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Kim SJ, Lai D, Park JY, Yokokawa R, Takayama S. Microfluidic automation using elastomeric valves and droplets: reducing reliance on external controllers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:2925-34. [PMID: 22761019 PMCID: PMC3463711 DOI: 10.1002/smll.201200456] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/02/2012] [Indexed: 05/04/2023]
Abstract
This paper gives an overview of elastomeric valve- and droplet-based microfluidic systems designed to minimize the need of external pressure to control fluid flow. This Concept article introduces the working principle of representative components in these devices along with relevant biochemical applications. This is followed by providing a perspective on the roles of different microfluidic valves and systems through comparison of their similarities and differences with transistors (valves) and systems in microelectronics. Despite some physical limitation of drawing analogies from electronic circuits, automated microfluidic circuit design can gain insights from electronic circuits to minimize external control units, while implementing high-complexity and high-throughput analysis.
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Affiliation(s)
- Sung-Jin Kim
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David Lai
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joong Yull Park
- School of Mechanical Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Ryuji Yokokawa
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Microengineering, Kyoto University, Yoshida-honmachi, Sakyo, Kyoto, 606-8501 JAPAN
| | - Shuichi Takayama
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA; Division of Nano-Bio and Chemical Engineering WCU Project, UNIST, Ulsan, Republic of Korea
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202
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Deschamps S, Llaca V, May GD. Genotyping-by-Sequencing in Plants. BIOLOGY 2012; 1:460-83. [PMID: 24832503 PMCID: PMC4009820 DOI: 10.3390/biology1030460] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 08/07/2012] [Accepted: 09/13/2012] [Indexed: 12/12/2022]
Abstract
The advent of next-generation DNA sequencing (NGS) technologies has led to the development of rapid genome-wide Single Nucleotide Polymorphism (SNP) detection applications in various plant species. Recent improvements in sequencing throughput combined with an overall decrease in costs per gigabase of sequence is allowing NGS to be applied to not only the evaluation of small subsets of parental inbred lines, but also the mapping and characterization of traits of interest in much larger populations. Such an approach, where sequences are used simultaneously to detect and score SNPs, therefore bypassing the entire marker assay development stage, is known as genotyping-by-sequencing (GBS). This review will summarize the current state of GBS in plants and the promises it holds as a genome-wide genotyping application.
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Affiliation(s)
- Stéphane Deschamps
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Victor Llaca
- DuPont Agricultural Biotechnology, Experimental Station, PO Box 80353, 200 Powder Mill Road, Wilmington, DE 19880-0353, USA.
| | - Gregory D May
- DuPont Pioneer, 7300 NW 62nd Ave., P.O. Box 1004, Johnston, IA 50131-1004, USA.
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203
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High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome 2012; 23:499-513. [PMID: 22991087 DOI: 10.1007/s00335-012-9424-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/19/2012] [Indexed: 12/19/2022]
Abstract
Phenotype-driven approaches in mice are powerful strategies for the discovery of genes and gene functions and for unravelling complex biological mechanisms. Traditional methods for mutation discovery are reliable and robust, but they can also be laborious and time consuming. Recently, high-throughput sequencing (HTS) technologies have revolutionised the process of forward genetics in mice by paving the way to rapid mutation discovery. However, successful application of HTS for mutation discovery relies heavily on the sequencing approach employed and strategies for data analysis. Here we review current HTS applications and resources for mutation discovery and provide an overview of the practical considerations for HTS implementation and data analysis.
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204
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Zec H, Rane TD, Wang TH. Microfluidic platform for on-demand generation of spatially indexed combinatorial droplets. LAB ON A CHIP 2012; 12:3055-62. [PMID: 22810353 PMCID: PMC3657393 DOI: 10.1039/c2lc40399d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We propose a highly versatile and programmable nanolitre droplet-based platform that accepts an unlimited number of sample plugs from a multi-well plate, performs digitization of these sample plugs into smaller daughter droplets and subsequent synchronization-free, robust injection of multiple reagents into the sample daughter droplets on-demand. This platform combines excellent control of valve-based microfluidics with the high-throughput capability of droplet microfluidics. We demonstrate the functioning of a proof-of-concept device which generates combinatorial mixture droplets from a linear array of sample plugs and four different reagents, using food dyes to mimic samples and reagents. Generation of a one dimensional array of the combinatorial mixture droplets on the device leads to automatic spatial indexing of these droplets, precluding the need to include a barcode in each droplet to identify its contents. We expect this platform to further expand the range of applications of droplet microfluidics to include applications requiring a high degree of multiplexing as well as high throughput analysis of multiple samples.
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Affiliation(s)
- Helena Zec
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Tel: +1 410 5164746
| | - Tushar D. Rane
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Tel: +1 410 5164746
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Tel: +1 410 5164746
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, USA.; Tel: +1 410 516 7086
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205
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Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, David P, Brown M, Wang S, Link DR, Olson J, Travers K, Schadt E, Bushman FD. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Res 2012; 40:10345-55. [PMID: 22923523 PMCID: PMC3488221 DOI: 10.1093/nar/gks753] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alternative RNA splicing greatly expands the repertoire of proteins encoded by genomes. Next-generation sequencing (NGS) is attractive for studying alternative splicing because of the efficiency and low cost per base, but short reads typical of NGS only report mRNA fragments containing one or few splice junctions. Here, we used single-molecule amplification and long-read sequencing to study the HIV-1 provirus, which is only 9700 bp in length, but encodes nine major proteins via alternative splicing. Our data showed that the clinical isolate HIV-1(89.6) produces at least 109 different spliced RNAs, including a previously unappreciated ∼1 kb class of messages, two of which encode new proteins. HIV-1 message populations differed between cell types, longitudinally during infection, and among T cells from different human donors. These findings open a new window on a little studied aspect of HIV-1 replication, suggest therapeutic opportunities and provide advanced tools for the study of alternative splicing.
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Affiliation(s)
- Karen E Ocwieja
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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206
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Sipos B, Massingham T, Stütz AM, Goldman N. An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing. PLoS One 2012; 7:e43359. [PMID: 22912860 PMCID: PMC3422288 DOI: 10.1371/journal.pone.0043359] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 07/19/2012] [Indexed: 11/24/2022] Open
Abstract
The rise of Next Generation Sequencing (NGS) technologies has transformed de novo genome sequencing into an accessible research tool, but obtaining high quality eukaryotic genome assemblies remains a challenge, mostly due to the abundance of repetitive elements. These also make it difficult to study nucleotide polymorphism in repetitive regions, including certain types of structural variations. One solution proposed for resolving such regions is Sequence Assembly aided by Mutagenesis (SAM), which relies on the fact that introducing enough random mutations breaks the repetitive structure, making assembly possible. Sequencing many different mutated copies permits the sequence of the repetitive region to be inferred by consensus methods. However, this approach relies on molecular cloning in order to isolate and amplify individual mutant copies, making it hard to scale-up the approach for use in conjunction with high-throughput sequencing technologies. To address this problem, we propose NG-SAM, a modified version of the SAM protocol that relies on PCR and dilution steps only, coupled to a NGS workflow. NG-SAM therefore has the potential to be scaled-up, e.g. using emerging microfluidics technologies. We built a realistic simulation pipeline to study the feasibility of NG-SAM, and our results suggest that under appropriate experimental conditions the approach might be successfully put into practice. Moreover, our simulations suggest that NG-SAM is capable of reconstructing robustly a wide range of potential target sequences of varying lengths and repetitive structures.
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Affiliation(s)
- Botond Sipos
- European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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207
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Bundock PC, Casu RE, Henry RJ. Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:657-67. [PMID: 22624722 DOI: 10.1111/j.1467-7652.2012.00707.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Large polyploid genomes of non-model species remain challenging targets for DNA polymorphism discovery despite the increasing throughput and continued reductions in cost of sequencing with new technologies. For these species especially, there remains a requirement to enrich genomic DNA to discover polymorphisms in regions of interest because of large genome size and to provide the sequence depth to enable estimation of copy number. Various methods of enriching DNA have been utilised, but some recent methods enable the efficient sampling of large regions (e.g. the exome). We have utilised one of these methods, solution-based hybridization (Agilent SureSelect), to capture regions of the genome of two sugarcane genotypes (one Saccharum officinarum and one Saccharum hybrid) based mainly on gene sequences from the close relative Sorghum bicolor. The capture probes span approximately 5.8 megabases (Mb). The enrichment over whole-genome shotgun sequencing was 10-11-fold for the two genotypes tested. This level of enrichment has important consequences for detecting single nucleotide polymorphisms (SNPs) from a single lane of Illumina (Genome Analyzer) sequence reads. The detection of polymorphisms was enabled by the depth of sequence at or near probe sites and enabled the detection of 270 000-280 000 SNPs within each genotype from a single lane of sequence using stringent detection parameters. The SNPs were present in 13 000-16 000 targeted genes, which would enable mapping of a large number of these chosen genes. SNP validation from 454 sequencing and between-genotype confirmations gave an 87%-91% validation rate.
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Affiliation(s)
- Peter C Bundock
- Co-operative Research Centre for Sugar Industry Innovation through Biotechnology, Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia.
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208
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Taly V, Pekin D, Abed AE, Laurent-Puig P. Detecting biomarkers with microdroplet technology. Trends Mol Med 2012; 18:405-16. [DOI: 10.1016/j.molmed.2012.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 05/07/2012] [Accepted: 05/07/2012] [Indexed: 12/15/2022]
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209
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Zellmer AJ, Hanes MM, Hird SM, Carstens BC. Deep Phylogeographic Structure and Environmental Differentiation in the Carnivorous Plant Sarracenia alata. Syst Biol 2012; 61:763-77. [DOI: 10.1093/sysbio/sys048] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Amanda J. Zellmer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Margaret M. Hanes
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Sarah M. Hird
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Bryan C. Carstens
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; and 2 Department of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USA
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210
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The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One 2012; 7:e38581. [PMID: 22745671 PMCID: PMC3380018 DOI: 10.1371/journal.pone.0038581] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 05/07/2012] [Indexed: 11/19/2022] Open
Abstract
Metagenome sequencing is becoming common and there is an increasing need for easily accessible tools for data analysis. An essential step is the taxonomic classification of sequence fragments. We describe a web server for the taxonomic assignment of metagenome sequences with PhyloPythiaS. PhyloPythiaS is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. Here, we demonstrate usage of our web server by taxonomic assignment of metagenome samples from an acidophilic biofilm community of an acid mine and of a microbial community from cow rumen.
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211
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Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R. Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis. Expert Rev Mol Diagn 2012; 12:159-73. [PMID: 22369376 DOI: 10.1586/erm.11.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The potential applications of next-generation sequencing technologies in diagnostic laboratories have become increasingly evident despite the various technical challenges that still need to be overcome to potentiate its widespread adoption in a clinical setting. Whole-genome sequencing is now both technically feasible and 'cost effective' using next-generation sequencing techniques. However, this approach is still considered to be 'expensive' for a diagnostic test. Although the goal of the US$1000 genome is fast approaching, neither the analytical hurdles nor the ethical issues involved are trivial. In addition, the cost of data analysis and storage has been much higher than initially expected. As a result, it is widely perceived that targeted sequencing and whole-exome sequencing are more likely to be adopted as diagnostic tools in the foreseeable future. However, the information-generating power of whole-exome sequencing has also sparked considerable debate in relation to its deployment in genetic diagnostics, particularly with reference to the revelation of incidental findings. In this review, we focus on the targeted sequencing approach and its potential as a genetic diagnostic tool.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.
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212
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Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L. Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. PLANT CELL REPORTS 2012; 31:973-85. [PMID: 22350316 PMCID: PMC3351601 DOI: 10.1007/s00299-012-1234-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/27/2012] [Accepted: 01/27/2012] [Indexed: 05/22/2023]
Abstract
Tomato (Solanum lycopersicum) is one of the world's most important vegetable crops. Managing the health of this crop can be particularly challenging; crop resistance may be overcome by new pathogen races while new pathogens have been introduced by global agricultural markets. Tomato is extensively used as a model plant for resistance studies and much has been attained through both genetic and biotechnological approaches. In this paper, we illustrate genomic methods currently employed to preserve resistant germplasm and to facilitate the study and transfer of resistance genes, and we describe the genomic organization of R-genes. Patterns of gene activation during disease resistance response, identified through functional approaches, are depicted. We also describe the opportunities offered by the use of new genomic technologies, including high-throughput DNA sequencing, large-scale expression data production and the comparative hybridization technique, whilst reporting multifaceted approaches to achieve genetic tomato disease control. Future strategies combining the huge amount of genomic and genetic data will be able to accelerate development of novel resistance varieties sustainably on a worldwide basis. Such strategies are discussed in the context of the latest insights obtained in this field.
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Affiliation(s)
- M R Ercolano
- Department of Soil, Plant, Environmental and Animal Production Sciences, University of Naples 'Federico II', Via Università 100, 80055 Portici, Italy.
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213
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Liao GJW, Chan KCA, Jiang P, Sun H, Leung TY, Chiu RWK, Lo YMD. Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 2012; 7:e38154. [PMID: 22666469 PMCID: PMC3362548 DOI: 10.1371/journal.pone.0038154] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 05/01/2012] [Indexed: 01/20/2023] Open
Abstract
Background Plasma DNA obtained from a pregnant woman contains a mixture of maternal and fetal DNA. The fetal DNA proportion in maternal plasma is relatively consistent as determined using polymorphic genetic markers across different chromosomes in euploid pregnancies. For aneuploid pregnancies, the observed fetal DNA proportion measured using polymorphic genetic markers for the aneuploid chromosome would be perturbed. In this study, we investigated the feasibility of analyzing single nucleotide polymorphisms using targeted massively parallel sequencing to detect such perturbations in mothers carrying trisomy 21 fetuses. Methodology/Principal Findings DNA was extracted from plasma samples collected from fourteen pregnant women carrying singleton fetuses. Hybridization-based targeted sequencing was used to enrich 2 906 single nucleotide polymorphism loci on chr7, chr13, chr18 and chr21. Plasma DNA libraries with and without target enrichment were analyzed by massively parallel sequencing. Genomic DNA samples of both the mother and fetus for each case were genotyped by single nucleotide polymorphism microarray analysis. For the targeted regions, the mean sequencing depth of the enriched samples was 225-fold higher than that of the non-enriched samples. From the targeted sequencing data, the ratio between fetus-specific and shared alleles increased by approximately 2-fold on chr21 in the paternally-derived trisomy 21 case. In comparison, the ratio is decreased by approximately 11% on chr21 in the maternally-derived trisomy 21 cases but with much overlap with the ratio of the euploid cases. Computer simulation revealed the relationship between the fetal DNA proportion, the number of informative alleles and the depth of sequencing. Conclusions/Significance Targeted massively parallel sequencing of single nucleotide polymorphism loci in maternal plasma DNA is a potential approach for trisomy 21 detection. However, the method appears to be less robust than approaches using non-polymorphism-based counting of sequence tags in plasma.
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Affiliation(s)
- Gary J. W. Liao
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - K. C. Allen Chan
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Peiyong Jiang
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Hao Sun
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Tak Y. Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Rossa W. K. Chiu
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - 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, New Territories, Hong Kong, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
- * E-mail:
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214
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Zieba A, Grannas K, Söderberg O, Gullberg M, Nilsson M, Landegren U. Molecular tools for companion diagnostics. N Biotechnol 2012; 29:634-40. [PMID: 22634023 DOI: 10.1016/j.nbt.2012.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 02/02/2023]
Abstract
The heterogeneous nature of cancer results in highly variable therapeutic responses even among patients with identical stages and grades of a malignancy. The move towards personalised medicine in cancer therapy has therefore been motivated by a need to customise therapy according to molecular features of individual tumours. Companion diagnostics serves to support early drug development, it can provide surrogate markers in clinical trials, and also guide selection of individual therapies and monitoring of responses in routine clinical care. The era of companion diagnostics can be said to have begun with the introduction of the HercepTest - a first-of-a-kind diagnostic tool developed by DakoCytomation in 1998 to select patients for therapy with the anticancer drug Herceptin (trastuzumab). Herceptin and the paired test proved that companion diagnostics can help guide patient-tailored therapies. We will discuss herein technologies to analyse companion diagnostics markers at the level of DNA, RNA or protein, focusing on a series of methods developed in our laboratory that can facilitate drug development and help stratify patients for therapy.
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Affiliation(s)
- Agata Zieba
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden.
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215
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Rizzo JM, Buck MJ. Key principles and clinical applications of "next-generation" DNA sequencing. Cancer Prev Res (Phila) 2012; 5:887-900. [PMID: 22617168 DOI: 10.1158/1940-6207.capr-11-0432] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Demand for fast, inexpensive, and accurate DNA sequencing data has led to the birth and dominance of a new generation of sequencing technologies. So-called "next-generation" sequencing technologies enable rapid generation of data by sequencing massive amounts of DNA in parallel using diverse methodologies which overcome the limitations of Sanger sequencing methods used to sequence the first human genome. Despite opening new frontiers of genomics research, the fundamental shift away from the Sanger sequencing that next-generation technologies has created has also left many unaware of the capabilities and applications of these new technologies, especially those in the clinical realm. Moreover, the brisk evolution of sequencing technologies has flooded the market with commercially available sequencing platforms, whose unique chemistries and diverse applications stand as another obstacle restricting the potential of next-generation sequencing. This review serves to provide a primer on next-generation sequencing technologies for clinical researchers and physician scientists. We provide an overview of the capabilities and clinical applications of DNA sequencing technologies to raise awareness among researchers about the power of these novel genomic tools. In addition, we discuss that key sequencing principles provide a comparison between existing and near-term technologies and outline key advantages and disadvantages between different sequencing platforms to help researchers choose an appropriate platform for their research interests.
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Affiliation(s)
- Jason M Rizzo
- Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Elicott St., Buffalo, NY 14203, USA.
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216
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Castellanos-Rizaldos E, Liu P, Milbury CA, Guha M, Brisci A, Cremonesi L, Ferrari M, Mamon H, Makrigiorgos GM. Temperature-tolerant COLD-PCR reduces temperature stringency and enables robust mutation enrichment. Clin Chem 2012; 58:1130-8. [PMID: 22587896 DOI: 10.1373/clinchem.2012.183095] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Low-level mutations in clinical tumor samples often reside below mutation detection limits, thus leading to false negatives that may impact clinical diagnosis and patient management. COLD-PCR (coamplification at lower denaturation temperature PCR) is a technology that magnifies unknown mutations during PCR, thus enabling downstream mutation detection. However, a practical difficulty in applying COLD-PCR has been the requirement for strict control of the denaturation temperature for a given sequence, to within ±0.3 °C. This requirement precludes simultaneous mutation enrichment in sequences of substantially different melting temperature (T(m)) and limits the technique to a single sequence at a time. We present a temperature-tolerant (TT) approach (TT-COLD-PCR) that reduces this obstacle. METHODS We describe thermocycling programs featuring a gradual increase of the denaturation temperature during COLD-PCR. This approach enabled enrichment of mutations when the cycling achieves the appropriate critical denaturation temperature of each DNA amplicon that is being amplified. Validation was provided for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) and TP53 (tumor protein p53) exons 6-9 by use of dilutions of mutated DNA, clinical cancer samples, and plasma-circulating DNA. RESULTS A single thermocycling program with a denaturation-temperature window of 2.5-3.0 °C enriches mutations in all DNA amplicons simultaneously, despite their different T(m)s. Mutation enrichments of 6-9-fold were obtained with TT-full-COLD-PCR. Higher mutation enrichments were obtained for the other 2 forms of COLD-PCR, fast-COLD-PCR, and ice-COLD-PCR. CONCLUSIONS Low-level mutations in diverse amplicons with different T(m)s can be mutation enriched via TT-COLD-PCR provided that their T(m)s fall within the denaturation-temperature window applied during amplification. This approach enables simultaneous enrichment of mutations in several amplicons and increases significantly the versatility of COLD-PCR.
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Affiliation(s)
- E Castellanos-Rizaldos
- Division of DNA Repair and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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217
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A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc Natl Acad Sci U S A 2012; 109:7665-70. [PMID: 22547789 DOI: 10.1073/pnas.1106752109] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a programmable droplet-based microfluidic device that combines the reconfigurable flow-routing capabilities of integrated microvalve technology with the sample compartmentalization and dispersion-free transport that is inherent to droplets. The device allows for the execution of user-defined multistep reaction protocols in 95 individually addressable nanoliter-volume storage chambers by consecutively merging programmable sequences of picoliter-volume droplets containing reagents or cells. This functionality is enabled by "flow-controlled wetting," a droplet docking and merging mechanism that exploits the physics of droplet flow through a channel to control the precise location of droplet wetting. The device also allows for automated cross-contamination-free recovery of reaction products from individual chambers into standard microfuge tubes for downstream analysis. The combined features of programmability, addressability, and selective recovery provide a general hardware platform that can be reprogrammed for multiple applications. We demonstrate this versatility by implementing multiple single-cell experiment types with this device: bacterial cell sorting and cultivation, taxonomic gene identification, and high-throughput single-cell whole genome amplification and sequencing using common laboratory strains. Finally, we apply the device to genome analysis of single cells and microbial consortia from diverse environmental samples including a marine enrichment culture, deep-sea sediments, and the human oral cavity. The resulting datasets capture genotypic properties of individual cells and illuminate known and potentially unique partnerships between microbial community members.
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218
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Theberge AB, Mayot E, El Harrak A, Kleinschmidt F, Huck WTS, Griffiths AD. Microfluidic platform for combinatorial synthesis in picolitre droplets. LAB ON A CHIP 2012; 12:1320-6. [PMID: 22344399 DOI: 10.1039/c2lc21019c] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This paper presents a droplet-based microfluidic platform for miniaturized combinatorial synthesis. As a proof of concept, a library of small molecules for early stage drug screening was produced. We present an efficient strategy for producing a 7 × 3 library of potential thrombin inhibitors that can be utilized for other combinatorial synthesis applications. Picolitre droplets containing the first type of reagent (reagents A(1), A(2), …, A(m)) were formed individually in identical microfluidic chips and then stored off chip with the aid of stabilizing surfactants. These droplets were then mixed to form a library of droplets containing reagents A(1-m), each individually compartmentalized, which was reinjected into a second microfluidic chip and combinatorially fused with picolitre droplets containing the second reagent (reagents B(1), B(2), …, B(n)) that were formed on chip. The concept was demonstrated with a three-component Ugi-type reaction involving an amine (reagents A(1-3)), an aldehyde (reagents B(1-7)), and an isocyanide (held constant), to synthesize a library of small molecules with potential thrombin inhibitory activity. Our technique produced 10(6) droplets of each reaction at a rate of 2.3 kHz. Each droplet had a reaction volume of 3.1 pL, at least six orders of magnitude lower than conventional techniques. The droplets can then be divided into aliquots for different downstream screening applications. In addition to medicinal chemistry applications, this combinatorial droplet-based approach holds great potential for other applications that involve sampling large areas of chemical parameter space with minimal reagent consumption; such an approach could be beneficial when optimizing reaction conditions or performing combinatorial reactions aimed at producing novel materials.
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Affiliation(s)
- Ashleigh B Theberge
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, CNRS UMR 7006, 8 Allée Gaspard Monge, 67083 Strasbourg Cedex, France
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219
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Yoshizawa S. Micro and nanotechnological tools for study of RNA. Biochimie 2012; 94:1588-94. [PMID: 22484393 DOI: 10.1016/j.biochi.2012.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 03/22/2012] [Indexed: 11/16/2022]
Abstract
Micro and nanotechnologies have originally contributed to engineering, especially in electronics. These technologies enable fabrication and assembly of materials at micrometer and nanometer scales and the manipulation of nano-objects. The power of these technologies has now been exploited in analyzes of biologically relevant molecules. In this review, the use of micro and nanotechnological tools in RNA research is described.
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Affiliation(s)
- Satoko Yoshizawa
- Centre de Génétique Moléculaire UPR 3404, CNRS, Université Paris-Sud, FRC3115 1 Ave de la Terrasse, 91190 Gif-sur-Yvette, France.
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220
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Targeted polymerase chain reaction-based enrichment and next generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 2012; 13:921-32. [PMID: 21811164 DOI: 10.1097/gim.0b013e318226fbf2] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Congenital disorders of glycosylation are a heterogeneous group of disorders caused by deficient glycosylation, primarily affecting the N-linked pathway. It is estimated that more than 40% of congenital disorders of glycosylation patients lack a confirmatory molecular diagnosis. The purpose of this study was to improve molecular diagnosis for congenital disorders of glycosylation by developing and validating a next generation sequencing panel for comprehensive mutation detection in 24 genes known to cause congenital disorders of glycosylation. METHODS Next generation sequencing validation was performed on 12 positive control congenital disorders of glycosylation patients. These samples were blinded as to the disease-causing mutations. Both RainDance and Fluidigm platforms were used for sequence enrichment and targeted amplification. The SOLiD platform was used for sequencing the amplified products. Bioinformatic analysis was performed using NextGENe® software. RESULTS The disease-causing mutations were identified by next generation sequencing for all 12 positive controls. Additional variants were also detected in three controls that are known or predicted to impair gene function and may contribute to the clinical phenotype. CONCLUSIONS We conclude that development of next generation sequencing panels in the diagnostic laboratory where multiple genes are implicated in a disorder is more cost-effective and will result in improved and faster patient diagnosis compared with a gene-by-gene approach. Recommendations are also provided for data analysis from the next generation sequencing-derived data in the clinical laboratory, which will be important for the widespread use of this technology.
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221
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Valencia CA, Rhodenizer D, Bhide S, Chin E, Littlejohn MR, Keong LM, Rutkowski A, Bonnemann C, Hegde M. Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy. J Mol Diagn 2012; 14:233-46. [PMID: 22426012 DOI: 10.1016/j.jmoldx.2012.01.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 01/02/2012] [Accepted: 01/18/2012] [Indexed: 11/30/2022] Open
Abstract
Sequencing individual genes by Sanger sequencing is a time-consuming and costly approach to resolve clinically heterogeneous genetic disorders. Panel testing offers the ability to efficiently and cost-effectively screen all of the genes for a particular genetic disorder. We assessed the analytical sensitivity and specificity of two different enrichment technologies, solution-based hybridization and microdroplet-based PCR target enrichment, in conjunction with next-generation sequencing (NGS), to identify mutations in 321 exons representing 12 different genes involved with congenital muscular dystrophies. Congenital muscular dystrophies present diagnostic challenges due to phenotypic variability, lack of standard access to and inherent difficulties with muscle immunohistochemical stains, and a general lack of clinician awareness. NGS results were analyzed across several parameters, including sequencing metrics and genotype concordance with Sanger sequencing. Genotyping data showed that both enrichment technologies produced suitable calls for use in clinical laboratories. However, microdroplet-based PCR target enrichment is more appropriate for a clinical laboratory, due to excellent sequence specificity and uniformity, reproducibility, high coverage of the target exons, and the ability to distinguish the active gene versus known pseudogenes. Regardless of the method, exons with highly repetitive and high GC regions are not well enriched and require Sanger sequencing for completeness. Our study demonstrates the successful application of targeted sequencing in conjunction with NGS to screen for mutations in hundreds of exons in a genetically heterogeneous human disorder.
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Affiliation(s)
- C Alexander Valencia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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222
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Fang WF, Ting SC, Hsu CW, Chen YT, Yang JT. Locally enhanced concentration and detection of oligonucleotides in a plug-based microfluidic device. LAB ON A CHIP 2012; 12:923-31. [PMID: 22240904 DOI: 10.1039/c2lc20917a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We propose a novel technique that allows oligonucleotides with specific end-modification within a plug in a plug-based microfluidic device to undergo a locally enhanced concentration at the rear of the plug as the plug moves downstream. DNA was enriched and detected in situ upon exploiting a combined effect underlain by an entropic force induced through fluid shear (i.e. a hydrodynamic-repellent effect) and the interfacial adsorption (aqueous/oil interface) attributed to affinity. Flow fields within a plug were visualized quantitatively using micro-particle image velocimetry (micro-PIV); the distribution of the fluid shear strain rate explains how the hydrodynamic-repellent effect engenders a dumbbell-like region with an increased concentration of DNA. The concentration of FAM (6-carboxy-fluorescein)-labeled DNA (FC-DNA) and of TAMRA (tetramethyl-6-carboxyrhodamine)-labeled DNA (TC-DNA), respectively, and the hybridization of probe DNA (modified with FAM) with target DNA (modified with TAMRA) were investigated in devices; a confocal fluorescence microscope (CFM) was utilized to monitor the processes and to resolve the corresponding 2D patterns and 3D reconstruction of the DNA distribution in a plug. TC-DNA, but not FC-DNA, concentrating within a plug was affected by the combined effect so as to achieve a concentration factor (C(r)) twice that of FC-DNA because of the lipophilicity of TAMRA. Using fluorescence resonance-energy transfer (FRET), we characterized the hybridization of the DNA in a plug; the detection limit of a system, improved by virtue of the proposed technique (the locally enhanced concentration), for DNA detection was estimated to be 20-50 nM. This technique enables DNA to concentrate locally in a nL-pL free-solution plug, the locally enhanced concentration to profit the hybridization efficiency and the detection of DNA, prospectively serving as a versatile means to accomplish a rapid DNA detection in a small volume for a Lab-on-a-Chip (LOC) system.
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Affiliation(s)
- Wei-Feng Fang
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
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223
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Jiang L, Zeng Y, Zhou H, Qu JY, Yao S. Visualizing millisecond chaotic mixing dynamics in microdroplets: A direct comparison of experiment and simulation. BIOMICROFLUIDICS 2012; 6:12810-1281012. [PMID: 22662077 PMCID: PMC3365329 DOI: 10.1063/1.3673254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 12/08/2011] [Indexed: 05/08/2023]
Abstract
In order to fully explore and utilize the advantages of droplet-based microfluidics, fast, sensitive, and quantitative measurements are indispensable for the diagnosis of biochemical reactions in microdroplets. Here, we report an optical detection technique using two-photon fluorescence lifetime imaging microscopy, with an aligning-summing and non-fitting division method, to depict two-dimensional (2D) maps of mixing dynamics by chaotic advection in microdroplets with high temporal and spatial resolution. The mixing patterns of two dye solutions inside droplets were quantitatively and accurately measured. The mixing efficiency in a serpentine droplet mixer was also quantified and compared with the simulation data. The mapped chaotic mixing dynamics agree well with the numerical simulation and theoretical prediction. This quantitative characterization is potentially applicable to the real-time kinetic study of biological and chemical reactions in droplet-based microfluidic systems.
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224
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Frommolt P, Abdallah AT, Altmüller J, Motameny S, Thiele H, Becker C, Stemshorn K, Fischer M, Freilinger T, Nürnberg P. Assessing the enrichment performance in targeted resequencing experiments. Hum Mutat 2012; 33:635-41. [PMID: 22290614 DOI: 10.1002/humu.22036] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 01/08/2012] [Indexed: 11/09/2022]
Abstract
Target enrichment strategies are a very common approach to sequence a predefined part of an individual's genome using second-generation sequencing technologies. While highly dependent on the technology and the target sequences selected, the performance of the various assays is also variable between samples and is influenced by the way how the libraries are handled in the laboratory. Here, we show how to find detailed information about the enrichment performance using a novel software package called NGSrich, which we developed as a part of a whole-exome resequencing pipeline in a medium-sized genomics center. Our software is suitable for high-throughput use and the results can be shared using HTML and a web server. Finally, we have sequenced exome-enriched DNA libraries of 18 human individuals using three different enrichment products and used our new software for a comparative analysis of their performance.
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Affiliation(s)
- Peter Frommolt
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Universität zu Köln, Cologne, Germany.
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225
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Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J. Targeted enrichment strategies for next-generation plant biology. AMERICAN JOURNAL OF BOTANY 2012; 99:291-311. [PMID: 22312117 DOI: 10.3732/ajb.1100356] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY The dramatic advances offered by modern DNA sequencers continue to redefine the limits of what can be accomplished in comparative plant biology. Even with recent achievements, however, plant genomes present obstacles that can make it difficult to execute large-scale population and phylogenetic studies on next-generation sequencing platforms. Factors like large genome size, extensive variation in the proportion of organellar DNA in total DNA, polyploidy, and gene number/redundancy contribute to these challenges, and they demand flexible targeted enrichment strategies to achieve the desired goals. METHODS In this article, we summarize the many available targeted enrichment strategies that can be used to target partial-to-complete organellar genomes, as well as known and anonymous nuclear targets. These methods fall under four categories: PCR-based enrichment, hybridization-based enrichment, restriction enzyme-based enrichment, and enrichment of expressed gene sequences. KEY RESULTS Examples of plant-specific applications exist for nearly all methods described. While some methods are well established (e.g., transcriptome sequencing), other promising methods are in their infancy (hybridization enrichment). A direct comparison of methods shows that PCR-based enrichment may be a reasonable strategy for accessing small genomic targets (e.g., ≤50 kbp), but that hybridization and transcriptome sequencing scale more efficiently if larger targets are desired. CONCLUSIONS While the benefits of targeted sequencing are greatest in plants with large genomes, nearly all comparative projects can benefit from the improved throughput offered by targeted multiplex DNA sequencing, particularly as the amount of data produced from a single instrument approaches a trillion bases per run.
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Affiliation(s)
- Richard Cronn
- Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331, USA.
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226
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Lin X, Tang W, Ahmad S, Lu J, Colby CC, Zhu J, Yu Q. Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities. Hear Res 2012; 288:67-76. [PMID: 22269275 DOI: 10.1016/j.heares.2012.01.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Revised: 01/04/2012] [Accepted: 01/06/2012] [Indexed: 01/25/2023]
Abstract
The goal of sequencing the entire human genome for $1000 is almost in sight. However, the total costs including DNA sequencing, data management, and analysis to yield a clear data interpretation are unlikely to be lowered significantly any time soon to make studies on a population scale and daily clinical uses feasible. Alternatively, the targeted enrichment of specific groups of disease and biological pathway-focused genes and the capture of up to an entire human exome (~1% of the genome) allowing an unbiased investigation of the complete protein-coding regions in the genome are now routine. Targeted gene capture followed by sequencing with massively parallel next-generation sequencing (NGS) has the advantages of 1) significant cost saving, 2) higher sequencing accuracy because of deeper achievable coverage, 3) a significantly shorter turnaround time, and 4) a more feasible data set for a bioinformatic analysis outcome that is functionally interpretable. Gene capture combined with NGS has allowed a much greater number of samples to be examined than is currently practical with whole-genome sequencing. Such an approach promises to bring a paradigm shift to biomedical research of Mendelian disorders and their clinical diagnoses, ultimately enabling personalized medicine based on one's genetic profile. In this review, we describe major methodologies currently used for gene capture and detection of genetic variations by NGS. We will highlight applications of this technology in studies of genetic disorders and discuss issues pertaining to applications of this powerful technology in genetic screening and the discovery of genes implicated in syndromic and non-syndromic hearing loss.
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Affiliation(s)
- Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322-3030, USA.
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227
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Smith M, Campino S, Gu Y, Clark TG, Otto TD, Maslen G, Manske M, Imwong M, Dondorp AM, Kwiatkowski DP, Quail MA, Swerdlow H. An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS. THE OPEN GENOMICS JOURNAL 2012; 5:10.2174/1875693X01205010018. [PMID: 24273626 PMCID: PMC3837216 DOI: 10.2174/1875693x01205010018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Studies on DNA from pathogenic organisms, within clinical samples, are often complicated by the presence of large amounts of host, e.g., human DNA. Isolation of pathogen DNA from these samples would improve the efficiency of next-generation sequencing (NGS) and pathogen identification. Here we describe a solution-based hybridisation method for isolation of pathogen DNA from a mixed population. This straightforward and inexpensive technique uses probes made from whole-genome DNA and off-the-shelf reagents. In this study, Escherichia coli DNA was successfully enriched from a mixture of E.coli and human DNA. After enrichment, genome coverage following NGS was significantly higher and the evenness of coverage and GC content were unaffected. This technique was also applied to samples containing a mixture of human and Plasmodium falciparum DNA. The P.falciparum genome is particularly difficult to sequence due to its high AT content (80.6%) and repetitive nature. Post enrichment, a bias in the recovered DNA was observed, with a poorer representation of the AT-rich non-coding regions. This uneven coverage was also observed in pre-enrichment samples, but to a lesser degree. Despite the coverage bias in enriched samples, SNP (single-nucleotide polymorphism) calling in coding regions was unaffected and the majority of samples had over 90% of their coding region covered at 5× depth. This technique shows significant promise as an effective method to enrich pathogen DNA from samples with heavy human contamination, particularly when applied to GC-neutral genomes.
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Affiliation(s)
- Miriam Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Susana Campino
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Yong Gu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Taane G. Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas D. Otto
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Gareth Maslen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Magnus Manske
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Arjen M. Dondorp
- Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Dominic P. Kwiatkowski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
- Wellcome Trust Centre of Human Genetics, University of Oxford, Oxford, UK
| | - Michael A. Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Harold Swerdlow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
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228
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Application of Next Generation Sequencing to Molecular Diagnosis of Inherited Diseases. CHEMICAL DIAGNOSTICS 2012; 336:19-45. [DOI: 10.1007/128_2012_325] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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229
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Abstract
This book chapter aims at providing an overview of all the aspects and procedures needed to develop a droplet-based workflow for single-cell analysis (see Fig. 10.1). The surfactant system used to stabilize droplets is a critical component of droplet microfluidics; its properties define the type of droplet-based assays and workflows that can be developed. The scope of this book chapter is limited to fluorinated surfactant systems that have proved to generate extremely stable droplets and allow to easily retrieve the encapsulated material. The formulation section discusses how the experimental parameters influence the choice of the surfactant system to use. The circuit design section presents recipes to design and integrate different droplet modules into a whole assay. The fabrication section describes the manufacturing of microfluidic chip including the surface treatment which is pivotal in droplet microfluidics. Finally, the last section reviews the experimental setup for fluorescence detection with an emphasis on cell injection and incubation.
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Affiliation(s)
- Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
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230
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Good JM. Reduced representation methods for subgenomic enrichment and next-generation sequencing. Methods Mol Biol 2012; 772:85-103. [PMID: 22065433 DOI: 10.1007/978-1-61779-228-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Several methods have been developed to enrich DNA for subsets of the genome prior to next-generation sequencing. These front-end enrichment strategies provide powerful and cost-effective tools for researchers interested in collecting large-scale genomic sequence data. In this review, I provide an overview of both general and targeted reduced representation enrichment strategies that are commonly used in tandem with next-generation sequencing. I focus on several key issues that are likely to be important when deciding which enrichment strategy is most appropriate for a given experiment. Overall, these techniques can enable the collection of large-scale genomic data in diverse species, providing a powerful tool for the study of evolutionary biology.
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Affiliation(s)
- Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, USA.
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231
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Multiplex Chromosomal Exome Sequencing Accelerates Identification of ENU-Induced Mutations in the Mouse. G3-GENES GENOMES GENETICS 2012; 2:143-50. [PMID: 22384391 PMCID: PMC3276189 DOI: 10.1534/g3.111.001669] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/21/2011] [Indexed: 12/22/2022]
Abstract
Forward genetic screens in Mus musculus have proved powerfully informative by revealing unsuspected mechanisms governing basic biological processes. This approach uses potent chemical mutagens, such as N-ethyl-N-nitrosourea (ENU), to randomly induce mutations in mice, which are then bred and phenotypically screened to identify lines that disrupt a specific biological process of interest. Although identifying a mutation using the rich resources of mouse genetics is straightforward, it is unfortunately neither fast nor cheap. Here we show that detecting newly induced causal variants in a forward genetic screen can be accelerated dramatically using a methodology that combines multiplex chromosome-specific exome capture, next-generation sequencing, rapid mapping, sequence annotation, and variation filtering. The key innovation of our method is multiplex capture and sequence that allows the simultaneous survey of both mutant, parental, and background strains in a single experiment. By comparing variants identified in mutant offspring with those found in dbSNP, the unmutagenized background strains, and parental lines, induced causative mutations can be distinguished immediately from preexisting variation or experimental artifact. Here we demonstrate this approach to find the causative mutations induced in four novel ENU lines identified from a recent ENU screen. In all four cases, after applying our method, we found six or fewer putative mutations (and sometimes only a single one). Determining the causative variant was then easily achieved through standard segregation approaches. We have developed this process into a community resource that will speed up individual labs’ ability to identify the genetic lesion in mutant mouse lines; all of our reagents and software tools are open source and available to the broader scientific community.
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232
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Desbois L, Padirac A, Kaneda S, Genot AJ, Rondelez Y, Hober D, Collard D, Fujii T. A microfluidic device for on-chip agarose microbead generation with ultralow reagent consumption. BIOMICROFLUIDICS 2012; 6:44101. [PMID: 24106525 PMCID: PMC3482248 DOI: 10.1063/1.4758460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/27/2012] [Indexed: 05/13/2023]
Abstract
Water-in-oil microdroplets offer microreactors for compartmentalized biochemical reactions with high throughput. Recently, the combination with a sol-gel switch ability, using agarose-in-oil microdroplets, has increased the range of possible applications, allowing for example the capture of amplicons in the gel phase for the preservation of monoclonality during a PCR reaction. Here, we report a new method for generating such agarose-in-oil microdroplets on a microfluidic device, with minimized inlet dead volume, on-chip cooling, and in situ monitoring of biochemical reactions within the gelified microbeads. We used a flow-focusing microchannel network and successfully generated agarose microdroplets at room temperature using the "push-pull" method. This method consists in pushing the oil continuous phase only, while suction is applied to the device outlet. The agarose phase present at the inlet is thus aspirated in the device, and segmented in microdroplets. The cooling system consists of two copper wires embedded in the microfluidic device. The transition from agarose microdroplets to microbeads provides additional stability and facilitated manipulation. We demonstrate the potential of this method by performing on-chip a temperature-triggered DNA isothermal amplification in agarose microbeads. Our device thus provides a new way to generate microbeads with high throughput and no dead volume for biochemical applications.
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Affiliation(s)
- Linda Desbois
- LIMMS/CNRS-IIS, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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233
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Ceulemans S, van der Ven K, Del-Favero J. Targeted screening and validation of copy number variations. Methods Mol Biol 2012; 838:311-28. [PMID: 22228019 DOI: 10.1007/978-1-61779-507-7_15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.
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Affiliation(s)
- Shana Ceulemans
- Applied Molecular Genomics Unit, VIB, Department of Molecular Genetics, Flanders, Belgium
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234
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Shirai M, Taniguchi T, Kambara H. Emerging applications of single-cell diagnostics. Top Curr Chem (Cham) 2012; 336:99-116. [PMID: 22610135 DOI: 10.1007/128_2012_327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The performance of DNA sequencers (next generation sequencing) is rapidly enhanced these days, being used for genetic diagnostics. Although many phenomena could be elucidated with such massive genome data, it is still a big challenge to obtain comprehensive understanding of diseases and the relevant biology at the cellular level. In general terms, the data obtained to date are averages of ensembles of cells, but it is not certain whether the same features are the same inside an individual cell. Accordingly, important information may be masked by the averaging process. As the technologies for analyzing bio-molecular components in single cells are being developed, single cell analysis seems promising to address the current limitations due to averaging problems. Although the technologies for single cell analysis are still at the infant stage, the single cell approach has the potential to improve the accuracy of diagnosis based on knowledge of intra- and inter-cellular networks. In this review several technologies and applications (especially medical applications) of genome and transcriptome analysis or single cells are described.
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Affiliation(s)
- M Shirai
- Central Research Laboratory, Hitachi, Ltd., 1-280, Higachi-koigakubo, Kokubunji-shi, Tokyo, Japan
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235
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Wei X, Ju X, Yi X, Zhu Q, Qu N, Liu T, Chen Y, Jiang H, Yang G, Zhen R, Lan Z, Qi M, Wang J, Yang Y, Chu Y, Li X, Guang Y, Huang J. Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing. PLoS One 2011; 6:e29500. [PMID: 22216297 PMCID: PMC3244462 DOI: 10.1371/journal.pone.0029500] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/29/2011] [Indexed: 01/17/2023] Open
Abstract
Background Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest. Methodology/Principal Findings To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR. Conclusions/Significance Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed.
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Affiliation(s)
- Xiaoming Wei
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiangchun Ju
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xin Yi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Qian Zhu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ning Qu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Tengfei Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yang Chen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Hui Jiang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Guanghui Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ruan Zhen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | | | - Ming Qi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jinming Wang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yi Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yuxing Chu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiaoyan Li
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yanfang Guang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jian Huang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Shanghai-Ministry Key Laboratory of Disease and Health Genomics, National Engineering Center for Biochip at Shanghai, Shanghai, China
- * E-mail:
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236
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Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer KA. Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing. Genome Biol 2011; 12:R124. [PMID: 22185227 PMCID: PMC3334619 DOI: 10.1186/gb-2011-12-12-r124] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/18/2011] [Accepted: 12/20/2011] [Indexed: 12/18/2022] Open
Abstract
Ultra-deep targeted sequencing (UDT-Seq) can identify subclonal somatic mutations in tumor samples. Early assays' limited breadth and depth restrict their clinical utility. Here, we target 71 kb of mutational hotspots in 42 cancer genes. We present novel methods enhancing both laboratory workflow and mutation detection. We evaluate UDT-Seq true sensitivity and specificity (> 94% and > 99%, respectively) for low prevalence mutations in a mixing experiment and demonstrate its utility using six tumor samples. With an improved performance when run on the Illumina Miseq, the UDT-Seq assay is well suited for clinical applications to guide therapy and study clonal selection in heterogeneous samples.
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Affiliation(s)
- Olivier Harismendy
- Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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237
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Myllykangas S, Natsoulis G, Bell JM, Ji HP. Targeted sequencing library preparation by genomic DNA circularization. BMC Biotechnol 2011; 11:122. [PMID: 22168766 PMCID: PMC3280942 DOI: 10.1186/1472-6750-11-122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For next generation DNA sequencing, we have developed a rapid and simple approach for preparing DNA libraries of targeted DNA content. Current protocols for preparing DNA for next-generation targeted sequencing are labor-intensive, require large amounts of starting material, and are prone to artifacts that result from necessary PCR amplification of sequencing libraries. Typically, sample preparation for targeted NGS is a two-step process where (1) the desired regions are selectively captured and (2) the ends of the DNA molecules are modified to render them compatible with any given NGS sequencing platform. RESULTS In this proof-of-concept study, we present an integrated approach that combines these two separate steps into one. Our method involves circularization of a specific genomic DNA molecule that directly incorporates the necessary components for conducting sequencing in a single assay and requires only one PCR amplification step. We also show that specific regions of the genome can be targeted and sequenced without any PCR amplification. CONCLUSION We anticipate that these rapid targeted libraries will be useful for validation of variants and may have diagnostic application.
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Affiliation(s)
- Samuel Myllykangas
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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238
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Cho SW, Kang DK, Choo JB, Demllo AJ, Chang SI. Recent advances in microfluidic technologies for biochemistry and molecular biology. BMB Rep 2011; 44:705-12. [DOI: 10.5483/bmbrep.2011.44.11.705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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239
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Mertes F, Elsharawy A, Sauer S, van Helvoort JMLM, van der Zaag PJ, Franke A, Nilsson M, Lehrach H, Brookes AJ. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics 2011; 10:374-86. [PMID: 22121152 PMCID: PMC3245553 DOI: 10.1093/bfgp/elr033] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.
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Affiliation(s)
- Florian Mertes
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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240
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Li Y, Guo SJ, Shao N, Tu S, Xu M, Ren ZR, Ling X, Wang GQ, Lin ZX, Tao SC. A universal multiplex PCR strategy for 100-plex amplification using a hydrophobically patterned microarray. LAB ON A CHIP 2011; 11:3609-3618. [PMID: 21909519 DOI: 10.1039/c1lc20526a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Both basic research and clinical medicine have urgent demands for highly efficient strategies to simultaneously identify many different DNA sequences within a single tube. Effective and simultaneous amplification of multiple target sequences is a prerequisite for any successful multiple nucleic acid detection method. Multiplex PCR is one of the best choices for this purpose. However, due to the intrinsic interference and competition among primer pairs in the same tube, multiple rounds of highly empirical optimization procedures are usually required to establish a successful multiplex PCR reaction. To address this challenge, we report here a universal multiplex PCR strategy that is capable of over 100-plex amplification using a specially designed microarray in which hydrophilic microwells are patterned on a hydrophobic chip. On such an array, primer pairs tagged with a universal sequence are physically separated in individual hydrophilic microwells on an otherwise hydrophobic chip, enabling many unique PCR reactions to be proceeded simultaneously during the first step of the procedure. The PCR products are then isolated and further amplified from the universal sequences, producing a sufficient amount of material for analysis by conventional gel electrophoresis or DNA microarray technology. This strategy is abbreviated as "MPH&HPM" for "Multiplex PCR on a Hydrophobically and Hydrophilically Patterned Microarray". The feasibility of this method is first demonstrated by a multiplex PCR reaction for the simultaneous detection of eleven pneumonia-causing pathogens. Further, we demonstrate the power of this strategy with a highly successful 116-plex PCR reaction that required only little prior optimization. The effectiveness of the MPH&HPM strategy with clinical samples is then illustrated with the detection of deleted exons of the Duchenne Muscular Dystrophy (DMD) gene, the results are in excellent agreement with the clinical records. Because of its generality, simplicity, flexibility, specificity and capacity of more than 100-plex amplification, the MPH&HPM strategy should have broad applications in both laboratory research and clinical applications when multiplex nucleic acid analysis is required.
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Affiliation(s)
- Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240, China
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241
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Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 2011; 32:177-195. [PMID: 22147957 PMCID: PMC3219767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Next-generation sequencing (NGS) is arguably one of the most significant technological advances in the biological sciences of the last 30 years. The second generation sequencing platforms have advanced rapidly to the point that several genomes can now be sequenced simultaneously in a single instrument run in under two weeks. Targeted DNA enrichment methods allow even higher genome throughput at a reduced cost per sample. Medical research has embraced the technology and the cancer field is at the forefront of these efforts given the genetic aspects of the disease. World-wide efforts to catalogue mutations in multiple cancer types are underway and this is likely to lead to new discoveries that will be translated to new diagnostic, prognostic and therapeutic targets. NGS is now maturing to the point where it is being considered by many laboratories for routine diagnostic use. The sensitivity, speed and reduced cost per sample make it a highly attractive platform compared to other sequencing modalities. Moreover, as we identify more genetic determinants of cancer there is a greater need to adopt multi-gene assays that can quickly and reliably sequence complete genes from individual patient samples. Whilst widespread and routine use of whole genome sequencing is likely to be a few years away, there are immediate opportunities to implement NGS for clinical use. Here we review the technology, methods and applications that can be immediately considered and some of the challenges that lie ahead.
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Affiliation(s)
- Cliff Meldrum
- Molecular Pathology, Hunter Area Pathology Service, Newcastle, NSW 2310
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne, Vic. 3002, Australia
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242
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Moorthie S, Mattocks CJ, Wright CF. Review of massively parallel DNA sequencing technologies. THE HUGO JOURNAL 2011. [PMID: 23205160 DOI: 10.1007/s11568-011-9156-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Since the development of technologies that can determine the base-pair sequence of DNA, the ability to sequence genes has contributed much to science and medicine. However, it has remained a relatively costly and laborious process, hindering its use as a routine biomedical tool. Recent times are seeing rapid developments in this field, both in the availability of novel sequencing platforms, as well as supporting technologies involved in processes such as targeting and data analysis. This is leading to significant reductions in the cost of sequencing a human genome and the potential for its use as a routine biomedical tool. This review is a snapshot of this rapidly moving field examining the current state of the art, forthcoming developments and some of the issues still to be resolved prior to the use of new sequencing technologies in routine clinical diagnosis.
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243
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Lai D, Frampton JP, Sriram H, Takayama S. Rounded multi-level microchannels with orifices made in one exposure enable aqueous two-phase system droplet microfluidics. LAB ON A CHIP 2011; 11:3551-4. [PMID: 21892481 DOI: 10.1039/c1lc20560a] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Exposure of a negative photoresist-coated glass slide with diffused light from the backside through a mask with disconnected features provides multi-level rounded channels with narrow orifices in one exposure. Using these structures, we construct microfluidic systems capable of creating aqueous two-phase system droplets where one aqueous phase forms droplets and the other aqueous phase forms the surrounding matrix. Unlike water-in-oil droplet systems, aqueous two-phase systems can have very low interfacial tensions that prevent spontaneous droplet formation. The multi-level channels fabricated by backside lithography satisfy two conflicting needs: (i) the requirement to have narrowed channels for efficient valve closure by channel deformation and (ii) the need to have wide channels to reduce the flow velocity, thus reducing the capillary number and enhancing droplet formation.
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Affiliation(s)
- David Lai
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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244
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Chen F, Zhan Y, Geng T, Lian H, Xu P, Lu C. Chemical transfection of cells in picoliter aqueous droplets in fluorocarbon oil. Anal Chem 2011; 83:8816-20. [PMID: 21967571 DOI: 10.1021/ac2022794] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The manipulation of cells inside water-in-oil droplets is essential for high-throughput screening of cell-based assays using droplet microfluidics. Cell transfection inside droplets is a critical step involved in functional genomics studies that examine in situ functions of genes using the droplet platform. Conventional water-in-hydrocarbon oil droplets are not compatible with chemical transfection due to its damage to cell viability and extraction of organic transfection reagents from the aqueous phase. In this work, we studied chemical transfection of cells encapsulated in picoliter droplets in fluorocarbon oil. The use of fluorocarbon oil permitted high cell viability and little loss of the transfection reagent into the oil phase. We varied the incubation time inside droplets, the DNA concentration, and the droplet size. After optimization, we were able to achieve similar transfection efficiency in droplets to that in the bulk solution. Interestingly, the transfection efficiency increased with smaller droplets, suggesting effects from either the microscale confinement or the surface-to-volume ratio.
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Affiliation(s)
- Fangyuan Chen
- Department of Chemistry, Nanjing University, Nanjing, PR China
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245
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Konry T, Bale SS, Bhushan A, Shen K, Seker E, Polyak B, Yarmush M. Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection. Mikrochim Acta 2011; 176:251-269. [PMID: 25378716 DOI: 10.1007/s00604-011-0705-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.
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Affiliation(s)
- Tania Konry
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Abhinav Bhushan
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Keyue Shen
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California, Davis, 3177 Kemper Hall, Davis, CA 95616, USA
| | - Boris Polyak
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Martin Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
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246
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Wang HY, Jain A. Novel sequencing-based strategies for high-throughput discovery of genetic mutations underlying inherited antibody deficiency disorders. Curr Allergy Asthma Rep 2011; 11:352-60. [PMID: 21792638 PMCID: PMC3179846 DOI: 10.1007/s11882-011-0211-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human inherited antibody deficiency disorders are generally caused by mutations in genes involved in the pathways regulating B-cell class switch recombination; DNA damage repair; and B-cell development, differentiation, and survival. Sequencing a large set of candidate genes involved in these pathways appears to be a highly efficient way to identify novel mutations. Herein we review several high-throughput sequencing approaches as well as recent improvements in target gene enrichment technologies. Systematic improvement of enrichment and sequencing methods, along with refinement of the experimental process is necessary to develop a cost-effective high-throughput resequencing assay for a large cohort of patient samples. The Hyper-IgM/CVID chip is one example of a resequencing platform that may be used to identify known or novel mutations in patents with various types of inherited antibody deficiency.
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Affiliation(s)
- Hong-Ying Wang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, CRC, 5W-3840, 10 Center Drive, Bethesda, MD 20892, USA
| | - Ashish Jain
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, CRC, 5W-3840, 10 Center Drive, Bethesda, MD 20892, USA
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247
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Paux E, Sourdille P, Mackay I, Feuillet C. Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 2011; 30:1071-88. [PMID: 21989506 DOI: 10.1016/j.biotechadv.2011.09.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 08/24/2011] [Accepted: 09/25/2011] [Indexed: 01/04/2023]
Abstract
In the past two decades, the wheat community has made remarkable progress in developing molecular resources for breeding. A wide variety of molecular tools has been established to accelerate genetic and physical mapping for facilitating the efficient identification of molecular markers linked to genes and QTL of agronomic interest. Already, wheat breeders are benefiting from a wide range of techniques to follow the introgression of the most favorable alleles in elite material and develop improved varieties. Breeders soon will be able to take advantage of new technological developments based on Next Generation Sequencing. In this paper, we review the molecular toolbox available to wheat scientists and breeders for performing fundamental genomic studies and breeding. Special emphasis is given on the production and detection of single nucleotide polymorphisms (SNPs) that should enable a step change in saturating the wheat genome for more efficient genetic studies and for the development of new selection methods. The perspectives offered by the access to an ordered full genome sequence for further marker development and enhanced precision breeding is also discussed. Finally, we discuss the advantages and limitations of marker-assisted selection for supporting wheat improvement.
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Affiliation(s)
- Etienne Paux
- INRA-UBP 1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brézet, Clermont-Ferrand, France
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248
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Haas J, Katus HA, Meder B. Next-generation sequencing entering the clinical arena. Mol Cell Probes 2011; 25:206-11. [PMID: 21914469 DOI: 10.1016/j.mcp.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 08/29/2011] [Accepted: 08/29/2011] [Indexed: 10/17/2022]
Abstract
Over the last decade the genetic etiology of many heritable diseases could be resolved. For heart muscle diseases, so called cardiomyopathies, mutations in more than 40 different genes have been identified. Due to this large genetic heterogeneity and missing of adequate gene-diagnostic tools, most patients are not genetically characterized, which would be important for individualized patient care. Currently, next-generation sequencing technologies are revolutionizing genetic and epigenetic research, since they are capable to produce billions of bases of sequence information in a single experiment. Accordingly, this powerful technology can now also open avenues for genetic diagnostics. The scope of this article is to illustrate technical approaches, clinical applications, and yet unsolved problems of next-generation sequencing entering the clinical arena.
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Affiliation(s)
- Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Im Neuenheimer Feld 350, Heidelberg 69120, Germany
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249
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Lee DH, Lee W, Um E, Park JK. Microbridge structures for uniform interval control of flowing droplets in microfluidic networks. BIOMICROFLUIDICS 2011; 5:34117-341179. [PMID: 22662043 PMCID: PMC3364831 DOI: 10.1063/1.3625604] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/26/2011] [Indexed: 05/10/2023]
Abstract
Precise temporal control of microfluidic droplets such as synchronization and combinatorial pairing of droplets is required to achieve a variety range of chemical and biochemical reactions inside microfluidic networks. Here, we present a facile and robust microfluidic platform enabling uniform interval control of flowing droplets for the precise temporal synchronization and pairing of picoliter droplets with a reagent. By incorporating microbridge structures interconnecting the droplet-carrying channel and the flow control channel, a fluidic pressure drop was derived between the two fluidic channels via the microbridge structures, reordering flowing droplets with a defined uniform interval. Through the adjustment of the control oil flow rate, the droplet intervals were flexibly and precisely adjustable. With this mechanism of droplet spacing, the gelation of the alginate droplets as well as control of the droplet interval was simultaneously achieved by additional control oil flow including calcified oleic acid. In addition, by parallel linking identical microfluidic modules with distinct sample inlet, controlled synchronization and pairing of two distinct droplets were demonstrated. This method is applicable to facilitate and develop many droplet-based microfluidic applications, including biological assay, combinatorial synthesis, and high-throughput screening.
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250
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Natrajan R, Reis-Filho JS. Next-generation sequencing applied to molecular diagnostics. Expert Rev Mol Diagn 2011; 11:425-44. [PMID: 21545259 DOI: 10.1586/erm.11.18] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Next-generation sequencing technologies have begun to revolutionize the field of cancer genetics through rapid and accurate assessment of a patient's DNA makeup with minimal cost. These technologies have already led to the realization of the inter- and intra-tumor genetic heterogeneity and the identification of novel mutations and chimeric genes, however, several challenges lie ahead. Given the low number of recurrent somatic genetic aberrations in common types of cancer, the identification of 'driver' genetic aberrations has proven challenging. Furthermore, implementation of next-generation sequencing and/or some of its derivatives into routine practice as diagnostic tests will require in-depth understanding of the pitfalls of these technologies and a great degree of bioinformatic expertise. This article focuses on the contribution of next-generation sequencing technologies to diagnosis and cancer prognostication and prediction.
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Affiliation(s)
- Rachael Natrajan
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
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