1
|
El-Tholoth M, Bau HH. Molecular Detection of Respiratory Tract Viruses in Chickens at the Point of Need by Loop-Mediated Isothermal Amplification (LAMP). Viruses 2024; 16:1248. [PMID: 39205222 PMCID: PMC11359210 DOI: 10.3390/v16081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
Accurate and timely molecular diagnosis of respiratory diseases in chickens is essential for implementing effective control measures, preventing the spread of diseases within poultry flocks, minimizing economic loss, and guarding food security. Traditional molecular diagnostic methods like polymerase chain reaction (PCR) require expensive equipment and trained personnel, limiting their use to centralized labs with a significant delay between sample collection and results. Loop-mediated isothermal amplification (LAMP) of nucleic acids offers an attractive alternative for detecting respiratory viruses in broiler chickens with sensitivity comparable to that of PCR. LAMP's main advantages over PCR are its constant incubation temperature (∼65 °C), high amplification efficiency, and contaminant tolerance, which reduce equipment complexity, cost, and power consumption and enable instrument-free tests. This review highlights effective LAMP methods and variants that have been developed for detecting respiratory viruses in chickens at the point of need.
Collapse
Affiliation(s)
- Mohamed El-Tholoth
- Department of Virology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
- Veterinary Sciences Program, Health Sciences Division, Al Ain Men’s Campus, Higher Colleges of Technology, Al Ain 17155, United Arab Emirates
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA;
| |
Collapse
|
2
|
Selva Sharma A, Lee NY. Advancements in visualizing loop-mediated isothermal amplification (LAMP) reactions: A comprehensive review of colorimetric and fluorometric detection strategies for precise diagnosis of infectious diseases. Coord Chem Rev 2024; 509:215769. [DOI: 10.1016/j.ccr.2024.215769] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
|
3
|
Liao Y, Liu Y, Feng Y, Zhen D, He F. Rapid Detection of Broad-Spectrum Pathogenic Bacteria Based on Highly Sensitive Proton Response of the Nucleic Acid Amplification SPQC Platform. Anal Chem 2024; 96:6756-6763. [PMID: 38625745 DOI: 10.1021/acs.analchem.4c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Pathogenic bacteria significantly contribute to elevated morbidity and mortality rates, highlighting the urgent need for early and precise detection. Currently, there is a paucity of effective broad-spectrum methods for detecting pathogenic bacteria. We have developed an innovative proton-responsive series piezoelectric quartz crystal (PR-SPQC) platform for the broad-spectrum identification of pathogenic bacteria. This was achieved by retrieving and aligning sequences from the NCBI GenBank database to identify and validate 16S rRNA oligonucleotide sequences that are signatures of pathogenic bacteria but absent in humans or fungi. The hyperbranched rolling circle amplification, activated exclusively by the screened target, exponentially generates protons that are detected by SPQC through a 2D polyaniline (PANI) film. The PR-SPQC platform demonstrates broad-spectrum capabilities in detecting pathogenic bacteria, with a detection limit of 2 CFU/mL within 90 min. Clinical testing of blood samples yielded satisfactory results. With its advantages in miniaturization, cost efficiency, and suitability for point-of-care testing, PR-SPQC has the potential to be extensively used for the rapid identification of diverse pathogenic bacteria within clinical practice and public health sectors.
Collapse
Affiliation(s)
- Yusheng Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Ye Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Deshuai Zhen
- Hunan Key Laboratory of Typical Environment Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, PR China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| |
Collapse
|
4
|
TABATA M, MIYAHARA Y. Control of interface functions in solid-state biosensors for stable detection of molecular recognition. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:32-56. [PMID: 38199246 PMCID: PMC10864167 DOI: 10.2183/pjab.100.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/25/2023] [Indexed: 01/12/2024]
Abstract
Significant progress has been achieved in the field of solid-state biosensors over the past 50 years. Various sensing devices with high-density integration and flexible configuration, as well as new applications for clinical diagnosis and healthcare, have been developed using blood, serum, and other body fluids such as sweat, tears, and saliva. A high-density array of ion-sensitive field effect transistors was developed by exploiting the advantages of advanced semiconductor technologies and commercialized in combination with an enzymatic primer extension reaction as a DNA sequencer in 2011. Different types of materials such as inorganic materials, metals, polymers, and biomolecules are mixed together on the surface of the gate while maintaining their own functions; therefore, compatibility among different materials has to be optimized so that the best detection performance of solid-state biosensors, including stability and reliability, is achieved as designed. Solid-state biosensors are suitable for the rapid, cost-effective, and noninvasive identification of biomarkers at various timepoints over the course of a disease.
Collapse
Affiliation(s)
- Miyuki TABATA
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Yuji MIYAHARA
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
5
|
Lee JY, Park JW. Modified cytosines versus cytosine in a DNA polymerase: retrieving thermodynamic and kinetic constants at the single molecule level. Analyst 2021; 147:341-348. [PMID: 34935781 DOI: 10.1039/d1an02108g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation plays key roles in various areas, such as gene expression, regulation, epigenetics, and cancers. Since 5-methylcytosine (5mC) is commonly present in methylated DNA, characterizing the binding kinetics and thermodynamics of the nucleotide to the enzymatic pocket can help to understand the DNA replication process. Furthermore, 5-carboxycytosine (5caC) is a form that appears through the iterative oxidation of 5mC, and its effect on the DNA replication process is still not well known. Here, we immobilized a DNA polymerase (DNAP) with an orientation control on a tip of an atomic force microscope (AFM), and observed the interaction between the immobilized deoxyguanosine triphosphate (dGTP) on the surface and the DNAP in the presence of a DNA duplex. The interaction probability increased as the concentration of the DNA strand, and the affinity constant between the DNAP and DNA was obtained by fitting the change. Increasing the concentration of dGTP in solution diminished the interaction probability, and a fitting allowed us to retrieve the affinity constant between dGTP and the DNAP holding the DNA in the reaction pocket. Because the dissociation constant could be obtained through the loading rate dependence of the unbinding force value, both affinity and kinetic constants for cytosine (C), 5mC, and 5caC in the DNAP were compared in the light of the steric and electronic effect of the substituents at 5-position of cytosine.
Collapse
Affiliation(s)
- Ji Yoon Lee
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea.
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea. .,Institute of Convergence Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
| |
Collapse
|
6
|
Salimova IO, Berezina AV, Shikholina IA, Zyk NV, Beloglazkina EK. Design and synthesis of novel terpyridine-based ligands with one and two terminal aurophilic moieties and their Rh(III) and Ru(II) complexes for the adsorption on metal surfaces. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
7
|
Wang C, Liu J, Kong J, Zhang X. Nitronyl nitroxide monoradical TEMPO as new electrochemical label for ultrasensitive detection of nucleic acids. Anal Chim Acta 2020; 1136:19-24. [PMID: 33081944 DOI: 10.1016/j.aca.2020.08.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/17/2020] [Accepted: 08/19/2020] [Indexed: 01/27/2023]
Abstract
In this work, a novel electrochemical biosensor based on nitronyl nitroxide monoradical 2,2,6,6-tetramethylpiperidine 1-Oxyl (TEMPO) as new electrochemical label for facile nucleic acids detection is developed. This fast and convenient functional microelectrode was designed by fixing the capture probe peptide nucleic acid (PNA) and using the coordination interaction of Zr4+ with both phosphate groups and carboxyl groups. Differential pulse voltammetry (DPV) was used to study the oxidation current of TEMPO which was combined with the electrode surface and labeled. TEMPO electrochemical signal related to target deoxyribonucleic acid (tDNA) concentration was finally detected when tDNA was added on the surface of glassy carbon electrode (GCE). The detection principle, optimization of key factors and performance analysis of the biosensor are also discussed. A great linear relation is acquired within the scope of 10 pM-100 nM under optimal conditions and the detection limit of this experiment is calculated as low as 2.57 pM (R2 = 0.996). In addition, complex serum samples were used to explore the practical application of this experiment. The results show the developed electrochemical DNA biosensor has wide application prospects in nucleic acids detection and clinical analysis.
Collapse
Affiliation(s)
- Chen Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China
| | - Jingliang Liu
- School of Environmental Science, Nanjing XiaoZhuang University, Nanjing, 211171, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, PR China
| |
Collapse
|
8
|
Gao G, Smith DI. Clinical Massively Parallel Sequencing. Clin Chem 2020; 66:77-88. [PMID: 31811004 DOI: 10.1373/clinchem.2019.303305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.
Collapse
Affiliation(s)
- Ge Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - David I Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| |
Collapse
|
9
|
Trotter M, Borst N, Thewes R, von Stetten F. Review: Electrochemical DNA sensing – Principles, commercial systems, and applications. Biosens Bioelectron 2020; 154:112069. [DOI: 10.1016/j.bios.2020.112069] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023]
|
10
|
Su X, Tayebi N, Credo GM, Wu K, Elibol OH, Liu DJ, Daniels JS, Li H, Hall DA, Varma M. Scalable Nanogap Sensors for Non-Redox Enzyme Assays. ACS Sens 2018; 3:1773-1781. [PMID: 30156096 DOI: 10.1021/acssensors.8b00500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clinical diagnostic assays that monitor redox enzyme activity are widely used in small, low-cost readout devices for point-of-care monitoring (e.g., a glucometer); however, monitoring non-redox enzymes in real-time using compact electronic devices remains a challenge. We address this problem by using a highly scalable nanogap sensor array to observe electrochemical signals generated by a model non-redox enzyme system, the DNA polymerase-catalyzed incorporation of four modified, redox-tagged nucleotides. Using deoxynucleoside triphosphates (dNTPs) tagged with para-aminophenyl monophosphate (pAPP) to form pAP-deoxyribonucleoside tetra-phosphates (AP-dN4Ps), incorporation of the nucleotide analogs by DNA polymerase results in the release of redox inactive pAP-triphosphates (pAPP3) that are converted to redox active small molecules para-aminophenol (pAP) in the presence of phosphatase. In this work, cyclic enzymatic reactions that generated many copies of pAP at each base incorporation site of a DNA template in combination with the highly confined nature of the planar nanogap transducers ( z = 50 nm) produced electrochemical signals that were amplified up to 100,000×. We observed that the maximum signal level and amplification level were dependent on a combination of factors including the base structure of the incorporated nucleotide analogs, nanogap electrode materials, and electrode surface coating. In addition, electrochemical signal amplification by redox cycling in the nanogap is independent of the in-plane geometry of the transducer, thus allowing the nanogap sensors to be highly scalable. Finally, when the DNA template concentration was constrained, the DNA polymerase assay exhibited different zero-order reaction kinetics for each type of base incorporation reaction, resolving the closely related nucleotide analogs.
Collapse
Affiliation(s)
- Xing Su
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Noureddine Tayebi
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Grace M. Credo
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Kai Wu
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Oguz H. Elibol
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - David J. Liu
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Jonathan S. Daniels
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Handong Li
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Drew A. Hall
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Madoo Varma
- Intel Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| |
Collapse
|
11
|
Nakagaki T, Tamura M, Kobashi K, Omori A, Koyama R, Idogawa M, Ogi K, Hiratsuka H, Tokino T, Sasaki Y. Targeted next-generation sequencing of 50 cancer-related genes in Japanese patients with oral squamous cell carcinoma. Tumour Biol 2018; 40:1010428318800180. [PMID: 30226113 DOI: 10.1177/1010428318800180] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Somatic mutation analysis is a standard of practice for human cancers to identify therapeutic sensitization and resistance mutations. We performed a multigene sequencing screen to explore mutational hotspots in cancer-related genes using a semiconductor-based sequencer. DNA from oral squamous cell carcinoma samples was used as a template to amplify 207 regions from 50 cancer-related genes. Of the 80 oral squamous cell carcinoma specimens from Japanese patients, including formalin-fixed paraffin-embedded samples, 56 specimens presented at least one somatic mutation among the 50 investigated genes, and 17 of these samples showed multiple gene somatic mutations. TP53 was the most commonly mutated gene (50.0%), followed by CDKN2A (16.3%), PIK3CA (7.5%), HRAS (5.0%), MET (2.5%), and STK11 (2.5%). In total, 32 cases (40.0%) were human papillomavirus positive and they were significantly less likely to have a TP53, mutation than human papillomavirus-negative oral squamous cell carcinomas (8/32, 25.0% vs 32/48, 66.7%, p = 0.00026). We also detected copy number variations, in which segments of the genome could be duplicated or deleted from the sequencing data. We detected the tumor-specific TP53 mutation in the plasma cell-free DNA from two oral squamous cell carcinoma patients, and after surgery, the test for these mutations became negative. Our approach facilitates the simultaneous high-throughput detection of somatic mutations and copy number variations in oral squamous cell carcinoma samples.
Collapse
Affiliation(s)
- Takafumi Nakagaki
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan.,2 Department of Oral Surgery, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Miyuki Tamura
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Kenta Kobashi
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Akina Omori
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Ryota Koyama
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masashi Idogawa
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Kazuhiro Ogi
- 2 Department of Oral Surgery, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hiroyoshi Hiratsuka
- 2 Department of Oral Surgery, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takashi Tokino
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Yasushi Sasaki
- 1 Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan.,3 Biology Division, Department of Liberal Arts and Sciences, Center for Medical Education, Sapporo Medical University, Sapporo, Japan
| |
Collapse
|
12
|
Nakagaki T, Tamura M, Kobashi K, Koyama R, Fukushima H, Ohashi T, Idogawa M, Ogi K, Hiratsuka H, Tokino T, Sasaki Y. Profiling cancer-related gene mutations in oral squamous cell carcinoma from Japanese patients by targeted amplicon sequencing. Oncotarget 2017; 8:59113-59122. [PMID: 28938622 PMCID: PMC5601718 DOI: 10.18632/oncotarget.19262] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/20/2017] [Indexed: 12/11/2022] Open
Abstract
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95.4% of total, 1.69 megabases of target sequence). The number of somatic mutations in 47 patients with OSCC ranged from 1 to 20 with a mean of 7.60. The most frequent mutations were in TP53 (61.7%), NOTCH1 (25.5%), CDKN2A (19.1%), SYNE1 (14.9%), PIK3CA (10.6%), ROS1 (10.6%), and TAF1L (10.6%). We also detected copy number variations (CNVs) in the segments of the genome that could be duplicated or deleted from deep sequencing data. Pathway assessment showed that the somatic aberrations within OSCC genomes are mainly involved in several important pathways, including cell cycle regulation and RTK–MAPK-PI3K. This study may enable better selection of therapies and deliver improved outcomes for OSCC patients when combined with clinical diagnostics.
Collapse
Affiliation(s)
- Takafumi Nakagaki
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan.,Department of Oral Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Miyuki Tamura
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Kenta Kobashi
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Ryota Koyama
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Hisayo Fukushima
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Tomoko Ohashi
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masashi Idogawa
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Kazuhiro Ogi
- Department of Oral Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroyoshi Hiratsuka
- Department of Oral Surgery, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Yasushi Sasaki
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| |
Collapse
|
13
|
Han D, Chand R, Kim YS. Microscale loop-mediated isothermal amplification of viral DNA with real-time monitoring on solution-gated graphene FET microchip. Biosens Bioelectron 2017; 93:220-225. [DOI: 10.1016/j.bios.2016.08.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 01/06/2023]
|
14
|
Feng C, Mao X, Shi H, Bo B, Chen X, Chen T, Zhu X, Li G. Detection of microRNA: A Point-of-Care Testing Method Based on a pH-Responsive and Highly Efficient Isothermal Amplification. Anal Chem 2017; 89:6631-6636. [PMID: 28553714 DOI: 10.1021/acs.analchem.7b00850] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Laborious and costly detection of miRNAs has brought challenges to its practical applications, especially for home health care, rigorous military medicine, and the third world. In this work, we present a pH-responsive miRNA amplification method, which allows the detection of miRNA just using a pH test paper. The operation is easy and no other costly instrument is involved, making the method very friendly. In our strategy, a highly efficient isothermal amplification of miRNA is achieved using an improved netlike rolling circle amplification (NRCA) technique. Large amounts of H+ can be produced as a byproduct during the amplification to induce significant changes of pH, which can be monitored directly using a pH test paper or pH-sensitive indicators. The degree of color changes depends on the amount of miRNA, making it possible for quantitative analysis. As an example, the method is successfully applied to quantify a miRNA (miR-21) in cancer cells. The results agree well with that from the prevalent qRT-PCR analysis. It is the first time that a paper-based point-of-care testing (POCT) is developed for the detection of miRNAs, which might promote the popularization of miRNAs working as biomarkers for diagnostic purposes.
Collapse
Affiliation(s)
- Chang Feng
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Xiaoxia Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China
| | - Bing Bo
- Department of Medical Oncology, Shanghai Pulmonary Hospital Tongji University School of Medicine , Shanghai 200433, P. R. China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, P. R. China.,Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University , Shanghai 200444, P. R. China
| |
Collapse
|
15
|
Jiang X, Dong D, Bian L, Zou D, He X, Ao D, Yang Z, Huang S, Liu N, Liu W, Huang L. Rapid Detection of Candida albicans by Polymerase Spiral Reaction Assay in Clinical Blood Samples. Front Microbiol 2016; 7:916. [PMID: 27379048 PMCID: PMC4905949 DOI: 10.3389/fmicb.2016.00916] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/27/2016] [Indexed: 12/21/2022] Open
Abstract
Candida albicans is the most common human yeast pathogen which causes mucosal infections and invasive fungal diseases. Early detection of this pathogen is needed to guide preventative and therapeutic treatment. The aim of this study was to establish a polymerase spiral reaction (PSR) assay that rapidly and accurately detects C. albicans and to assess the clinical applicability of PSR-based diagnostic testing. Internal transcribed spacer 2 (ITS2), a region between 5.8S and 28S fungal ribosomal DNA, was used as the target sequence. Four primers were designed for amplification of ITS2 with the PSR method, which was evaluated using real time turbidity monitoring and visual detection using a pH indicator. Fourteen non-C. albicans yeast strains were negative for detection, which indicated the specificity of PSR assay was 100%. A 10-fold serial dilution of C. albicans genomic DNA was subjected to PSR and conventional polimerase chain reaction (PCR) to compare their sensitivities. The detection limit of PSR was 6.9 pg/μl within 1 h, 10-fold higher than that of PCR (69.0 pg/μl). Blood samples (n = 122) were collected from intensive care unit and hematological patients with proven or suspected C. albicans infection at two hospitals in Beijing, China. Both PSR assay and the culture method were used to analyze the samples. Of the 122 clinical samples, 34 were identified as positive by PSR. The result was consistent with those obtained by the culture method. In conclusion, a novel and effective C. albicans detection assay was developed that has a great potential for clinical screening and point-of-care testing.
Collapse
Affiliation(s)
- Xiaoqun Jiang
- School of Environment and Natural Resources, Renmin University of China Beijing, China
| | - Derong Dong
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Lihong Bian
- Department of Gynecology, 307th Hospital of Chinese People's Liberation Army Beijing, China
| | - Dayang Zou
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xiaoming He
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Da Ao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Zhan Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Simo Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Ningwei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Liuyu Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| |
Collapse
|
16
|
Sasaki Y, Tamura M, Koyama R, Nakagaki T, Adachi Y, Tokino T. Genomic characterization of esophageal squamous cell carcinoma: Insights from next-generation sequencing. World J Gastroenterol 2016; 22:2284-2293. [PMID: 26900290 PMCID: PMC4735002 DOI: 10.3748/wjg.v22.i7.2284] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/29/2015] [Accepted: 12/19/2015] [Indexed: 02/06/2023] Open
Abstract
Two major types of cancer occur in the esophagus: squamous cell carcinoma, which is associated with chronic smoking and alcohol consumption, and adenocarcinoma, which typically arises in gastric reflux-associated Barrett's esophagus. Although there is increasing incidence of esophageal adenocarcinoma in Western counties, esophageal squamous cell carcinoma (ESCC) accounts for most esophageal malignancies in East Asia, including China and Japan. Technological advances allowing for massively parallel, high-throughput next-generation sequencing (NGS) of DNA have enabled comprehensive characterization of somatic mutations in large numbers of tumor samples. Recently, several studies were published in which whole exome or whole genome sequencing was performed in ESCC tumors and compared with matched normal DNA. Mutations were validated in several genes, including in TP53, CDKN2A, FAT1, NOTCH1, PIK3CA, KMT2D and NFE2L2, which had been previously implicated in ESCC. Several new recurrent alterations have also been identified in ESCC. Combining the clinicopathological characteristics of patients with information obtained from NGS studies may lead to the development of effective diagnostic and therapeutic approaches for ESCC. As this research becomes more prominent, it is important that gastroenterologist become familiar with the various NGS technologies and the results generated using these methods. In the present study, we describe recent research approaches using NGS in ESCC.
Collapse
|
17
|
Feng H, Wang X, Zhang Z, Tang C, Ye H, Jones L, Lou F, Zhang D, Jiang S, Sun H, Dong H, Zhang G, Liu Z, Dong Z, Guo B, Yan H, Yan C, Wang L, Su Z, Li Y, Nandakumar V, Huang XF, Chen SY, Liu D. Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing. Cancer Inform 2015; 14:83-93. [PMID: 26244006 PMCID: PMC4489668 DOI: 10.4137/cin.s22941] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/21/2015] [Accepted: 01/22/2015] [Indexed: 12/18/2022] Open
Abstract
Lung cancer remains the most prevalent malignancy and the primary cause of cancer-related deaths worldwide. Unique mutations patterns can be found in lung cancer subtypes, in individual cancers, or within a single tumor, and drugs that target these genetic mutations and signal transduction pathways are often beneficial to patients. In this study, we used the Ion Torrent AmpliSeq Cancer Panel to sequence 737 loci from 45 cancer-related genes and oncogenes to identify genetic mutations in 48 formalin-fixed, paraffin-embedded (FFPE) human lung cancer samples from Chinese patients. We found frequent mutations in EGFR, KRAS, PIK3CA, and TP53 genes. Moreover, we observed that a portion of the lung cancer samples harbored two or more mutations in these key genes. This study demonstrates the feasibility of using the Ion Torrent sequencing to efficiently identify genetic mutations in individual tumors for targeted lung cancer therapy.
Collapse
Affiliation(s)
- Hongxiang Feng
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Xiaowei Wang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Zhenrong Zhang
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | | | - Hua Ye
- San Valley Biotechnology Inc., Beijing, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Feng Lou
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - Hong Sun
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - Zhiyuan Liu
- San Valley Biotechnology Inc., Beijing, China
| | | | | | - He Yan
- San Valley Biotechnology Inc., Beijing, China
| | - Chaowei Yan
- San Valley Biotechnology Inc., Beijing, China
| | - Lu Wang
- San Valley Biotechnology Inc., Beijing, China
| | - Ziyi Su
- San Valley Biotechnology Inc., Beijing, China
| | - Yangyang Li
- San Valley Biotechnology Inc., Beijing, China
| | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xue F Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Deruo Liu
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| |
Collapse
|
18
|
Huang X, Yu H, Liu X, Jiang Y, Yan M, Wu D. A Dual-Mode Large-Arrayed CMOS ISFET Sensor for Accurate and High-Throughput pH Sensing in Biomedical Diagnosis. IEEE Trans Biomed Eng 2015; 62:2224-33. [PMID: 25850082 DOI: 10.1109/tbme.2015.2419233] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
GOAL The existing ISFET-based DNA sequencing detects hydrogen ions released during the polymerization of DNA strands on microbeads, which are scattered into microwell array above the ISFET sensor with unknown distribution. However, false pH detection happens at empty microwells due to crosstalk from neighboring microbeads. In this paper, a dual-mode CMOS ISFET sensor is proposed to have accurate pH detection toward DNA sequencing. METHODS Dual-mode sensing, optical and chemical modes, is realized by integrating a CMOS image sensor (CIS) with ISFET pH sensor, and is fabricated in a standard 0.18-μm CIS process. With accurate determination of microbead physical locations with CIS pixel by contact imaging, the dual-mode sensor can correlate local pH for one DNA slice at one location-determined microbead, which can result in improved pH detection accuracy. Moreover, toward a high-throughput DNA sequencing, a correlated-double-sampling readout that supports large array for both modes is deployed to reduce pixel-to-pixel nonuniformity such as threshold voltage mismatch. RESULTS The proposed CMOS dual-mode sensor is experimentally examined to show a well correlated pH map and optical image for microbeads with a pH sensitivity of 26.2 mV/pH, a fixed pattern noise (FPN) reduction from 4% to 0.3%, and a readout speed of 1200 frames/s. CONCLUSION A dual-mode CMOS ISFET sensor with suppressed FPN for accurate large-arrayed pH sensing is proposed and demonstrated with state-of-the-art measured results toward accurate and high-throughput DNA sequencing. SIGNIFICANCE The developed dual-mode CMOS ISFET sensor has great potential for future personal genome diagnostics with high accuracy and low cost.
Collapse
|
19
|
Reshetilov AN. Biosensors and biofuel cells: Research focused on practical application (Review). APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815020167] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Visual detection of isothermal nucleic acid amplification using pH-sensitive dyes. Biotechniques 2015; 58:59-68. [PMID: 25652028 DOI: 10.2144/000114253] [Citation(s) in RCA: 407] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/20/2014] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid amplification is the basis for many molecular diagnostic assays. In these cases, the amplification product must be detected and analyzed, typically requiring extended workflow time, sophisticated equipment, or both. Here we present a novel method of amplification detection that harnesses the pH change resulting from amplification reactions performed with minimal buffering capacity. In loop-mediated isothermal amplification (LAMP) reactions, we achieved rapid (<30 min) and sensitive (<10 copies) visual detection using pH-sensitive dyes. Additionally, the detection can be performed in real time, enabling high-throughput or quantitative applications. We also demonstrate this visual detection for another isothermal amplification method (strand-displacement amplification), PCR, and reverse transcription LAMP (RT-LAMP) detection of RNA. The colorimetric detection of amplification presented here represents a generally applicable approach for visual detection of nucleic acid amplification, enabling molecular diagnostic tests to be analyzed immediately without the need for specialized and expensive instrumentation.
Collapse
|
21
|
Molecular diagnostics of the HBB gene in an Omani cohort using bench-top DNA Ion Torrent PGM technology. Blood Cells Mol Dis 2014; 53:133-7. [DOI: 10.1016/j.bcmd.2014.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/06/2014] [Indexed: 11/22/2022]
|
22
|
Xu Z, Huo X, Tang C, Ye H, Nandakumar V, Lou F, Zhang D, Jiang S, Sun H, Dong H, Zhang G, Liu Z, Dong Z, Guo B, Yan H, Yan C, Wang L, Su Z, Li Y, Gu D, Zhang X, Wu X, Wei X, Hong L, Zhang Y, Yang J, Gong Y, Tang C, Jones L, Huang XF, Chen SY, Chen J. Frequent KIT mutations in human gastrointestinal stromal tumors. Sci Rep 2014; 4:5907. [PMID: 25080996 PMCID: PMC4118194 DOI: 10.1038/srep05907] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 05/07/2014] [Indexed: 01/07/2023] Open
Abstract
Identifying gene mutations in individual tumors is critical to improve the efficacy of cancer therapy by matching targeted drugs to specific mutations. Gastrointestinal stromal tumors (GIST) are stromal or mesenchymal subepithelial neoplasms affecting the gastrointestinal tract and frequently contain activating gene mutations in either KIT or platelet-derived growth factor A (PDGFRA). Although GIST is highly responsive to several selective tyrosine kinase inhibitors, combined use of inhibitors targeting other mutations is needed to further prolong survival in patients with GIST. In this study, we aim to screen and identify genetic mutations in GIST for targeted therapy using the new Ion Torrent next-generation sequencing platform. Utilizing the Ion Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes using DNA extracted from formalin-fixed and paraffin-embedded (FFPE) samples of 121 human gastrointestinal stromal tumors, set up stringent parameters for reliable variant calling by filtering out potential raw base calling errors, and identified frequent mutations in the KIT gene. This study demonstrates the utility of using Ion Torrent sequencing to efficiently identify human cancer mutations. This may provide a molecular basis for clinically developing new drugs targeting these gene mutations for GIST therapy.
Collapse
Affiliation(s)
- Zhi Xu
- 1] Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China [2]
| | - Xinying Huo
- 1] Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China [2]
| | | | - Hua Ye
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Feng Lou
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Dandan Zhang
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Shouwen Jiang
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Hong Sun
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Haichao Dong
- San Valley Biotechnology Inc., Beijing 100044, China
| | | | - Zhiyuan Liu
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Zhishou Dong
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Baishuai Guo
- San Valley Biotechnology Inc., Beijing 100044, China
| | - He Yan
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Chaowei Yan
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Lu Wang
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Ziyi Su
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Yangyang Li
- San Valley Biotechnology Inc., Beijing 100044, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xiaojing Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xiaomin Wu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xiaowei Wei
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Lingzhi Hong
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yangmei Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Jinsong Yang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yonglin Gong
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Cuiju Tang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xue F Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| |
Collapse
|
23
|
Mahdavi M, Samaeian A, Hajmirzaheydarali M, Shahmohammadi M, Mohajerzadeh S, Malboobi MA. Label-free detection of DNA hybridization using a porous poly-Si ion-sensitive field effect transistor. RSC Adv 2014. [DOI: 10.1039/c4ra07433e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
24
|
Xu Z, Huo X, Ye H, Tang C, Nandakumar V, Lou F, Zhang D, Dong H, Sun H, Jiang S, Zhang G, Liu Z, Dong Z, Guo B, He Y, Yan C, Wang L, Su Z, Li Y, Gu D, Zhang X, Wu X, Wei X, Hong L, Zhang Y, Yang J, Gong Y, Tang C, Jones L, Huang XF, Chen SY, Chen J. Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform. PLoS One 2014; 9:e100442. [PMID: 25025766 PMCID: PMC4098916 DOI: 10.1371/journal.pone.0100442] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 05/28/2014] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7%) in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.
Collapse
Affiliation(s)
- Zhi Xu
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xinying Huo
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hua Ye
- San Valley Biotechnology Incorporated, Beijing, China
| | | | - Vijayalakshmi Nandakumar
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Feng Lou
- San Valley Biotechnology Incorporated, Beijing, China
| | - Dandan Zhang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Haichao Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | - Hong Sun
- San Valley Biotechnology Incorporated, Beijing, China
| | - Shouwen Jiang
- San Valley Biotechnology Incorporated, Beijing, China
| | | | - Zhiyuan Liu
- San Valley Biotechnology Incorporated, Beijing, China
| | - Zhishou Dong
- San Valley Biotechnology Incorporated, Beijing, China
| | - Baishuai Guo
- San Valley Biotechnology Incorporated, Beijing, China
| | - Yan He
- San Valley Biotechnology Incorporated, Beijing, China
| | - Chaowei Yan
- San Valley Biotechnology Incorporated, Beijing, China
| | - Lu Wang
- San Valley Biotechnology Incorporated, Beijing, China
| | - Ziyi Su
- San Valley Biotechnology Incorporated, Beijing, China
| | - Yangyang Li
- San Valley Biotechnology Incorporated, Beijing, China
| | - Dongying Gu
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaojing Zhang
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaomin Wu
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xiaowei Wei
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lingzhi Hong
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yangmei Zhang
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jinsong Yang
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yonglin Gong
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Cuiju Tang
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lindsey Jones
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Xue F. Huang
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Si-Yi Chen
- Norris Comprehensive Cancer Center, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jinfei Chen
- Department of Oncology, The Affiliated Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
25
|
Crescentini M, Bennati M, Carminati M, Tartagni M. Noise limits of CMOS current interfaces for biosensors: a review. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2014; 8:278-292. [PMID: 24875287 DOI: 10.1109/tbcas.2013.2262998] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Current sensing readout is one of the most frequent techniques used in biosensing due to the charge-transfer phenomena occurring at solid-liquid interfaces. The development of novel nanodevices for biosensing determines new challenges for electronic interface design based on current sensing, especially when compact and efficient arrays need to be organized, such as in recent trends of rapid label-free electronic detection of DNA synthesis. This paper will review the basic noise limitations of current sensing interfaces with particular emphasis on integrated CMOS technology. Starting from the basic theory, the paper presents, investigates and compares charge-sensitive amplifier architectures used in both continuous-time and discrete-time approaches, along with their design trade-offs involving noise floor, sensitivity to stray capacitance and bandwidth. The ultimate goal of this review is providing analog designers with helpful design rules and analytical tools. Also, in order to present a comprehensive overview of the state-of-the-art, the most relevant papers recently appeared in the literature about this topic are discussed and compared.
Collapse
|
26
|
Ebrahimi A, Dak P, Salm E, Dash S, Garimella SV, Bashir R, Alam MA. Nanotextured superhydrophobic electrodes enable detection of attomolar-scale DNA concentration within a droplet by non-faradaic impedance spectroscopy. LAB ON A CHIP 2013; 13:4248-4256. [PMID: 24056864 PMCID: PMC3886286 DOI: 10.1039/c3lc50517k] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Label-free, rapid detection of biomolecules in microliter volumes of highly diluted solutions (sub-femtomolar) is of essential importance for numerous applications in medical diagnostics, food safety, and chem-bio sensing for homeland security. At ultra-low concentrations, regardless of the sensitivity of the detection approach, the sensor response time is limited by physical diffusion of molecules towards the sensor surface. We have developed a fast, low cost, non-faradaic impedance sensing method for detection of synthetic DNA molecules in DI water at attomolar levels by beating the diffusion limit through evaporation of a micro-liter droplet of DNA on a nanotextured superhydrophobic electrode array. Continuous monitoring of the impedance of individual droplets as a function of evaporation time is exploited to dramatically improve the sensitivity and robustness of detection. Formation of the nanostructures on the electrode surface not only increases the surface hydrophobicity, but also allows robust pinning of the droplet contact area to the sensor surface. These two features are critical for performing highly stable impedance measurements as the droplet evaporates. Using this scheme, the detection limit of conventional non-faradaic methods is improved by five orders of magnitude. The proposed platform represents a step-forward towards realization of ultra-sensitive lab-on-chip biomolecule detectors for real time point-of-care application. Further works are however needed to ultimately realize the full potential of the proposed approach to appraise biological samples in complex buffer solutions rather than in DI water.
Collapse
Affiliation(s)
- Aida Ebrahimi
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | | | | | | | | | | | | |
Collapse
|
27
|
Krüger F, Clare EL, Greif S, Siemers BM, Symondson WOC, Sommer RS. An integrative approach to detect subtle trophic niche differentiation in the sympatric trawling bat speciesMyotis dasycnemeandMyotis daubentonii. Mol Ecol 2013; 23:3657-71. [DOI: 10.1111/mec.12512] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/16/2013] [Accepted: 08/24/2013] [Indexed: 02/02/2023]
Affiliation(s)
- F. Krüger
- Ecology Centre, Landscape Ecology; University of Kiel; Olshausenstr. 75 24418 Kiel Germany
- Echolot Gbr; Eulerstr. 12 48155 Münster Germany
| | - E. L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Rd E1 4NS London UK
| | - S. Greif
- Max Planck Institute for Ornithology, Sensory Ecology; Eberhard-Gwinner-Straβe 4 82319 Seewiesen Germany
| | - B. M. Siemers
- Max Planck Institute for Ornithology, Sensory Ecology; Eberhard-Gwinner-Straβe 4 82319 Seewiesen Germany
| | - W. O. C. Symondson
- Cardiff School of Biosciences; Cardiff University; The Sir Martin Evans Building, Museum Avenue Cardiff CF10 3AX UK
| | - R. S. Sommer
- Ecology Centre, Landscape Ecology; University of Kiel; Olshausenstr. 75 24418 Kiel Germany
| |
Collapse
|
28
|
Akhras MS, Pettersson E, Diamond L, Unemo M, Okamoto J, Davis RW, Pourmand N. The Sequencing Bead Array (SBA), a next-generation digital suspension array. PLoS One 2013; 8:e76696. [PMID: 24116138 PMCID: PMC3792038 DOI: 10.1371/journal.pone.0076696] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/24/2013] [Indexed: 01/26/2023] Open
Abstract
Here we describe the novel Sequencing Bead Array (SBA), a complete assay for molecular diagnostics and typing applications. SBA is a digital suspension array using Next-Generation Sequencing (NGS), to replace conventional optical readout platforms. The technology allows for reducing the number of instruments required in a laboratory setting, where the same NGS instrument could be employed from whole-genome and targeted sequencing to SBA broad-range biomarker detection and genotyping. As proof-of-concept, a model assay was designed that could distinguish ten Human Papillomavirus (HPV) genotypes associated with cervical cancer progression. SBA was used to genotype 20 cervical tumor samples and, when compared with amplicon pyrosequencing, was able to detect two additional co-infections due to increased sensitivity. We also introduce in-house software Sphix, enabling easy accessibility and interpretation of results. The technology offers a multi-parallel, rapid, robust, and scalable system that is readily adaptable for a multitude of microarray diagnostic and typing applications, e.g. genetic signatures, single nucleotide polymorphisms (SNPs), structural variations, and immunoassays. SBA has the potential to dramatically change the way we perform probe-based applications, and allow for a smooth transition towards the technology offered by genomic sequencing.
Collapse
Affiliation(s)
- Michael S. Akhras
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Erik Pettersson
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Lisa Diamond
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Swedish Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Örebro University Hospital, Örebro, Sweden
| | - Jennifer Okamoto
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, California, United States of America
| | - Nader Pourmand
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
| |
Collapse
|
29
|
De Novo DNA Synthesis and Its Biosensor Detection. ACTA ACUST UNITED AC 2013. [DOI: 10.1201/b15589-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
30
|
Toumazou C, Shepherd LM, Reed SC, Chen GI, Patel A, Garner DM, Wang CJA, Ou CP, Amin-Desai K, Athanasiou P, Bai H, Brizido IMQ, Caldwell B, Coomber-Alford D, Georgiou P, Jordan KS, Joyce JC, La Mura M, Morley D, Sathyavruthan S, Temelso S, Thomas RE, Zhang L. Simultaneous DNA amplification and detection using a pH-sensing semiconductor system. Nat Methods 2013; 10:641-6. [PMID: 23749303 DOI: 10.1038/nmeth.2520] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 05/08/2013] [Indexed: 12/11/2022]
Abstract
We developed an integrated chip for real-time amplification and detection of nucleic acid using pH-sensing complementary metal-oxide semiconductor (CMOS) technology. Here we show an amplification-coupled detection method for directly measuring released hydrogen ions during nucleotide incorporation rather than relying on indirect measurements such as fluorescent dyes. This is a label-free, non-optical, real-time method for detecting and quantifying target sequences by monitoring pH signatures of native amplification chemistries. The chip has ion-sensitive field effect transistor (ISFET) sensors, temperature sensors, resistive heating, signal processing and control circuitry all integrated to create a full system-on-chip platform. We evaluated the platform using two amplification strategies: PCR and isothermal amplification. Using this platform, we genotyped and discriminated unique single-nucleotide polymorphism (SNP) variants of the cytochrome P450 family from crude human saliva. We anticipate this semiconductor technology will enable the creation of devices for cost-effective, portable and scalable real-time nucleic acid analysis.
Collapse
|
31
|
Samuel N, Hudson TJ. Translating genomics to the clinic: implications of cancer heterogeneity. Clin Chem 2012; 59:127-37. [PMID: 23151419 DOI: 10.1373/clinchem.2012.184580] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Sequencing of cancer genomes has become a pivotal method for uncovering and understanding the deregulated cellular processes driving tumor initiation and progression. Whole-genome sequencing is evolving toward becoming less costly and more feasible on a large scale; consequently, thousands of tumors are being analyzed with these technologies. Interpreting these data in the context of tumor complexity poses a challenge for cancer genomics. CONTENT The sequencing of large numbers of tumors has revealed novel insights into oncogenic mechanisms. In particular, we highlight the remarkable insight into the pathogenesis of breast cancers that has been gained through comprehensive and integrated sequencing analysis. The analysis and interpretation of sequencing data, however, must be considered in the context of heterogeneity within and among tumor samples. Only by adequately accounting for the underlying complexity of cancer genomes will the potential of genome sequencing be understood and subsequently translated into improved management of patients. SUMMARY The paradigm of personalized medicine holds promise if patient tumors are thoroughly studied as unique and heterogeneous entities and clinical decisions are made accordingly. Associated challenges will be ameliorated by continued collaborative efforts among research centers that coordinate the sharing of mutation, intervention, and outcomes data to assist in the interpretation of genomic data and to support clinical decision-making.
Collapse
Affiliation(s)
- Nardin Samuel
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | |
Collapse
|
32
|
Elliott AM, Radecki J, Moghis B, Li X, Kammesheidt A. Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. J Biomol Tech 2012; 23:24-30. [PMID: 22468138 DOI: 10.7171/jbt.12-2301-003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cystic fibrosis (CF) is one of the most frequently diagnosed autosomal-recessive diseases in the Caucasian population. For general-population CF carrier screening, the American College of Medical Genetics (ACMG)/American College of Obstetricians and Gynecologists (ACOG) have recommended a core panel of 23 mutations that will identify 49-98% of carriers, depending on ethnic background. Using a genotyping technology that can rapidly identify disease-causing mutations is important for high-throughput general-population carrier screening, confirming clinical diagnosis, determining treatment options, and prenatal diagnosis. Here, we describe a proof-of-concept study to determine whether the Ion Torrent Personal Genome Machine (PGM) sequencer platform can reliably identify all ACMG/ACOG 23 CF transmembrane conductance regulator (CFTR) mutations. A WT CF specimen along with mutant DNA specimens representing all 23 CFTR mutations were sequenced bidirectionally on the Ion Torrent 314 chip to determine the accuracy of the PGM for CFTR variant detection. We were able to reliably identify all of the targeted mutations except for 2184delA, which lies in a difficult, 7-mer homopolymer tract. Based on our study, we believe PGM sequencing may be a suitable technology for identifying CFTR mutations in the future. However, as a result of the elevated rate of base-calling errors within homopolymer stretches, mutations within such regions currently need to be evaluated carefully using an alternative method.
Collapse
|
33
|
Stranneheim H, Lundeberg J. Stepping stones in DNA sequencing. Biotechnol J 2012; 7:1063-73. [PMID: 22887891 PMCID: PMC3472021 DOI: 10.1002/biot.201200153] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/21/2012] [Accepted: 07/04/2012] [Indexed: 12/11/2022]
Abstract
In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read-length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics.
Collapse
Affiliation(s)
- Henrik Stranneheim
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
| | | |
Collapse
|
34
|
Lindsay S. Biochemistry and semiconductor electronics--the next big hit for silicon? JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:164201. [PMID: 22465874 PMCID: PMC3489000 DOI: 10.1088/0953-8984/24/16/164201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two recent developments portend a new era for silicon electronics in biomedical applications. Firstly, highly specific chemical recognition and massively parallel sample preparation techniques are being combined with VLSI to make new kinds of analytical chips. Secondly, critical dimensions are beginning to approach the size of biomolecules, opening new pathways for physical interactions between molecules and semiconductor structures. Future generations of hybrid chemical-CMOS devices could revolutionize diagnosis and make personalized medicine cheap enough to become widespread.
Collapse
Affiliation(s)
- Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| |
Collapse
|
35
|
Abstract
Today, resequencing of a human genome can be performed in approximately a week using a single instrument. Thanks to a steady logarithmic rate of increase in performance for DNA sequencing platforms over the past seven years, DNA sequencing is one of the fastest developing technology fields. As the process becomes faster, it opens up possibilities within health care, diagnostics, and entirely new fields of research. Immediate genetic characterization of contagious outbreaks has been exemplified, and with such applications for the direct benefit of human health, expectations of future sensitive, rapid, high-throughput, and cost-effective technologies are steadily growing. Simultaneously, some of the limitations of a rapidly growing field have become apparent, and questions regarding the quality of some of the data deposited into databases have been raised. A human genome sequenced in only an hour is likely to become a reality in the future, but its definition may not be as certain.
Collapse
Affiliation(s)
- Patrik L Ståhl
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
| | | |
Collapse
|
36
|
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011; 21:2224-41. [PMID: 21926179 DOI: 10.1101/gr.126599.111] [Citation(s) in RCA: 320] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
Collapse
Affiliation(s)
- Dent Earl
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HOK, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 2011. [PMID: 21926179 DOI: 10.1101/gr.126599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
Collapse
Affiliation(s)
- Dent Earl
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
|
39
|
Ahmadian A, Svahn HA. Massively parallel sequencing platforms using lab on a chip technologies. LAB ON A CHIP 2011; 11:2653-2655. [PMID: 21503304 DOI: 10.1039/c1lc90035h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Afshin Ahmadian
- Albanova University Center and Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, Sweden
| | | |
Collapse
|
40
|
Schweiger MR, Kerick M, Timmermann B, Isau M. The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations. Cancer Metastasis Rev 2011; 30:199-210. [PMID: 21267768 DOI: 10.1007/s10555-011-9278-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The development of cancer is characterized by the joined occurrence of alterations on different levels--from single nucleotide changes via structural and copy number variations to epigenetic alterations. With the advent of advanced technologies such as next generation sequencing, we have now the tools in hands to put some light on complex processes and recognize systematic patterns that develop throughout cancer progression. The combination of single hypothesis-driven experiments with a system-wide genetic view enables us to prove so far not addressable questions such as the influence of DNA methylation on gene expression or the disruption of genome homeostasis by structural variations and miRNA expression patterns. Out of this enormous amount of information, specific biomarkers for cancer progression have been discovered, which pave the way for the development of new therapeutic strategies. Here, we will review the status quo of integrative cancer genomic approaches, give an overview over the power of next generation sequencing technologies in oncology, and outline future perspective. Both sides--clinical as well as basic research aspects--will be considered.
Collapse
Affiliation(s)
- Michal R Schweiger
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | | | | | | |
Collapse
|
41
|
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475:348-52. [PMID: 21776081 DOI: 10.1038/nature10242] [Citation(s) in RCA: 1141] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 05/26/2011] [Indexed: 12/16/2022]
|
42
|
Sun Z, Qiang W, Li H, Hao N, Xu D, Chen HY. Electric detection of DNA with PDMS microgap electrodes and silver nanoparticles. Analyst 2010; 136:540-4. [PMID: 21079881 DOI: 10.1039/c0an00512f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work a novel microdevice sensor has been developed by plating gold on the PDMS surface to generate a sandwich-type gap electrode for DNA detection. The microdevice utilizes a gold band electrode-PDMS-gold band electrode configuration and the minimum detectable volume could be as low as 5 μL. The 20 μm PDMS-based gap was chemically modified with DNA capture probes and DNA sandwich hybrids were formed with the addition of DNA target and silver nanoparticle probes. To increase detection sensitivity, parallel detection zones have been developed in which the relevant resistances decrease substantially upon hybridyzation. By measuring the change in electrical conductivity, the DNA target in the concentration range of 1000-0.1 nM can be assayed and the limit of lowest detectable concentration was achieved at 0.01 nM.
Collapse
Affiliation(s)
- Ziyin Sun
- Key Lab of Analytical Chemistry for Life Science, Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, China
| | | | | | | | | | | |
Collapse
|
43
|
The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics. Anal Bioanal Chem 2010; 399:2313-29. [DOI: 10.1007/s00216-010-3968-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 06/23/2010] [Indexed: 10/19/2022]
|
44
|
Electrochemical detection of oligonucleotide by attaching redox probes onto its backbone. Biosens Bioelectron 2010; 26:2670-4. [PMID: 20400286 DOI: 10.1016/j.bios.2010.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 02/26/2010] [Accepted: 03/13/2010] [Indexed: 11/23/2022]
Abstract
An approach was demonstrated to detect oligonucleotide by attaching redox probes onto its backbone. First, peptide nucleic acid (PNA) with a neutral backbone was immobilized onto a gold (Au) electrode surface as a capture. Second, when the PNA capture hybridized with a target oligonucleotide (a short DNA), an assembly of Au-PNA-DNA formed and phosphate groups were thus brought into the assembly from the DNA's backbone. The linker ion of Zr(4+) exhibits a strong coordination interaction with the phosphate group and the carboxylic group. The hybridized target DNA provides the phosphate group while a derivatized redox probe of ferrocene (Fc) carboxyl acid offers the carboxylic group. Therefore, the redox probe can be attached to the phosphate group by the linker to form an assembly of Au-PNA-DNA-Zr-Fc. Its redox process was studied and the detection conditions of oligonucleotide were optimized. A limit of detection of 1.0×10(-12) M or ∼2 attomol was reached.
Collapse
|
45
|
Fang C, Fan Y, Kong J, Gao Z, Balasubramanian N. Electrical detection of oligonucleotide using an aggregate of gold nanoparticles as a conductive tag. Anal Chem 2009; 80:9387-94. [PMID: 19072259 DOI: 10.1021/ac801433z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-specific DNA detection is a routine job in medical diagnostics and genetic screening. Alternative to a fluorescence readout scheme or electrophoresis approach, various kinds of rapid, low-cost, facile, and label-free methods have also been developed in last decades. Among these, direct electrical detection of DNA received increasing attention but more research is desirable. Particularly, enhancement with high discrimination must be employed to selectively amplify the responding signal. A chip-based biosensor was developed in this work to electrically detect 22-mer oligonucleotide DNA at low concentration, from 50 fM to 10 pM. First, a gold nanoparticle (NP) was capped with 3-mercaptopropionic acid through a thiol-gold bond. The derivatized carboxylic acid group showed strong complex interaction with an inorganic linker, Zr(4+). As a result, Zr(4+) could link several hundreds of individual gold NPs together to form an aggregate of nanoparticles (ANP), which was capable of being used as a conductive tag for the electrical detection of DNA. Second, in order to achieve the discriminative localization of ANP to bridge two comb-shaped electrodes (with height of approximately 50 nm and interdistance of 300-350 nm) gapped with insulative material of silicon oxide, peptide nucleic acids were covalently bonded to the silicon oxide in the gap as capture sites for DNA. After hybridization with target DNA, the charged phosphate-containing backbone of DNA was introduced into the gap. Phosphate groups also exhibited strong complex interaction with the linker of Zr(4+) and could react with the residual Zr(4+) on the ANP surface. As a consequence, the conductive tags were linked to the phosphate groups and localized into the gap, which could modify the conductance between the two comb-shaped electrodes in turn. The degree of modification correlated directly to the amount of hybridized DNA and to the concentration of target DNA in sample solution. Compared with the individual NPs used as the tag, a strong enhancement from the gold ANP was obtained.
Collapse
Affiliation(s)
- Cheng Fang
- Institute of Microelectronics, Agency for Science, Technology and Research, 11 Science Park Road, Science Park II, 117685, Republic of Singapore.
| | | | | | | | | |
Collapse
|
46
|
Scaini D, Castronovo M, Casalis L, Scoles G. Electron transfer mediating properties of hydrocarbons as a function of chain length: a differential scanning conductive tip atomic force microscopy investigation. ACS NANO 2008; 2:507-515. [PMID: 19206577 DOI: 10.1021/nn700342p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The development of novel molecular and biomolecular devices relies on the understanding of charge transport across molecule-substrate interfaces. However, different strategies adopted so far for fabricating and studying transport through metal-molecule-metal junctions yield values for the transport coefficients that differ by up to orders of magnitude even for the same junction. Conductive tip atomic force microscopy (CT-AFM) allows for the simultaneous measurement of transport and morphological properties of molecular assemblies, but absolute transport measurements depend on the nature of the AFM tip-molecule contact. In this work we present a differential approach to the study of metal-molecule-metal junctions based on the combination of AFM-driven nanolithography and CT-AFM. We nanograft patches of alkanethiol molecules in a self-assembled monolayer of alkanethiol molecules of different chain length and measure by CT-AFM the morphology and the transport properties of the nanopatches and of the reference layer. The method allows for the determination of the differential resistance between the two molecular layers and is thus independent of environmental factors. The validity of this approach is demonstrated by measuring the tunneling decay constant of alkanethiols as a function of their length.
Collapse
Affiliation(s)
- Denis Scaini
- SISSA/ETTRA NanoInnovation Laboratory, Sincrotrone Trieste, S.S.14 Km 163.5, 34012 Basovizza, Trieste, Italy
| | | | | | | |
Collapse
|
47
|
Anderson EP, Daniels JS, Yu H, Karhanek M, Lee TH, Davis RW, Pourmand N. A System for Multiplexed Direct Electrical Detection of DNA Synthesis. SENSORS AND ACTUATORS. B, CHEMICAL 2008; 129:79-86. [PMID: 19183700 PMCID: PMC2344141 DOI: 10.1016/j.snb.2007.07.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
An electronic system for the multiplexed detection of DNA polymerization is designed and characterized. DNA polymerization is detected by the measurement of small transient currents arising from ion diffusion during polymerization. A transimpedance amplifier is used to detect these small currents; we implemented a twenty-four channel recording system on a single printed circuit board. Various contributions to the input-referred current noise are analyzed and characterized, as it limits the minimum detectable current and thus the biological limit of detection. We obtained 8.5 pA RMS mean noise current (averaged over all 24 channels) over the recording bandwidth (DC to 2 kHz). With digital filtering, the input-referred current noise of the acquisition system is reduced to 2.4 pA, which is much lower than the biological noise. Electrical crosstalk between channels is measured, and a model for the crosstalk is presented. Minimizing the crosstalk is critical because it can lead to erroneous microarray data. With proper precautions, crosstalk is reduced to a negligible value (less than 1.4%). Using a micro-fabricated array of 24 gold electrodes, we demonstrated system functionality by detecting the presence of a target DNA oligonucleotide which hybridized onto its corresponding target.
Collapse
Affiliation(s)
- Erik P Anderson
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
| | | | | | | | | | | | | |
Collapse
|
48
|
Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
Collapse
Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| |
Collapse
|