101
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Fujiki R, Ikeda M, Yoshida A, Akiko M, Yao Y, Nishimura M, Matsushita K, Ichikawa T, Tanaka T, Morisaki H, Morisaki T, Ohara O. Assessing the Accuracy of Variant Detection in Cost-Effective Gene Panel Testing by Next-Generation Sequencing. J Mol Diagn 2018; 20:572-582. [PMID: 29953964 DOI: 10.1016/j.jmoldx.2018.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/20/2018] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
There is significant debate within the diagnostics community regarding the accuracy of variant identification by next-generation sequencing and the necessity of confirmatory testing of detected variants. Because the quality threshold to discriminate false positives depends on the workflow, no regulatory standard regarding this matter has yet been published. The goal of this study was to empirically determine the threshold to perform additional Sanger sequencing and to reduce the experimental cost to a practical level. Using 278 model genes, a hybridization capture-based protocol was examined to meet the clinical requirements of low cost, high efficiency, and high-quality data. To reduce excessive false-positive detection, filtering processes were introduced to remove mismapped reads and strand-biased detection to a published best-practices pipeline. With seven samples from the 1000 Genomes Project, 2750 single-nucleotide polymorphisms and 142 insertions/deletions were identified by our designed workflow. Compared with variants registered in the single nucleotide polymorphism database (dbSNP), a zero false-positive threshold value was determined (quality score > 1000). The variants satisfying these criteria accounted for 95.6% of single-nucleotide polymorphisms and 50.7% of insertions/deletions. Except for deletions located within the highly repeated sequences, the workflow achieved 100% sensitivity. The established threshold allowed us to discriminate between convincing variants and those requiring validation, a design that reconciles the competing objectives of cost minimization and quality maximization of clinical gene panel testing.
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Affiliation(s)
- Ryoji Fujiki
- Department of Technology Development, Kazusa DNA Research Institute, Chiba, Japan.
| | | | - Akiko Yoshida
- Retinal Regeneration Laboratory, Center for Developmental Biology, RIKEN, Kobe, Japan; Department of Ophthalmology, Institute of Biomedical Research and Innovation Hospital, Kobe, Japan
| | - Maeda Akiko
- Retinal Regeneration Laboratory, Center for Developmental Biology, RIKEN, Kobe, Japan; Department of Ophthalmology, Institute of Biomedical Research and Innovation Hospital, Kobe, Japan; Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Yue Yao
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motio Nishimura
- Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | | | - Tomohiko Ichikawa
- Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Hiroko Morisaki
- Department of Medical Genetics, Sakakibara Heart Institute, Tokyo, Japan
| | - Takayuki Morisaki
- School of Health Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Chiba, Japan
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102
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Paul JL, Leslie H, Trainer AH, Gaff C. A theory-informed systematic review of clinicians' genetic testing practices. Eur J Hum Genet 2018; 26:1401-1416. [PMID: 29891880 DOI: 10.1038/s41431-018-0190-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/13/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
This systematic literature review investigates factors impacting on clinicians' decisions to offer genetic tests in their practice, and maps them to a theoretical behaviour change framework. Better understanding of these factors will inform the design of effective interventions to integrate genomics tests into clinical care. We conducted a narrative synthesis of empirical research of medical specialists' perspectives on and experiences of offering genetic tests to their patients. This review was based upon the PRISMA statement and guidelines for reviewing qualitative research. Four electronic data sources were searched-MEDLINE, EMBASE, CINAHL, PubMed. Studies were independently assessed by two authors. Content analysis was applied to map the findings of included studies to a framework validated for behaviour and implementation research, the Theoretical Domains Framework (TDF). The TDF describes 14 factors known to influence behaviour and has been applied in diverse clinical settings to understand and/or modify health professional behaviour. Thirty-four studies published in 39 articles met inclusion and quality criteria. Most studies were published after 2011 (54%), Northern American (82%), quantitative in design (68%) and addressed familial cancer genetic tests (53%). Of the 14 TDF factors, 13 were identified. The three most common factors were: Environmental Context and Resources (n = 33), Beliefs about Consequences (n = 26), and Knowledge (n = 23). To support the adoption of genomic tests beyond specialist services, nuanced interventions targeting considerations beyond clinician education are needed. For instance, interventions addressing organisational constraints which may restrict clinicians' ability to offer genomic tests are required alongside those targeting factors intrinsic to the clinician.
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Affiliation(s)
- Jean L Paul
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Hanna Leslie
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia.,Paediatric & Reproductive Unit, SA Clinical Genetics Service, Adelaide, South Australia, Australia
| | - Alison H Trainer
- Faculty of Medicine, University of Melbourne, Melbourne, VIC, Australia.,Parkville integrated Familial Cancer Centre and Genomic Medicine, Peter McCallum Cancer Centre and Royal Melbourne Hospitals, Melbourne, VIC, Australia
| | - Clara Gaff
- Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,Faculty of Medicine, University of Melbourne, Melbourne, VIC, Australia. .,Melbourne Genomics Health Alliance, Melbourne, VIC, Australia.
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103
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Wang Z, Zhao Y. Gut microbiota derived metabolites in cardiovascular health and disease. Protein Cell 2018; 9:416-431. [PMID: 29725935 PMCID: PMC5960473 DOI: 10.1007/s13238-018-0549-0] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/16/2018] [Indexed: 02/08/2023] Open
Abstract
Trillions of microbes inhabit the human gut, not only providing nutrients and energy to the host from the ingested food, but also producing metabolic bioactive signaling molecules to maintain health and elicit disease, such as cardiovascular disease (CVD). CVD is the leading cause of mortality worldwide. In this review, we presented gut microbiota derived metabolites involved in cardiovascular health and disease, including trimethylamine-N-oxide (TMAO), uremic toxins, short chain fatty acids (SCFAs), phytoestrogens, anthocyanins, bile acids and lipopolysaccharide. These gut microbiota derived metabolites play critical roles in maintaining a healthy cardiovascular function, and if dysregulated, potentially causally linked to CVD. A better understanding of the function and dynamics of gut microbiota derived metabolites holds great promise toward mechanistic predicative CVD biomarker discoveries and precise interventions.
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Affiliation(s)
- Zeneng Wang
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| | - Yongzhong Zhao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
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104
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Abstract
PURPOSE OF REVIEW The development of next-generation sequencing (NGS) technologies is transforming the practice of medical genetics and revolutionizing the approach to heterogeneous hereditary conditions, including skeletal muscle disorders. Here, we review the different NGS approaches described in the literature so far for the characterization of myopathic patients and the results obtained from the implementation of such approaches in a clinical setting. RECENT FINDINGS The overall diagnostic rate of NGS strategies for patients affected by skeletal muscle disorders is higher than the success rate obtained using the traditional gene-by-gene approach. Moreover, many recent articles have been expanding the clinical phenotypes associated with already known disease genes. SUMMARY NGS applications will soon be the first-tier test for skeletal muscle disorders. They will improve the diagnosis in myopathic patients, promoting their inclusion into novel therapeutic trials. At the same time, they will improve our knowledge about the molecular mechanisms causing skeletal muscle disorders, favoring the development of novel therapeutic approaches.
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105
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Salazar JL, Yamamoto S. Integration of Drosophila and Human Genetics to Understand Notch Signaling Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:141-185. [PMID: 30030826 PMCID: PMC6233323 DOI: 10.1007/978-3-319-89512-3_8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Notch signaling research dates back to more than one hundred years, beginning with the identification of the Notch mutant in the fruit fly Drosophila melanogaster. Since then, research on Notch and related genes in flies has laid the foundation of what we now know as the Notch signaling pathway. In the 1990s, basic biological and biochemical studies of Notch signaling components in mammalian systems, as well as identification of rare mutations in Notch signaling pathway genes in human patients with rare Mendelian diseases or cancer, increased the significance of this pathway in human biology and medicine. In the 21st century, Drosophila and other genetic model organisms continue to play a leading role in understanding basic Notch biology. Furthermore, these model organisms can be used in a translational manner to study underlying mechanisms of Notch-related human diseases and to investigate the function of novel disease associated genes and variants. In this chapter, we first briefly review the major contributions of Drosophila to Notch signaling research, discussing the similarities and differences between the fly and human pathways. Next, we introduce several biological contexts in Drosophila in which Notch signaling has been extensively characterized. Finally, we discuss a number of genetic diseases caused by mutations in genes in the Notch signaling pathway in humans and we expand on how Drosophila can be used to study rare genetic variants associated with these and novel disorders. By combining modern genomics and state-of-the art technologies, Drosophila research is continuing to reveal exciting biology that sheds light onto mechanisms of disease.
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Affiliation(s)
- Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.
- Program in Developmental Biology, BCM, Houston, TX, USA.
- Department of Neuroscience, BCM, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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106
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Panigrahi M, Panigrahi A. Curbing Malaria: A New Hope through Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Technology. J Arthropod Borne Dis 2017; 11:539-540. [PMID: 29367930 PMCID: PMC5775160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Manjit Panigrahi
- Animal Genetics Division, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Ansuman Panigrahi
- Department of Community Medicine, Kalinga Institute of Medical Sciences, KIIT University, Bhubaneswar, India,Corresponding author: Dr Ansuman Panigrahi, E-mail:
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107
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Perumal S, Waminal NE, Lee J, Lee J, Choi BS, Kim HH, Grandbastien MA, Yang TJ. Elucidating the major hidden genomic components of the A, C, and AC genomes and their influence on Brassica evolution. Sci Rep 2017; 7:17986. [PMID: 29269833 PMCID: PMC5740159 DOI: 10.1038/s41598-017-18048-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022] Open
Abstract
Decoding complete genome sequences is prerequisite for comprehensive genomics studies. However, the currently available reference genome sequences of Brassica rapa (A genome), B. oleracea (C) and B. napus (AC) cover 391, 540, and 850 Mbp and represent 80.6, 85.7, and 75.2% of the estimated genome size, respectively, while remained are hidden or unassembled due to highly repetitive nature of these genome components. Here, we performed the first comprehensive genome-wide analysis using low-coverage whole-genome sequences to explore the hidden genome components based on characterization of major repeat families in the B. rapa and B. oleracea genomes. Our analysis revealed 10 major repeats (MRs) including a new family comprising about 18.8, 10.8, and 11.5% of the A, C and AC genomes, respectively. Nevertheless, these 10 MRs represented less than 0.7% of each assembled reference genome. Genomic survey and molecular cytogenetic analyses validates our insilico analysis and also pointed to diversity, differential distribution, and evolutionary dynamics in the three Brassica species. Overall, our work elucidates hidden portions of three Brassica genomes, thus providing a resource for understanding the complete genome structures. Furthermore, we observed that asymmetrical accumulation of the major repeats might be a cause of diversification between the A and C genomes.
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Affiliation(s)
- Sampath Perumal
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.,Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Jonghoon Lee
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do, 28051, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seongnam, 13558, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | | | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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108
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Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Bonn S, Kollmar M. The landscape of human mutually exclusive splicing. Mol Syst Biol 2017; 13:959. [PMID: 29242366 PMCID: PMC5740500 DOI: 10.15252/msb.20177728] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.
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Affiliation(s)
- Klas Hatje
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Raza-Ur Rahman
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ramon O Vidal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science Georg-August-University, Göttingen, Germany
| | - Björn Hammesfahr
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vikas Bansal
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ashish Rajput
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Michel Edwar Mickael
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Ting Sun
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany.,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany .,Center for Molecular Neurobiology, Institute of Medical Systems Biology University Clinic Hamburg-Eppendorf, Hamburg, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins Department of NMR-Based Structural Biology Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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109
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Reid ES, Papandreou A, Drury S, Boustred C, Yue WW, Wedatilake Y, Beesley C, Jacques TS, Anderson G, Abulhoul L, Broomfield A, Cleary M, Grunewald S, Varadkar SM, Lench N, Rahman S, Gissen P, Clayton PT, Mills PB. Advantages and pitfalls of an extended gene panel for investigating complex neurometabolic phenotypes. Brain 2017; 139:2844-2854. [PMID: 27604308 PMCID: PMC5091046 DOI: 10.1093/brain/aww221] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022] Open
Abstract
Neurometabolic disorders are markedly heterogeneous, both clinically and genetically, and are characterized by variable neurological dysfunction accompanied by suggestive neuroimaging or biochemical abnormalities. Despite early specialist input, delays in diagnosis and appropriate treatment initiation are common. Next-generation sequencing approaches still have limitations but are already enabling earlier and more efficient diagnoses in these patients. We designed a gene panel targeting 614 genes causing inborn errors of metabolism and tested its diagnostic efficacy in a paediatric cohort of 30 undiagnosed patients presenting with variable neurometabolic phenotypes. Genetic defects that could, at least partially, explain observed phenotypes were identified in 53% of cases. Where biochemical abnormalities pointing towards a particular gene defect were present, our panel identified diagnoses in 89% of patients. Phenotypes attributable to defects in more than one gene were seen in 13% of cases. The ability of in silico tools, including structure-guided prediction programmes to characterize novel missense variants were also interrogated. Our study expands the genetic, clinical and biochemical phenotypes of well-characterized (POMGNT1, TPP1) and recently identified disorders (PGAP2, ACSF3, SERAC1, AFG3L2, DPYS). Overall, our panel was accurate and efficient, demonstrating good potential for applying similar approaches to clinically and biochemically diverse neurometabolic disease cohorts.
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Affiliation(s)
- Emma S Reid
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Apostolos Papandreou
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Yehani Wedatilake
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Clare Beesley
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Developmental Biology and Cancer Programme, UCL Institute of Child Health, London, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lara Abulhoul
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alex Broomfield
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Maureen Cleary
- Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephanie Grunewald
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sophia M Varadkar
- Neurology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Nick Lench
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shamima Rahman
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Paul Gissen
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK.,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Peter T Clayton
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
| | - Philippa B Mills
- Genetics and Genomics Medicine Programme, UCL Institute of Child Health, London, UK
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110
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Liang Y, Kelemen A. Bayesian state space models for dynamic genetic network construction across multiple tissues. Stat Appl Genet Mol Biol 2017; 15:273-90. [PMID: 27343475 DOI: 10.1515/sagmb-2014-0055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes.
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111
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Worthey EA. Analysis and Annotation of Whole-Genome or Whole-Exome Sequencing Derived Variants for Clinical Diagnosis. ACTA ACUST UNITED AC 2017; 95:9.24.1-9.24.28. [PMID: 29044471 DOI: 10.1002/cphg.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.
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112
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Dwivedi SL, Lammerts van Bueren ET, Ceccarelli S, Grando S, Upadhyaya HD, Ortiz R. Diversifying Food Systems in the Pursuit of Sustainable Food Production and Healthy Diets. TRENDS IN PLANT SCIENCE 2017; 22:842-856. [PMID: 28716581 DOI: 10.1016/j.tplants.2017.06.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/09/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
Increasing demand for nutritious, safe, and healthy food because of a growing population, and the pledge to maintain biodiversity and other resources, pose a major challenge to agriculture that is already threatened by a changing climate. Diverse and healthy diets, largely based on plant-derived food, may reduce diet-related illnesses. Investments in plant sciences will be necessary to design diverse cropping systems balancing productivity, sustainability, and nutritional quality. Cultivar diversity and nutritional quality are crucial. We call for better cooperation between food and medical scientists, food sector industries, breeders, and farmers to develop diversified and nutritious cultivars that reduce soil degradation and dependence on external inputs, such as fertilizers and pesticides, and to increase adaptation to climate change and resistance to emerging pests.
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Affiliation(s)
- Sangam L Dwivedi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Edith T Lammerts van Bueren
- Louis Bolk Institute, Hoofdstraat 24, 3972 LA Driebergen, The Netherlands; Wageningen University and Research, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | | | - Stefania Grando
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, 23053 Alnarp, Sweden.
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113
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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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114
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Ahn YJ, Markkandan K, Baek IP, Mun S, Lee W, Kim HS, Han K. An efficient and tunable parameter to improve variant calling for whole genome and exome sequencing data. Genes Genomics 2017; 40:39-47. [PMID: 29892897 DOI: 10.1007/s13258-017-0608-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/23/2017] [Indexed: 12/30/2022]
Abstract
Next generation sequencing (NGS) has traditionally been performed in various fields including agricultural to clinical and there are so many sequencing platforms available in order to obtain accurate and consistent results. However, these platforms showed amplification bias when facilitating variant calls in personal genomes. Here, we sequenced whole genomes and whole exomes from ten Korean individuals using Illumina and Ion Proton, respectively to find the vulnerability and accuracy of NGS platform in the GC rich/poor area. Overall, a total of 1013 Gb reads from Illumina and ~39.1 Gb reads from Ion Proton were analyzed using BWA-GATK variant calling pipeline. Furthermore, conjunction with the VQSR tool and detailed filtering strategies, we achieved high-quality variants. Finally, each of the ten variants from Illumina only, Ion Proton only, and intersection was selected for Sanger validation. The validation results revealed that Illumina platform showed higher accuracy than Ion Proton. The described filtering methods are advantageous for large population-based whole genome studies designed to identify common and rare variations associated with complex diseases.
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Affiliation(s)
- Yong Ju Ahn
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.,Theragen Etex Inc., Suwon, Republic of Korea
| | | | - In-Pyo Baek
- Theragen Etex Inc., Suwon, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.,DKU-Theragen Institute for NGS analysis (DTiNa), Cheonan, Republic of Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.,DKU-Theragen Institute for NGS analysis (DTiNa), Cheonan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea. .,DKU-Theragen Institute for NGS analysis (DTiNa), Cheonan, Republic of Korea.
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115
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Krier JB, Kalia SS, Green RC. Genomic sequencing in clinical practice: applications, challenges, and opportunities. DIALOGUES IN CLINICAL NEUROSCIENCE 2017. [PMID: 27757064 PMCID: PMC5067147 DOI: 10.31887/dcns.2016.18.3/jkrier] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The development of massively parallel sequencing (or next-generation sequencing) has facilitated a rapid implementation of genomic sequencing in clinical medicine. Genomic sequencing (GS) is now an essential tool for evaluating rare disorders, identifying therapeutic targets in neoplasms, and screening for prenatal aneuploidy. Emerging applications, such as GS for preconception carrier screening and predisposition screening in healthy individuals, are being explored in research settings and utilized by members of the public eager to incorporate genomic information into their health management. The rapid pace of adoption has created challenges for all stakeholders in clinical GS, from standardizing variant interpretation approaches in clinical molecular laboratories to ensuring that nongeneticist clinicians are prepared for new types of clinical information. Clinical GS faces a pivotal moment, as the vast potential of new quantities and types of data enable further clinical innovation and complicated implementation questions continue to be resolved.
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Affiliation(s)
- Joel B Krier
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | | | - Robert C Green
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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116
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Kim BY, Park JH, Jo HY, Koo SK, Park MH. Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. PLoS One 2017; 12:e0182272. [PMID: 28792971 PMCID: PMC5549930 DOI: 10.1371/journal.pone.0182272] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection.
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Affiliation(s)
- Bo-Young Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Hye-Yeong Jo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
| | - Soo Kyung Koo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
- * E-mail: (SKK); (MHP)
| | - Mi-Hyun Park
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
- * E-mail: (SKK); (MHP)
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117
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Tegtmeyer D, Seidl M, Gerner P, Baumann U, Klemann C. Inflammatory bowel disease caused by primary immunodeficiencies-Clinical presentations, review of literature, and proposal of a rational diagnostic algorithm. Pediatr Allergy Immunol 2017; 28:412-429. [PMID: 28513998 DOI: 10.1111/pai.12734] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel diseases (IBD) including Crohn's disease (CD) and ulcerative colitis have a multifactorial pathogenesis with complex interactions between polygenetic predispositions and environmental factors. However, IBD can also be caused by monogenic diseases, such as primary immunodeficiencies (PID). Recently, an increasing number of these altogether rare diseases have been described to present often primarily, or solely, as IBD. Early recognition of these conditions enables adaption of therapies and thus directly benefits the course of IBDs. Here, we discuss the different clinical presentations in IBD and characteristic features of patient's history, clinical findings, and diagnostic results indicative for a causative PID. Possible predictors are early onset of disease, necessity of parenteral nutrition, failure to respond to standard immunosuppressive therapy, parental consanguinity, increased susceptibility for infections, certain histopathologic findings, and blood tests that are atypical for classic IBD. We illustrate this with exemplary case studies of IBD due to NEMO deficiency, chronic granulomatous disease, common variable immunodeficiency, CTLA-4 and LRBA deficiency. Taking these factors into account, we propose a diagnostic pathway to enable early diagnosis of IBD due to PID.
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Affiliation(s)
- Daniel Tegtmeyer
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany.,University Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Seidl
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Surgical Pathology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Patrick Gerner
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Ulrich Baumann
- Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christian Klemann
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany.,Center of Pediatric Surgery, Hannover Medical School, Hannover, Germany
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118
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Navarrete HP, Soler LH, Mares RE, Ramos MA. Frequency of Alu insertions within the ACE and PR loci in Northwestern Mexicans. BMC Res Notes 2017; 10:339. [PMID: 28750672 PMCID: PMC5530943 DOI: 10.1186/s13104-017-2673-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 07/22/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Presently, non-LTR retrotransposons are the most active mobile elements in the human genome. Among these, Alu elements are highly represented in the modern population. Worldwide, distribution of Alu polymorphisms (insertion/deletion; I/D) shows variability between different populations. Two Alu insertion loci, ACE and PR, are significant biomarkers that have served in several genotype-phenotype association studies. In Mexico, studies concerning the frequency of these biomarkers have been conducted mainly in subpopulations from central and southern regions. Here, we screened a population sample of the northwestern region to gain further knowledge regarding the prevalence of Alu polymorphisms within ACE and PR loci. RESULTS For ACE locus, the observed genotype frequencies were 26.5, 51.0 and 22.5% for II, ID, and DD, respectively; and allelic frequencies for I and D were 52 and 48%. Whereas respective genotype frequencies for PR locus were 2.7, 26.5 and 70.8%, and the corresponding allele frequencies were 16 and 84%. Furthermore, the insertion frequency within ACE locus was similar between central, western and northwestern subpopulations, and rather higher in southeastern subpopulation (p < 0.05). Although the occurrence of Alu polymorphisms within PR locus has not been widely examined, the insertion frequency was higher in northwestern subpopulation, as compared with western and southeastern subpopulations (p < 0.05). Based on the frequency of Alu insertions found in ACE and PR loci, subpopulations from the northwestern, western and central regions share a common genetic origin, but apparently not with the subpopulation from the southeastern region, in accordance with the notion that assumes the existence of a broad genomic diversity in the Mexican population. In addition, the high prevalence of Alu insertions reveals their potential application as biomarkers with prognostic value for the associated diseases; e.g., as part of the standard protocols for clinical diagnosis.
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Affiliation(s)
- Hilda P Navarrete
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Linda H Soler
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Rosa E Mares
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico
| | - Marco A Ramos
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, 22390, Tijuana, BCN, Mexico.
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119
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Sabo A, Mishra P, Dugan-Perez S, Voruganti VS, Kent JW, Kalra D, Cole SA, Comuzzie AG, Muzny DM, Gibbs RA, Butte NF. Exome sequencing reveals novel genetic loci influencing obesity-related traits in Hispanic children. Obesity (Silver Spring) 2017; 25:1270-1276. [PMID: 28508493 PMCID: PMC5687071 DOI: 10.1002/oby.21869] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To perform whole exome sequencing in 928 Hispanic children and identify variants and genes associated with childhood obesity. METHODS Single-nucleotide variants (SNVs) were identified from Illumina whole exome sequencing data using integrated read mapping, variant calling, and an annotation pipeline (Mercury). Association analyses of 74 obesity-related traits and exonic variants were performed using SeqMeta software. Rare autosomal variants were analyzed using gene-based association analyses, and common autosomal variants were analyzed at the SNV level. RESULTS (1) Rare exonic variants in 10 genes and 16 common SNVs in 11 genes that were associated with obesity traits in a cohort of Hispanic children were identified, (2) novel rare variants in peroxisome biogenesis factor 1 (PEX1) associated with several obesity traits (weight, weight z score, BMI, BMI z score, waist circumference, fat mass, trunk fat mass) were discovered, and (3) previously reported SNVs associated with childhood obesity were replicated. CONCLUSIONS Convergence of whole exome sequencing, a family-based design, and extensive phenotyping discovered novel rare and common variants associated with childhood obesity. Linking PEX1 to obesity phenotypes poses a novel mechanism of peroxisomal biogenesis and metabolism underlying the development of childhood obesity.
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Affiliation(s)
- Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Pamela Mishra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - V. Saroja Voruganti
- Department of Nutrition and UNC Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Jack W. Kent
- Department of Genetics, Texas Biomedical Research institute, San Antonio, TX, USA
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research institute, San Antonio, TX, USA
| | - Anthony G. Comuzzie
- Department of Genetics, Texas Biomedical Research institute, San Antonio, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Nancy F. Butte
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX
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120
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Kalatskaya I, Trinh QM, Spears M, McPherson JD, Bartlett JMS, Stein L. ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. Genome Med 2017; 9:59. [PMID: 28659176 PMCID: PMC5490163 DOI: 10.1186/s13073-017-0446-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022] Open
Abstract
Background A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison. Results In this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded tissues; we tested our algorithm with both deep targeted and whole-exome sequencing data. Our algorithm correctly classified between 95 and 98% of somatic mutations with F1-measure ranges from 75.9 to 98.6% depending on the tumor type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues). Conclusions In this work, we describe the development, implementation, and validation of ISOWN, an accurate algorithm for predicting somatic mutations in cancer tissues in the absence of matching normal tissues. ISOWN is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0446-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina Kalatskaya
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Quang M Trinh
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California, USA
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Lincoln Stein
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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121
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Jepsen K, Jepsen S. Antibiotics/antimicrobials: systemic and local administration in the therapy of mild to moderately advanced periodontitis. Periodontol 2000 2017; 71:82-112. [PMID: 27045432 DOI: 10.1111/prd.12121] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 02/06/2023]
Abstract
This review gives an update of the current scientific evidence on the efficacy of the adjunctive use of systemic and local antibiotics/antimicrobials in the treatment of periodontitis. In particular, it addresses whether their use can improve the results of nonsurgical mechanical therapy in mild-to-moderate forms of the disease. Large numbers of randomized clinical trials and systematic reviews with meta-analyses have clearly established that adjunctive systemic antibiotics, combined with mechanical debridement, offer clinical improvements additional to those obtained with scaling and root planing alone. These effects are more pronounced in aggressive periodontitis and in initially deep pockets, whereas more limited additional improvements, of 0.3 mm for additional pocket reduction and 0.2 mm for additional clinical attachment gain, have been documented for moderately deep sites (4-6 mm) in patients with chronic periodontitis. The marginal clinical benefit in patients with moderate disease has to be balanced against possible side effects. Notably, it has to be realized that an increasing number of warnings have been articulated against the unrestricted use of antibiotics in treating periodontal diseases because of the emerging global public health issue of bacterial resistance. The effects of the adjunctive local administration of antimicrobials have also been very well documented in several systematic reviews. Overall, in persistent or recurrent localized deep sites, the application of antimicrobials by sustained-delivery devices may offer a benefit of an additional 0.4 mm in pocket depth reduction and 0.3 mm in clinical attachment level gain. In conclusion, the slight additional benefits of adjunctive antimicrobials, which were shown for moderate forms of periodontitis, have to be balanced against their side effects and therefore their prescription should be limited as much as possible.
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122
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Girelli D, Piubelli C, Martinelli N, Corrocher R, Olivieri O. A decade of progress on the genetic basis of coronary artery disease. Practical insights for the internist. Eur J Intern Med 2017; 41:10-17. [PMID: 28395986 DOI: 10.1016/j.ejim.2017.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 12/24/2022]
Abstract
Clinicians are well aware of the importance of a positive family history for coronary artery disease (CAD). Nonetheless, elucidation of the genetic basis of CAD has long proven difficult. The scenario changed in the last decade through the application of modern genomic technologies, like genome-wide association studies (GWAS) and next generation sequencing (NGS). GWAS have discovered over 60 common variants highly associated with CAD. For predictive purposes, such variants have been used to build up Genetic Risk Scores (GRSs), but their incorporation into classical prediction models does not appear substantially outperform the simple addition of family history. To date, the only strong case for the utility of incorporating genetic testing into clinical practice is represented by the diagnosis of Familial Hypercholesterolemia (FH). On the other hand, utilization of genomic techniques has driven formidable advances into the knowledge of CAD pathophysiology, particularly by addressing controversies on the causality of some lipid fractions that had long remained unsolved because of limitations of observational epidemiology. For example, NGS-derived rare variants with strong functional effects on key-genes like ANGPTL4, APOA5, APOC3, LPL, and SCARB1, have proven useful as proxies to demonstrate the causality of triglyceride-rich lipoproteins (TRLs) at variance with HDL-cholesterol concentration, thus contributing to tear down a dogma from classical epidemiology. Moreover, such variants have paved the way for the development of new biologic drugs (i.e. monoclonal antibodies or antisense oligonucleotides) targeting key proteins like PCSK9, Lipoprotein(a), and apolipoprotein C3. Such drugs are currently under active investigation, with first results being extremely promising.
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Affiliation(s)
- Domenico Girelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy.
| | - Chiara Piubelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Nicola Martinelli
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Roberto Corrocher
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
| | - Oliviero Olivieri
- Department of Medicine, Section of Internal Medicine, University of Verona, Italy
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123
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Alfares A, Alfadhel M, Wani T, Alsahli S, Alluhaydan I, Al Mutairi F, Alothaim A, Albalwi M, Al Subaie L, Alturki S, Al-Twaijri W, Alrifai M, Al-Rumayya A, Alameer S, Faqeeh E, Alasmari A, Alsamman A, Tashkandia S, Alghamdi A, Alhashem A, Tabarki B, AlShahwan S, Hundallah K, Wali S, Al-Hebbi H, Babiker A, Mohamed S, Eyaid W, Zada AAP. A multicenter clinical exome study in unselected cohorts from a consanguineous population of Saudi Arabia demonstrated a high diagnostic yield. Mol Genet Metab 2017; 121:91-95. [PMID: 28454995 DOI: 10.1016/j.ymgme.2017.04.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 11/20/2022]
Affiliation(s)
- Ahmed Alfares
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia.
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Tariq Wani
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Saud Alsahli
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Iram Alluhaydan
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Fuad Al Mutairi
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ali Alothaim
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Mohammed Albalwi
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Lamia Al Subaie
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Saeed Alturki
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Waleed Al-Twaijri
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Muhammad Alrifai
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al-Rumayya
- King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia; Division of Neurology, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Seham Alameer
- Department of Pediatrics, King Khaled National Guard Hospital, Jeddah, Saudi Arabia
| | - Eissa Faqeeh
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulaziz Alsamman
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Soha Tashkandia
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | - Amal Alhashem
- Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Brahim Tabarki
- Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Saad AlShahwan
- Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Sami Wali
- Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | | | - Amir Babiker
- King Saud University Medical City and College of Medicine, Riyadh, Saudi Arabia
| | - Sarar Mohamed
- King Saud University Medical City and College of Medicine, Riyadh, Saudi Arabia
| | - Wafaa Eyaid
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Abdul Ali Peer Zada
- Molecular Genetics Section, Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh, Saudi Arabia
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Zare F, Dow M, Monteleone N, Hosny A, Nabavi S. An evaluation of copy number variation detection tools for cancer using whole exome sequencing data. BMC Bioinformatics 2017; 18:286. [PMID: 28569140 PMCID: PMC5452530 DOI: 10.1186/s12859-017-1705-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/22/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has become primary strategy for sequencing patient samples and study their genomics aberrations. However, compared to whole genome sequencing, WES introduces more biases and noise that make CNV detection very challenging. Additionally, tumors' complexity makes the detection of cancer specific CNVs even more difficult. Although many CNV detection tools have been developed since introducing NGS data, there are few tools for somatic CNV detection for WES data in cancer. RESULTS In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations. We compared the performance of the tools in terms of sensitivity and false discovery rate (FDR) using real data and simulated data. Comparative analysis of the results of the tools showed that there is a low consensus among the tools in calling CNVs. Using real data, tools show moderate sensitivity (~50% - ~80%), fair specificity (~70% - ~94%) and poor FDRs (~27% - ~60%). Also, using simulated data we observed that increasing the coverage more than 10× in exonic regions does not improve the detection power of the tools significantly. CONCLUSIONS The limited performance of the current CNV detection tools for WES data in cancer indicates the need for developing more efficient and precise CNV detection methods. Due to the complexity of tumors and high level of noise and biases in WES data, employing advanced novel segmentation, normalization and de-noising techniques that are designed specifically for cancer data is necessary. Also, CNV detection development suffers from the lack of a gold standard for performance evaluation. Finally, developing tools with user-friendly user interfaces and visualization features can enhance CNV studies for a broader range of users.
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Affiliation(s)
- Fatima Zare
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Michelle Dow
- Biomedical Informatics Department, University of California San Diego, San Diego, CA, USA
| | - Nicholas Monteleone
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Abdelrahman Hosny
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Sheida Nabavi
- Computer Science and Engineering Department and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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125
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Yang M, Wei H, Wang Y, Deng J, Tang Y, Zhou L, Guo G, Tong A. Targeted Disruption of V600E-Mutant BRAF Gene by CRISPR-Cpf1. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 8:450-458. [PMID: 28918044 PMCID: PMC5542387 DOI: 10.1016/j.omtn.2017.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 02/05/2023]
Abstract
BRAF-V600E (1799T > A) is one of the most frequently reported driver mutations in multiple types of cancers, and patients with such mutations could benefit from selectively inactivating the mutant allele. Near this mutation site, there are two TTTN and one NGG protospacer-adjacent motifs (PAMs) for Cpf1 and Cas9 CRISPR nucleases, respectively. The 1799T > A substitution also leads to the occurrence of a novel NGNG PAM for the EQR variant of Cas9. We examined the editing efficacy and selectivity of Cpf1, Cas9, and EQR variant to this mutation site. Only Cpf1 demonstrated robust activity to induce specific disruption of only mutant BRAF, not wild-type sequence. Cas9 recognized and cut both normal and mutant alleles, and no obvious gene editing events were observed using EQR variant. Our results support the potential applicability of Cpf1 in precision medicine through highly specific inactivation of many other gain-of-function mutations.
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Affiliation(s)
- Meijia Yang
- The State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Heng Wei
- College of Life Science, Sichuan University, Chengdu 610064, China
| | - Yuelong Wang
- Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Jiaojiao Deng
- Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yani Tang
- The State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Liangxue Zhou
- Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Gang Guo
- The State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Aiping Tong
- The State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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Eldomery MK, Coban-Akdemir Z, Harel T, Rosenfeld JA, Gambin T, Stray-Pedersen A, Küry S, Mercier S, Lessel D, Denecke J, Wiszniewski W, Penney S, Liu P, Bi W, Lalani SR, Schaaf CP, Wangler MF, Bacino CA, Lewis RA, Potocki L, Graham BH, Belmont JW, Scaglia F, Orange JS, Jhangiani SN, Chiang T, Doddapaneni H, Hu J, Muzny DM, Xia F, Beaudet AL, Boerwinkle E, Eng CM, Plon SE, Sutton VR, Gibbs RA, Posey JE, Yang Y, Lupski JR. Lessons learned from additional research analyses of unsolved clinical exome cases. Genome Med 2017; 9:26. [PMID: 28327206 PMCID: PMC5361813 DOI: 10.1186/s13073-017-0412-6] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 02/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.
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Affiliation(s)
- Mohammad K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Present Address: Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, 350 W. 11th Street, Indianapolis, IN 46202 USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Women and Children’s Division, Oslo University Hospital, 0424 Oslo, Norway
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093 Nantes, CEDEX 1 France
- Atlantic Gene Therapies, UMR1089, Nantes, France
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030 USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Brett H. Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - John W. Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Jordan S. Orange
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital Center for Human Immuno-Biology, Houston, TX USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Theodore Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Christine M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sharon E. Plon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, TX 7703 USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor-Hopkins Center for Mendelian Genomics, Baltimore, MD USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Texas Children’s Hospital, Houston, TX 77030 USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030 USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX 77030-3498 USA
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127
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Gschwind AR, Singh A, Certa U, Reymond A, Heckel T. Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis. BMC Genomics 2017; 18:144. [PMID: 28183275 PMCID: PMC5301398 DOI: 10.1186/s12864-017-3531-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 02/01/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) are a significant source of genetic diversity and commonly found in mammalian genomes. We have generated a genome-wide CNV map for Cynomolgus monkeys (Macaca fascicularis). This crab-eating macaque is the closest animal model to humans that is used in biomedical research. RESULTS We show that Cynomolgus monkey CNVs are in general much smaller in size than gene loci and are specific to the population of origin. Genome-wide expression data from five vitally important organs demonstrates that CNVs in close proximity to transcription start sites associate strongly with expression changes. Among these eQTL genes we find an overrepresentation of genes involved in metabolism, receptor activity, and transcription. CONCLUSION These results provide evidence that CNVs shape tissue transcriptomes in monkey populations, potentially offering an adaptive advantage. We suggest that this genetic diversity should be taken into account when using Cynomolgus macaques as models.
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Affiliation(s)
- Andreas R Gschwind
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics SIB, Lausanne, Switzerland
| | - Anjali Singh
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Ulrich Certa
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Tobias Heckel
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, 4070, Basel, Switzerland.
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Schoch K, Meng L, Szelinger S, Bearden DR, Stray-Pedersen A, Busk OL, Stong N, Liston E, Cohn RD, Scaglia F, Rosenfeld JA, Tarpinian J, Skraban CM, Deardorff MA, Friedman JN, Akdemir ZC, Walley N, Mikati MA, Kranz PG, Jasien J, McConkie-Rosell A, McDonald M, Wechsler SB, Freemark M, Kansagra S, Freedman S, Bali D, Millan F, Bale S, Nelson SF, Lee H, Dorrani N, Goldstein DB, Xiao R, Yang Y, Posey JE, Martinez-Agosto JA, Lupski JR, Wangler MF, Shashi V. A Recurrent De Novo Variant in NACC1 Causes a Syndrome Characterized by Infantile Epilepsy, Cataracts, and Profound Developmental Delay. Am J Hum Genet 2017; 100:343-351. [PMID: 28132692 PMCID: PMC5294886 DOI: 10.1016/j.ajhg.2016.12.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/22/2016] [Indexed: 02/08/2023] Open
Abstract
Whole-exome sequencing (WES) has increasingly enabled new pathogenic gene variant identification for undiagnosed neurodevelopmental disorders and provided insights into both gene function and disease biology. Here, we describe seven children with a neurodevelopmental disorder characterized by microcephaly, profound developmental delays and/or intellectual disability, cataracts, severe epilepsy including infantile spasms, irritability, failure to thrive, and stereotypic hand movements. Brain imaging in these individuals reveals delay in myelination and cerebral atrophy. We observe an identical recurrent de novo heterozygous c.892C>T (p.Arg298Trp) variant in the nucleus accumbens associated 1 (NACC1) gene in seven affected individuals. One of the seven individuals is mosaic for this variant. NACC1 encodes a transcriptional repressor implicated in gene expression and has not previously been associated with germline disorders. The probability of finding the same missense NACC1 variant by chance in 7 out of 17,228 individuals who underwent WES for diagnoses of neurodevelopmental phenotypes is extremely small and achieves genome-wide significance (p = 1.25 × 10-14). Selective constraint against missense variants in NACC1 makes this excess of an identical missense variant in all seven individuals more remarkable. Our findings are consistent with a germline recurrent mutational hotspot associated with an allele-specific neurodevelopmental phenotype in NACC1.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Szabolcs Szelinger
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David R Bearden
- Division of Child Neurology, Department of Neurology, University of Rochester School of Medicine, Rochester, NY 14627, USA
| | - Asbjorg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Norwegian National Unit for Newborn Screening, Oslo University Hospital, 0424 Oslo, Norway
| | - Oyvind L Busk
- Section of Medical Genetics, Department of Laboratory Medicine, Telemark Hospital, 3710 Skien, Norway
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Eriskay Liston
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Ronald D Cohn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Tarpinian
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cara M Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeremy N Friedman
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Zeynep Coban Akdemir
- Norwegian National Unit for Newborn Screening, Oslo University Hospital, 0424 Oslo, Norway
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Stephanie Burns Wechsler
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA; Division of Cardiology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Michael Freemark
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | | | - Deeksha Bali
- Department of Pathology, Duke Health, Durham, NC 27710, USA
| | | | | | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Naghmeh Dorrani
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julian A Martinez-Agosto
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor-Hopkins Center for Mendelian Genomics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA.
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA.
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Psychological and behavioural impact of returning personal results from whole-genome sequencing: the HealthSeq project. Eur J Hum Genet 2017; 25:280-292. [PMID: 28051073 PMCID: PMC5315514 DOI: 10.1038/ejhg.2016.178] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 10/18/2016] [Accepted: 11/01/2016] [Indexed: 11/29/2022] Open
Abstract
Providing ostensibly healthy individuals with personal results from whole-genome sequencing could lead to improved health and well-being via enhanced disease risk prediction, prevention, and diagnosis, but also poses practical and ethical challenges. Understanding how individuals react psychologically and behaviourally will be key in assessing the potential utility of personal whole-genome sequencing. We conducted an exploratory longitudinal cohort study in which quantitative surveys and in-depth qualitative interviews were conducted before and after personal results were returned to individuals who underwent whole-genome sequencing. The participants were offered a range of interpreted results, including Alzheimer's disease, type 2 diabetes, pharmacogenomics, rare disease-associated variants, and ancestry. They were also offered their raw data. Of the 35 participants at baseline, 29 (82.9%) completed the 6-month follow-up. In the quantitative surveys, test-related distress was low, although it was higher at 1-week than 6-month follow-up (Z=2.68, P=0.007). In the 6-month qualitative interviews, most participants felt happy or relieved about their results. A few were concerned, particularly about rare disease-associated variants and Alzheimer's disease results. Two of the 29 participants had sought clinical follow-up as a direct or indirect consequence of rare disease-associated variants results. Several had mentioned their results to their doctors. Some participants felt having their raw data might be medically useful to them in the future. The majority reported positive reactions to having their genomes sequenced, but there were notable exceptions to this. The impact and value of returning personal results from whole-genome sequencing when implemented on a larger scale remains to be seen.
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Qian M, Spada C, Wang X. Approach, Application, and Bioethics of mtDNA Sequencing in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:23-38. [DOI: 10.1007/978-981-10-6674-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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131
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Vasaikar S, Bhatia P, Bhatia PG, Chu Yaiw K. Complementary Approaches to Existing Target Based Drug Discovery for Identifying Novel Drug Targets. Biomedicines 2016; 4:E27. [PMID: 28536394 PMCID: PMC5344266 DOI: 10.3390/biomedicines4040027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 02/07/2023] Open
Abstract
In the past decade, it was observed that the relationship between the emerging New Molecular Entities and the quantum of R&D investment has not been favorable. There might be numerous reasons but few studies stress the introduction of target based drug discovery approach as one of the factors. Although a number of drugs have been developed with an emphasis on a single protein target, yet identification of valid target is complex. The approach focuses on an in vitro single target, which overlooks the complexity of cell and makes process of validation drug targets uncertain. Thus, it is imperative to search for alternatives rather than looking at success stories of target-based drug discovery. It would be beneficial if the drugs were developed to target multiple components. New approaches like reverse engineering and translational research need to take into account both system and target-based approach. This review evaluates the strengths and limitations of known drug discovery approaches and proposes alternative approaches for increasing efficiency against treatment.
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Affiliation(s)
- Suhas Vasaikar
- Integrative Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Pooja Bhatia
- School of Biological Sciences, Indian Institute of Technology, Delhi 110016, India.
| | - Partap G Bhatia
- Department of Pharmaceutics and Pharmaceutical Microbiology, Usmanu Danfodiyo University, Sokoto 840231, Nigeria.
| | - Koon Chu Yaiw
- Experimental Cardiovascular Research Unit, Department of Medicine-Solna, Center for Molecular Medicine, Karolinska Institute, Stockholm 17177, Sweden.
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132
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Jackson RA, Nguyen ML, Barrett AN, Tan YY, Choolani MA, Chen ES. Synthetic combinations of missense polymorphic genetic changes underlying Down syndrome susceptibility. Cell Mol Life Sci 2016; 73:4001-17. [PMID: 27245382 PMCID: PMC11108497 DOI: 10.1007/s00018-016-2276-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 02/08/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are important biomolecular markers in health and disease. Down syndrome, or Trisomy 21, is the most frequently occurring chromosomal abnormality in live-born children. Here, we highlight associations between SNPs in several important enzymes involved in the one-carbon folate metabolic pathway and the elevated maternal risk of having a child with Down syndrome. Our survey highlights that the combination of SNPs may be a more reliable predictor of the Down syndrome phenotype than single SNPs alone. We also describe recent links between SNPs in p53 and its related pathway proteins and Down syndrome, as well as highlight several proteins that help to associate apoptosis and p53 signaling with the Down syndrome phenotype. In addition to a comprehensive review of the literature, we also demonstrate that several SNPs reside within the same regions as these Down syndrome-linked SNPs, and propose that these closely located nucleotide changes may provide new candidates for future exploration.
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Affiliation(s)
- Rebecca A Jackson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Mai Linh Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Yuan Yee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore
| | - Mahesh A Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore.
- National University Health System, Singapore, Singapore.
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, #05-05, MD7, 8 Medical Drive, Singapore, 117597, Singapore.
- National University Health System, Singapore, Singapore.
- NUS Graduate School of Science and Engineering, National University of Singapore, Singapore, Singapore.
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133
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Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Genet Med 2016; 19:412-420. [PMID: 27657687 PMCID: PMC5362362 DOI: 10.1038/gim.2016.131] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/20/2016] [Indexed: 12/19/2022] Open
Abstract
Purpose To investigate the utility of whole-exome sequencing (WES) to define a molecular diagnosis in patients clinically diagnosed with congenital anomalies of kidney and urinary tract (CAKUT). Methods WES was performed in 62 families with CAKUT. WES data were analyzed for Single Nucleotide Variants (SNVs) in 35 known CAKUT genes, putatively deleterious sequence changes in new candidate genes, and potentially disease-associated copy-number variants (CNVs). Results In approximately 5% of families, pathogenic SNVs were identified in PAX2, HNF1B, and EYA1. Observed phenotypes in these families expand the current understanding about the role of these genes in CAKUT. Four pathogenic CNVs were also identified using two CNV detection tools. In addition, we found one deleterious de novo SNV in FOXP1 among the 62 families with CAKUT. Database of clinical BMGL laboratory was queried and seven additional unrelated individuals with novel de novo SNVs in FOXP1 were identified. Six of these 8 individuals with FOXP1 SNVs, have syndromic urinary tract defects, implicating this gene in urinary tract development. Conclusion We conclude that WES can be used to identify the molecular etiology (SNVs, CNVs) in a subset of individuals with CAKUT. WES can also help identify novel CAKUT genes.
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134
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Martin-Sanchez FJ, Lopez-Campos GH. The New Role of Biomedical Informatics in the Age of Digital Medicine. Methods Inf Med 2016; 55:392-402. [PMID: 27523651 DOI: 10.3414/me15-02-0005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/11/2015] [Indexed: 01/13/2023]
Abstract
OBJECTIVES To reflect on the recent rise of Digital Medicine, as well as to analyse main research opportunities in this area. Through the use of several examples, this article aims to highlight the new role that Biomedical Informatics (BMI) can play to facilitate progress in research fields such as participatory and precision medicine. This paper also examines the potential impact and associated risks for BMI due to the development of digital medicine and other recent trends. Lastly, possible strategies to place BMI in a better position to face these challenges are suggested. METHODS The core content of this article is based on a recent invited keynote lecture delivered by one of the authors (Martin-Sanchez) at the Medical Informatics Europe conference (MIE 2015) held in Madrid in May 2015. Both authors (Lopez-Campos and Martin-Sanchez) have collaborated during the last four years in projects such as the ones described in section 3 and have also worked in reviewing relevant articles and initiatives to prepare this talk. RESULTS AND CONCLUSIONS Challenges for BMI posed by the rise of technologically driven fields such as Digital Medicine are explored. New opportunities for BMI, in the context of two main avenues for biomedical and clinical research (participatory and precision medicine) are also emphasised. Several examples of current research illustrate that BMI plays a key role in the new area of Digital Medicine. Embracing these opportunities will allow academic groups in BMI to maintain their leadership, identify new research funding opportunities and design new educational programs to train the next generation of BMI scientists.
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Affiliation(s)
- Fernando J Martin-Sanchez
- Fernando J. Martin-Sanchez, PhD, FACHI, FACMI, Weill Cornell Medicine, Department of Healthcare Policy and Research, Division of Health Informatics, 425 61st Street, Suite 301, New York, NY 10021, USA, E-mail:
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135
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Noll AC, Miller NA, Smith LD, Yoo B, Fiedler S, Cooley LD, Willig LK, Petrikin JE, Cakici J, Lesko J, Newton A, Detherage K, Thiffault I, Saunders CJ, Farrow EG, Kingsmore SF. Clinical detection of deletion structural variants in whole-genome sequences. NPJ Genom Med 2016; 1:16026. [PMID: 29263817 PMCID: PMC5685307 DOI: 10.1038/npjgenmed.2016.26] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022] Open
Abstract
Optimal management of acutely ill infants with monogenetic diseases requires rapid identification of causative haplotypes. Whole-genome sequencing (WGS) has been shown to identify pathogenic nucleotide variants in such infants. Deletion structural variants (DSVs, >50 nt) are implicated in many genetic diseases, and tools have been designed to identify DSVs using short-read WGS. Optimisation and integration of these tools into a WGS pipeline could improve diagnostic sensitivity and specificity of WGS. In addition, it may improve turnaround time when compared with current CNV assays, enhancing utility in acute settings. Here we describe DSV detection methods for use in WGS for rapid diagnosis in acutely ill infants: SKALD (Screening Konsensus and Annotation of Large Deletions) combines calls from two tools (Breakdancer and GenomeStrip) with calibrated filters and clinical interpretation rules. In four WGS runs, the average analytic precision (positive predictive value) of SKALD was 78%, and recall (sensitivity) was 27%, when compared with validated reference DSV calls. When retrospectively applied to a cohort of 36 families with acutely ill infants SKALD identified causative DSVs in two. The first was heterozygous deletion of exons 1–3 of MMP21 in trans with a heterozygous frame-shift deletion in two siblings with transposition of the great arteries and heterotaxy. In a newborn female with dysmorphic features, ventricular septal defect and persistent pulmonary hypertension, SKALD identified the breakpoints of a heterozygous, de novo 1p36.32p36.13 deletion. In summary, consensus DSV calling, implemented in an 8-h computational pipeline with parameterised filtering, has the potential to increase the diagnostic yield of WGS in acutely ill neonates and discover novel disease genes.
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Affiliation(s)
- Aaron C Noll
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Stephanie Fiedler
- Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Linda D Cooley
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Julie Cakici
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - John Lesko
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Angela Newton
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kali Detherage
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA.,Department of Pathology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Stephen F Kingsmore
- Heartland Institute for Clinical and Translational Research, University of Kansas Medical Center, Kansas City, KS, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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136
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Cayer DM, Nazor KL, Schork NJ. Mission critical: the need for proteomics in the era of next-generation sequencing and precision medicine. Hum Mol Genet 2016; 25:R182-R189. [DOI: 10.1093/hmg/ddw214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
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137
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Li L, Liu P, Sun L, Bin Zhou, Fei J. PiggyBac transposon-based polyadenylation-signal trap for genome-wide mutagenesis in mice. Sci Rep 2016; 6:27788. [PMID: 27292714 PMCID: PMC4904408 DOI: 10.1038/srep27788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 05/23/2016] [Indexed: 12/12/2022] Open
Abstract
We designed a new type of polyadenylation-signal (PAS) trap vector system in living mice, the piggyBac (PB) (PAS-trapping (EGFP)) gene trapping vector, which takes advantage of the efficient transposition ability of PB and efficient gene trap and insertional mutagenesis of PAS-trapping. The reporter gene of PB(PAS-trapping (EGFP)) is an EGFP gene with its own promoter, but lacking a poly(A) signal. Transgenic mouse lines carrying PB(PAS-trapping (EGFP)) and protamine 1 (Prm1) promoter-driven PB transposase transgenes (Prm1-PBase) were generated by microinjection. Male mice doubly positive for PB(PAS-trapping (EGFP)) and Prm1-PBase were crossed with WT females, generating offspring with various insertion mutations. We found that 44.8% (26/58) of pups were transposon-positive progenies. New transposon integrations comprised 26.9% (7/26) of the transposon-positive progenies. We found that 100% (5/5) of the EGFP fluorescence-positive mice had new trap insertions mediated by a PB transposon in transcriptional units. The direction of the EGFP gene in the vector was consistent with the direction of the endogenous gene reading frame. Furthermore, mice that were EGFP-PCR positive, but EGFP fluorescent negative, did not show successful gene trapping. Thus, the novel PB(PAS-trapping (EGFP)) system is an efficient genome-wide gene-trap mutagenesis in mice.
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Affiliation(s)
- Limei Li
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Department of vascular surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Liu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liangliang Sun
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, 200003, PR China
| | - Bin Zhou
- Department of vascular surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jian Fei
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- Metastasis research institute, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
- School of Life Science and Technology, Tongji University, Shanghai, China
- Shanghai Research Center for Model Organisms, Shanghai, 201203, China
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138
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McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol 2016. [PMID: 27268795 DOI: 10.1186/s13059-016–0974-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
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Affiliation(s)
- William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Graham R S Ritchie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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139
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McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biol 2016; 17:122. [PMID: 27268795 PMCID: PMC4893825 DOI: 10.1186/s13059-016-0974-4] [Citation(s) in RCA: 4261] [Impact Index Per Article: 532.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/03/2016] [Indexed: 02/06/2023] Open
Abstract
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
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Affiliation(s)
- William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Harpreet Singh Riat
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Graham R S Ritchie
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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Koringa PG, Jakhesara SJ, Rank DN, Joshi CG. Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing. 3 Biotech 2016; 6:38. [PMID: 28330108 PMCID: PMC4729760 DOI: 10.1007/s13205-015-0351-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/04/2015] [Indexed: 11/04/2022] Open
Abstract
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget.
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141
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Lupski JR. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 2016; 135:591-601. [PMID: 27221143 DOI: 10.1007/s00439-016-1682-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 12/23/2022]
Abstract
The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 604B, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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143
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Uzun A, Schuster J, McGonnigal B, Schorl C, Dewan A, Padbury J. Targeted Sequencing and Meta-Analysis of Preterm Birth. PLoS One 2016; 11:e0155021. [PMID: 27163930 PMCID: PMC4862658 DOI: 10.1371/journal.pone.0155021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/22/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the genetic contribution(s) to the risk of preterm birth may lead to the development of interventions for treatment, prediction and prevention. Twin studies suggest heritability of preterm birth is 36-40%. Large epidemiological analyses support a primary maternal origin for recurrence of preterm birth, with little effect of paternal or fetal genetic factors. We exploited an "extreme phenotype" of preterm birth to leverage the likelihood of genetic discovery. We compared variants identified by targeted sequencing of women with 2-3 generations of preterm birth with term controls without history of preterm birth. We used a meta-genomic, bi-clustering algorithm to identify gene sets coordinately associated with preterm birth. We identified 33 genes including 217 variants from 5 modules that were significantly different between cases and controls. The most frequently identified and connected genes in the exome library were IGF1, ATM and IQGAP2. Likewise, SOS1, RAF1 and AKT3 were most frequent in the haplotype library. Additionally, SERPINB8, AZU1 and WASF3 showed significant differences in abundance of variants in the univariate comparison of cases and controls. The biological processes impacted by these gene sets included: cell motility, migration and locomotion; response to glucocorticoid stimulus; signal transduction; metabolic regulation and control of apoptosis.
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Affiliation(s)
- Alper Uzun
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
- Brown Alpert Medical School, Providence, Rhode Island, United States of America
| | - Jessica Schuster
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
| | - Bethany McGonnigal
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
| | - Christoph Schorl
- Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Andrew Dewan
- Department of Epidemiology and Public Health, Yale University, New Haven, Connecticut, United States of America
| | - James Padbury
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
- Brown Alpert Medical School, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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144
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Tripathi R, Sharma P, Chakraborty P, Varadwaj PK. Next-generation sequencing revolution through big data analytics. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1178180] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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145
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Millan F, Cho MT, Retterer K, Monaghan KG, Bai R, Vitazka P, Everman DB, Smith B, Angle B, Roberts V, Immken L, Nagakura H, DiFazio M, Sherr E, Haverfield E, Friedman B, Telegrafi A, Juusola J, Chung WK, Bale S. Whole exome sequencing reveals de novo pathogenic variants in KAT6A as a cause of a neurodevelopmental disorder. Am J Med Genet A 2016; 170:1791-8. [PMID: 27133397 DOI: 10.1002/ajmg.a.37670] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/06/2016] [Indexed: 01/06/2023]
Abstract
Neurodevelopmental disorders (NDD) are common, with 1-3% of general population being affected, but the etiology is unknown in most individuals. Clinical whole-exome sequencing (WES) has proven to be a powerful tool for the identification of pathogenic variants leading to Mendelian disorders, among which NDD represent a significant percentage. Performing WES with a trio-approach has proven to be extremely effective in identifying de novo pathogenic variants as a common cause of NDD. Here we report six unrelated individuals with a common phenotype consisting of NDD with severe speech delay, hypotonia, and facial dysmorphism. These patients underwent WES with a trio approach and de novo heterozygous predicted pathogenic novel variants in the KAT6A gene were identified. The KAT6A gene encodes a histone acetyltransfrease protein and it has long been known for its structural involvement in acute myeloid leukemia; however, it has not previously been associated with any congenital disorder. In animal models the KAT6A ortholog is involved in transcriptional regulation during development. Given the similar findings in animal models and our patient's phenotypes, we hypothesize that KAT6A could play a role in development of the brain, face, and heart in humans. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | | | | | | | | | | | - Brooke Smith
- Greenwood Genetic Center, Greenville, South Carolina
| | - Brad Angle
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Victoria Roberts
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | | | | | - Marc DiFazio
- Children's Outpatient Center of Montgomery County, Rockville, Maryland
| | - Elliott Sherr
- Institute of Human Genetics, University of California, San Francisco, California
| | | | | | | | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York
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146
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Goldfeder RL, Priest JR, Zook JM, Grove ME, Waggott D, Wheeler MT, Salit M, Ashley EA. Medical implications of technical accuracy in genome sequencing. Genome Med 2016; 8:24. [PMID: 26932475 PMCID: PMC4774017 DOI: 10.1186/s13073-016-0269-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/21/2016] [Indexed: 12/31/2022] Open
Abstract
Background As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome. Methods We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation. Results We observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6 % of the exonic bases in ClinVar and OMIM genes and 82.1 % of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50 % of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2. Conclusions Together, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0269-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel L Goldfeder
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - James R Priest
- Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA. .,Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| | - Justin M Zook
- Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Megan E Grove
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Daryl Waggott
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Matthew T Wheeler
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA.
| | - Marc Salit
- Genome-scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA.
| | - Euan A Ashley
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA. .,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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147
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Abstract
New high-throughput DNA sequencing (HTS) technologies developed in the past decade have begun to be applied to the study of the complex gene rearrangements that encode human antibodies. This article first reviews the genetic features of Ig loci and the HTS technologies that have been applied to human repertoire studies, then discusses key choices for experimental design and data analysis in these experiments and the insights gained in immunological and infectious disease studies with the use of these approaches.
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148
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Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PLoS Comput Biol 2016; 12:e1004711. [PMID: 26845687 PMCID: PMC4742230 DOI: 10.1371/journal.pcbi.1004711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
Although many human diseases have a genetic component involving many loci, the majority of studies are statistically underpowered to isolate the many contributing variants, raising the question of the existence of alternate processes to identify disease mutations. To address this question, we collect ancestral transcription factor binding sites disrupted by an individual's variants and then look for their most significant congregation next to a group of functionally related genes. Strikingly, when the method is applied to five different full human genomes, the top enriched function for each is invariably reflective of their very different medical histories. For example, our method implicates "abnormal cardiac output" for a patient with a longstanding family history of heart disease, "decreased circulating sodium level" for an individual with hypertension, and other biologically appealing links for medical histories spanning narcolepsy to axonal neuropathy. Our results suggest that erosion of gene regulation by mutation load significantly contributes to observed heritable phenotypes that manifest in the medical history. The test we developed exposes a hitherto hidden layer of personal variants that promise to shed new light on human disease penetrance, expressivity and the sensitivity with which we can detect them.
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149
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Souzeau E, Burdon KP, Mackey DA, Hewitt AW, Savarirayan R, Otlowski M, Craig JE. Ethical Considerations for the Return of Incidental Findings in Ophthalmic Genomic Research. Transl Vis Sci Technol 2016; 5:3. [PMID: 26929883 PMCID: PMC4757467 DOI: 10.1167/tvst.5.1.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 12/25/2022] Open
Abstract
Whole genome and whole exome sequencing technologies are being increasingly used in research. However, they have the potential to identify incidental findings (IF), findings not related to the indication of the test, raising questions regarding researchers' responsibilities toward the return of this information to participants. In this study we discuss the ethical considerations related to the return of IF to research participants, emphasizing that the type of the study matters and describing the current practice standards. There are currently no legal obligations for researchers to return IF to participants, but some viewpoints consider that researchers might have an ethical one to return IF of clinical validity and clinical utility and that are actionable. The reality is that most IF are complex to interpret, especially since they were not the indication of the test. The clinical utility often depends on the participants' preferences, which can be challenging to conciliate and relies on participants' understanding. In summary, in the context of a lack of clear guidance, researchers need to have a clear plan for the disclosure or nondisclosure of IF from genomic research, balancing their research goals and resources with the participants' rights and their duty not to harm.
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Affiliation(s)
- Emmanuelle Souzeau
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
| | - Kathryn P. Burdon
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
| | - David A. Mackey
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Alex W. Hewitt
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Service, Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Australia
| | | | - Jamie E. Craig
- Department of Ophthalmology Flinders University, Flinders Medical Centre, Adelaide, Australia
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150
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White J, Beck CR, Harel T, Posey JE, Jhangiani SN, Tang S, Farwell KD, Powis Z, Mendelsohn NJ, Baker JA, Pollack L, Mason KJ, Wierenga KJ, Arrington DK, Hall M, Psychogios A, Fairbrother L, Walkiewicz M, Person RE, Niu Z, Zhang J, Rosenfeld JA, Muzny DM, Eng C, Beaudet AL, Lupski JR, Boerwinkle E, Gibbs RA, Yang Y, Xia F, Sutton VR. POGZ truncating alleles cause syndromic intellectual disability. Genome Med 2016; 8:3. [PMID: 26739615 PMCID: PMC4702300 DOI: 10.1186/s13073-015-0253-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/08/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Large-scale cohort-based whole exome sequencing of individuals with neurodevelopmental disorders (NDDs) has identified numerous novel candidate disease genes; however, detailed phenotypic information is often lacking in such studies. De novo mutations in pogo transposable element with zinc finger domain (POGZ) have been identified in six independent and diverse cohorts of individuals with NDDs ranging from autism spectrum disorder to developmental delay. METHODS Whole exome sequencing was performed on five unrelated individuals. Sanger sequencing was used to validate variants and segregate mutations with the phenotype in available family members. RESULTS We identified heterozygous truncating mutations in POGZ in five unrelated individuals, which were confirmed to be de novo or not present in available parental samples. Careful review of the phenotypes revealed shared features that included developmental delay, intellectual disability, hypotonia, behavioral abnormalities, and similar facial characteristics. Variable features included short stature, microcephaly, strabismus and hearing loss. CONCLUSIONS While POGZ has been associated with neurodevelopmental disorders in large cohort studies, our data suggest that loss of function variants in POGZ lead to an identifiable syndrome of NDD with specific phenotypic traits. This study exemplifies the era of human reverse clinical genomics ushered in by large disease-directed cohort studies; first defining a new syndrome molecularly and, only subsequently, phenotypically.
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Affiliation(s)
- Janson White
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Nancy J Mendelsohn
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN, 55102, USA
| | - Janice A Baker
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN, 55102, USA
| | - Lynda Pollack
- Arnold Palmer Medical Center, Division of Genetics, Orlando, FL, 32806, USA
| | - Kati J Mason
- Arnold Palmer Medical Center, Division of Genetics, Orlando, FL, 32806, USA
| | - Klaas J Wierenga
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Daniel K Arrington
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Melissa Hall
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Apostolos Psychogios
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Laura Fairbrother
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37212, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Richard E Person
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Zhiyv Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- University of Texas Health Science Center, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA
- Exome Laboratory, Baylor Miraca Genetics Laboratory, Houston, TX, 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, 77030, USA.
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