1
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Srivathsan A, Meier R. Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing. Methods Mol Biol 2024; 2744:223-238. [PMID: 38683322 DOI: 10.1007/978-1-0716-3581-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.
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Affiliation(s)
- Amrita Srivathsan
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.
- Institute for Biology, Humboldt University, Berlin, Germany.
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2
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Cheng J, Siejka-Zielińska P, Liu Y, Chandran A, Kriaucionis S, Song CX. Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection. Nucleic Acids Res 2021; 49:e76. [PMID: 33905495 PMCID: PMC8287915 DOI: 10.1093/nar/gkab291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
Whole genome base-resolution methylome sequencing allows for the most comprehensive analysis of DNA methylation, however, the considerable sequencing cost often limits its applications. While reduced representation sequencing can be an affordable alternative, over 80% of CpGs in the genome are not covered. Building on our recently developed TET-assisted pyridine borane sequencing (TAPS) method, we here described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-cleaving endonuclease digestion of TAPS-converted DNA to enrich methylated CpG sites (mCpGs). eeTAPS can accurately detect 87% of mCpGs in the mouse genome with a sequencing depth equivalent to 4× whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of mCpGs with 2.5× sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.
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Affiliation(s)
- Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paulina Siejka-Zielińska
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Anandhakumar Chandran
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Skirmantas Kriaucionis
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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3
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Abstract
The introduction of next generation sequencing (NGS; also known as massively parallel sequencing) technology in the field of forensic genetics has been welcomed by the scientific community, above all because it complements the weaknesses of capillary electrophoresis (CE) in the analysis of genetic markers, such as single nucleotide polymorphism (SNP) typing. However, one of the main obstacles to its adoption does not seem to be the cost of the instrumentation, but rather the cost of the NGS library preparation kits. With the aim of reducing the cost of library preparation without compromising the quality of the results, we tried to scale down reaction volumes for the first two polymerase chain reactions in the amplification and enrichment phases of the targeted loci of library preparation using the ForenSeq™ DNA Signature Prep kit. We used 1 µL templated DNA input to a concentration of 1 ng/µL, instead of the 5 µL at 0.2 ng/µL recommended by the manufacturer. Our findings indicate that reduction of the library preparation volume using the ForenSeq™ DNA Signature Prep kit did not interfere with the quality and reproducibility of the DNA profiles obtained and can help lower the overall cost of NGS.
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Affiliation(s)
- Stefania Turrina
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
| | - Domenico De Leo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine - Forensic Genetics Laboratory, University of Verona, Italy
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4
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Zhou K, Mo Q, Guo S, Liu Y, Yin C, Ji X, Guo X, Xing J. A Novel Next-Generation Sequencing-Based Approach for Concurrent Detection of Mitochondrial DNA Copy Number and Mutation. J Mol Diagn 2020; 22:1408-1418. [PMID: 33011442 DOI: 10.1016/j.jmoldx.2020.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/17/2020] [Accepted: 09/03/2020] [Indexed: 01/06/2023] Open
Abstract
Numerous studies have identified essential contributions of altered mitochondrial DNA (mtDNA) copy number and mutations in many common disorders, including cancer. To date, capture-based next-generation sequencing (NGS) has been widely applied to detect mtDNA mutations, although it lacks the ability to assess mtDNA copy number. The current strategy for quantifying mtDNA copy number relies mainly on real-time quantitative PCR, which is limited in degraded samples. A novel capture-based NGS approach was developed using both mtDNA and nuclear DNA probes to capture target fragments, enabling simultaneous detection of mtDNA mutations and copy number in different sample types. First, the impact of selecting reference genes on mtDNA copy number calculation was evaluated, and finally, 3 nuclear DNA fragments of 4000 bp were selected as an internal reference for detection. Then, the effective application of this approach was verified in DNA samples of formalin-fixed, paraffin-embedded specimens and body fluids, indicating the widespread applicability. This approach showed more accurate and stable results in detecting mtDNA copy number compared with real-time quantitative PCR in degraded DNA samples. Moreover, data indicated this approach had good reproducibility in detecting both mtDNA copy number and mutations among three sample types. Altogether, a versatile and cost-effective capture-based NGS approach has been developed for concurrent detection of mtDNA copy number and mutations, which has numerous applications in research and diagnosis.
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Affiliation(s)
- Kaixiang Zhou
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Qinqin Mo
- Department of Laboratory Medicine, Medical College of Yanan University, Yan'an, China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Yang Liu
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Chun Yin
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xiaoying Ji
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Xu Guo
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, China.
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5
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Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 PMCID: PMC7272069 DOI: 10.1371/journal.pone.0233800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 12/14/2022] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Georgios Joannis Pappas
- Department of Cell Biology, University of Brasília, Brasília, Distrito Federal, Brazil
- * E-mail:
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6
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Pereira WJ, Pappas MDCR, Grattapaglia D, Pappas GJ. A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing. PLoS One 2020; 15:e0233800. [PMID: 32497070 DOI: 10.1371/journal.pone.00233800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 05/27/2023] Open
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
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Affiliation(s)
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
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Meyer F, Bagchi S, Chaterji S, Gerlach W, Grama A, Harrison T, Paczian T, Trimble WL, Wilke A. MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. Brief Bioinform 2020; 20:1151-1159. [PMID: 29028869 DOI: 10.1093/bib/bbx105] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/21/2017] [Indexed: 11/12/2022] Open
Abstract
As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline. Currently, we use well-understood data sets in MG-RAST as platform for benchmarking. The use of artificial data sets for pipeline performance optimization has not added value, as these data sets are not presenting the same challenges as real-world data sets. In addition, the MG-RAST team welcomes suggestions for improvements of the workflow. We are currently working on versions 4.02 and 4.1, both of which contain significant input from the community and our partners that will enable double barcoding, stronger inferences supported by longer-read technologies, and will increase throughput while maintaining sensitivity by using Diamond and SortMeRNA. On the technical platform side, the MG-RAST team intends to support the Common Workflow Language as a standard to specify bioinformatics workflows, both to facilitate development and efficient high-performance implementation of the community's data analysis tasks.
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8
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Krych Ł, Castro-Mejía JL, Forero-Junco LM, Moesby DN, Mikkelsen MB, Rasmussen MA, Sykulski M, Nielsen DS. DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq. Commun Biol 2019; 2:369. [PMID: 31633060 PMCID: PMC6787052 DOI: 10.1038/s42003-019-0617-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 09/17/2019] [Indexed: 11/10/2022] Open
Abstract
Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.
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Affiliation(s)
- Łukasz Krych
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- GenXone S.A., 60-476 Poznań, Poland
| | - Josué L. Castro-Mejía
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Laura M. Forero-Junco
- Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Daniel N. Moesby
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten B. Mikkelsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten A. Rasmussen
- Chemometrics and Analytical Technology, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S. Nielsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
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9
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De Maio N, Shaw LP, Hubbard A, George S, Sanderson ND, Swann J, Wick R, AbuOun M, Stubberfield E, Hoosdally SJ, Crook DW, Peto TEA, Sheppard AE, Bailey MJ, Read DS, Anjum MF, Walker AS, Stoesser N. Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microb Genom 2019; 5:e000294. [PMID: 31483244 PMCID: PMC6807382 DOI: 10.1099/mgen.0.000294] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/19/2019] [Indexed: 01/23/2023] Open
Abstract
Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strategies, as well as comparing to long-read-only assembly with Flye followed by short-read polishing with Pilon. Hybrid assembly with either PacBio or ONT reads facilitated high-quality genome reconstruction, and was superior to the long-read assembly and polishing approach evaluated with respect to accuracy and completeness. Combining ONT and Illumina reads fully resolved most genomes without additional manual steps, and at a lower consumables cost per isolate in our setting. Automated hybrid assembly is a powerful tool for complete and accurate bacterial genome assembly.
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Affiliation(s)
- Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Liam P. Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alasdair Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | | | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ryan Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | | | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Mark J. Bailey
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Daniel S. Read
- Centre for Ecology & Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, Surrey, KT15 3NB, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Colman RE, Mace A, Seifert M, Hetzel J, Mshaiel H, Suresh A, Lemmer D, Engelthaler DM, Catanzaro DG, Young AG, Denkinger CM, Rodwell TC. Whole-genome and targeted sequencing of drug-resistant Mycobacterium tuberculosis on the iSeq100 and MiSeq: A performance, ease-of-use, and cost evaluation. PLoS Med 2019; 16:e1002794. [PMID: 31039166 PMCID: PMC6490892 DOI: 10.1371/journal.pmed.1002794] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Accurate, comprehensive, and timely detection of drug-resistant tuberculosis (TB) is essential to inform patient treatment and enable public health surveillance. This is crucial for effective control of TB globally. Whole-genome sequencing (WGS) and targeted next-generation sequencing (NGS) approaches have potential as rapid in vitro diagnostics (IVDs), but the complexity of workflows, interpretation of results, high costs, and vulnerability of instrumentation have been barriers to broad uptake outside of reference laboratories, especially in low- and middle-income countries. A new, solid-state, tabletop sequencing instrument, Illumina iSeq100, has the potential to decentralize NGS for individual patient care. METHODS AND FINDINGS In this study, we evaluated WGS and targeted NGS for TB on both the new iSeq100 and the widely used MiSeq (both manufactured by Illumina) and compared sequencing performance, costs, and usability. We utilized DNA libraries produced from Mycobacterium tuberculosis clinical isolates for the evaluation. We conducted WGS on three strains and observed equivalent uniform genome coverage with both platforms and found the depth of coverage obtained was consistent with the expected data output. Utilizing the standardized, cloud-based ReSeqTB bioinformatics pipeline for variant analysis, we found the two platforms to have 94.0% (CI 93.1%-94.8%) agreement, in comparison to 97.6% (CI 97%-98.1%) agreement for the same libraries on two MiSeq instruments. For the targeted NGS approach, 46 M. tuberculosis-specific amplicon libraries had 99.6% (CI 98.0%-99.9%) agreement between the iSeq100 and MiSeq data sets in drug resistance-associated SNPs. The upfront capital costs are almost 5-fold lower for the iSeq100 ($19,900 USD) platform in comparison to the MiSeq ($99,000 USD); however, because of difference in the batching capabilities, the price per sample for WGS was higher on the iSeq100. For WGS of M. tuberculosis at the minimum depth of coverage of 30x, the cost per sample on the iSeq100 was $69.44 USD versus $28.21 USD on the MiSeq, assuming a 2 × 150 bp run on a v3 kit. In terms of ease of use, the sequencing workflow of iSeq100 has been optimized to only require 27 minutes total of hands-on time pre- and post-run, and the maintenance is simplified by a single-use cartridge-based fluidic system. As these are the first sequencing attempts on the iSeq100 for M. tuberculosis, the sequencing pool loading concentration still needs optimization, which will affect sequencing error and depth of coverage. Additionally, the costs are based on current equipment and reagent costs, which are subject to change. CONCLUSIONS The iSeq100 instrument is capable of running existing TB WGS and targeted NGS library preparations with comparable accuracy to the MiSeq. The iSeq100 has reduced sequencing workflow hands-on time and is able to deliver sequencing results in <24 hours. Reduced capital and maintenance costs and lower-throughput capabilities also give the iSeq100 an advantage over MiSeq in settings of individualized care but not in high-throughput settings such as reference laboratories, where sample batching can be optimized to minimize cost at the expense of workflow complexity and time.
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Affiliation(s)
- Rebecca E. Colman
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
- * E-mail:
| | - Aurélien Mace
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
| | - Marva Seifert
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - Jonathan Hetzel
- Illumina Inc., San Diego, California, United States of America
| | - Haifa Mshaiel
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
| | - Anita Suresh
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Donald G. Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Amanda G. Young
- Illumina Inc., San Diego, California, United States of America
| | | | - Timothy C. Rodwell
- Foundation for Innovative New Diagnostics, Campus Biotech, Geneva, Switzerland
- Department of Medicine, University of California, San Diego, San Diego, California, United States of America
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11
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Paajanen P, Kettleborough G, López-Girona E, Giolai M, Heavens D, Baker D, Lister A, Cugliandolo F, Wilde G, Hein I, Macaulay I, Bryan GJ, Clark MD. A critical comparison of technologies for a plant genome sequencing project. Gigascience 2019; 8:giy163. [PMID: 30624602 PMCID: PMC6423373 DOI: 10.1093/gigascience/giy163] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 09/26/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND A high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read-only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates. RESULTS Here, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs. CONCLUSIONS The field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.
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Affiliation(s)
- Pirita Paajanen
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - George Kettleborough
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Elena López-Girona
- Cell and Molcular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North 4442, New Zealand
| | - Michael Giolai
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Darren Heavens
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - David Baker
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ashleigh Lister
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Fiorella Cugliandolo
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Gail Wilde
- Cell and Molcular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Ingo Hein
- Cell and Molcular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Iain Macaulay
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Glenn J Bryan
- Cell and Molcular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Matthew D Clark
- Technology Development, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London WC2 5BD, UK
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12
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Abstract
Attention has been focused on the field of genetics and genomics in Iran in recent years and some efforts have been enforced and implemented. However, they are totally not adequate, considering the advances in medical genetics and genomics in the past two decades around the world. Overall, considering the lack of medical genetics residency programs in the Iranian health education system, big demand due to high consanguinity and intraethnic marriages, there is a lag in genetic services and necessity to an immediate response to fill this big gap in Iran. As clarified in the National constitution fundamental law and re-emphasized in the 6th National Development Plan, the Iranian government authority is in charge of providing the standard level of health including genetic services to all Iranian individuals who are in need.
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MESH Headings
- Databases, Genetic
- Facilities and Services Utilization
- Genetic Diseases, Inborn/diagnosis
- Genetic Diseases, Inborn/epidemiology
- Genetic Diseases, Inborn/genetics
- Genetic Testing/economics
- Genetic Testing/legislation & jurisprudence
- Genetic Testing/statistics & numerical data
- Genetics, Medical/economics
- Genetics, Medical/legislation & jurisprudence
- Genetics, Medical/organization & administration
- Genetics, Medical/statistics & numerical data
- Humans
- Iran
- Prenatal Diagnosis/economics
- Prenatal Diagnosis/statistics & numerical data
- Sequence Analysis, DNA/economics
- Sequence Analysis, DNA/statistics & numerical data
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Affiliation(s)
- Babak Behnam
- Department of Medical Genetics and Molecular BiologyCollege of MedicineIran University of Medical Sciences (IUMS)TehranIran
| | - Maryam Zakeri
- Non‐Communicable Disease (NCD) GroupDepartment of HealthHormozgan University of Medical SciencesBandarabbasIran
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13
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Gao M, Callari M, Beddowes E, Sammut SJ, Grzelak M, Biggs H, Jones L, Boumertit A, Linn SC, Cortes J, Oliveira M, Baird R, Chin SF, Caldas C. Next Generation-Targeted Amplicon Sequencing (NG-TAS): an optimised protocol and computational pipeline for cost-effective profiling of circulating tumour DNA. Genome Med 2019; 11:1. [PMID: 30609936 PMCID: PMC6320579 DOI: 10.1186/s13073-018-0611-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023] Open
Abstract
Circulating tumour DNA (ctDNA) detection and monitoring have enormous potential clinical utility in oncology. We describe here a fast, flexible and cost-effective method to profile multiple genes simultaneously in low input cell-free DNA (cfDNA): Next Generation-Targeted Amplicon Sequencing (NG-TAS). We designed a panel of 377 amplicons spanning 20 cancer genes and tested the NG-TAS pipeline using cell-free DNA from two HapMap lymphoblastoid cell lines. NG-TAS consistently detected mutations in cfDNA when mutation allele fraction was > 1%. We applied NG-TAS to a clinical cohort of metastatic breast cancer patients, demonstrating its potential in monitoring the disease. The computational pipeline is available at https://github.com/cclab-brca/NGTAS_pipeline .
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Affiliation(s)
- Meiling Gao
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Maurizio Callari
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Emma Beddowes
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Stephen-John Sammut
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Marta Grzelak
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Heather Biggs
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Linda Jones
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Abdelhamid Boumertit
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Sabine C. Linn
- Netherland Cancer Institute, 1006 BE Amsterdam, Netherlands
| | - Javier Cortes
- Ramon y Cajal University Hospital, 28034 Madrid, Spain
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | | | - Richard Baird
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE UK
- Breast Cancer Programme, Cancer Research UK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 2QQ UK
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14
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Yu TM, Morrison C, Gold EJ, Tradonsky A, Arnold RJG. Budget Impact of Next-Generation Sequencing for Molecular Assessment of Advanced Non-Small Cell Lung Cancer. Value Health 2018; 21:1278-1285. [PMID: 30442274 DOI: 10.1016/j.jval.2018.04.1372] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 03/27/2018] [Accepted: 04/02/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Genetic testing for nonsquamous advanced non-small cell lung cancer (aNSCLC) is recommended to guide first-line therapy. Activating mutations can be identified via single-gene testing or next-generation sequencing (NGS). OBJECTIVES To evaluate the budget impact of NGS instead of single-gene testing for tissue-based molecular assessment of aNSCLC from the US health care payer perspective. METHODS An annual cohort of newly diagnosed patients with nonsquamous aNSCLC in a hypothetical 1-million-member health care plan was evaluated using a Markov model over 5 years. Epidemiology and testing rates (EGFR, ALK, ROS1, BRAF, MET, HER2, and RET) were from the literature. Treatments were determined by available genetic information. Safety, progression, and survival with targeted therapy or chemotherapy were from randomized clinical trials. Single-gene testing and first-line and maintenance treatment costs were from RED BOOK and Medicare fee schedules; NGS testing, adverse event, and progression costs to payers were from the literature. RESULTS Three hundred sixteen testing-eligible patients with aNSCLC were expected annually, of whom 179 undergo genetic testing. Of 57 patients expected to have activating mutations, single-gene testing identified 35, whereas NGS identified 54. NGS, instead of single-gene testing, decreased expected testing procedure-related costs to the health plan payer by $24,651. First-line and maintenance treatment costs increased by $842,205, offset by a $385,000 decrease in second-line treatment and palliative care costs. Over 5 years, total budget impact was $432,554 ($0.0072 per member per month). CONCLUSIONS NGS is expected to identify more patients with activating mutations, thereby better enabling selection for targeted therapy and clinical trial enrollment. The budget impact to US payers is expected to be minimally cost-additive.
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Affiliation(s)
- Tiffany M Yu
- Navigant Consulting, Inc., San Francisco, CA, USA.
| | | | | | | | - Renée J G Arnold
- Navigant Consulting, Inc., San Francisco, CA, USA; Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Pel J, Choi WWY, Leung A, Shibahara G, Gelinas L, Despotovic M, Ung WL, Marziali A. Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy. PLoS One 2018; 13:e0204265. [PMID: 30278055 PMCID: PMC6168144 DOI: 10.1371/journal.pone.0204265] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 01/15/2023] Open
Abstract
A challenge in the clinical adoption of cell-free DNA (cfDNA) liquid biopsies for cancer care is their high cost compared to potential reimbursement. The most common approach used in liquid biopsies to achieve high specificity detection of circulating tumor DNA (ctDNA) among a large background of normal cfDNA is to attach molecular barcodes to each DNA template, amplify it, and then sequence it many times to reach a low-error consensus. In applications where the highest possible specificity is required, error rate can be lowered further by independently detecting the sequences of both strands of the starting cfDNA. While effective in error reduction, the additional sequencing redundancy required by such barcoding methods can increase the cost of sequencing up to 100-fold over standard next-generation sequencing (NGS) of equivalent depth. We present a novel library construction and analysis method for NGS that achieves comparable performance to the best barcoding methods, but without the increase in sequencing and subsequent sequencing cost. Named Proximity-Sequencing (Pro-Seq), the method merges multiple copies of each template into a single sequencing read by physically linking the molecular copies so they seed a single sequencing cluster. Since multiple DNA copies of the same template are compared for consensus within the same cluster, sequencing accuracy is improved without the use of redundant reads. Additionally, it is possible to represent both senses of the starting duplex in a single cluster. The resulting workflow is simple, and can be completed by a single technician in a work day with minimal hands on time. Using both cfDNA and cell line DNA, we report the average per-mutation detection threshold and per-base analytical specificity to be 0.003% and >99.9997% respectively, demonstrating that Pro-Seq is among the highest performing liquid biopsy technologies in terms of both sensitivity and specificity, but with greatly reduced sequencing costs compared to existing methods of comparable accuracy.
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Affiliation(s)
- Joel Pel
- Boreal Genomics Inc., Vancouver, British Columbia, Canada
| | | | - Amy Leung
- Boreal Genomics Inc., Vancouver, British Columbia, Canada
| | | | - Laura Gelinas
- Boreal Genomics Inc., Vancouver, British Columbia, Canada
| | | | - W. Lloyd Ung
- Boreal Genomics Inc., Vancouver, British Columbia, Canada
| | - Andre Marziali
- Boreal Genomics Inc., Vancouver, British Columbia, Canada
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
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16
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Affiliation(s)
- David H Spencer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, The McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri
| | - Timothy J Ley
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, The McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri
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17
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Marino P, Touzani R, Perrier L, Rouleau E, Kossi DS, Zhaomin Z, Charrier N, Goardon N, Preudhomme C, Durand-Zaleski I, Borget I, Baffert S. Cost of cancer diagnosis using next-generation sequencing targeted gene panels in routine practice: a nationwide French study. Eur J Hum Genet 2018; 26:314-323. [PMID: 29367707 PMCID: PMC5838982 DOI: 10.1038/s41431-017-0081-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/21/2017] [Accepted: 12/05/2017] [Indexed: 12/25/2022] Open
Abstract
It is currently unclear if next-generation sequencing (NGS) technologies can be implemented in the diagnosis setting at an affordable cost. The aim of this study was to measure the total cost of performing NGS in clinical practice in France, in both germline and somatic cancer genetics.The study was performed on 15 French representative cancer molecular genetics laboratories performing NGS panels' tests. The production cost was estimated using a micro-costing method with resources consumed collected in situ in each laboratory from a healthcare provider perspective. In addition, we used a top-down methodology for specific post-sequencing steps including bioinformatics, technical validation, and biological validation. Additional non-specific costs were also included. Costs were detailed per step of the process (from the pre-analytical phase to delivery of results), and per cost driver (consumables, staff, equipment, maintenance, overheads). Sensitivity analyses were performed.The mean total cost of NGS for targeted gene panels was estimated to 607€ (±207) in somatic genetics and 550€ (±140) in germline oncogenetic analysis. Consumables were the highest cost driver of the sequencing process. The sensitivity analysis showed that a 25% reduction of consumables resulted in a 15% decrease in total NGS cost in somatic genetics, and 13% in germline analysis. Additional costs accounted for 30-32% of the total NGS costs.Beyond cost assessment considerations, the diffusion of NGS technologies will raise questions about their efficiency when compared to more targeted approaches, and their added value in a context of routine diagnosis.
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Affiliation(s)
- Patricia Marino
- Institut Paoli Calmettes, SESSTIM, Marseille, France.
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Aix Marseille Univ, Marseille, France.
| | - Rajae Touzani
- Institut Paoli Calmettes, SESSTIM, Marseille, France
- INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, Aix Marseille Univ, Marseille, France
| | - Lionel Perrier
- Léon Berard Cancer Centre, GATE L-SE, UMR-CNRS 5824, Lyon, France
| | - Etienne Rouleau
- Department of Pathology and Medical Biology, Gustave Roussy, Villejuif, France
| | | | - Zou Zhaomin
- Gustave Roussy, Etudes et Recherche en économie de la santé, Villejuif, France
| | | | - Nicolas Goardon
- Cancer Comprehensive Center François Baclesse, Cancer Biology and Genetics Laboratory, Caen, France
| | - Claude Preudhomme
- CHRU of Lille, Biology & Pathology Center, Laboratory of Hematology, Lille, France
| | | | - Isabelle Borget
- Gustave Roussy, Etudes et Recherche en économie de la santé, Villejuif, France
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18
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Affiliation(s)
- Julian Barwell
- University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 5WW, UK
- University of Leicester, Department of Cancer Studies & Molecular Medicine, Leicester LE1 7RH, UK
| | - Jacqui Shaw
- University of Leicester, Department of Cancer Studies & Molecular Medicine, Leicester LE1 7RH, UK
| | - Ming Lim
- University of Liverpool, Management School, Foundation Building, Brownlow Hill, Liverpool L69 7ZX, UK
| | - Riddhi Y Shukla
- University of Leicester, Department of Cancer Studies & Molecular Medicine, Leicester LE1 7RH, UK
| | - Joanna Lowry
- University Hospitals of Leicester, Leicester Royal Infirmary, Leicester LE1 5WW, UK
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20
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Abstract
BACKGROUND Alpha-1 antitrypsin deficiency (AATD) is a genetic condition characterized by low serum levels of the protein alpha-1 antitrypsin. Because there are no unique clinical symptoms that point to a definitive diagnosis of AATD, laboratory testing is crucial to differentiate this disease from others. OBJECTIVE To summarize advances in laboratory techniques used to test for AATD. METHODS Data were sourced from a nonsystematic literature review of MEDLINE and the author's personal literature collection, and by checking reference lists of sourced articles. RESULTS Since the original description of AATD by Laurell and Eriksson in 1963, testing methods have undergone major changes. Currently, alpha-1 antitrypsin protein is quantified by immunologic measurement in serum, and the phenotype is characterized by isoelectric focusing and/or targeted genotyping of predefined mutations. In addition, whole-gene sequencing of the gene SERPINA1 can be undertaken. However, this is costly and generally used only if targeted genotyping cannot conclusively identify the variant. The introduction of next-generation sequencing (NGS), which enables rapid and accurate sequencing of large quantities of DNA fragments in a single reaction, may help reduce costs. With its increasing availability, NGS may begin to appear in testing protocols. Clinical guidelines recommend that patients are tested for AATD if they have chronic irreversible airflow obstruction, especially those with early onset disease or a positive family history of AATD. Despite this, AATD is still underrecognized, and significant delays exist between symptom onset and diagnosis. CONCLUSION Traditional testing practices have limitations. Screening programs that incorporate NGS are the most comprehensive methods available for accurate diagnosis of AATD.
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Abstract
We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4–5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms.
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Affiliation(s)
- Joaquin C. B. Nunez
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, Department of Marine Biology and Ecology, Miami, Florida, United States of America
| | - Marjorie F. Oleksiak
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, Department of Marine Biology and Ecology, Miami, Florida, United States of America
- * E-mail:
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22
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Chen YE, Kao SS, Chung RH. Cost-Effectiveness Analysis of Different Genetic Testing Strategies for Lynch Syndrome in Taiwan. PLoS One 2016; 11:e0160599. [PMID: 27482709 PMCID: PMC4970721 DOI: 10.1371/journal.pone.0160599] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/21/2016] [Indexed: 01/01/2023] Open
Abstract
Patients with Lynch syndrome (LS) have a significantly increased risk of developing colorectal cancer (CRC) and other cancers. Genetic screening for LS among patients with newly diagnosed CRC aims to identify mutations in the disease-causing genes (i.e., the DNA mismatch repair genes) in the patients, to offer genetic testing for relatives of the patients with the mutations, and then to provide early prevention for the relatives with the mutations. Several genetic tests are available for LS, such as DNA sequencing for MMR genes and tumor testing using microsatellite instability and immunohistochemical analyses. Cost-effectiveness analyses of different genetic testing strategies for LS have been performed in several studies from different countries such as the US and Germany. However, a cost-effectiveness analysis for the testing has not yet been performed in Taiwan. In this study, we evaluated the cost-effectiveness of four genetic testing strategies for LS described in previous studies, while population-specific parameters, such as the mutation rates of the DNA mismatch repair genes and treatment costs for CRC in Taiwan, were used. The incremental cost-effectiveness ratios based on discounted life years gained due to genetic screening were calculated for the strategies relative to no screening and to the previous strategy. Using the World Health Organization standard, which was defined based on Taiwan’s Gross Domestic Product per capita, the strategy based on immunohistochemistry as a genetic test followed by BRAF mutation testing was considered to be highly cost-effective relative to no screening. Our probabilistic sensitivity analysis results also suggest that the strategy has a probability of 0.939 of being cost-effective relative to no screening based on the commonly used threshold of $50,000 to determine cost-effectiveness. To the best of our knowledge, this is the first cost-effectiveness analysis for evaluating different genetic testing strategies for LS in Taiwan. The results will be informative for the government when considering offering screening for LS in patients newly diagnosed with CRC.
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Affiliation(s)
- Ying-Erh Chen
- Department of Insurance, Tamkang University, Tamsui Dist., New Taipei City, 251, Taiwan
- * E-mail:
| | - Sung-Shuo Kao
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, 813, Taiwan
| | - Ren-Hua Chung
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, 350, Taiwan
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Sabatini LM, Mathews C, Ptak D, Doshi S, Tynan K, Hegde MR, Burke TL, Bossler AD. Genomic Sequencing Procedure Microcosting Analysis and Health Economic Cost-Impact Analysis: A Report of the Association for Molecular Pathology. J Mol Diagn 2016; 18:319-328. [PMID: 27080370 PMCID: PMC7212689 DOI: 10.1016/j.jmoldx.2015.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/13/2015] [Accepted: 11/13/2015] [Indexed: 01/07/2023] Open
Abstract
The increasing use of advanced nucleic acid sequencing technologies for clinical diagnostics and therapeutics has made vital understanding the costs of performing these procedures and their value to patients, providers, and payers. The Association for Molecular Pathology invested in a cost and value analysis of specific genomic sequencing procedures (GSPs) newly coded by the American Medical Association Current Procedural Terminology Editorial Panel. Cost data and work effort, including the development and use of data analysis pipelines, were gathered from representative laboratories currently performing these GSPs. Results were aggregated to generate representative cost ranges given the complexity and variability of performing the tests. Cost-impact models for three clinical scenarios were generated with assistance from key opinion leaders: impact of using a targeted gene panel in optimizing care for patients with advanced non-small-cell lung cancer, use of a targeted gene panel in the diagnosis and management of patients with sensorineural hearing loss, and exome sequencing in the diagnosis and management of children with neurodevelopmental disorders of unknown genetic etiology. Each model demonstrated value by either reducing health care costs or identifying appropriate care pathways. The templates generated will aid laboratories in assessing their individual costs, considering the value structure in their own patient populations, and contributing their data to the ongoing dialogue regarding the impact of GSPs on improving patient care.
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Affiliation(s)
- Linda M Sabatini
- Genomic Sequencing Procedures Pricing Project Oversight Committee, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois.
| | | | - Devon Ptak
- Boston Healthcare Associates, Boston, Massachusetts
| | | | | | - Madhuri R Hegde
- Genomic Sequencing Procedures Pricing Project Oversight Committee, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Bethesda, Maryland; Division of Medical Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Tara L Burke
- Association for Molecular Pathology, Bethesda, Maryland
| | - Aaron D Bossler
- Genomic Sequencing Procedures Pricing Project Oversight Committee, a Working Group of the Association for Molecular Pathology Economic Affairs Committee, Bethesda, Maryland; Department of Pathology, University of Iowa, Iowa City, Iowa
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Wade L. BRAIN DRAIN. Mexico struggles to woo expat genome jocks. Science 2016; 352:507. [PMID: 27126019 DOI: 10.1126/science.352.6285.507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Delaunay A, Dallot S, Filloux D, Dupuy V, Roumagnac P, Jacquot E. SNaPshot and CE-SSCP: Two Simple and Cost-Effective Methods to Reveal Genetic Variability Within a Virus Species. Methods Mol Biol 2016; 1302:187-206. [PMID: 25981256 DOI: 10.1007/978-1-4939-2620-6_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-stranded DNA, and (3) migration of fluorescent-labeled molecules in capillary electrophoresis system. The SNaPshot technology was used to describe the diversity of 20 targeted single nucleotide polymorphisms (SNPs) selected from alignment of viral genomic sequences retrieved from public database. The CE-SSCP procedure was applied to identify the polymorphisms of two small (<500 bases in length) genomic regions of viral genomes. The different steps of SNaPshot and CE-SSCP setup procedures are presented using Potato virus Y (PVY, Potyvirus) and Plum pox virus (PPV, Potyvirus) RNA viruses as molecular targets, respectively.
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Affiliation(s)
- Agnès Delaunay
- INRA-Cirad-Montpellier SupAgro, UMR 385 BGPI, Cirad TA A-54K, Montpellier cedex, 34398, France
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Inagaki S, Henry IM, Lieberman MC, Comai L. High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture. PLoS One 2015; 10:e0139672. [PMID: 26445462 PMCID: PMC4596565 DOI: 10.1371/journal.pone.0139672] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/16/2015] [Indexed: 01/19/2023] Open
Abstract
Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA—genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.
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Affiliation(s)
- Soichi Inagaki
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
- Department of Integrative Genetics, National Institute of Genetics, Mishima, Japan
| | - Isabelle M. Henry
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
| | - Meric C. Lieberman
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
| | - Luca Comai
- Plant Biology Department and Genome Center, University of California Davis, Davis, California, United States of America
- * E-mail:
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Tenedini E, Artuso L, Bernardis I, Artusi V, Percesepe A, De Rosa L, Contin R, Manfredini R, Pellacani G, Giannetti A, Pagani J, De Luca M, Tagliafico E. Amplicon-based next-generation sequencing: an effective approach for the molecular diagnosis of epidermolysis bullosa. Br J Dermatol 2015; 173:731-8. [PMID: 25913354 DOI: 10.1111/bjd.13858] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Epidermolysis bullosa (EB) is caused by mutations in genes that encode proteins belonging to the epidermal-dermal junction assembly. Due to the extreme clinical/genetic heterogeneity of the disease, the current methods available for diagnosing EB involve immunohistochemistry of biopsy samples and transmission electron microscopy followed by single-candidate gene Sanger sequencing (SS), which are labour-intensive and expensive clinical pathways. OBJECTIVES According to the recently published recommendations for the diagnosis and treatment of EB, the assessment of the mutational landscape is now a fundamental step for developing a comprehensive diagnostic path. We aimed to develop a customized, cost-effective amplicon panel for the complete and accurate sequencing of all the pathogenic genes already identified in EB, and to minimize the processing time required for the execution of the test and to refine the analysis pipeline to achieve cost-effective results from the perspective of a routine laboratory set-up. Next-generation sequencing (NGS) via the parallel ultra-deep sequencing of many genes represents a proper method for reducing the processing time and costs of EB diagnostics. MATERIALS AND METHODS We developed an EB disease-comprehensive AmpliSeq panel to accomplish the NGS on an Ion Torrent Personal Genome Machine platform. The panel was performed on 10 patients with known genetic diagnoses and was then employed in eight family trios with unknown molecular footprints. RESULTS The panel was successful in finding the causative mutations in all 10 patients with known mutations, fully confirming the SS data and providing proof of concept of the sensitivity, specificity and accuracy of this procedure. In addition to being consistent with the clinical diagnosis, it was also effective in the trios, identifying all of the variants, including ones that the SS missed or de novo mutations. CONCLUSIONS The NGS and AmpliSeq were shown to be an effective approach for the diagnosis of EB, resulting in a cost- and time-effective 72-h procedure.
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Affiliation(s)
- E Tenedini
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - L Artuso
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - I Bernardis
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - V Artusi
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - A Percesepe
- Department of Medical and Surgical Sciences for Children and Adults, Medical Genetics Unit, University Hospital of Modena, Largo del Pozzo 71, Modena, 41126, Italy
| | - L De Rosa
- Centre for Regenerative Medicine 'Stefano Ferrari', University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - R Contin
- Centre for Regenerative Medicine 'Stefano Ferrari', University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - R Manfredini
- Centre for Regenerative Medicine 'Stefano Ferrari', University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - G Pellacani
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplants, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - A Giannetti
- Emeritus of Dermatology, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - J Pagani
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - M De Luca
- Centre for Regenerative Medicine 'Stefano Ferrari', University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
| | - E Tagliafico
- Centre for Genome Research, University of Modena and Reggio Emilia, Via Campi 287, Modena, 41125, Italy
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Abstract
The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders.
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Affiliation(s)
- Lyn S Chitty
- UCL Institute of Child Health, Genetics and Genomic Medicine, London WC1N 1EH, United Kingdom; University College London Hospitals NHS Foundation Trust, London NW1 2PG, United Kingdom; NE Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, 37 Queen Square, London WC1N 3BH, United Kingdom
| | - Y M Dennis Lo
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong SAR, China
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Abstract
PURPOSE OF REVIEW Many international recommendations for the management of familial hypercholesterolaemia propose the use of cascade testing using the family mutation to unambiguously identify affected relatives. In the current economic climate DNA information is often regarded as too expensive. Here, we review the literature and suggest strategies to improve cost-effectiveness of cascade testing. RECENT FINDINGS Advances in next-generation sequencing have both speeded up the time taken for a genetic diagnosis and reduced costs. Also, it is now clear that, in the majority of patients with a clinical diagnosis of familial hypercholesterolaemia in whom no mutation can be found, the most likely cause of their elevated LDL-cholesterol (LDL-C) is because they have inherited a greater number than average of common LDL-C raising variants in many different genes. The major cost driver for cascade testing is not DNA testing but treatment over the remaining lifetime of the identified relative. With potent statins now off-patent, the overall cost has reduced considerably, and combining these three factors, a familial hypercholesterolaemia service based around DNA-cascade testing is now less than 25% of that estimated by NICE in 2008. SUMMARY Although all patients with a clinical diagnosis of familial hypercholesterolaemia need to have their LDL-C lowered, cascade testing should be focused on those with the monogenic form and not the polygenic form.
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Affiliation(s)
- Robert Pears
- Public Health Department, Corporate Services, Hampshire County Council, Winchester, Hampshire
| | - Michael Griffin
- Solutions for Public Health, Oxford Business Park South, Cowley, Oxfordshire
| | - Marta Futema
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
| | - Steve E. Humphries
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, UK
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Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One 2015; 10:e0128036. [PMID: 26000737 PMCID: PMC4441430 DOI: 10.1371/journal.pone.0128036] [Citation(s) in RCA: 426] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/21/2015] [Indexed: 11/23/2022] Open
Abstract
Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the standard Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples. Several hundred samples can then be pooled on the same HiSeq lane via custom barcodes. Our method will be useful for re-sequencing of microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples, as well as for other sequencing applications including large amplicon, open chromosome, artificial chromosomes, and RNA sequencing.
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Affiliation(s)
- Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sergey Kryazhimskiy
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tami D. Lieberman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hattie Chung
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael M. Desai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail: (MB); (RK)
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Faculty of Biology and Department of Computer Science, Technion-Israel Institute of Technology, Haifa, Israel
- * E-mail: (MB); (RK)
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32
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Rosenstein J. The promise of nanopore technology: Nanopore DNA sequencing represents a fundamental change in the way that genomic information is read, with potentially big savings. IEEE Pulse 2015; 5:52-4. [PMID: 25029683 DOI: 10.1109/mpul.2014.2321214] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Wang Y, Cui Y, Zhou X, Han J. Development of a high-throughput resequencing array for the detection of pathogenic mutations in osteogenesis imperfecta. PLoS One 2015; 10:e0119553. [PMID: 25742658 PMCID: PMC4350936 DOI: 10.1371/journal.pone.0119553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/30/2015] [Indexed: 01/29/2023] Open
Abstract
Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found.
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Affiliation(s)
- Yao Wang
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- Shandong Institute of Endocrine and Metabolic Diseases, Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Yazhou Cui
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Xiaoyan Zhou
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Jinxiang Han
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- * E-mail:
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Abstract
Next-generation sequencing methods based on nanopore technology have recently gained considerable attention, mainly because they promise affordable and fast genome sequencing by providing long read lengths (5 kbp) and do not require additional DNA amplification or enzymatic incorporation of modified nucleotides. This permits health care providers and research facilities to decode a genome within hours for less than $1000. This review summarizes past, present, and future DNA sequencing techniques, which are realized by nanopore approaches such as those pursued by Oxford Nanopore Technologies.
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Psifidi A, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G, Banos G. Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PLoS One 2015; 10:e0115960. [PMID: 25635817 PMCID: PMC4312062 DOI: 10.1371/journal.pone.0115960] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/28/2014] [Indexed: 12/21/2022] Open
Abstract
Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.
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Affiliation(s)
- Androniki Psifidi
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Chrysostomos I. Dovas
- Microbiology and Infectious Diseases Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Bramis
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Thomai Lazou
- Food safety Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Claire L. Russel
- Department of Clinical Veterinary Sciences, University of Bristol, Langford House, Langford, Bristol, United Kingdom
| | - Georgios Arsenos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Banos
- Animal Production Laboratory, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
- Scotland’s Rural College, Edinburgh, United Kingdom
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Lázaro-Muñoz G, Conley JM, Davis AM, Van Riper M, Walker RL, Juengst ET. Looking for Trouble: Preventive Genomic Sequencing in the General Population and the Role of Patient Choice. Am J Bioeth 2015; 15:3-14. [PMID: 26147254 PMCID: PMC4493927 DOI: 10.1080/15265161.2015.1039721] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in genomics have led to calls for developing population-based preventive genomic sequencing (PGS) programs with the goal of identifying genetic health risks in adults without known risk factors. One critical issue for minimizing the harms and maximizing the benefits of PGS is determining the kind and degree of control individuals should have over the generation, use, and handling of their genomic information. In this article we examine whether PGS programs should offer individuals the opportunity to selectively opt out of the sequencing or analysis of specific genomic conditions (the menu approach) or whether PGS should be implemented using an all-or-nothing panel approach. We conclude that any responsible scale-up of PGS will require a menu approach that may seem impractical to some, but that draws its justification from a rich mix of normative, legal, and practical considerations.
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Tso KY, Lee SD, Lo KW, Yip KY. Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts? BMC Genomics 2014; 15:1172. [PMID: 25539684 PMCID: PMC4326289 DOI: 10.1186/1471-2164-15-1172] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/11/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data. RESULTS We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two special handling strategies was too small for special handling to be cost-effective, but it was found crucial when false non-synonymous SNVs should be minimized, especially in exome sequencing. CONCLUSIONS Our study systematically analyzes the effects of mouse contamination in the sequencing data of human-in-mouse xenografts. Our findings provide information for designing data analysis pipelines for these data.
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Affiliation(s)
- Kai-Yuen Tso
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Sau Dan Lee
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwok-Wai Lo
- />Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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Kundu S, Ghosh SK. Trend of different molecular markers in the last decades for studying human migrations. Gene 2014; 556:81-90. [PMID: 25510397 DOI: 10.1016/j.gene.2014.12.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/15/2022]
Abstract
Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration.
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Affiliation(s)
- Sharbadeb Kundu
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India
| | - Sankar Kumar Ghosh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Pin-788011 Assam, India.
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Abstract
Background Rapid advances in next-generation sequencing technologies facilitate genetic association studies of an increasingly wide array of rare variants. To capture the rare or less common variants, a large number of individuals will be needed. However, the cost of a large scale study using whole genome or exome sequencing is still high. DNA pooling can serve as a cost-effective approach, but with a potential limitation that the identity of individual genomes would be lost and therefore individual characteristics and environmental factors could not be adjusted in association analysis, which may result in power loss and a biased estimate of genetic effect. Methods For case-control studies, we propose a design strategy for pool creation and an analysis strategy that allows covariate adjustment, using multiple imputation technique. Results Simulations show that our approach can obtain reasonable estimate for genotypic effect with only slight loss of power compared to the much more expensive approach of sequencing individual genomes. Conclusion Our design and analysis strategies enable more powerful and cost-effective sequencing studies of complex diseases, while allowing incorporation of covariate adjustment.
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Affiliation(s)
- Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail: (WG); (CL)
| | - Chun Li
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, United States of America
- * E-mail: (WG); (CL)
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Erickson RP. Next generation sequencing is here now. Lymphology 2014; 47:196-197. [PMID: 25915980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The availability of massively parallel DNA sequencers has brought the cost of sequencing genes to affordable levels but the cost of analyzing the huge amount of data has not decreased to the same extent. Thus, only analyzing the sequences of the genes relevant to the patient's condition makes the cost manageable. A panel of genes relevant to lymphedematous conditions is described.
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Chang YS, Lee CC, Liu TY, Chen YC, Lu HC, Chang JG. Direct assessment of cytochrome P450 2D6 genotypes by high-resolution melting analysis and DNA sequencing. Environ Toxicol Pharmacol 2014; 38:821-828. [PMID: 25461541 DOI: 10.1016/j.etap.2014.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 09/18/2014] [Accepted: 09/21/2014] [Indexed: 06/04/2023]
Abstract
We developed a CYP2D6 genotyping method that required only one polymerase chain reaction (PCR) followed by a high-resolution melting curve analysis (HRM) and DNA sequencing. DNA was extracted from peripheral blood samples obtained from 100 normal individuals. From the HRM analysis using three fragments of amplicons (exons 1, 6, and 9), we successfully identified four common CYP2D6 gene polymorphisms (100C>T, 2850C>T, 2988G>A, and 4180G>C). Exons 3 and 7 were also screened by HRM analysis. The heteroduplexes, wild-type homoduplexes, and homoduplexes of compound mutations showed distinct melting plots. The other four exons (exons 2, 4, 5, and 8) were directly analyzed by DNA sequencing. In conclusion, we developed an HRM and DNA sequencing based method to assess the CYP2D6 gene directly without the need for nested PCR. This method is quick and cost-effective; it reduces the chance of PCR contamination and is suitable for clinical application.
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Affiliation(s)
- Ya-Sian Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Chin Lee
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Chia Chen
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsiu-Chin Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan; Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan.
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Abstract
The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model organisms. Here, we show that a high-quality draft genome of a eukaryote can be obtained at relatively low cost by exploiting a hybrid combination of sequencing strategies.
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Affiliation(s)
- Luigi Faino
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Toumazou C, Thay TSLK, Georgiou P. A new era of semiconductor genetics using ion-sensitive field-effect transistors: the gene-sensitive integrated cell. Philos Trans A Math Phys Eng Sci 2014; 372:20130112. [PMID: 24567478 DOI: 10.1098/rsta.2013.0112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Semiconductor genetics is now disrupting the field of healthcare owing to the rapid parallelization and scaling of DNA sensing using ion-sensitive field-effect transistors (ISFETs) fabricated using commercial complementary metal -oxide semiconductor technology. The enabling concept of DNA reaction monitoring introduced by Toumazou has made this a reality and we are now seeing relentless scaling with Moore's law ultimately achieving the $100 genome. In this paper, we present the next evolution of this technology through the creation of the gene-sensitive integrated cell (GSIC) for label-free real-time analysis based on ISFETs. This device is derived from the traditional metal-oxide semiconductor field-effect transistor (MOSFET) and has electrical performance identical to that of a MOSFET in a standard semiconductor process, yet is capable of incorporating DNA reaction chemistries for applications in single nucleotide polymorphism microarrays and DNA sequencing. Just as application-specific integrated circuits, which are developed in much the same way, have shaped our consumer electronics industry and modern communications and memory technology, so, too, do GSICs based on a single underlying technology principle have the capacity to transform the life science and healthcare industries.
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Affiliation(s)
- Christofer Toumazou
- Centre for Bio-inspired Technology, Department of Electrical and Electronic Engineering, Imperial College, London, UK
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Chaturbhuj DN, Nirmalkar AP, Paranjape RS, Tripathy SP. Evaluation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. PLoS One 2014; 9:e87441. [PMID: 24533056 PMCID: PMC3922725 DOI: 10.1371/journal.pone.0087441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/25/2013] [Indexed: 11/18/2022] Open
Abstract
Objectives Validation of a cost effective in-house method for HIV-1 drug resistance genotyping using plasma samples. Design The validation includes the establishment of analytical performance characteristics such as accuracy, reproducibility, precision and sensitivity. Methods The accuracy was assessed by comparing 26 paired Virological Quality Assessment (VQA) proficiency testing panel sequences generated by in-house and ViroSeq Genotyping System 2.0 (Celera Diagnostics, US) as a gold standard. The reproducibility and precision were carried out on five samples with five replicates representing multiple HIV-1 subtypes (A, B, C) and resistance patterns. The amplification sensitivity was evaluated on HIV-1 positive plasma samples (n = 88) with known viral loads ranges from 1000–1.8 million RNA copies/ml. Results Comparison of the nucleotide sequences generated by ViroSeq and in-house method showed 99.41±0.46 and 99.68±0.35% mean nucleotide and amino acid identity respectively. Out of 135 Stanford HIVdb listed HIV-1 drug resistance mutations, partial discordance was observed at 15 positions and complete discordance was absent. The reproducibility and precision study showed high nucleotide sequence identities i.e. 99.88±0.10 and 99.82±0.20 respectively. The in-house method showed 100% analytical sensitivity on the samples with HIV-1 viral load >1000 RNA copies/ml. The cost of running the in-house method is only 50% of that for ViroSeq method (112$ vs 300$), thus making it cost effective. Conclusions The validated cost effective in-house method may be used to collect surveillance data on the emergence and transmission of HIV-1 drug resistance in resource limited countries. Moreover, the wide applications of a cost effective and validated in-house method for HIV-1 drug resistance testing will facilitate the decision making for the appropriate management of HIV infected patients.
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Affiliation(s)
- Devidas N. Chaturbhuj
- Drug Resistance Lab, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Amit P. Nirmalkar
- Department of Epidemiology & Biostatistics, National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Ramesh S. Paranjape
- National AIDS Research Institute, Indian Council of Medical Research, Bhosari, Pune, India
| | - Srikanth P. Tripathy
- National JALMA Institute Of Leprosy And Other Mycobacterial Diseases, Indian Council of Medical Research, Bhosari, Agra, India
- * E-mail:
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Middha S, Baheti S, Hart SN, Kocher JPA. From days to hours: reporting clinically actionable variants from whole genome sequencing. PLoS One 2014; 9:e86803. [PMID: 24505267 PMCID: PMC3914798 DOI: 10.1371/journal.pone.0086803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/13/2013] [Indexed: 11/19/2022] Open
Abstract
As the cost of whole genome sequencing (WGS) decreases, clinical laboratories will be looking at broadly adopting this technology to screen for variants of clinical significance. To fully leverage this technology in a clinical setting, results need to be reported quickly, as the turnaround rate could potentially impact patient care. The latest sequencers can sequence a whole human genome in about 24 hours. However, depending on the computing infrastructure available, the processing of data can take several days, with the majority of computing time devoted to aligning reads to genomics regions that are to date not clinically interpretable. In an attempt to accelerate the reporting of clinically actionable variants, we have investigated the utility of a multi-step alignment algorithm focused on aligning reads and calling variants in genomic regions of clinical relevance prior to processing the remaining reads on the whole genome. This iterative workflow significantly accelerates the reporting of clinically actionable variants with no loss of accuracy when compared to genotypes obtained with the OMNI SNP platform or to variants detected with a standard workflow that combines Novoalign and GATK.
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Affiliation(s)
- Sumit Middha
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Steven N. Hart
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jean-Pierre A. Kocher
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
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Kitpipit T, Chotigeat W, Linacre A, Thanakiatkrai P. Forensic animal DNA analysis using economical two-step direct PCR. Forensic Sci Med Pathol 2014; 10:29-38. [PMID: 24435950 DOI: 10.1007/s12024-013-9521-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2013] [Indexed: 11/25/2022]
Abstract
Wildlife forensic DNA analysis by amplification of a mitochondrial locus followed by DNA sequencing is routine, yet suffers from being costly and time-consuming. To address these disadvantages we report on a low-cost two-step direct PCR assay to efficiently analyze 12 forensically relevant mammalian sample types without DNA extraction. A cytochrome oxidase I degenerate-universal primer pair was designed and validated for the developed assay. The 12 sample types, which included bone, horn, feces, and urine, were amplified successfully by the assay using a pre-direct PCR dilution protocol. The average amplification success rate was as high as 92.5 % (n = 350), with an average PCR product concentration of 220.71 ± 180.84 ng/μL. Differences in amplification success rate and PCR product quantity between sample types were observed; however, most samples provided high quality sequences, permitting a 100 % nucleotide similarity to their respective species via BLAST database queries. The combination of PBS and Phire(®) Hot Start II DNA polymerase gave comparable amplification success rate and amplicon quantity with the proprietary commercial kits (P > 0.05, n = 350) but at considerably lower cost. The stability of the assay was tested by successfully amplifying samples that had been stored for up to 12 months. Our data indicate that this low-cost two-step direct amplification assay has the potential to be a valuable tool for the forensic DNA community.
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Affiliation(s)
- Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand,
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Buonaccorsi V, Peterson M, Lamendella G, Newman J, Trun N, Tobin T, Aguilar A, Hunt A, Praul C, Grove D, Roney J, Roberts W. Vision and change through the genome consortium for active teaching using next-generation sequencing (GCAT-SEEK). CBE Life Sci Educ 2014; 13:1-2. [PMID: 24591495 PMCID: PMC3940450 DOI: 10.1187/cbe.13-10-0195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Development of the Genome Consortium on Active Teaching using Next Generation Sequencing (GCAT-SEEK) is described. Workshops, educational modules, assessment resources, data analysis software and computer hardware available for faculty are described.
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Affiliation(s)
- Vincent Buonaccorsi
- *Department of Biology, Juniata College, Huntingdon, PA 16652
- Address correspondence to: Vincent P. Buonaccorsi ()
| | - Mark Peterson
- *Department of Biology, Juniata College, Huntingdon, PA 16652
| | - Gina Lamendella
- *Department of Biology, Juniata College, Huntingdon, PA 16652
| | - Jeff Newman
- Department of World Languages and Cultures, Juniata College, Huntingdon, PA 16652
| | - Nancy Trun
- **Department of Philosophy, Juniata College, Huntingdon, PA 16652
| | - Tammy Tobin
- Department of Biology, Lycoming College, Williamsport, PA 17701
| | - Andres Aguilar
- Department of Biology, Duquesne University, Pittsburgh, PA 15282
| | - Arthur Hunt
- Department of Biology, Susquehanna University, Selinsgrove, PA 17870
| | - Craig Praul
- Department of Biological Sciences, California State University, Los Angeles, CA 90032
| | - Deborah Grove
- Department of Biological Sciences, California State University, Los Angeles, CA 90032
| | - Jim Roney
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546
| | - Wade Roberts
- University Park Genomics Core Facility, Pennsylvania State University, State College, PA 16802
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Schorderet DF, Bernasconi M, Tiab L, Favez T, Escher P. IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies-a price comparison with Sanger sequencing. Adv Exp Med Biol 2014; 801:171-6. [PMID: 24664695 DOI: 10.1007/978-1-4614-3209-8_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the number of exons/length of the candidate genes. Payment for these procedures was complicated and the sequential billing of several genes created endless paperwork. We therefore evaluated the costs of generating and sequencing a hybridization-based DNA library enriched for the 64 most frequently mutated genes in RD, called IROme, and compared them to the costs of amplifying and sequencing these genes by the Sanger method. The production cost generated by the high-throughput (HT) sequencing of IROme was established at CHF 2,875.75 per case. Sanger sequencing of the same exons cost CHF 69,399.02. Turnaround time of the analysis was 3 days for IROme. For Sanger sequencing, it could only be estimated, as we never sequenced all 64 genes in one single patient. Sale cost for IROme calculated on the basis of the sale cost of one exon by Sanger sequencing is CHF 8,445.88, which corresponds to the sale price of 40 exons. In conclusion, IROme is cheaper and faster than Sanger sequencing and therefore represents a sound approach for the diagnosis of RD, both scientifically and economically. As a drop in the costs of HT sequencing is anticipated, target resequencing might become the new gold standard in the molecular diagnosis of RD.
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Affiliation(s)
- Daniel F Schorderet
- IRO, Institute for Research in Ophthalmology, 64 Avenue du Grand-Champsec, 1950, Sion, Switzerland,
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Affiliation(s)
- Francis S Collins
- From the Office of the Director, National Institutes of Health, Bethesda, MD (F.S.C.); and the Office of the Commissioner, Food and Drug Administration, Department of Health and Human Services, Silver Spring, MD (M.A.H.)
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