a GS FLX Titanium 454 platform. The patients selected were likely to have an underlying immunodeficiency. In one patient with hepatosplenomegaly, recurrent infections and an elevated IgM level, sequence analysis of the patient and his two unaffected parents identified ATM (ataxia telangiectasia mutated) as the underlying defect. In a second child with a clinical SCID phenotype, we detected a mutation in the ARTEMIS gene after focusing on SCID-associated genes. 454 sequencing yielded 152,000-397,000 high-quality reads per patient. 78-99% of the targeted nucleotides were covered at least one time, 76-82% at least five times. Array-based sequence capture expands our capacities to sequence large targeted DNA regions in a less laborious and time-consuming approach. Our array was capable to find the underlying genetic defect in two patients with suspected primary immunodeficiency. Upcoming whole-exome sequencing definitely will add more valuable data, but bioinformatical analysis and validation of variants already pose major challenges.
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Affiliation(s)
- S Ghosh
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Hospital Düsseldorf, Düsseldorf, Germany
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Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R. Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis. Expert Rev Mol Diagn 2012; 12:159-73. [PMID: 22369376 DOI: 10.1586/erm.11.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The potential applications of next-generation sequencing technologies in diagnostic laboratories have become increasingly evident despite the various technical challenges that still need to be overcome to potentiate its widespread adoption in a clinical setting. Whole-genome sequencing is now both technically feasible and 'cost effective' using next-generation sequencing techniques. However, this approach is still considered to be 'expensive' for a diagnostic test. Although the goal of the US$1000 genome is fast approaching, neither the analytical hurdles nor the ethical issues involved are trivial. In addition, the cost of data analysis and storage has been much higher than initially expected. As a result, it is widely perceived that targeted sequencing and whole-exome sequencing are more likely to be adopted as diagnostic tools in the foreseeable future. However, the information-generating power of whole-exome sequencing has also sparked considerable debate in relation to its deployment in genetic diagnostics, particularly with reference to the revelation of incidental findings. In this review, we focus on the targeted sequencing approach and its potential as a genetic diagnostic tool.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing. Genet Med 2012; 14:823-6. [DOI: 10.1038/gim.2012.50] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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AlSaadi MM, Gaunt TR, Boustred CR, Guthrie PAI, Liu X, Lenzi L, Rainbow L, Hall N, Alharbi KK, Day INM. From a single whole exome read to notions of clinical screening: primary ciliary dyskinesia and RSPH9 p.Lys268del in the Arabian Peninsula. Ann Hum Genet 2012; 76:211-20. [PMID: 22384920 PMCID: PMC3575730 DOI: 10.1111/j.1469-1809.2012.00704.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a genetic disorder, usually autosomal recessive, causing early respiratory disease and later subfertility. Whole exome sequencing may enable efficient analysis for locus heterogeneous disorders such as PCD. We whole-exome-sequenced one consanguineous Saudi Arabian with clinically diagnosed PCD and normal laterality, to attempt ab initio molecular diagnosis. We reviewed 13 known PCD genes and potentially autozygous regions (extended homozygosity) for homozygous exon deletions, non-dbSNP codon, splice-site base variants or small indels. Homozygous non-dbSNP changes were also reviewed exome-wide. One single molecular read representing RSPH9 p.Lys268del was observed, with no wild-type reads, and a notable deficiency of mapped reads at this location. Among all observations, RSPH9 was the strongest candidate for causality. Searching unmapped reads revealed seven more mutant reads. Direct assay for p.Lys268del (MboII digest) confirmed homozygosity in the affected individual, then confirmed homozygosity in three siblings with bronchiectasis. Our finding in southwest Saudi Arabia indicates that p.Lys268del, previously observed in two Bedouin families (Israel, UAE), is geographically widespread in the Arabian Peninsula. Analogous with cystic fibrosis CFTR p.Phe508del, screening for RSPH9 p.Lys268del (which lacks sentinel dextrocardia) in those at risk would help in early diagnosis, tailored clinical management, genetic counselling and primary prevention.
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Affiliation(s)
- Muslim M AlSaadi
- College of Medicine, King Saud University, P O Box 2925 Riyadh 11472, Kingdom of Saudi Arabia
| | - Tom R Gaunt
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Christopher R Boustred
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Philip AI Guthrie
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Xuan Liu
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Luca Lenzi
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Lucille Rainbow
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Neil Hall
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Khalid K Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, P.O.Box 10219, Riyadh 11433, Kingdom of Saudi Arabia
| | - Ian NM Day
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
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Dewey FE, Pan S, Wheeler MT, Quake SR, Ashley EA. DNA sequencing: clinical applications of new DNA sequencing technologies. Circulation 2012; 125:931-44. [PMID: 22354974 DOI: 10.1161/circulationaha.110.972828] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederick E Dewey
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Falk CVRB, 300 Pasteur Dr, Stanford, CA 94305, USA
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Green RC, Berg JS, Berry GT, Biesecker LG, Dimmock DP, Evans JP, Grody WW, Hegde MR, Kalia S, Korf BR, Krantz I, McGuire AL, Miller DT, Murray MF, Nussbaum RL, Plon SE, Rehm HL, Jacob HJ. Exploring concordance and discordance for return of incidental findings from clinical sequencing. Genet Med 2012; 14:405-10. [PMID: 22422049 DOI: 10.1038/gim.2012.21] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
PURPOSE The aim of this study was to explore specific conditions and types of genetic variants that specialists in genetics recommend should be returned as incidental findings in clinical sequencing. METHODS Sixteen specialists in clinical genetics and/or molecular medicine selected variants in 99 common conditions to return to the ordering physician if discovered incidentally through whole-genome sequencing. For most conditions, the specialists independently considered three molecular scenarios for both adults and minor children: a known pathogenic mutation, a truncating variant presumed pathogenic (where other truncating variants are known to be pathogenic), and a missense variant predicted in silico to be pathogenic. RESULTS On average, for adults and children, respectively, each specialist selected 83.5 and 79.0 conditions or genes of 99 in the known pathogenic mutation categories, 57.0 and 53.5 of 72 in the truncating variant categories, and 33.4 and 29.7 of 72 in the missense variant categories. Concordance in favor of disclosure within the adult/known pathogenic mutation category was 100% for 21 conditions or genes and 80% or higher for 64 conditions or genes. CONCLUSION Specialists were highly concordant for the return of findings for 64 conditions or genes if discovered incidentally during whole-exome sequencing or whole-genome sequencing.Genet Med 2012:14(4):405-410.
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Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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Xie S, Lan Z, Qu N, Wei X, Yu P, Zhu Q, Yang G, Wang J, Shi Q, Wang W, Yang L, Yi X. Detection of truncated dystrophin lacking the C-terminal domain in a Chinese pedigree by next-generation sequencing. Gene 2012; 499:139-42. [PMID: 22425969 DOI: 10.1016/j.gene.2012.03.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/15/2012] [Accepted: 03/04/2012] [Indexed: 01/06/2023]
Abstract
Dystrophin (DMD) gene is the largest gene containing 79 exons involving various mutation types and regions, and targeted next-generation sequencing (NGS) was employed in detecting DMD gene mutation in the present study. A literature-annotated disease nonsense mutation (c.10141C>T, NM_004006.1) in exon 70 that has been reported as Duchenne Muscular Dystrophy (DMD)-causing mutation was found in our two patients, the proband and his cousin. In the present study two main methods were used, the next-generation sequencing and the classic Sanger sequencing. The exon capture followed by HiSeq2000 sequencing was specifically used in this study. Combined applications of the next-generation sequencing platform and bioinformatics are proved to be effective methods for DMD diagnosis.
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Affiliation(s)
- Shuqi Xie
- Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
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Ku CS, Cooper DN, Polychronakos C, Naidoo N, Wu M, Soong R. Exome sequencing: dual role as a discovery and diagnostic tool. Ann Neurol 2012; 71:5-14. [PMID: 22275248 DOI: 10.1002/ana.22647] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Recent developments in high-throughput sequence capture methods and next-generation sequencing technologies have now made exome sequencing a viable approach to elucidate the genetic basis of Mendelian disorders with hitherto unknown etiology. In addition, exome sequencing is increasingly being employed as a diagnostic tool for specific genetic diseases, particularly in the context of those disorders characterized by significant genetic and phenotypic heterogeneity, for example, Charcot-Marie-Tooth disease and congenital disorders of glycosylation. Such disorders are challenging to interrogate with conventional polymerase chain reaction-Sanger sequencing methods, because of the inherent difficulty in prioritizing candidate genes for diagnostic testing. Here, we explore the value of exome sequencing as a diagnostic tool and discuss whether exome sequencing can come to serve a dual role in diagnosis and discovery. We summarize the current status of exome sequencing, the technical challenges facing it, and its adaptation to diagnostics, and make recommendations for the use of exome sequencing as a routine diagnostic tool. Finally, we discuss pertinent ethical concerns, such as the use of exome sequencing data, originally generated in a diagnostic context, in research investigations.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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Lucas JS, Adam EC, Goggin PM, Jackson CL, Powles-Glover N, Patel SH, Humphreys J, Fray MD, Falconnet E, Blouin JL, Cheeseman MT, Bartoloni L, Norris DP, Lackie PM. Static respiratory cilia associated with mutations in Dnahc11/DNAH11: a mouse model of PCD. Hum Mutat 2012; 33:495-503. [PMID: 22102620 DOI: 10.1002/humu.22001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 11/16/2011] [Indexed: 01/09/2023]
Abstract
Primary ciliary dyskinesia (PCD) is an inherited disorder causing significant upper and lower respiratory tract morbidity and impaired fertility. Half of PCD patients show abnormal situs. Human disease loci have been identified but a mouse model without additional deleterious defects is elusive. The inversus viscerum mouse, mutated at the outer arm dynein heavy chain 11 locus (Dnahc11) is a known model of heterotaxy. We demonstrated immotile tracheal cilia with normal ultrastructure and reduced sperm motility in the Dnahc11(iv) mouse. This is accompanied by gross rhinitis, sinusitis, and otitis media, all indicators of human PCD. Strikingly, age-related progression of the disease is evident. The Dnahc11(iv) mouse is robust, lacks secondary defects, and requires no intervention to precipitate the phenotype. Together these findings show the Dnahc11(iv) mouse to be an excellent model of many aspects of human PCD. Mutation of the homologous human locus has previously been associated with hyperkinetic tracheal cilia in PCD. Two PCD patients with normal ciliary ultrastructure, one with immotile and one with hyperkinetic cilia were found to carry DNAH11 mutations. Three novel DNAH11 mutations were detected indicating that this gene should be investigated in patients with normal ciliary ultrastructure and static, as well as hyperkinetic cilia.
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Affiliation(s)
- Jane S Lucas
- Primary Ciliary Dyskinesia Group, Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton NIHR Respiratory Biomedical Research Unit, Southampton General Hospital, Southampton, UK
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Wei X, Ju X, Yi X, Zhu Q, Qu N, Liu T, Chen Y, Jiang H, Yang G, Zhen R, Lan Z, Qi M, Wang J, Yang Y, Chu Y, Li X, Guang Y, Huang J. Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing. PLoS One 2011; 6:e29500. [PMID: 22216297 PMCID: PMC3244462 DOI: 10.1371/journal.pone.0029500] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/29/2011] [Indexed: 01/17/2023] Open
Abstract
Background Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest. Methodology/Principal Findings To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR. Conclusions/Significance Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed.
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Affiliation(s)
- Xiaoming Wei
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiangchun Ju
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xin Yi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Qian Zhu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ning Qu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Tengfei Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yang Chen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Hui Jiang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Guanghui Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ruan Zhen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | | | - Ming Qi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jinming Wang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yi Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yuxing Chu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiaoyan Li
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yanfang Guang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jian Huang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Shanghai-Ministry Key Laboratory of Disease and Health Genomics, National Engineering Center for Biochip at Shanghai, Shanghai, China
- * E-mail:
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Current world literature. Curr Opin Pediatr 2011; 23:700-7. [PMID: 22068136 DOI: 10.1097/mop.0b013e32834dda34] [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: 11/26/2022]
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Wagle N, Berger MF, Davis MJ, Blumenstiel B, Defelice M, Pochanard P, Ducar M, Van Hummelen P, Macconaill LE, Hahn WC, Meyerson M, Gabriel SB, Garraway LA. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2011; 2:82-93. [PMID: 22585170 DOI: 10.1158/2159-8290.cd-11-0184] [Citation(s) in RCA: 448] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
UNLABELLED Knowledge of "actionable" somatic genomic alterations present in each tumor (e.g., point mutations, small insertions/deletions, and copy-number alterations that direct therapeutic options) should facilitate individualized approaches to cancer treatment. However, clinical implementation of systematic genomic profiling has rarely been achieved beyond limited numbers of oncogene point mutations. To address this challenge, we utilized a targeted, massively parallel sequencing approach to detect tumor genomic alterations in formalin-fixed, paraffin-embedded (FFPE) tumor samples. Nearly 400-fold mean sequence coverage was achieved, and single-nucleotide sequence variants, small insertions/deletions, and chromosomal copynumber alterations were detected simultaneously with high accuracy compared with other methods in clinical use. Putatively actionable genomic alterations, including those that predict sensitivity or resistance to established and experimental therapies, were detected in each tumor sample tested. Thus, targeted deep sequencing of clinical tumor material may enable mutation-driven clinical trials and, ultimately, "personalized" cancer treatment. SIGNIFICANCE Despite the rapid proliferation of targeted therapeutic agents, systematic methods to profile clinically relevant tumor genomic alterations remain underdeveloped. We describe a sequencingbased approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.
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Affiliation(s)
- Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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Hagiwara K, Morino H, Shiihara J, Tanaka T, Miyazawa H, Suzuki T, Kohda M, Okazaki Y, Seyama K, Kawakami H. Homozygosity mapping on homozygosity haplotype analysis to detect recessive disease-causing genes from a small number of unrelated, outbred patients. PLoS One 2011; 6:e25059. [PMID: 21949849 PMCID: PMC3176806 DOI: 10.1371/journal.pone.0025059] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 08/26/2011] [Indexed: 01/23/2023] Open
Abstract
Genes involved in disease that are not common are often difficult to identify; a method that pinpoints them from a small number of unrelated patients will be of great help. In order to establish such a method that detects recessive genes identical-by-descent, we modified homozygosity mapping (HM) so that it is constructed on the basis of homozygosity haplotype (HM on HH) analysis. An analysis using 6 unrelated patients with Siiyama-type α1-antitrypsin deficiency, a disease caused by a founder gene, the correct gene locus was pinpointed from data of any 2 patients (length: 1.2–21.8 centimorgans, median: 1.6 centimorgans). For a test population in which these 6 patients and 54 healthy subjects were scrambled, the approach accurately identified these 6 patients and pinpointed the locus to a 1.4-centimorgan fragment. Analyses using synthetic data revealed that the analysis works well for IBD fragment derived from a most recent common ancestor (MRCA) who existed less than 60 generations ago. The analysis is unsuitable for the genes with a frequency in general population more than 0.1. Thus, HM on HH analysis is a powerful technique, applicable to a small number of patients not known to be related, and will accelerate the identification of disease-causing genes for recessive conditions.
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Affiliation(s)
- Koichi Hagiwara
- Department of Respiratory Medicine, Saitama Medical University, Moroyama, Saitama, Japan.
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