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Lin W, Hu S, Wu Z, Xu Z, Zhong Y, Lv Z, Qiu W, Xiao X. iCancer-Pred: A tool for identifying cancer and its type using DNA methylation. Genomics 2022; 114:110486. [PMID: 36126833 DOI: 10.1016/j.ygeno.2022.110486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/11/2022] [Accepted: 09/16/2022] [Indexed: 01/14/2023]
Abstract
DNA methylation is an important epigenetics, which occurs in the early stages of tumor formation. And it also is of great significance to find the relationship between DNA methylation and cancer. This paper proposes a novel model, iCancer-Pred, to identify cancer and classify its types further. The datasets of DNA methylation information of 7 cancer types have been collected from The Cancer Genome Atlas (TCGA). The coefficient of variation firstly is used to reduce the number of features, and then the elastic network is applied to select important features. Finally, a fully connected neural network is constructed with these selected features. In predicting seven types of cancers, iCancer-Pred has achieved an overall accuracy of over 97% accuracy with 5-fold cross-validation. For the convenience of the application, a user-friendly web server: http://bioinfo.jcu.edu.cn/cancer or http://121.36.221.79/cancer/ is available. And the source codes are freely available for download at https://github.com/Huerhu/iCancer-Pred.
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Affiliation(s)
- Weizhong Lin
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China.
| | - Siqin Hu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Zhicheng Wu
- Wuhan Ammunition Life Science & Technology Co., Ltd., Wuhan 430000, China
| | - Zhaochun Xu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Yu Zhong
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Zhe Lv
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Wangren Qiu
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
| | - Xuan Xiao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen 333000, China
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Huang F, Wang TJ, Cho WH, Chen YH, Wu PC, Kuo HK. Mutation survey in Taiwanese patients with Stickler syndrome. Taiwan J Ophthalmol 2022; 12:423-429. [PMID: 36660125 PMCID: PMC9843582 DOI: 10.4103/tjo.tjo_3_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/06/2022] [Indexed: 01/22/2023] Open
Abstract
PURPOSE The purpose of this study was to identify gene mutation and phenotype correlations in a cohort of Taiwanese patients with Stickler syndrome. MATERIALS AND METHODS Patients clinically diagnosed with Stickler syndrome or suspected Stickler syndrome were enrolled. DNA was extracted from venous blood samples. For the targeted next-generation sequencing (NGS) approach, specific primers were designed for all COL2A1, COL11A1, COL11A2, COL9A1, and COL9A2 exons and flanking intron sequences. RESULTS Twenty-three patients from 12 families were enrolled in this study. The myopia power in these 23 cases (35 eyes) ranged from -4.625 to -25.625 D, with a median of -10.00 D. Four patients had retinal detachment. Fourteen patients had a cleft palate. These 23 patients and 13 healthy controls were enrolled in the NGS study. Three families had significant single nucleotide variants (SNVs) in COL2A1. The mutation rates in this survey were 25% (3/12 families) and 35% (8/23 cases). The SNV of family #1, located at exon 27, c.1753G >T, p. Gly585Val, was novel and has not yet been reported in the ClinVar database. Families #10 and #11 had the same SNV, located in exon 33, c.2101C >T, p. Arg701X. Both variants were classified as likely pathogenic according to the American College of Medical Genetics and Genomics guidelines. CONCLUSION Genetic mutations in COL2A1 were found in 25% of Taiwanese families with Stickler syndrome. One novel variant was identified using NGS, which expanded the COL2A1 mutation spectrum. Molecular genetic analysis is helpful to confirm the clinical diagnosis of patients with suspected Stickler syndrome.
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Affiliation(s)
- Faye Huang
- Department of Plastic and Reconstructive Surgery, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan,School of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Tzu-Jou Wang
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan,Department of Pediatrics, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Wan-Hua Cho
- Department of Ophthalmology, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yi-Hao Chen
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan,Department of Ophthalmology, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Pei-Chang Wu
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan,Department of Ophthalmology, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Hsi-Kung Kuo
- School of Medicine, Chang Gung University, Taoyuan City, Taiwan,Department of Ophthalmology, Kaohsiung Chang-Gung Memorial Hospital, Kaohsiung, Taiwan,Address for correspondence: Dr. Hsi-Kung Kuo, Department of Ophthalmology, Kaohsiung Chang Gung Memorial Hospital, 123 Ta-Pei Road, Niao-Sung District, Kaohsiung, Taiwan. E-mail:
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Genetic Characteristics and Phenotype of Korean Patients with Stickler Syndrome: A Korean Multicenter Analysis Report No. 1. Genes (Basel) 2021; 12:genes12101578. [PMID: 34680973 PMCID: PMC8536015 DOI: 10.3390/genes12101578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Stickler syndrome is an inherited connective tissue disorder of collagen. There are relatively few reports of East Asian patients, and no large-scale studies have been conducted in Korean patients yet. In this study, we retrospectively analyzed the genetic characteristics and clinical features of Korean Stickler syndrome patients. Among 37 genetically confirmed Stickler syndrome patients, 21 types of gene variants were identified, of which 12 were novel variants. A total of 30 people had variants in the COL2A1 gene and 7 had variants in the COL11A1 gene. Among the types of pathogenic variants, missense variants were found in 11, nonsense variants in 8, and splice site variants in 7. Splicing variants were frequently associated with retinal detachment (71%) followed by missense variants. This is the first large-scale study of Koreans with Stickler syndrome, which will expand the spectrum of genetic variations of Stickler syndrome.
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Ali Khan I. Do second generation sequencing techniques identify documented genetic markers for neonatal diabetes mellitus? Heliyon 2021; 7:e07903. [PMID: 34584998 PMCID: PMC8455689 DOI: 10.1016/j.heliyon.2021.e07903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/15/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Neonatal diabetes mellitus (NDM) is noted as a genetic, heterogeneous, and rare disease in infants. NDM occurs due to a single-gene mutation in neonates. A common source for developing NDM in an infant is the existence of mutations/variants in the KCNJ11 and ABCC8 genes, encoding the subunits of the voltage-dependent potassium channel. Both KCNJ11 and ABCC8 genes are useful in diagnosing monogenic diabetes during infancy. Genetic analysis was previously performed using first-generation sequencing techniques, such as DNA-Sanger sequencing, which uses chain-terminating inhibitors. Sanger sequencing has certain limitations; it can screen a limited region of exons in one gene, but it cannot screen large regions of the human genome. In the last decade, first generation sequencing techniques have been replaced with second-generation sequencing techniques, such as next-generation sequencing (NGS), which sequences nucleic-acids more rapidly and economically than Sanger sequencing. NGS applications are involved in whole exome sequencing (WES), whole genome sequencing (WGS), and targeted gene panels. WES characterizes a substantial breakthrough in human genetics. Genetic testing for custom genes allows the screening of the complete gene, including introns and exons. The aim of this review was to confirm if the 22 genetic variations previously documented to cause NDM by Sanger sequencing could be detected using second generation sequencing techniques. The author has cross-checked global studies performed in NDM using NGS, ES/WES, WGS, and targeted gene panels as second-generation sequencing techniques; WES confirmed the similar variants, which have been previously documented with Sanger sequencing. WES is documented as a powerful tool and WGS as the most comprehensive test for verified the documented variants, as well as novel enhancers. This review recommends for the future studies should be performed with second generation sequencing techniques to identify the verified 22 genetic and novel variants by screening in NDM (PNDM or TNMD) children.
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Affiliation(s)
- Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, PO Box-10219, Riyadh, 11433, Saudi Arabia
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Chiou CC, Wang CL, Luo JD, Liu CY, Ko HW, Yang CT. Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients. Cancer Genomics Proteomics 2021; 17:417-423. [PMID: 32576586 DOI: 10.21873/cgp.20200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/14/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Circulating tumor DNA (ctDNA) bears specific mutations derived from tumor cells. The amount of mutant ctDNA may reflect tumor burden. In this study, we detected epidermal growth factor receptor (EGFR) mutations in ctDNA as a monitoring marker for the response of non-small cell lung cancer (NSCLC) patients to tyrosine kinase inhibitors (TKIs). PATIENTS AND METHODS Serial plasma samples from eight NSCLC patients during TKI treatment were collected. Libraries with barcoded adapters were constructed from ctDNA of these plasma samples using a PCR-based targeted DNA panel. The libraries were then sequenced for measuring EGFR mutations. In addition, carcinoembryonic antigen (CEA) was also measured in these patients. RESULTS In six patients who suffered disease progression (PD), five had elevated EGFR mutation reads before PD. In the two patients who did not develop PD, EGFR mutations remained undetectable in their plasma. The CEA levels were higher than the cutoff value in most samples and had a poor correlation with disease status. CONCLUSION The mutation count of tumor-specific mutations can be a monitoring marker of TKI treatment in NSCLC patients.
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Affiliation(s)
- Chiuan-Chian Chiou
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.,Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Chih-Liang Wang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, U.S.A
| | - Chien-Ying Liu
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - How-Wen Ko
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Cheng-Ta Yang
- Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. .,Department of Respiratory Therapy, College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
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Teske D, Peters A, Möllers A, Fischer M. Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14323-14333. [PMID: 32917087 DOI: 10.1021/acs.jafc.0c03001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.
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Affiliation(s)
- Doreen Teske
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alina Peters
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alexander Möllers
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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Urban A. "…This Has to Do With My Identity. And I Don't Want to Make it Totally Transparent." Identity Relevance in the Attitudes of Affected People and Laypersons to the Handling of High-Throughput Genomic Data. FRONTIERS IN SOCIOLOGY 2020; 5:532357. [PMID: 33869478 PMCID: PMC8022580 DOI: 10.3389/fsoc.2020.532357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
With the establishment of genome sequencing, the influence of genomic information on self-understanding and identity construction has become increasingly important. New sequencing methods far exceed previous genetic tests in terms of scope and quantity. Despite theoretical approaches, however, there are few empirical findings on the identity-relevant influence of genomic information. The present study examines genomic information's identity-relevant influences and considers whether developments in the field of genome sequencing may generate problems that are not yet addressed by existing identity concepts based on traditional genetic tests. The study is based on 10 partially standardized interviews with personally affected persons and four focus groups with medical laypersons as representatives of the public, which were evaluated on the basis of qualitative content analysis. As a result, this paper presents five thematic areas with identity-relevant references within subjective attitudes toward the handling of genomic information, and also derives two basic identity concepts. The results indicate that the lay discourse is still strongly based on older debates about genetic testing and that the view on the complexity of genomic information established in the scientific context has thus far no influence on the perspectives either of those affected or laypersons.
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Affiliation(s)
- Alexander Urban
- Department of Medical Ethics and History of Medicine, University Medical Center Göttingen, Göttingen, Germany
- Faculty of Social Sciences, Georg-August-University Göttingen, Göttingen, Germany
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Udar N, Iyer A, Porter M, Haigis R, Smith S, Dhillon S, Meier K, Ward D, Lu J, Wenz P, Buchner L, Dunn T, Wise A, Mueller A, Gutekunst K. Development and Analytical Validation of a DNA Dual-Strand Approach for the US Food and Drug Administration-Approved Next-Generation Sequencing-Based Praxis Extended RAS Panel for Metastatic Colorectal Cancer Samples. J Mol Diagn 2019; 22:159-178. [PMID: 31837434 DOI: 10.1016/j.jmoldx.2019.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 09/03/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022] Open
Abstract
A next-generation sequencing method was developed that can distinguish single-stranded modifications from low-frequency somatic mutations present on both strands of DNA in formalin-fixed paraffin-embedded colorectal cancer samples. We applied this method for analytical validation of the Praxis Extended RAS Panel, a US Food and Drug Administration-approved companion diagnostic for panitumumab, on the Illumina MiSeqDx platform. With the use of the TruSeq amplicon workflow, both strands of DNA from the starting material were interrogated independently. Mutations were reported only if found on both strands; artifacts usually present on only one strand would not be reported. A total of 56 mutations were targeted within the KRAS and NRAS genes. A minimum read depth of 1800× per amplicon is required per sample but averaged >30,000× at maximum multiplexing levels. Analytical validation studies were performed to determine the simultaneous detection of mutations on both strands, reproducibility, assay detection level, precision of the assay across various factors, and the impact of interfering substances. In conclusion, this assay can clearly distinguish single-stranded artifacts from low-frequency mutations. Furthermore, the assay is accurate, precise, and reproducible, can achieve consistent detection of a mutation at 5% mutation frequency, exhibits minimal impact from tested interfering substances, and can simultaneously detect 56 mutations in a single run using 10 samples plus controls.
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Affiliation(s)
- Nitin Udar
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Anita Iyer
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California.
| | - Margaret Porter
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Robert Haigis
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Shannon Smith
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Shivani Dhillon
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Kristen Meier
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Diane Ward
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Jing Lu
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Paul Wenz
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Leonard Buchner
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Tamsen Dunn
- Department of Bioinformatics, Illumina, Inc., San Diego, California
| | - Aaron Wise
- Department of Bioinformatics, Illumina, Inc., San Diego, California
| | - Amy Mueller
- Department of Medical Affairs, Illumina, Inc., San Diego, California
| | - Karen Gutekunst
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
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Coppola G, Corrado E, Curnis A, Maglia G, Oriente D, Mignano A, Brugada P. Update on Brugada Syndrome 2019. Curr Probl Cardiol 2019; 46:100454. [PMID: 31522883 DOI: 10.1016/j.cpcardiol.2019.100454] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
Abstract
Brugada syndrome (BrS) was first described in 1992 as an aberrant pattern of ST segment elevation in right precordial leads with a high incidence of sudden cardiac death (SCD) in patients with structurally normal heart. It represents 4% ∼ 12% of all SCD and 20% of SCD in patients with structurally normal heart. The extremely wide genetic heterogeneity of BrS and other inherited cardiac disorders makes this new area of genetic arrhytmology a fascinating one. This review shows the state of art in diagnosis, management, and treatment of BrS focusing all the aspects regarding genetics and Preimplant Genetic Diagnosis (PGD) of embryos, overlapping syndromes, risk stratification, familial screening, and future perspectives. Moreover the review analyzes key points like electrocardiogram (ECG) criteria, the role of electrophysiological study (the role of ventricular programmed stimulation and the need of universal accepted protocol) and the importance of a correct risk stratification to clarify when implantable cardioverter defibrillator or a close follow-up is needed. In recent years, cardiovascular studies have been focused on personalized risk assessment and to determine the most optimal therapy for an individual. The BrS syndrome has also benefited of these advances although there remain several key points to be elucidated. We will review the present knowledge, progress made, and future research directions on BrS.
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Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019; 25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.
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Affiliation(s)
- V Mintzer
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; Leumit Health Services, Israel
| | - J Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - T Simon-Tuval
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel.
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Berberich AJ, Hegele RA. The role of genetic testing in dyslipidaemia. Pathology 2019; 51:184-192. [DOI: 10.1016/j.pathol.2018.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/28/2023]
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12
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Humangenetik. PÄDIATRIE 2019. [PMCID: PMC7498390 DOI: 10.1007/978-3-662-57295-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetische Erkrankungen haben in der Kinderheilkunde eine größere Bedeutung erlangt. Durch Weiterentwicklung zytogenetischer, biochemischer und molekulargenetischer Diagnostik ist das Spektrum der bekannten genetischen und genetisch mitbedingten Erkrankungen größer geworden: im Katalog monogener Erkrankungen von McKusick stehen inzwischen über 8.500 Erkrankungen. Die häufigsten genetischen Erkrankungen werden in diesem Kapitel ebenso beschrieben wie die Aufgaben der humangenetischen Beratung, pränataler Diagnostik sowie des „next generation sequencing“.
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Weymann D, Pataky R, Regier DA. Economic Evaluations of Next-Generation Precision Oncology: A Critical Review. JCO Precis Oncol 2018; 2:1-23. [DOI: 10.1200/po.17.00311] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose Precision oncology has the potential to improve patient health and reduce treatment costs. Yet the up-front cost of genomic testing with next-generation sequencing (NGS) technologies can be prohibitive. Our study is a structured review of economic evaluations of precision oncology informed by NGS. The aim is to characterize the availability and scope of economic evidence. Materials and Methods We searched Medline (PubMed), Embase (Ovid), and Web of Science databases for English-language full-text peer-reviewed articles published between 2000 and 2016. We focused our search on articles that estimated the benefit of precision oncology in relation to its costs. We excluded studies that did not undertake full economic evaluations or did not focus on NGS technologies. We reviewed all included studies and summarized key methodological and empirical study characteristics. Results Fifty-five economic evaluations met our inclusion criteria. The number of published studies increased steadily, from three studies between 2005 and 2007 to 26 between 2014 and 2016. Most studies evaluated multiplex panels (86%). We found testing was frequently used to predict prognosis (67%), to diagnose patients (24%), or to identify targeted therapeutic options (7%). Methods and cost effectiveness differed according to NGS technology, test strategy, and cancer type. Deterministic and probabilistic analyses were typically used to characterize parameter and decision uncertainty (91% and 75%). Conclusion Although the availability of economic evidence examining precision oncology increased over time, methods used often did not align with current guidelines. Future evaluations should undertake extensive sensitivity analysis to address all sources of uncertainty associated with rapidly changing NGS technologies. Furthermore, additional research is needed evaluating the cost effectiveness of more comprehensive next-generation technologies before implementing these on a wider scale.
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Affiliation(s)
- Deirdre Weymann
- All authors, Canadian Centre for Applied Research in Cancer Control, BC Cancer; and Dean A. Regier, University of British Columbia, Vancouver, British Columbia, Canada
| | - Reka Pataky
- All authors, Canadian Centre for Applied Research in Cancer Control, BC Cancer; and Dean A. Regier, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dean A. Regier
- All authors, Canadian Centre for Applied Research in Cancer Control, BC Cancer; and Dean A. Regier, University of British Columbia, Vancouver, British Columbia, Canada
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Li W, Liao B, Zhu W, Chen M, Li Z, Wei X, Peng L, Huang G, Cai L, Chen H. Fisher Discrimination Regularized Robust Coding Based on a Local Center for Tumor Classification. Sci Rep 2018; 8:9152. [PMID: 29904059 PMCID: PMC6002553 DOI: 10.1038/s41598-018-27364-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/31/2018] [Indexed: 11/29/2022] Open
Abstract
Tumor classification is crucial to the clinical diagnosis and proper treatment of cancers. In recent years, sparse representation-based classifier (SRC) has been proposed for tumor classification. The employed dictionary plays an important role in sparse representation-based or sparse coding-based classification. However, sparse representation-based tumor classification models have not used the employed dictionary, thereby limiting their performance. Furthermore, this sparse representation model assumes that the coding residual follows a Gaussian or Laplacian distribution, which may not effectively describe the coding residual in practical tumor classification. In the present study, we formulated a novel effective cancer classification technique, namely, Fisher discrimination regularized robust coding (FDRRC), by combining the Fisher discrimination dictionary learning method with the regularized robust coding (RRC) model, which searches for a maximum a posteriori solution to coding problems by assuming that the coding residual and representation coefficient are independent and identically distributed. The proposed FDRRC model is extensively evaluated on various tumor datasets and shows superior performance compared with various state-of-the-art tumor classification methods in a variety of classification tasks.
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Affiliation(s)
- Weibiao Li
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Bo Liao
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China.
| | - Wen Zhu
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Min Chen
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Zejun Li
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaohui Wei
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Lihong Peng
- Hunan University of Technology, Zhu Zhou, Hunan, 412007, China
| | - Guohua Huang
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Lijun Cai
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - HaoWen Chen
- College of Information Science and Engineering, Hunan University, Changsha, Hunan, 410082, China
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15
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Borràs N, Batlle J, Pérez-Rodríguez A, López-Fernández MF, Rodríguez-Trillo Á, Lourés E, Cid AR, Bonanad S, Cabrera N, Moret A, Parra R, Mingot-Castellano ME, Balda I, Altisent C, Pérez-Montes R, Fisac RM, Iruín G, Herrero S, Soto I, de Rueda B, Jiménez-Yuste V, Alonso N, Vilariño D, Arija O, Campos R, Paloma MJ, Bermejo N, Berrueco R, Mateo J, Arribalzaga K, Marco P, Palomo Á, Sarmiento L, Iñigo B, Nieto MDM, Vidal R, Martínez MP, Aguinaco R, César JM, Ferreiro M, García-Frade J, Rodríguez-Huerta AM, Cuesta J, Rodríguez-González R, García-Candel F, Cornudella R, Aguilar C, Vidal F, Corrales I. Molecular and clinical profile of von Willebrand disease in Spain (PCM-EVW-ES): comprehensive genetic analysis by next-generation sequencing of 480 patients. Haematologica 2017; 102:2005-2014. [PMID: 28971901 PMCID: PMC5709099 DOI: 10.3324/haematol.2017.168765] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 09/20/2017] [Indexed: 01/10/2023] Open
Abstract
Molecular diagnosis of patients with von Willebrand disease is pending in most populations due to the complexity and high cost of conventional molecular analyses. The need for molecular and clinical characterization of von Willebrand disease in Spain prompted the creation of a multicenter project (PCM-EVW-ES) that resulted in the largest prospective cohort study of patients with all types of von Willebrand disease. Molecular analysis of relevant regions of the VWF, including intronic and promoter regions, was achieved in the 556 individuals recruited via the development of a simple, innovative, relatively low-cost protocol based on microfluidic technology and next-generation sequencing. A total of 704 variants (237 different) were identified along VWF, 155 of which had not been previously recorded in the international mutation database. The potential pathogenic effect of these variants was assessed by in silico analysis. Furthermore, four short tandem repeats were analyzed in order to evaluate the ancestral origin of recurrent mutations. The outcome of genetic analysis allowed for the reclassification of 110 patients, identification of 37 asymptomatic carriers (important for genetic counseling) and re-inclusion of 43 patients previously excluded by phenotyping results. In total, 480 patients were definitively diagnosed. Candidate mutations were identified in all patients except 13 type 1 von Willebrand disease, yielding a high genotype-phenotype correlation. Our data reinforce the capital importance and usefulness of genetics in von Willebrand disease diagnostics. The progressive implementation of molecular study as the first-line test for routine diagnosis of this condition will lead to increasingly more personalized and effective care for this patient population.
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Affiliation(s)
- Nina Borràs
- Banc de Sang i Teixits, Barcelona, Spain
- Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Spain
| | - Javier Batlle
- Complexo Hospitalario Universitario A Coruña, INIBIC, Spain
| | | | | | | | - Esther Lourés
- Complexo Hospitalario Universitario A Coruña, INIBIC, Spain
| | - Ana Rosa Cid
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Noelia Cabrera
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Andrés Moret
- Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Rafael Parra
- Banc de Sang i Teixits, Barcelona, Spain
- Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Ignacia Balda
- Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | | | | | | | - Gemma Iruín
- Hospital Universitario Cruces, Barakaldo, Spain
| | | | | | | | | | | | - Dolores Vilariño
- Complejo Hospitalario Universitario Santiago de Compostela, Spain
| | - Olga Arija
- Hospital Universitario Lucus Augusti, Lugo, Spain
| | | | | | | | | | - José Mateo
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rosa Cornudella
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | | | - Francisco Vidal
- Banc de Sang i Teixits, Barcelona, Spain
- Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Spain
- CIBER de Enfermedades Cardiovasculares, Spain
| | - Irene Corrales
- Banc de Sang i Teixits, Barcelona, Spain
- Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona (VHIR-UAB), Spain
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16
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Aymé S, Bockenhauer D, Day S, Devuyst O, Guay-Woodford LM, Ingelfinger JR, Klein JB, Knoers NVAM, Perrone RD, Roberts J, Schaefer F, Torres VE, Cheung M, Wheeler DC, Winkelmayer WC. Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2017; 92:796-808. [PMID: 28938953 PMCID: PMC6685068 DOI: 10.1016/j.kint.2017.06.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
Rare kidney diseases encompass at least 150 different conditions, most of which are inherited. Although individual rare kidney diseases raise specific issues, as a group these rare diseases can have overlapping challenges in diagnosis and treatment. These challenges include small numbers of affected patients, unidentified causes of disease, lack of biomarkers for monitoring disease progression, and need for complex care. To address common clinical and patient issues among rare kidney diseases, the KDIGO Controversies Conference entitled, Common Elements in Rare Kidney Diseases, brought together a panel of multidisciplinary clinical providers and patient advocates to address five central issues for rare kidney diseases. These issues encompassed diagnostic challenges, management of kidney functional decline and progression of chronic kidney disease, challenges in clinical study design, translation of advances in research to clinical care, and provision of practical and integrated patient support. Thus, by a process of consensus, guidance for addressing these challenges was developed and is presented here.
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Affiliation(s)
- Ségolène Aymé
- Institut du Cerveau et de la Moelle Épinière, Centre National de la Recherche Scientifique Unite Mixte de Recherche 7225, Institut National de la Santé et de la Recherche Médicale U 1127, Université Pierre et Marie Curie-P6 Unite Mixte de Recherche S 1127, Paris, France
| | - Detlef Bockenhauer
- University College of London Centre for Nephrology, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, UK
| | - Simon Day
- Clinical Trials Consulting and Training Limited, Buckingham, UK
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland.
| | - Lisa M Guay-Woodford
- Center for Translational Science, Children's National Health System, Washington, DC, USA.
| | - Julie R Ingelfinger
- MassGeneral Hospital for Children at Massachusetts General Hospital, Harvard University, Boston, Massachusetts, USA
| | - Jon B Klein
- Division of Nephrology and Hypertension, The University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ronald D Perrone
- Department of Medicine, Division of Nephrology, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Julia Roberts
- Polycystic Kidney Disease Foundation, Kansas City, Missouri, USA
| | - Franz Schaefer
- Division of Pediatric Nephrology, Centre for Pediatrics and Adolescent Medicine, Heidelberg University Medical Centre, Heidelberg, Germany
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael Cheung
- Kidney Disease: Improving Global Outcomes, Brussels, Belgium
| | | | - Wolfgang C Winkelmayer
- Selzman Institute for Kidney Health, Section of Nephrology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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17
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Ma H, Brosens LAA, Elias SG, Morsink FHM, Nijman IJ, Hylind LM, Montgomery EA, Offerhaus GJA, Giardiello FM, de Leng WWJ. Longitudinal analysis of colon crypt stem cell dynamics in sulindac treated Familial Adenomatous Polyposis patients. Sci Rep 2017; 7:11972. [PMID: 28931879 PMCID: PMC5607292 DOI: 10.1038/s41598-017-11865-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/24/2017] [Indexed: 02/06/2023] Open
Abstract
The non-steroidal anti-inflammatory drug sulindac decreases size and number of adenomas after 4-6 months of treatment for familial adenomatous polyposis (FAP) patients. However, the underlying mechanism remains unknown. As stem cells are thought to be the tumor precursor cells, visualizing their behavior is crucial for monitoring tumor progression. Increased tag diversity in inactive genes is indicative of a protracted clonal evolution and consequently, increased risk for tumor formation. Therefore, the effect of sulindac on stem cell dynamics was studied. Normal appearing single crypts were laser microdissected in placebo- and sulindac- treated FAP patient tissue after which the methylation patterns were visualized by Next Generation Sequencing. A significant difference in tag diversity over time was found in the sulindac group compared to the placebo group (*p = 0.018), indicative of a shortened clonal evolution treated sulindac. The rate of change in tag diversity over time was correlated with polyp number change over time. No significant difference over time was observed in the percent methylation when comparing placebo vs sulindac. In conclusion, daily sulindac administration in FAP patients significantly altered colorectal stem cell dynamics, which might explain the chemopreventive action of this drug indicating that tag diversity may be used as a predictive biomarker.
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Affiliation(s)
- Huiying Ma
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lodewijk A A Brosens
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd G Elias
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Folkert H M Morsink
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Linda M Hylind
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Montgomery
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - G Johan A Offerhaus
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Francis M Giardiello
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands.
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18
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Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing. J Mol Diagn 2017; 19:776-787. [DOI: 10.1016/j.jmoldx.2017.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
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19
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Du H, Pan B, Chen T. Evaluation of chemical mutagenicity using next generation sequencing: A review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2017; 35:140-158. [PMID: 28506110 DOI: 10.1080/10590501.2017.1328831] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations are heritable changes in the nucleotide sequence of DNA that can lead to many adverse effects. Genotoxicity assays have been used to identify chemical mutagenicity. Recently, next generation sequencing (NGS) has been used for this purpose. In this review, we present the progress in NGS application for assessing mutagenicity of chemicals, including the methods used for detecting the induced mutations, bioinformatics tools for analyzing the sequencing data, and chemicals whose mutagenicity has been evaluated using NGS. Available information suggests that NGS technology has unparalleled advantages for evaluating mutagenicity of chemicals can be applied for the next generation of mutagenicity tests.
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Affiliation(s)
- Hua Du
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Bohu Pan
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Tao Chen
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
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20
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The Unravelling of the Genetic Architecture of Plasminogen Deficiency and its Relation to Thrombotic Disease. Sci Rep 2016; 6:39255. [PMID: 27976734 PMCID: PMC5157013 DOI: 10.1038/srep39255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/22/2016] [Indexed: 01/16/2023] Open
Abstract
Although plasminogen is a key protein in fibrinolysis and several mutations in the plasminogen gene (PLG) have been identified that result in plasminogen deficiency, there are conflicting reports to associate it with the risk of thrombosis. Our aim was to unravel the genetic architecture of PLG in families with plasminogen deficiency and its relationship with spontaneous thrombotic events in these families. A total of 13 individuals from 4 families were recruited. Their genetic risk profile of thromboembolism was characterized using the Thrombo inCode kit. Only one family presented genetic risk of thromboembolism (homozygous carrier of F12 rs1801020 and F13A1 rs5985). The whole PLG was tested using Next Generation Sequencing (NGS) and 5 putative pathogenic mutations were found (after in silico predictions) and associated with plasminogen deficiency. Although we can not find genetic risk factors of thrombosis in 3 of 4 families, even the mutations associated with plasminogen deficiency do not cosegregated with thrombosis, we can not exclude plasminogen deficiency as a susceptibility risk factor for thrombosis, since thrombosis is a multifactorial and complex disease where unknown genetic risk factors, in addition to plasminogen deficiency, within these families may explain the thrombotic tendency.
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21
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The cost of molecular-guided therapy in oncology: a prospective cost study alongside the MOSCATO trial. Genet Med 2016; 19:683-690. [DOI: 10.1038/gim.2016.174] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/21/2016] [Indexed: 12/28/2022] Open
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22
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Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis. Pathol Oncol Res 2016; 23:225-234. [PMID: 27722982 DOI: 10.1007/s12253-016-0124-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/04/2016] [Indexed: 12/22/2022]
Abstract
With the advancement and improvement of new sequencing technology, next-generation sequencing (NGS) has been applied increasingly in cancer genomics research fields. More recently, NGS has been adopted in clinical oncology to advance personalized treatment of cancer. NGS is utilized to novel diagnostic and rare cancer mutations, detection of translocations, inversions, insertions and deletions, detection of copy number variants, detect familial cancer mutation carriers, provide the molecular rationale for appropriate targeted, therapeutic and prognostic. NGS holds many advantages, such as the ability to fully sequence all types of mutations for a large number of genes (hundreds to thousands) and the sensitivity, speed in a single test at a relatively low cost compared to be other sequencing modalities. Here we described the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
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23
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Orue A, Rieber M. Optimized Multiplex Detection of 7 KRAS Mutations by Taqman Allele-Specific qPCR. PLoS One 2016; 11:e0163070. [PMID: 27632281 PMCID: PMC5025196 DOI: 10.1371/journal.pone.0163070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Establishing the KRAS mutational status of tumor samples is essential to manage patients with colorectal or lung cancer, since these mutations preclude treatment with monoclonal anti-epidermal growth factor receptor (EGFR) antibodies. We report an inexpensive, rapid multiplex allele-specific qPCR method detecting the 7 most clinically relevant KRAS somatic mutations with concomitant amplification of non-mutated KRAS in tumor cells and tissues from CRC patients. Positive samples evidenced in the multiplex assay were further subjected to individual allele-specific analysis, to define the specific mutation. Reference human cancer DNA harbouring either G12A, G12C, G12D, G12R, G12S, G12V and G13D confirmed assay specificity with ≤1% sensitivity of mutant alleles. KRAS multiplex mutation analysis usefulness was also demonstrated with formalin-fixed paraffin embedded (FFPE) from CRC biopsies. CONCLUSION Co-amplification of non-mutated DNA avoided false negatives from degraded samples. Moreover, this cost effective assay is compatible with mutation detection by DNA sequencing in FFPE tissues, but with a greater sensitivity when mutant DNA concentrations are limiting.
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Affiliation(s)
- Andrea Orue
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
| | - Manuel Rieber
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
- * E-mail:
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24
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Bertier G, Hétu M, Joly Y. Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views. BMC Med Genomics 2016; 9:52. [PMID: 27514372 PMCID: PMC4982236 DOI: 10.1186/s12920-016-0213-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature. METHODS In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users. RESULTS Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles. CONCLUSIONS WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.
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Affiliation(s)
- Gabrielle Bertier
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
- UMR 1027, Inserm, University of Toulouse III - Paul Sabatier, 37 allées Jules Guesde, F-31000 Toulouse, France
| | - Martin Hétu
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
| | - Yann Joly
- Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
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25
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Ahmed A. Analysis of Metagenomics Next Generation Sequence Data for Fungal ITS Barcoding: Do You Need Advance Bioinformatics Experience? Front Microbiol 2016; 7:1061. [PMID: 27507959 PMCID: PMC4960088 DOI: 10.3389/fmicb.2016.01061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/23/2016] [Indexed: 11/13/2022] Open
Abstract
During the last few decades, most of microbiology laboratories have become familiar in analyzing Sanger sequence data for ITS barcoding. However, with the availability of next-generation sequencing platforms in many centers, it has become important for medical mycologists to know how to make sense of the massive sequence data generated by these new sequencing technologies. In many reference laboratories, the analysis of such data is not a big deal, since suitable IT infrastructure and well-trained bioinformatics scientists are always available. However, in small research laboratories and clinical microbiology laboratories the availability of such resources are always lacking. In this report, simple and user-friendly bioinformatics work-flow is suggested for fast and reproducible ITS barcoding of fungi.
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Affiliation(s)
- Abdalla Ahmed
- College of Medicine, Umm Al-Qura University Makkah, Saudi Arabia
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26
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Maclachlan A, Watson SP, Morgan NV. Inherited platelet disorders: Insight from platelet genomics using next-generation sequencing. Platelets 2016; 28:14-19. [PMID: 27348543 PMCID: PMC5359778 DOI: 10.1080/09537104.2016.1195492] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inherited platelet disorders (IPDs) are a heterogeneous group of disorders associated with normal or reduced platelet counts and bleeding diatheses of varying severities. The identification of the underlying cause of IPDs is clinically challenging due to the absence of a gold-standard platelet test, and is often based on a clinical presentation and normal values in other hematology assays. As a consequence, a DNA-based approach has a potentially important role in the investigation of these patients. Next-generation sequencing (NGS) technologies are allowing the rapid analysis of genes that have been previously implicated in IPDs or that are known to have a key role in platelet regulation, as well as novel genes that have not been previously implicated in platelet dysfunction. The potential limitations of NGS arise with the interpretation of the sheer volume of genetic information obtained from whole exome sequencing (WES) or whole genome sequencing (WGS) in order to identify function-disrupting variants. Following on from bioinformatic analysis, a number of candidate genetic variants usually remain, therefore adding to the difficulty of phenotype–genotype segregation verification. Linking genetic changes to an underlying bleeding disorder is an ongoing challenge and may not always be feasible due to the multifactorial nature of IPDs. Nevertheless, NGS will play a key role in our understanding of the mechanisms of platelet function and the genetics involved.
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Affiliation(s)
- Annabel Maclachlan
- a Institute of Cardiovascular Sciences, College of Medical and Dental Sciences , University of Birmingham , Birmingham , B15 2TT , UK
| | - Steve P Watson
- a Institute of Cardiovascular Sciences, College of Medical and Dental Sciences , University of Birmingham , Birmingham , B15 2TT , UK
| | - Neil V Morgan
- a Institute of Cardiovascular Sciences, College of Medical and Dental Sciences , University of Birmingham , Birmingham , B15 2TT , UK
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27
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Roy-Chowdhuri S, Stewart J. Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing—The MD Anderson Experience. Arch Pathol Lab Med 2016; 140:1191-1199. [DOI: 10.5858/arpa.2016-0117-ra] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
As our understanding of genomic alterations underlying solid tumor malignancies continues to evolve, molecular testing of tumor samples is increasingly used to guide therapeutic management. Next-generation sequencing (NGS) provides a novel platform for the simultaneous screening of multiple genes using small amounts of DNA. Several recent studies have described NGS mutational analysis using cytologic specimens. The cytopathologist's role in specimen assessment and triaging is critical to effectively implementing NGS in routine cytology practice.
Objectives.—
To review the NGS experience and a variety of preanalytic factors that affect NGS success rates of cytologic specimens at our institution.
Data Sources.—
To evaluate cytology specimen adequacy rates for NGS, we reviewed a 14-month period of image-guided fine-needle aspiration and core needle biopsies used for testing. In addition, we reviewed data from our previously published studies to evaluate preanalytic factors affecting NGS success in these specimens.
Conclusions.—
Identifying factors that affect NGS success rates in cytology specimens is crucial for a better understanding of specimen adequacy requirements and for proper use of limited-volume tissue samples. In our practice, which uses direct smears as well as cell block sections, NGS success rates in core needle biopsy and fine-needle aspiration samples are comparable. The chance of successful testing is further increased by procuring concurrent fine-needle aspiration and core needle biopsy samples. The type of glass slides used for direct smears and the method of tissue extraction affect our DNA yield. Validating a DNA input for cytology samples that is lower than that recommended by the manufacturer has significantly increased our NGS success rate.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- From the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
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28
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Sommen M, Schrauwen I, Vandeweyer G, Boeckx N, Corneveaux JJ, van den Ende J, Boudewyns A, De Leenheer E, Janssens S, Claes K, Verstreken M, Strenzke N, Predöhl F, Wuyts W, Mortier G, Bitner-Glindzicz M, Moser T, Coucke P, Huentelman MJ, Van Camp G. DNA Diagnostics of Hereditary Hearing Loss: A Targeted Resequencing Approach Combined with a Mutation Classification System. Hum Mutat 2016; 37:812-9. [PMID: 27068579 DOI: 10.1002/humu.22999] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
Abstract
Although there are nearly 100 different causative genes identified for nonsyndromic hearing loss (NSHL), Sanger sequencing-based DNA diagnostics usually only analyses three, namely, GJB2, SLC26A4, and OTOF. As this is seen as inadequate, there is a need for high-throughput diagnostic methods to detect disease-causing variations, including single-nucleotide variations (SNVs), insertions/deletions (Indels), and copy-number variations (CNVs). In this study, a targeted resequencing panel for hearing loss was developed including 79 genes for NSHL and selected forms of syndromic hearing loss. One-hundred thirty one presumed autosomal-recessive NSHL (arNSHL) patients of Western-European ethnicity were analyzed for SNVs, Indels, and CNVs. In addition, we established a straightforward variant classification system to deal with the large number of variants encountered. We estimate that combining prescreening of GJB2 with our panel leads to a diagnosis in 25%-30% of patients. Our data show that after GJB2, the most commonly mutated genes in a Western-European population are TMC1, MYO15A, and MYO7A (3.1%). CNV analysis resulted in the identification of causative variants in two patients in OTOA and STRC. One of the major challenges for diagnostic gene panels is assigning pathogenicity for variants. A collaborative database collecting all identified variants from multiple centers could be a valuable resource for hearing loss diagnostics.
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Affiliation(s)
- Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nele Boeckx
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Jason J Corneveaux
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jenneke van den Ende
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - An Boudewyns
- Department of Otorhinolaryngology, Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Els De Leenheer
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Kathleen Claes
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Margriet Verstreken
- University Department Otolaryngology, St. Augustinus Hospital, Antwerp, Belgium
| | - Nicola Strenzke
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Friederike Predöhl
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany
| | - Wim Wuyts
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.,Antwerp University Hospital, Antwerp, Belgium
| | - Maria Bitner-Glindzicz
- Clinical and Molecular Genetics Unit, UCL Institute of Child Health and Great Ormond Street Hospital NHS Trust, London, UK
| | - Tobias Moser
- Inner Ear Lab, Department of Otolaryngology, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Paul Coucke
- Center of Medical Genetics, Ghent University, Ghent, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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29
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Sener EF, Canatan H, Ozkul Y. Recent Advances in Autism Spectrum Disorders: Applications of Whole Exome Sequencing Technology. Psychiatry Investig 2016; 13:255-64. [PMID: 27247591 PMCID: PMC4878959 DOI: 10.4306/pi.2016.13.3.255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 09/22/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorders (ASD) is characterized by three core symptoms with impaired reciprocal social interaction and communication, a pattern of repetitive behavior and/or restricted interests in early childhood. The prevalence is higher in male children than in female children. As a complex neurodevelopmental disorder, the phenotype and severity of autism are extremely heterogeneous with differences from one patient to another. Genetics has a key role in the etiology of autism. Environmental factors are also interacting with the genetic profile and cause abnormal changes in neuronal development, brain growth, and functional connectivity. The term of exome represents less than 1% of the human genome, but contains 85% of known disease-causing variants. Whole-exome sequencing (WES) is an application of the next generation sequencing technology to determine the variations of all coding regions, or exons of known genes. For this reason, WES has been extensively used for clinical studies in the recent years. WES has achieved great success in the past years for identifying Mendelian disease genes. This review evaluates the potential of current findings in ASD for application in next generation sequencing technology, particularly WES. WES and whole-genome sequencing (WGS) approaches may lead to the discovery of underlying genetic factors for ASD and may thereby identify novel therapeutic targets for this disorder.
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Affiliation(s)
- Elif Funda Sener
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
- Erciyes University Genome and Stem Cell Center, Kayseri, Turkey
| | - Halit Canatan
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Erciyes University Medical Faculty, Kayseri, Turkey
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30
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Milicchio F, Rose R, Bian J, Min J, Prosperi M. Visual programming for next-generation sequencing data analytics. BioData Min 2016; 9:16. [PMID: 27127540 PMCID: PMC4848821 DOI: 10.1186/s13040-016-0095-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/21/2016] [Indexed: 11/10/2022] Open
Abstract
Background High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a ‘cultural’ gap between the end user and the developer. Text Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users’ needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. Conclusion In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.
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Affiliation(s)
| | | | - Jiang Bian
- Department of Health Outcomes and Policy, University of Florida, Gainesville, FL USA
| | - Jae Min
- Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA
| | - Mattia Prosperi
- Department of Epidemiology, College of Public Health and Health Professions & College of Medicine, University of Florida, 2004 Mowry Road, Gainesville, 32610-0231 FL USA
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31
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Mer AS, Klevebring D, Grönberg H, Rantalainen M. Study design requirements for RNA sequencing-based breast cancer diagnostics. Sci Rep 2016; 6:20200. [PMID: 26830453 PMCID: PMC4735337 DOI: 10.1038/srep20200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022] Open
Abstract
Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.
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Affiliation(s)
- Arvind Singh Mer
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden
| | - Daniel Klevebring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden
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32
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Tsourounis M, Stuart J, Pignato W, Toscani M, Barone J. Current Trends in Personalized Medicine and Companion Diagnostics: A Summary From the DIA Meeting on Personalized Medicine and Companion Diagnostics. Ther Innov Regul Sci 2015; 49:530-543. [PMID: 30222427 DOI: 10.1177/2168479015570330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Personalized medicine has reached the mainstream, accounting for more new drug approvals and a promising pipeline of candidate therapeutics. Recent advances in genomics, computational biology, medical imaging, diagnostic technologies, and translational medicine are creating the possibility for scientists to develop diagnostic tools and new treatments for cancer, genetic disorders, and infectious diseases that may be particularly effective in biomarker-defined subpopulations. Drug development under this model creates new challenges that will require the need for increased regulatory flexibility, novel clinical trial designs, and translational science development. In this review, the authors highlight key developmental and regulatory challenges in the advancement of personalized medicines and their associated companion diagnostics with the need for innovative clinical trial designs to support drug/diagnostic development and registration. Further, the clinical complexities of implementing new technologies are considered, such as high-throughput next-generation sequencing in personalized medicine, and offer a glimpse of the regulatory and policy considerations shaping this methodology in multimarker diagnostic development.
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Affiliation(s)
| | | | | | | | - Joseph Barone
- 2 Ernest Mario School of Pharmacy, Piscataway, NJ, USA
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33
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Vicini P, Fields O, Lai E, Litwack ED, Martin AM, Morgan TM, Pacanowski MA, Papaluca M, Perez OD, Ringel MS, Robson M, Sakul H, Vockley J, Zaks T, Dolsten M, Søgaard M. Precision medicine in the age of big data: The present and future role of large-scale unbiased sequencing in drug discovery and development. Clin Pharmacol Ther 2015; 99:198-207. [PMID: 26536838 DOI: 10.1002/cpt.293] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
High throughput molecular and functional profiling of patients is a key driver of precision medicine. DNA and RNA characterization has been enabled at unprecedented cost and scale through rapid, disruptive progress in sequencing technology, but challenges persist in data management and interpretation. We analyze the state-of-the-art of large-scale unbiased sequencing in drug discovery and development, including technology, application, ethical, regulatory, policy and commercial considerations, and discuss issues of LUS implementation in clinical and regulatory practice.
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Affiliation(s)
- P Vicini
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
| | - O Fields
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
| | - E Lai
- Takeda Pharmaceuticals International, Deerfield, Illinois, USA
| | - E D Litwack
- Food and Drug Administration, Silver Spring, Maryland, USA
| | - A-M Martin
- GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - T M Morgan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, and East Hanover, New Jersey, USA
| | - M A Pacanowski
- Food and Drug Administration, Silver Spring, Maryland, USA
| | | | - O D Perez
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
| | - M S Ringel
- Boston Consulting Group, Boston, Massachusetts, USA
| | - M Robson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, and East Hanover, New Jersey, USA
| | - H Sakul
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
| | - J Vockley
- Inova Translational Medicine Institute, Falls Church, Virginia, USA
| | - T Zaks
- Sanofi, Cambridge, Massachusetts, USA
| | - M Dolsten
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
| | - M Søgaard
- Pfizer Worldwide Research & Development, La Jolla, California, Collegeville, Pennsylvania, and New York, New York, USA
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34
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Shaheen R, Patel N, Shamseldin H, Alzahrani F, Al-Yamany R, ALMoisheer A, Ewida N, Anazi S, Alnemer M, Elsheikh M, Alfaleh K, Alshammari M, Alhashem A, Alangari AA, Salih MA, Kircher M, Daza RM, Ibrahim N, Wakil SM, Alaqeel A, Altowaijri I, Shendure J, Al-Habib A, Faqieh E, Alkuraya FS. Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. Genet Med 2015; 18:686-95. [PMID: 26633546 DOI: 10.1038/gim.2015.147] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/03/2015] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Dysmorphology syndromes are among the most common referrals to clinical genetics specialists. Inability to match the dysmorphology pattern to a known syndrome can pose a major diagnostic challenge. With an aim to accelerate the establishment of new syndromes and their genetic etiology, we describe our experience with multiplex consanguineous families that appeared to represent novel autosomal recessive dysmorphology syndromes at the time of evaluation. METHODS Combined autozygome/exome analysis of multiplex consanguineous families with apparently novel dysmorphology syndromes. RESULTS Consistent with the apparent novelty of the phenotypes, our analysis revealed a strong candidate variant in genes that were novel at the time of the analysis in the majority of cases, and 10 of these genes are published here for the first time as novel candidates (CDK9, NEK9, ZNF668, TTC28, MBL2, CADPS, CACNA1H, HYAL2, CTU2, and C3ORF17). A significant minority of the phenotypes (6/31, 19%), however, were caused by genes known to cause Mendelian phenotypes, thus expanding the phenotypic spectrum of the diseases linked to these genes. The conspicuous inheritance pattern and the highly specific phenotypes appear to have contributed to the high yield (90%) of plausible molecular diagnoses in our study cohort. CONCLUSION Reporting detailed clinical and genomic analysis of a large series of apparently novel dysmorphology syndromes will likely lead to a trend to accelerate the establishment of novel syndromes and their underlying genes through open exchange of data for the benefit of patients, their families, health-care providers, and the research community.Genet Med 18 7, 686-695.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ruah Al-Yamany
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Agaadir ALMoisheer
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shamsa Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maha Alnemer
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Elsheikh
- Department of Obstetrics and Gynecology, Suliman AlHabib Hospital, Riyadh, Saudi Arabia
| | - Khaled Alfaleh
- Department of Obstetrics and Gynecology, Suliman AlHabib Hospital, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muneera Alshammari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Abdullah A Alangari
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Salma M Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Alaqeel
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ikhlas Altowaijri
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Amro Al-Habib
- Department of Surgery, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Eissa Faqieh
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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35
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Duncan R, Kourout M, Grigorenko E, Fisher C, Dong M. Advances in multiplex nucleic acid diagnostics for blood-borne pathogens: promises and pitfalls. Expert Rev Mol Diagn 2015; 16:83-95. [PMID: 26581018 DOI: 10.1586/14737159.2016.1112272] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The large number of blood-borne viruses, bacteria and parasites currently of concern, as well as many newly emerging pathogens, presents a daunting challenge to protection of the safety of blood for transfusion and diagnosing infectious diseases. Focusing on nucleic acid diagnostic tests, multiplex devices are coming into use with many more in various developmental stages that promise to offer solutions to the clinical need. The characteristics, advantages and disadvantages of platforms in clinical use and at the research and development stage are examined here. The presence of multiple assays and associated reagents operating simultaneously on one platform, implementation in traditional clinical laboratories and regulatory review will present special challenges. Fortunately, clinical laboratories have made dramatic technical progress in the last two decades and regulatory agencies have publicly expressed support for development of multiplex devices.
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Affiliation(s)
- Robert Duncan
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Moussa Kourout
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | | | - Carolyn Fisher
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
| | - Ming Dong
- a Center for Biologics Evaluation and Research , US FDA , Silver Spring , MD , USA
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36
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Lu H, Tang Y, Dunn PA, Wallner-Pendleton EA, Lin L, Knoll EA. Isolation and molecular characterization of newly emerging avian reovirus variants and novel strains in Pennsylvania, USA, 2011-2014. Sci Rep 2015; 5:14727. [PMID: 26469681 PMCID: PMC4606735 DOI: 10.1038/srep14727] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 09/07/2015] [Indexed: 11/26/2022] Open
Abstract
Avian reovirus (ARV) infections of broiler and turkey flocks have caused significant clinical disease and economic losses in Pennsylvania (PA) since 2011. Most of the ARV-infected birds suffered from severe arthritis, tenosynovitis, pericarditis and depressed growth or runting-stunting syndrome (RSS). A high morbidity (up to 20% to 40%) was observed in ARV-affected flocks, and the flock mortality was occasionally as high as 10%. ARV infections in turkeys were diagnosed for the first time in PA in 2011. From 2011 to 2014, a total of 301 ARV isolations were made from affected PA poultry. The molecular characterization of the Sigma C gene of 114 field isolates, representing most ARV outbreaks, revealed that only 21.93% of the 114 sequenced ARV isolates were in the same genotyping cluster (cluster 1) as the ARV vaccine strains (S1133, 1733, and 2048), whereas 78.07% of the sequenced isolates were in genotyping clusters 2, 3, 4, 5, and 6 (which were distinct from the vaccine strains) and represented newly emerging ARV variants. In particular, genotyping cluster 6 was a new ARV genotype that was identified for the first time in 10 novel PA ARV variants of field isolates.
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Affiliation(s)
- Huaguang Lu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Yi Tang
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Patricia A. Dunn
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Eva A. Wallner-Pendleton
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Lin Lin
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Eric A. Knoll
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
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Souilmi Y, Lancaster AK, Jung JY, Rizzo E, Hawkins JB, Powles R, Amzazi S, Ghazal H, Tonellato PJ, Wall DP. Scalable and cost-effective NGS genotyping in the cloud. BMC Med Genomics 2015; 8:64. [PMID: 26470712 PMCID: PMC4608296 DOI: 10.1186/s12920-015-0134-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
Background While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10’s of dollars. Results We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Conclusions Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0134-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yassine Souilmi
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA. .,Department of Biology, Mohamed Vth University, 4 Ibn Battouta Avenue, B.P: 1014RP, Rabat, Morocco.
| | - Alex K Lancaster
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA. .,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
| | - Jae-Yoon Jung
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA.
| | - Ettore Rizzo
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 1, Pavia, 27100, Italy.
| | - Jared B Hawkins
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA.
| | - Ryan Powles
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA.
| | - Saaïd Amzazi
- Department of Biology, Mohamed Vth University, 4 Ibn Battouta Avenue, B.P: 1014RP, Rabat, Morocco.
| | - Hassan Ghazal
- Department of Biology, Mohamed First University, Oujda, Nador, Morocco.
| | - Peter J Tonellato
- Department of Biomedical Informatics, Harvard Medical School 10 Shattuck Street, Boston, MA, 02115, USA. .,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02215, USA.
| | - Dennis P Wall
- Department of Pediatrics and Psychiatry (by courtesy), Division of Systems Medicine & Program in Biomedical Informatics, Stanford University, Stanford, CA, 94305, USA.
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Song C, Castellanos-Rizaldos E, Bejar R, Ebert BL, Makrigiorgos GM. DMSO Increases Mutation Scanning Detection Sensitivity of High-Resolution Melting in Clinical Samples. Clin Chem 2015; 61:1354-62. [PMID: 26432802 DOI: 10.1373/clinchem.2015.245357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mutation scanning provides the simplest, lowest-cost method for identifying DNA variations on single PCR amplicons, and it may be performed before sequencing to avoid screening of noninformative wild-type samples. High-resolution melting (HRM) is the most commonly used method for mutation scanning. With PCR-HRM, however, mutations less abundant than approximately 3%-10% that can still be clinically significant may often be missed. Therefore, enhancing HRM detection sensitivity is important for mutation scanning and its clinical application. METHODS We used serial dilution of cell lines containing the TP53 exon 8 mutation to demonstrate the improvement in detection sensitivity for conventional-PCR-HRM in the presence of DMSO. We also conducted coamplification at lower denaturation temperature (COLD)-PCR with an extra step for cross-hybridization, followed by preferential denaturation and amplification at optimized critical temperature (full-COLD-PCR), to further enrich low-level mutations before HRM with or without DMSO, and we used droplet-digital PCR to derive the optimal conditions for mutation enrichment. Both conventional PCR-HRM and full-COLD-PCR-HRM with and without DMSO were used for mutation scanning of TP53 exon 8 in cancer samples containing known mutations and myelodysplastic syndrome samples with unknown mutations. Mutations in other genes were also examined. RESULTS The detection sensitivity of PCR-HRM scanning increases 2- to 5-fold in the presence of DMSO, depending on mutation type and sequence context, and can typically detect mutation abundance of approximately 1%. When mutation enrichment is applied during amplification with full-COLD-PCR followed by HRM in the presence of DMSO, mutations with 0.2%-0.3% abundance in TP53 exon 8 can be detected. CONCLUSIONS DMSO improves HRM mutation scanning sensitivity with saturating dyes. When full-COLD-PCR is used, followed by DMSO-HRM, the overall improvement is about 20-fold compared with conventional PCR-HRM.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Elena Castellanos-Rizaldos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Rafael Bejar
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, CA
| | - Benjamin L Ebert
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;
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Moens LNJ, Falk-Sörqvist E, Ljungström V, Mattsson J, Sundström M, La Fleur L, Mathot L, Micke P, Nilsson M, Botling J. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples. J Mol Diagn 2015; 17:729-39. [PMID: 26354930 DOI: 10.1016/j.jmoldx.2015.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/29/2015] [Accepted: 06/17/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings.
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Affiliation(s)
- Lotte N J Moens
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Elin Falk-Sörqvist
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Johanna Mattsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Magnus Sundström
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Linnéa La Fleur
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Mats Nilsson
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden.
| | - Johan Botling
- Department of Immunology Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, Sweden.
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Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies. Cancers (Basel) 2015; 7:1699-715. [PMID: 26343728 PMCID: PMC4586792 DOI: 10.3390/cancers7030859] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 01/28/2023] Open
Abstract
Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.
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42
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Roy-Chowdhuri S, Goswami RS, Chen H, Patel KP, Routbort MJ, Singh RR, Broaddus RR, Barkoh BA, Manekia J, Yao H, Medeiros LJ, Staerkel G, Luthra R, Stewart J. Factors affecting the success of next-generation sequencing in cytology specimens. Cancer Cytopathol 2015; 123:659-68. [PMID: 26230354 DOI: 10.1002/cncy.21597] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of cytology specimens for next-generation sequencing (NGS) is particularly challenging because of the unconventional substrate of smears and the often limited sample volume. An analysis of factors affecting NGS testing in cytologic samples may help to increase the frequency of successful testing. METHODS This study reviewed variables associated with all in-house cytology cases (n = 207) that were analyzed by NGS with the Ion Torrent platform during a 10-month interval. A statistical analysis was performed to measure the effects of the DNA input threshold, specimen preparation, slide type, tumor fraction, DNA yield, and cytopathologist bias. RESULTS One hundred sixty-four of 207 cases (79%) were successfully sequenced by NGS; 43 (21%) failed because of either a low DNA yield or a template/library preparation failure. The median estimated tumor fraction and DNA concentration for the successfully sequenced cases were 70% and 2.5 ng/μL, respectively, whereas they were 60% and 0.2 ng/μL, respectively, for NGS failures. Cell block sections were tested in 91 cases, and smears were used in 116 cases. NGS success positively correlated with the DNA yield but not the tumor fraction. Cell block preparations showed a higher success rate than smears. Frosted-tip slides yielded significantly more DNA than fully frosted slides. Lowering the input DNA concentration below the manufacturer's recommended threshold of 10 ng (>0.85 ng/μL) resulted in a marked increase in the NGS success rate from 58.6% to 89.8%. CONCLUSIONS The failure of NGS with cytology samples is usually a result of suboptimal DNA due to multiple pre-analytical factors. Knowledge of these factors will allow better selection of cytology material for mutational analysis.
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Affiliation(s)
- Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rashmi S Goswami
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Chen
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajesh R Singh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Russell R Broaddus
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bedia A Barkoh
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jawad Manekia
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregg Staerkel
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015; 3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023] Open
Abstract
Structural variants are genomic rearrangements larger than 50 bp accounting for around 1% of the variation among human genomes. They impact on phenotypic diversity and play a role in various diseases including neurological/neurocognitive disorders and cancer development and progression. Dissecting structural variants from next-generation sequencing data presents several challenges and a number of approaches have been proposed in the literature. In this mini review, we describe and summarize the latest tools – and their underlying algorithms – designed for the analysis of whole-genome sequencing, whole-exome sequencing, custom captures, and amplicon sequencing data, pointing out the major advantages/drawbacks. We also report a summary of the most recent applications of third-generation sequencing platforms. This assessment provides a guided indication – with particular emphasis on human genetics and copy number variants – for researchers involved in the investigation of these genomic events.
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Affiliation(s)
- Lorenzo Tattini
- Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence , Florence , Italy
| | - Romina D'Aurizio
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council , Pisa , Italy
| | - Alberto Magi
- Department of Clinical and Experimental Medicine, University of Florence , Florence , Italy
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44
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Milner LC, Garrison NA, Cho MK, Altman RB, Hudgins L, Galli SJ, Lowe HJ, Schrijver I, Magnus DC. Genomics in the clinic: ethical and policy challenges in clinical next-generation sequencing programs at early adopter USA institutions. Per Med 2015; 12:269-282. [PMID: 29771644 DOI: 10.2217/pme.14.88] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Next-generation sequencing (NGS) technologies are poised to revolutionize clinical diagnosis and treatment, but raise significant ethical and policy challenges. This review examines NGS program challenges through a synthesis of published literature, website and conference presentation content, and interviews at early-adopting institutions in the USA. Institutions are proactively addressing policy challenges related to the management and technical aspects of program development. However, ethical challenges related to patient-related aspects have not been fully addressed. These complex challenges present opportunities to develop comprehensive and standardized regulations across programs. Understanding the strengths, weaknesses and current practices of evolving NGS program approaches are important considerations for institutions developing NGS services, policymakers regulating or funding NGS programs and physicians and patients considering NGS services.
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Affiliation(s)
- Lauren C Milner
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nanibaa' A Garrison
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA.,Center for Biomedical Ethics & Society, Departments of Pediatrics & Anthropology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen J Galli
- Stanford Center for Genomics & Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Henry J Lowe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Iris Schrijver
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Center for Genomics & Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David C Magnus
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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45
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Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses. Virchows Arch 2015; 467:203-10. [PMID: 25838078 DOI: 10.1007/s00428-015-1765-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/12/2015] [Accepted: 03/19/2015] [Indexed: 01/25/2023]
Abstract
Desmoid-type fibromatoses are locally aggressive and frequently recurrent tumours, and an accurate diagnosis is essential for patient management. The majority of sporadic lesions harbour beta-catenin (CTNNB1) mutations. We used next-generation sequencing to detect CTNNB1 mutations and to compare the sensitivity and specificity of next-generation sequencing with currently employed mutation detection techniques: mutation-specific restriction enzyme digestion and polymerase chain reaction amplification. DNA was extracted from formalin-fixed paraffin-embedded needle biopsy or resection tissue sections from 144 patients with sporadic desmoid-type fibromatoses, four patients with syndrome-related desmoid-type fibromatoses and 11 morphological mimics. Two primer pairs were designed for CTNNB1 mutation hotspots. Using ≥10 ng of DNA, libraries were generated by Fluidigm and sequenced on the Ion Torrent Personal Genome Machine. Next-generation sequencing had a sensitivity of 92.36 % (133/144, 95 % CIs: 86.74 to 96.12 %) and a specificity of 100 % for the detection of CTNNB1 mutations in desmoid-type fibromatoses-like spindle cell lesions. All mutations detected by mutation-specific restriction enzyme digestion were identified by next-generation sequencing. Next-generation sequencing identified additional mutations in 11 tumours that were not detected by mutation-specific restriction enzyme digestion, two of which have not been previously described. Next-generation sequencing is highly sensitive for the detection of CTNNB1 mutations. This multiplex assay has the advantage of detecting additional mutations compared to those detected by mutation-specific restriction enzyme digestion (sensitivity 82.41 %). The technology requires minimal DNA and is time- and cost-efficient.
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Savarese M, Di Fruscio G, Tasca G, Ruggiero L, Janssens S, De Bleecker J, Delpech M, Musumeci O, Toscano A, Angelini C, Sacconi S, Santoro L, Ricci E, Claes K, Politano L, Nigro V. Next generation sequencing on patients with LGMD and nonspecific myopathies: Findings associated with ANO5 mutations. Neuromuscul Disord 2015; 25:533-41. [PMID: 25891276 PMCID: PMC4502439 DOI: 10.1016/j.nmd.2015.03.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/24/2015] [Accepted: 03/25/2015] [Indexed: 11/30/2022]
Abstract
We studied 786 undiagnosed patients with LGMD or nonspecific myopathic features to investigate the role of ANO5 mutations in limb-girdle muscular dystrophies (LGMDs) and in nonspecific myopathies using the next generation sequencing (NGS) approach. In 160 LGMD patients, we first sequenced hotspot exons 5 and 20 and then sequenced the remaining part of the coding region. Another 626 patients, recruited using broader inclusion criteria, were directly analyzed by targeted NGS. By combining NGS and Sanger sequencing, we identified 33/786 (4%) patients carrying putative pathogenic changes in both alleles and 23 ANO5 heterozygotes (3%). The phenotypic spectrum is broader than expected, from hyperCKemia to myopathies, with lack of genotype/phenotype correlations. In particular, this is currently the largest screening of the ANO5 gene. The large number of heterozygotes for damaging mutations suggests that anoctaminopathies should be frequent and often nonpenetrant. We propose the multiple genetic testing by targeted NGS as a first step to analyze patients with nonspecific myopathic presentations. This represents a straightforward approach to overcome the difficulties of clinical heterogeneity of ANO5 patients, and to test, at the same time, many other genes involved in neuromuscular disorders.
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Affiliation(s)
- Marco Savarese
- Telethon Institute of Genetics and Medicine, Pozzuoli (NA), Italy; Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Napoli, Italy
| | - Giuseppina Di Fruscio
- Telethon Institute of Genetics and Medicine, Pozzuoli (NA), Italy; Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Napoli, Italy
| | | | - Lucia Ruggiero
- Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Università di Napoli "Federico II", Napoli, Italy
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Jan De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - Marc Delpech
- Biochimie et génétique moléculaire, Centre hospitalier Cochin, Paris, France
| | - Olimpia Musumeci
- Dipartimento di Neuroscienze, Università di Messina, Messina, Italy
| | - Antonio Toscano
- Dipartimento di Neuroscienze, Università di Messina, Messina, Italy
| | - Corrado Angelini
- Dipartimento di Neuroscienze, Università di Padova, Padova, Italy
| | - Sabrina Sacconi
- Centre de Référence Maladies Neuromusculaires - SLA, Hôpital Archet 1, CHU de Nice, Nice, France
| | - Lucio Santoro
- Dipartimento di Neuroscienze e Scienze riproduttive ed odontostomatologiche, Università di Napoli "Federico II", Napoli, Italy
| | | | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Luisa Politano
- Dipartimento di Medicina Sperimentale, Seconda Università di Napoli, Napoli, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli (NA), Italy; Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università di Napoli, Napoli, Italy.
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Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J, Cogulu O. Evolution of genetic techniques: past, present, and beyond. BIOMED RESEARCH INTERNATIONAL 2015; 2015:461524. [PMID: 25874212 PMCID: PMC4385642 DOI: 10.1155/2015/461524] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 12/05/2022]
Abstract
Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.
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Affiliation(s)
- Asude Alpman Durmaz
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology, Warsaw University Faculty of Medicine, 61 02-091 Warsaw, Poland
| | - Gokce Toruner
- Institute of Genomic Medicine, UMDNJ-NJ Medical School, Newark, NJ 07103, USA
| | - Jacqueline Schoumans
- Department of Medical Genetics, Cancer Cytogenetic Unit, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ozgur Cogulu
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
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48
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Yoon KL. Update of genetic susceptibility in patients with Kawasaki disease. KOREAN JOURNAL OF PEDIATRICS 2015; 58:84-8. [PMID: 25861330 PMCID: PMC4388975 DOI: 10.3345/kjp.2015.58.3.84] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/20/2015] [Indexed: 12/23/2022]
Abstract
Kawasaki disease (KD) is an acute systemic vasculitis that predominantly affects children, and can result in coronary artery lesions (CAL). A patient with KD who is resistant to treatment with intravenous immunoglobulin (IVIG) has a higher risk of developing CAL. Incomplete KD has increased in prevalence in recent years, and is another risk factor for the development of CAL. Although the pathogenesis of KD remains unclear, there has been increasing evidence for the role of genetic susceptibility to the disease since it was discovered in 1967. We retrospectively reviewed previous genetic research for known susceptibility genes in the pathogenesis of KD, IVIG resistance, and the development of CAL. This review revealed numerous potential susceptibility genes including genetic polymorphisms of ITPKC, CASP3, the transforming growth factor-β signaling pathway, B lymphoid tyrosine kinase, FCGR2A, KCNN2, and other genes, an imbalance of Th17/Treg, and a range of suggested future treatment options. The results of genetic research may improve our understanding of the pathogenesis of KD, and aid in the discovery of new treatment modalities for high-risk patients with KD.
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Affiliation(s)
- Kyung Lim Yoon
- Department of Pediatrics, Kyung Hee University Hospital at Gangdong, Seoul, Korea
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Kelly BJ, Fitch JR, Hu Y, Corsmeier DJ, Zhong H, Wetzel AN, Nordquist RD, Newsom DL, White P. Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics. Genome Biol 2015; 16:6. [PMID: 25600152 PMCID: PMC4333267 DOI: 10.1186/s13059-014-0577-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/23/2014] [Indexed: 12/18/2022] Open
Abstract
While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter White
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus 43205, OH, USA.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio, USA
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50
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Black JS, Salto-Tellez M, Mills KI, Catherwood MA. The impact of next generation sequencing technologies on haematological research – A review. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pathog.2015.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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