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Khan MYA, Dai D, Su X, Tian J, Zhou J, Ma L, Wang Y, Wen W, Zhang Y. Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet 2024; 55:457-464. [PMID: 38622758 DOI: 10.1111/age.13432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
The common deleterious genetic defects in Holstein cattle include haplotypes 1-6 (HH1-HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single-tube multiplex fluorescent amplification-refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3' end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf-ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf-ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.
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Affiliation(s)
- Md Yousuf Ali Khan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | - Dongmei Dai
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Su
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia Tian
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Jiamin Zhou
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Liqin Ma
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wan Wen
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Tong Z, Shen C, Li Q, Yin H, Mao H. Combining sensors and actuators with electrowetting-on-dielectric (EWOD): advanced digital microfluidic systems for biomedical applications. Analyst 2023; 148:1399-1421. [PMID: 36752059 DOI: 10.1039/d2an01707e] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The concept of digital microfluidics (DMF) enables highly flexible and precise droplet manipulation at a picoliter scale, making DMF a promising approach to realize integrated, miniaturized "lab-on-a-chip" (LOC) systems for research and clinical purposes. Owing to its simplicity and effectiveness, electrowetting-on-dielectric (EWOD) is one of the most commonly studied and applied effects to implement DMF. However, complex biomedical assays usually require more sophisticated sample handling and detection capabilities than basic EWOD manipulation. Alternatively, combined systems integrating EWOD actuators and other fluidic handling techniques are essential for bringing DMF into practical use. In this paper, we briefly review the main approaches for the integration/combination of EWOD with other microfluidic manipulation methods or additional external fields for specified biomedical applications. The form of integration ranges from independently operating sub-systems to fully coupled hybrid actuators. The corresponding biomedical applications of these works are also summarized to illustrate the significance of these innovative combination attempts.
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Affiliation(s)
- Zhaoduo Tong
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China. .,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanjie Shen
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China. .,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiushi Li
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
| | - Hao Yin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China. .,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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Feng L, Wu H, Yue H, Chu Y, Zhang J, Huang X, Pang S, Zhang L, Li Y, Wang W, Zou B, Zhou G. Multiplexed and Rapid AST for Escherichia coli Infection by Simultaneously Pyrosequencing Multiple Barcodes Each Specific to an Antibiotic Exposed to a Sample. Anal Chem 2022; 94:8633-8641. [PMID: 35675678 DOI: 10.1021/acs.analchem.2c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antimicrobial susceptibility testing (AST) is an effective way to guide antibiotic selection. However, conventional culture-based phenotypic AST is time-consuming. The key point to shorten the test is to quantify the small change in the bacterial number after the antibiotic exposure. To achieve rapid AST, we proposed a combination of multiplexed PCR with barcoded pyrosequencing to significantly shorten the time for antibiotic exposure. First, bacteria exposed to each antibiotic were labeled with a unique barcode. Then, the pool of the barcoded products was amplified by PCR with a universal primer pair. Finally, barcodes in the amplicons were individually and quantitatively decoded by pyrosequencing. As pyrosequencing is able to discriminate as low as 5% variation in target concentrations, as short as 7.5 min was enough for cultivation to detect the susceptibility of Escherichia coli to an antibiotic. The barcodes enable more than six kinds of drugs or six kinds of concentrations of a drug to be tested at a time. The susceptibility of 6 antibiotics to 43 E. coli-positive samples from 482 clinical urine samples showed a consistency of 99.3% for drug-resistant samples and of 95.7% for drug-sensitive samples in comparison with the conventional method. In addition, the minimum inhibitory concentration (MIC) of 29 E. coli samples was successfully measured. The proposed AST is dye free (pyrosequencing), multiplexed (six antibiotics), fast (a half-working day for reporting the results), and able to detect the MIC, thus having a great potential for clinical use in quick antibiotic selection.
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Affiliation(s)
- Liying Feng
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, China
| | - Huijie Yue
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Jieyu Zhang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Xiaohui Huang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Shuyun Pang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Likun Zhang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Yujiao Li
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China
| | - Weiping Wang
- Department of Clinical Laboratory, Jinling Hospital, Medical School of Nanjing University, Nanjing 210002, China
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing 210002, China.,School of Pharmaceutical Science, Southern Medical University, Guangzhou 510515, China
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Cheng C, Xiao P. Evaluation of the correctable decoding sequencing as a new powerful strategy for DNA sequencing. Life Sci Alliance 2022; 5:5/8/e202101294. [PMID: 35422436 PMCID: PMC9012935 DOI: 10.26508/lsa.202101294] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/01/2022] Open
Abstract
This article proposed the correctable decoding sequencing technology with conservative theoretical error rate of 0.0009%, and evaluated its robustness by simulation. This technology can provide a powerful new protocol for NGS platforms, enabling accurate identification of rare mutations in medicine. Next-generation sequencing (NGS) promises to revolutionize precision medicine, but the existing sequencing technologies are limited in accuracy. To overcome this limitation, we propose the correctable decoding sequencing strategy, which is a duplex sequencing protocol with conservative theoretical error rates of 0.0009%. This rate is lower than that for Sanger sequencing. Here, we simulate the sequencing reactions by the self-developed software, and find that this approach has great potential in NGS in terms of sequence decoding, reassembly, error correction, and sequencing accuracy. Besides, this approach can be compatible with most SBS-based sequencing platforms, and also has the ability to compensate for some of the shortcomings of NGS platforms, thereby broadening its application for researchers. Hopefully, it can provide a powerful new protocol that can be used as an alternative to the existing NGS platforms, enabling accurate identification of rare mutations in a variety of applications in biology and medicine.
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Affiliation(s)
- Chu Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Iqbal F, Shabbir MI. Genetic analysis with pyrosequencing using loop pipetting and a light dependent resistor. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5035-5047. [PMID: 34647115 DOI: 10.1039/d1ay01123e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA sequencing is among the most important techniques in biology to decipher the key genetic players of health and disease. The existing laboratory instruments for DNA sequencing are well established and reliable. However, these instruments are still out of reach of most laboratories in the world due to very high equipment and running costs and require trained personnel to keep them running. These instruments are also large and bulky making them unsuitable for analysis in remote settings away from laboratories. Here we describe a proof-of-concept of a DNA sequencing device LoopSeeq using a simple approach to address the said problems without minimizing the quality of results. The device was designed to perform pyrosequencing by iterative addition of dNTPs by contact dispensing through a loop pipette (loopette) and detection of chemiluminiscence with the cheapest sensor in the market, a light dependent resistor (LDR). Two small geared motors drive the moving parts in a controlled and coordinated manner with the help of a motor driver circuit, an Arduino Nano microcontroller and two small neodymium magnets. The real-time light intensity data from the LDR were transferred to a laptop computer for further analysis. Pyrosequencing was optimized using 55 nt self-primed oligo. In order to demonstrate the DNA sequencing ability with real samples, molecular genetic analysis was performed for a previously identified novel mutation from our lab in exon4 of the OCA2 gene. LoopSeeq successfully identified the homozygous normal (c.408-409_AA), homozygous mutant (c.408-409_delAA) and heterozygous carrier (c.408-409_AA/delAA) alleles in three individuals of a family affected with oculocutaneous albinism (OCA). Further, this can be implemented for molecular diagnostic applications for bacterial, viral or other pathogen detection and genotyping among different subtypes following some reports described earlier. A few drawbacks in the current implementation including the evaporation of liquid reagents, possible loopette contamination, etc. associated with use for longer times are also described along with suggestions to rectify these problems in future designs. With the described capabilities, the LoopSeeq device can be implemented in routine labs as well as in several real-world situations where conventional DNA sequencing instruments are unfeasible, for example, diagnostic testing at remote settings or at the point-of-care.
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Affiliation(s)
- Faisal Iqbal
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
| | - Muhammad Imran Shabbir
- Department of Biological Sciences, Faculty of Basic & Applied Sciences, International Islamic University, Sector H-10, Islamabad, Pakistan.
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8
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Radhakrishnan A, Kuppusamy G, Ponnusankar S, Mutalik S. Towards next-generation personalization of tacrolimus treatment: a review on advanced diagnostic and therapeutic approaches. Pharmacogenomics 2021; 22:1151-1175. [PMID: 34719935 DOI: 10.2217/pgs-2021-0008] [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: 11/21/2022] Open
Abstract
The benefit of personalized medicine is that it allows the customization of drug therapy - maximizing efficacy while avoiding side effects. Genetic polymorphisms are one of the major contributors to interindividual variability. Currently, the only gold standard for applying personalized medicine is dose titration. Because of technological advancements, converting genotypic data into an optimum dose has become easier than in earlier years. However, for many medications, determining a personalized dose may be difficult, leading to a trial-and-error method. On the other hand, the technologically oriented pharmaceutical industry has a plethora of smart drug delivery methods that are underutilized in customized medicine. This article elaborates the genetic polymorphisms of tacrolimus as case study, and extensively covers the diagnostic and therapeutic technologies which aid in the delivery of personalized tacrolimus treatment for better clinical outcomes, thereby providing a new strategy for implementing personalized medicine.
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Affiliation(s)
- Arun Radhakrishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Sivasankaran Ponnusankar
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Karnataka, India
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Ghemrawi M, Fischinger F, Duncan G, Dukes MJ, Guilliano M, McCord B. Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Sci Int Genet 2021; 55:102560. [PMID: 34507077 DOI: 10.1016/j.fsigen.2021.102560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In crime scenes, biological exhibits are often human in origin, yet biological stains from other fauna may also be present at a crime scene, creating confusion during an investigation. Furthermore, identifying the source of a biological sample can be critical during an investigation. To identify the presence of biological material from non-human sources, it is common to use genetic markers within mitochondrial DNA such as cytochrome b, 16S rRNA, and 12S rRNA genes. This process usually requires DNA sequencing, a process that is neither quick nor easy. In general, a faster, more standardized method for species identification from tissue and body fluids is desirable.For this reason, we have developed a vertebrate specific real-time quantitation method that is followed by an automated pyrosequencing-based procedure that sequences a short fragment within the 12S rRNA gene. Using no more than 35 bases, the assay can distinguish between 32 different species commonly found in and around a household with a turnaround time of 6 h from extraction to sequencing. -Using this procedure, up to 48 samples can be run at a time without the need for expensive reagents or bioinformatic skills.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Dania Beach, Fl 33004, United State
| | | | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
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Wei R, Fei Z, Liu Y, Fu B, Chen L, Wang L, Xiao P. A digital coding combination analysis for mutational genotyping using pyrosequencing. Electrophoresis 2021; 42:1262-1269. [PMID: 33641189 DOI: 10.1002/elps.202000327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/25/2021] [Accepted: 02/16/2021] [Indexed: 11/07/2022]
Abstract
In the present study, we developed a novel digital coding combination analysis (DCCA) to analyze the gene mutation based on the sample combination principle. The principle is that any numerically named sample is divided into two groups, any two samples are not grouped in the same two groups, and any sample can be tested within the detection limit. Therefore, we proposed a specific combination that N samples were divided into M groups. Then N samples were analyzed, which could obtain the mutation results of M mixed groups. If only two groups showed positive (mutant type) signals, the same sample number from two positive signal groups would be the positive sample, and the remaining samples were negative (wild type). If three groups or more exhibited positive results, the same sample number from three positive signal groups would be the positive sample. If some samples remained uncertain, individual samples could be analyzed on a small scale. In the present study, we used the two genotypes of a mutation site (A5301G) to verify whether it was a useful and promising method. The results showed that we could quantitatively detect mutations and demonstrate 100% consistent results against a panel of defined mixtures with the detection limit using pyrosequencing. This method was suitable, sensitive, and reproducible for screening and analyzing low-frequency mutation samples, which could reduce reagent consumption and cost by approximately 70-80% compared with conventional clinical methods.
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Affiliation(s)
- Rongbin Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Zhongjie Fei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Yanrong Liu
- Heze Center for Disease Control and Prevention, Heze, P. R. China
| | - Bangwen Fu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Ling Chen
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Liu Wang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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11
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Recent developments in molecular sensor designs for inorganic pyrophosphate detection and biological imaging. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213744] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Photocatalytic Inactivation as a Method of Elimination of E. coli from Drinking Water. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11031313] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The presence of microorganisms, specifically the Escherichia coli, in drinking water is of global concern. This is mainly due to the health implications of these pathogens. Several conventional methods have been developed for their removal; however, this pathogen is still found in most drinking water. In the continuous quest for a more effective removal approach, photocatalysis has been considered as an alternative method for the elimination of pathogens including E. coli from water. Photocatalysis has many advantages compared to the conventional methods. It offers the advantage of non-toxicity and utilizes the energy from sunlight, thereby making it a completely green route. Since most photocatalysts could only be active in the ultraviolet region of the solar spectrum, which is less than 5% of the entire spectrum, the challenge associated with photocatalysis is the design of a system for the effective harvest and complete utilization of the solar energy for the photocatalytic process. In this review, different photocatalysts for effective inactivation of E. coli and the mechanism involved in the process were reviewed. Various strategies that have been adopted in order to modulate the band gap energy of these photocatalysts have been explored. In addition, different methods of estimating and detecting E. coli in drinking water were presented. Furthermore, different photocatalytic reactor designs for photocatalytic inactivation of E. coli were examined. Finally, the kinetics of E. coli inactivation was discussed.
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Yu H, Du L, Yi S, Wang Q, Zhu Y, Qiu Y, Jiang Y, Li M, Wang D, Wang Q, Yuan G, Cao Q, Kijlstra A, Yang P. Epigenome-wide association study identifies Behçet's disease-associated methylation loci in Han Chinese. Rheumatology (Oxford) 2020; 58:1574-1584. [PMID: 30863869 DOI: 10.1093/rheumatology/kez043] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVE The aetiology of Behçet's disease (BD), known as a systemic vasculitis, is not completely understood. Increasing evidence suggests that aberrant DNA methylation may contribute to the pathogenesis of BD. The aim of this epigenome-wide association study was to identify BD-associated methylation loci in Han Chinese. METHODS Genome-wide DNA methylation profiles were compared between 60 BD patients and 60 healthy controls using the Infinium Human Methylation 450 K Beadchip. BD-associated methylation loci were validated in 100 BD patients and 100 healthy controls by pyrosequencing. Gene expression and cytokine production was quantified by real-time PCR and ELISA. RESULTS A total of 4332 differentially methylated CpG sites were associated with BD. Five differentially methylated CpG sites (cg03546163, cg25114611, cg20228731, cg23261343 and cg14290576) revealed a significant hypomethylation status across four different genes (FKBP5, FLJ43663, RUNX2 and NFIL3) and were validated by pyrosequencing. Validation results showed that the most significant locus was located in the 5'UTR of FKBP5 (cg03546163, P = 3.81E-13). Four CpG sites with an aberrant methylation status, including cg03546163, cg25114611, cg23261343 and cg14290576, may serve as a diagnostic marker for BD (area under the receiver operating curve curve = 83.95%, 95% CI 78.20, 89.70%). A significantly inverse correlation was found between the degree of methylation at cg03546163 as well as cg25114611 and FKBP5 mRNA expression. Treatment with a demethylation agent, 5-Aza-2'-deoxycytidine resulted in an increase of FKBP5 mRNA expression and a stimulated IL-1β production. CONCLUSION Our findings suggest that aberrant DNA methylation, independently of previously known genetic variants, plays a vital role in the pathogenesis of BD. TRIAL REGISTRATION Chinese Clinical Trial Registry, chictr.org.cn, ChiCTR-CCC-12002184.
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Affiliation(s)
- Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Liping Du
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Shenglan Yi
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yunyun Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yiguo Qiu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Yan Jiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Minghui Li
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Detao Wang
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Qing Wang
- Shanghai Biotechnology Corporation, Shanghai, China and
| | - Gangxiang Yuan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
| | - Aize Kijlstra
- Department of Ophthalmology, University Eye Clinic Maastricht, Maastricht, The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, and Chongqing Eye Institute, Chongqing
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14
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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15
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Robles M, Couturier-Tarrade A, Derisoud E, Geeverding A, Dubois C, Dahirel M, Aioun J, Prezelin A, Calvez J, Richard C, Wimel L, Chavatte-Palmer P. Effects of dietary arginine supplementation in pregnant mares on maternal metabolism, placental structure and function and foal growth. Sci Rep 2019; 9:6461. [PMID: 31015538 PMCID: PMC6478728 DOI: 10.1038/s41598-019-42941-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/27/2019] [Indexed: 12/17/2022] Open
Abstract
Foals born to primiparous mares are lighter and less mature than those born to multiparous dams. Factors driving this difference are not totally understood. Using 7 multiparous and 6 primiparous standardbred mares, we demonstrated that, in late gestation, primiparous mares were less insulin resistant compared to multiparous mares, and that their foals had reduced plasma amino-acid concentrations at birth compared to foals born to multiparous mares. Vascular development, as observed through structure and gene expression, and global DNA methylation were also reduced in primiparous placentas. Another group of 8 primiparous mares was orally supplemented with L-arginine (100 g/day, 210d to term). L-arginine improved pregnancy-induced insulin resistance and increased maternal L-arginine and L-ornithine plasma concentrations but foal plasma amino acid concentrations were not affected at birth. At birth, foal weight and placental biometry, structure, ultra-structure and DNA methylation were not modified. Placental expression of genes involved in glucose and fatty acid transfers was increased. In conclusion, maternal insulin resistance in response to pregnancy and placental function are reduced in primiparous pregnancies. Late-gestation L-arginine supplementation may help primiparous mares to metabolically adapt to pregnancy and improve placental function. More work is needed to confirm these effects and ascertain optimal treatment conditions.
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Affiliation(s)
- Morgane Robles
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | | | - Emilie Derisoud
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Audrey Geeverding
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Cedric Dubois
- IFCE, Station Expérimentale de la Valade, 19370 Chamberet, France
| | - Michele Dahirel
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Josiane Aioun
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Audrey Prezelin
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Juliane Calvez
- UMR PNCA, AgroParisTech, INRA, Université Paris Saclay, 75005 Paris, France
| | - Christophe Richard
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Laurence Wimel
- IFCE, Station Expérimentale de la Valade, 19370 Chamberet, France
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16
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Nie P, Li Z, Wang Y, Zhang Y, Zhao M, Luo J, Du S, Deng Z, Chen J, Wang Y, Chen S, Wang L. Gut microbiome interventions in human health and diseases. Med Res Rev 2019; 39:2286-2313. [PMID: 30994937 DOI: 10.1002/med.21584] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/27/2019] [Accepted: 03/24/2019] [Indexed: 02/06/2023]
Abstract
Ongoing studies have determined that the gut microbiota is a major factor influencing both health and disease. Host genetic factors and environmental factors contribute to differences in gut microbiota composition and function. Intestinal dysbiosis is a cause or a contributory cause for diseases in multiple body systems, ranging from the digestive system to the immune, cardiovascular, respiratory, and even nervous system. Investigation of pathogenesis has identified specific species or strains, bacterial genes, and metabolites that play roles in certain diseases and represent potential drug targets. As research progresses, gut microbiome-based diagnosis and therapy are proposed and applied, which might lead to considerable progress in precision medicine. We further discuss the limitations of current studies and potential solutions.
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Affiliation(s)
- Pengqing Nie
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yimeng Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yubing Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Mengna Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Jie Luo
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shiming Du
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Yunfu Wang
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.,Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
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17
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Zou F, Ruan Q, Lin X, Zhang M, Song Y, Zhou L, Zhu Z, Lin S, Wang W, Yang CJ. Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing. Biosens Bioelectron 2019; 126:551-557. [DOI: 10.1016/j.bios.2018.09.092] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/17/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
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18
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Noronha V, Rajendra A, Joshi A, Patil V, Menon N, Prabhash K. Epidermal growth factor receptor-mutated non-small-cell lung cancer: A primer on contemporary management. CANCER RESEARCH, STATISTICS, AND TREATMENT 2019. [DOI: 10.4103/crst.crst_51_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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19
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Cameron SJ, Takáts Z. Mass spectrometry approaches to metabolic profiling of microbial communities within the human gastrointestinal tract. Methods 2018; 149:13-24. [DOI: 10.1016/j.ymeth.2018.04.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/22/2018] [Indexed: 12/14/2022] Open
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20
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Shi Y, Liu M, Long X, Chen D, Zheng H, Chen S. Effect of abnormal GpG methylation in the second trimester of pregnancy on adverse health risk of offspring. Exp Ther Med 2018; 16:2875-2880. [PMID: 30214509 PMCID: PMC6125837 DOI: 10.3892/etm.2018.6560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/04/2018] [Indexed: 01/18/2023] Open
Abstract
Effect of abnormal GpG methylation in amniotic fluid cells during the second trimester of pregnancy on adverse health risk of offspring was investigated. In total, 237 sets of amniotic fluid cells were collected from patients who received prenatal diagnosis in the Third Affiliated Hospital of Guangzhou Medical University (Guangzhou, China) from April 2010 to October 2011. Among them, 156 sets were from singleton and 81 sets were from twins. H19 gene was amplified by PCR, and the product was purified and pyrosequencing was used to detect the DNA methylation level of GapG. Follow-up records of the birth outcomes of pregnant women's offspring were collected. Positive rate of DNA amplification in 200 cases of amniotic fluid cells was 84.4% (200/237). Average age of singleton pregnancies was higher than that of twins (P<0.05), and no significant differences were found in gestational age and PCR amplification rate (P>0.05). There was no difference in the methylation level of GapG between singleton and twins (P>0.05), but the abnormal methylation rate of GapG1 in twin fetuses was significantly higher than that of singleton (20.3 vs. 3.6%, χ2=8.364, P=0.004). Offspring sex, singleton or twins, mode of delivery, time of pregnancy, and low birth weight showed no significant effect on GapG methylation level of H19 in the second trimester of pregnancy. No offspring deformities were found regardless of the increased or decreased degree of methylation (P>0.05). The number of fetuses born may cause abnormal GapG1 methylation, but no effect of GapG methylation on the adverse health risk of offspring was found.
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Affiliation(s)
- Yu Shi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher-Education Institutes, Guangzhou Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Mingxing Liu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher-Education Institutes, Guangzhou Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Xiaolin Long
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher-Education Institutes, Guangzhou Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Dunjin Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher-Education Institutes, Guangzhou Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Haiyan Zheng
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory for Reproduction and Genetics of Guangdong Higher-Education Institutes, Guangzhou Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510150, P.R. China
| | - Shiling Chen
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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21
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Chen W, Shang Y, Ren L, Xie K, Zhang X, Zhang C, Sun S, Wang Y, Zha L, Guo Y. Developing a MtSNP-based genotyping system for genetic identification of forensically important flesh flies (Diptera: Sarcophagidae). Forensic Sci Int 2018; 290:178-188. [DOI: 10.1016/j.forsciint.2018.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/05/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022]
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22
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Oh Y, Song IC, Kim J, Kwon GC, Koo SH, Kim SY. Pyrosequencing-based quantitative measurement of CALR mutation allele burdens and their clinical implications in patients with myeloproliferative neoplasms. Clin Chim Acta 2018; 483:183-191. [DOI: 10.1016/j.cca.2018.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/17/2018] [Accepted: 05/01/2018] [Indexed: 12/26/2022]
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23
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Busato F, Dejeux E, El Abdalaoui H, Gut IG, Tost J. Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®. Methods Mol Biol 2018; 1708:427-445. [PMID: 29224157 DOI: 10.1007/978-1-4939-7481-8_22] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many protocols for gene-specific DNA methylation analysis are either labor intensive, not quantitative and/or limited to the measurement of the methylation status of only one or very few CpG positions. Pyrosequencing is a real-time sequencing technology that overcomes these limitations. After bisulfite modification of genomic DNA, a region of interest is amplified by PCR with one of the two primers being biotinylated. The PCR generated template is rendered single-stranded and a pyrosequencing primer is annealed to analyze quantitatively cytosine methylation. In comparative studies, pyrosequencing has been shown to be among the most accurate and reproducible technologies for locus-specific DNA methylation analyses and has become a widely used tool for the validation of DNA methylation changes identified in genome-wide studies as well as for locus-specific analyses with clinical impact such as methylation analysis of the MGMT promoter. Advantages of the Pyrosequencing technology are the ease of its implementation, the high quality and the quantitative nature of the results, and its ability to identify differentially methylated positions in close proximity.
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Affiliation(s)
- Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Emelyne Dejeux
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Hafida El Abdalaoui
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Ivo Glynne Gut
- Biomedical Genomics Group, Centro Nacional de Analisis Genomico, CNAG-CRG, Center for Genomic Regulation, Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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24
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Mikata Y, Ohnishi R, Nishijima R, Matsumoto A, Konno H. Pyrophosphate-Induced Intramolecular Excimer Formation in Dinuclear Zinc(II) Complexes with Tetrakisquinoline Ligands. Inorg Chem 2018; 57:7724-7734. [PMID: 29905465 DOI: 10.1021/acs.inorgchem.8b00726] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dinuclear Zn2+ complexes with HTQHPN ( N,N,N' ,N'-tetrakis(2-quinolylmethyl)-2-hydroxy-1,3-propanediamine) derivatives have been prepared, and their pyrophosphate (PPi, P2O74-) sensing properties were examined. The ligand library includes six HTQHPN derivatives with electron-donating/withdrawing substituents, an extended aromatic ring, and six-membered chelates upon zinc binding. Complexation of ligand with 2 equiv of Zn2+ promotes small to moderate fluorescence enhancement around 380 nm, but in the cases of HTQHPN, HT(6-FQ)HPN ( N,N,N' ,N'-tetrakis(6-fluoro-2-quinolylmethyl)-2-hydroxy-1,3-propanediamine), and HT(8Q)HPN ( N,N,N' ,N'-tetrakis(8-quinolylmethyl)-2-hydroxy-1,3-propanediamine), subsequent addition of PPi induced a significant fluorescence increase around 450 nm. This fluorescence enhancement in the long-wavelength region is attributed to the conformational change of the bis-(quinolylmethyl)amine moiety which promotes intramolecular excimer formation between adjacent quinolines upon binding with PPi. The structures of PPi- and phosphate-bound dizinc complexes were revealed by X-ray crystallography utilizing phenyl-substituted analogues. The zinc complex with HT(8Q)HPN exhibits the highest signal enhancement ( IPPi/ I0 = 12.5) and selectivity toward PPi sensing ( IATP/ IPPi = 20% and IADP/ IPPi = 25%). The fluorescence enhancement turned to decrease gradually after the addition of more than 1 equiv of PPi due to the removal of zinc ion from the ligand-zinc-PPi ternary complex, allowing the accurate determination of PPi concentrations at the fluorescence maximum composition. The practical application of the present method was demonstrated monitoring the enzymatic activity of pyrophosphatase.
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Affiliation(s)
- Yuji Mikata
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science , Nara Women's University , Nara 630-8506 , Japan.,KYOUSEI Science Center , Nara Women's University , Nara 630-8506 , Japan.,Department of Chemistry, Faculty of Science , Nara Women's University , Nara 630-8506 , Japan
| | - Risa Ohnishi
- Department of Chemistry, Faculty of Science , Nara Women's University , Nara 630-8506 , Japan
| | - Risa Nishijima
- Department of Chemistry, Faculty of Science , Nara Women's University , Nara 630-8506 , Japan
| | - Arimasa Matsumoto
- Department of Chemistry, Biology, and Environmental Science, Faculty of Science , Nara Women's University , Nara 630-8506 , Japan
| | - Hideo Konno
- National Institute of Advanced Industrial Science and Technology (AIST) , 1-1-1 Higashi , Tsukuba , Ibaraki 305-8565 , Japan
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25
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Mueller JW, Idkowiak J, Gesteira TF, Vallet C, Hardman R, van den Boom J, Dhir V, Knauer SK, Rosta E, Arlt W. Human DHEA sulfation requires direct interaction between PAPS synthase 2 and DHEA sulfotransferase SULT2A1. J Biol Chem 2018; 293:9724-9735. [PMID: 29743239 PMCID: PMC6016456 DOI: 10.1074/jbc.ra118.002248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/28/2018] [Indexed: 12/30/2022] Open
Abstract
The high-energy sulfate donor 3′-phosphoadenosine-5′-phosphosulfate (PAPS), generated by human PAPS synthase isoforms PAPSS1 and PAPSS2, is required for all human sulfation pathways. Sulfotransferase SULT2A1 uses PAPS for sulfation of the androgen precursor dehydroepiandrosterone (DHEA), thereby reducing downstream activation of DHEA to active androgens. Human PAPSS2 mutations manifest with undetectable DHEA sulfate, androgen excess, and metabolic disease, suggesting that ubiquitous PAPSS1 cannot compensate for deficient PAPSS2 in supporting DHEA sulfation. In knockdown studies in human adrenocortical NCI-H295R1 cells, we found that PAPSS2, but not PAPSS1, is required for efficient DHEA sulfation. Specific APS kinase activity, the rate-limiting step in PAPS biosynthesis, did not differ between PAPSS1 and PAPSS2. Co-expression of cytoplasmic SULT2A1 with a cytoplasmic PAPSS2 variant supported DHEA sulfation more efficiently than co-expression with nuclear PAPSS2 or nuclear/cytosolic PAPSS1. Proximity ligation assays revealed protein–protein interactions between SULT2A1 and PAPSS2 and, to a lesser extent, PAPSS1. Molecular docking studies showed a putative binding site for SULT2A1 within the PAPSS2 APS kinase domain. Energy-dependent scoring of docking solutions identified the interaction as specific for the PAPSS2 and SULT2A1 isoforms. These findings elucidate the mechanistic basis for the selective requirement for PAPSS2 in human DHEA sulfation.
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Affiliation(s)
- Jonathan W Mueller
- From the Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham B15 2TT, United Kingdom, .,the Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom
| | - Jan Idkowiak
- From the Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham B15 2TT, United Kingdom.,the Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom
| | - Tarsis F Gesteira
- the Department of Chemistry, King's College London, London SE1 1DB, United Kingdom, and
| | - Cecilia Vallet
- the Departments of Molecular Biology II, Centre for Medical Biotechnology (ZMB) and
| | - Rebecca Hardman
- From the Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Johannes van den Boom
- Molecular Biology I, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45141 Essen, Germany
| | - Vivek Dhir
- From the Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Shirley K Knauer
- the Departments of Molecular Biology II, Centre for Medical Biotechnology (ZMB) and
| | - Edina Rosta
- the Department of Chemistry, King's College London, London SE1 1DB, United Kingdom, and
| | - Wiebke Arlt
- From the Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham B15 2TT, United Kingdom.,the Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham B15 2TH, United Kingdom
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26
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Chan KK, Wong ESY, Wong OGW, Ngan HYS, Cheung ANY. Identification of nonsynonymous TP53 mutations in hydatidiform moles. Mutat Res 2018; 809:20-23. [PMID: 29655027 DOI: 10.1016/j.mrfmmm.2018.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/11/2018] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Hydatidiform mole (HM), an unusual pregnancy with pure or predominant paternal genetic contribution, is the most common form of gestational trophoblastic disease. Most HM regress after uterine evacuation but some will develop into persistent disease or even frank malignancy. Although p53 is highly expressed in HM, TP53 mutations have rarely been detected in previous studies. Here we screened for specific missense mutations on several TP53 hotspots in 49 HMs using a highly sensitive pyrosequencing approach and revealed the significant existence of such mutations in HM tissues. A particularly high frequency (∼59% of the cases) of p53 inactivating mutation on exon 7 has been detected. Our identification of hitherto unreported TP53 mutations in HM suggests the presence of p53 mutants and reflects the advantages of using pyrosequencing for point mutation detection in clinical samples. Traditional sequencing method may have overlooked such mutations that only occur in a small population of trophoblasts.
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Affiliation(s)
- Ka-Kui Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Esther Shuk-Ying Wong
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Oscar Gee-Wan Wong
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Hextan Yuen-Sheung Ngan
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Annie Nga-Yin Cheung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China.
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27
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Ivády G, Madar L, Dzsudzsák E, Koczok K, Kappelmayer J, Krulisova V, Macek M, Horváth A, Balogh I. Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system. BMC Genomics 2018; 19:158. [PMID: 29466940 PMCID: PMC5822529 DOI: 10.1186/s12864-018-4544-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/13/2018] [Indexed: 01/14/2023] Open
Abstract
Background Current technologies in next-generation sequencing are offering high throughput reads at low costs, but still suffer from various sequencing errors. Although pyro- and ion semiconductor sequencing both have the advantage of delivering long and high quality reads, problems might occur when sequencing homopolymer-containing regions, since the repeating identical bases are going to incorporate during the same synthesis cycle, which leads to uncertainty in base calling. The aim of this study was to evaluate the analytical performance of a pyrosequencing-based next-generation sequencing system in detecting homopolymer sequences using homopolymer-preintegrated plasmid constructs and human DNA samples originating from patients with cystic fibrosis. Results In the plasmid system average correct genotyping was 95.8% in 4-mers, 87.4% in 5-mers and 72.1% in 6-mers. Despite the experienced low genotyping accuracy in 5- and 6-mers, it was possible to generate amplicons with more than a 90% adequate detection rate in every homopolymer tract. When homopolymers in the CFTR gene were sequenced average accuracy was 89.3%, but varied in a wide range (52.2 – 99.1%). In all but one case, an optimal amplicon-sequencing primer combination could be identified. In that single case (7A tract in exon 14 (c.2046_2052)), none of the tested primer sets produced the required analytical performance. Conclusions Our results show that pyrosequencing is the most reliable in case of 4-mers and as homopolymer length gradually increases, accuracy deteriorates. With careful primer selection, the NGS system was able to correctly genotype all but one of the homopolymers in the CFTR gene. In conclusion, we configured a plasmid test system that can be used to assess genotyping accuracy of NGS devices and developed an accurate NGS assay for the molecular diagnosis of CF using self-designed primers for amplification and sequencing. Electronic supplementary material The online version of this article (10.1186/s12864-018-4544-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gergely Ivády
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - László Madar
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Erika Dzsudzsák
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Katalin Koczok
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.,Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - János Kappelmayer
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Veronika Krulisova
- Department of Biology and Medical Genetics, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine and University Hospital Motol, Charles University, Prague, Czech Republic
| | - Attila Horváth
- Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary
| | - István Balogh
- Department of Laboratory Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary. .,Division of Clinical Genetics, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary.
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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29
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Haplotype-Contained PCR Products Analysis by Sequencing with Selective Restriction of Primer Extension. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1397902. [PMID: 29376065 PMCID: PMC5742430 DOI: 10.1155/2017/1397902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 10/30/2017] [Accepted: 11/14/2017] [Indexed: 11/24/2022]
Abstract
We develop a strategy for haplotype analysis of PCR products that contained two adjacent heterozygous loci using sequencing with specific primers, allele-specific primers, and ddNTP-blocked primers. To validate its feasibility, two sets of PCR products, including two adjacent heterozygous SNPs, UGT1A1⁎6 (rs4148323) and UGT1A1⁎28 (rs8175347), and two adjacent heterozygous SNPs, K1637K (rs11176013) and S1647T (rs11564148), were analyzed. Haplotypes of PCR products, including UGT1A1⁎6 and UGT1A1⁎28, were successfully analyzed by Sanger sequencing with allele-specific primers. Also, haplotypes of PCR products, including K1637K and S1647T, could not be determined by Sanger sequencing with allele-specific primers but were successfully analyzed by pyrosequencing with ddNTP-blocked primers. As a result, this method is able to effectively haplotype two adjacent heterozygous PCR products. It is simple, fast, and irrespective of short read length of pyrosequencing. Overall, we fully hope it will provide a new promising technology to identify haplotypes of conventional PCR products in clinical samples.
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30
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Determination of multiple-clone infection at allelic dimorphism site of Plasmodium vivax merozoite surface protein-1 in the Republic of Korea by pyrosequencing assay. Acta Trop 2017; 176:300-304. [PMID: 28847673 DOI: 10.1016/j.actatropica.2017.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 11/21/2022]
Abstract
Allelic diversity leading to multiple gene polymorphisms of vivax malaria parasites has been shown to greatly contribute to antigenic variation and drug resistance, increasing the potential for multiple-clone infections within the host. Therefore, to identify multiple-clone infections and the predominant haplotype of Plasmodium vivax in a South Korean population, P. vivax merozoite surface protein-1 (PvMSP-1) was analyzed by pyrosequencing. Pyrosequencing of 156 vivax malaria-infected samples yielded 97 (62.18%) output pyrograms showing two main types of peak patterns of the dimorphic allele for threonine and alanine (T1476A). Most of the samples evaluated (88.66%) carried multiple-clone infections (wild- and mutant-types), whereas 11.34% of the same population carried only the mutant-type (1476A). In addition, each allele showed a high frequency of guanine (G) base substitution at both the first and third positions (86.07% and 81.13%, respectively) of the nucleotide combinations. Pyrosequencing of the PvMSP-1 42-kDa fragment revealed a heterogeneous parasite population, with the mutant-type dominant compared to the wild-type. Understanding the genetic diversity and multiple-clone infection rates may lead to improvements in vivax malaria prevention and strategic control plans. Further studies are needed to improve the efficacy of the pyrosequencing assay with large sample sizes and additional nucleotide positions.
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Swaminathan V, Rajaram G, Abhishek V, Reddy BS, Kannan K. A Novel Hypergraph-Based Genetic Algorithm (HGGA) Built on Unimodular and Anti-homomorphism Properties for DNA Sequencing by Hybridization. Interdiscip Sci 2017; 11:397-411. [PMID: 29110287 DOI: 10.1007/s12539-017-0267-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 11/29/2022]
Abstract
The sequencing by hybridization (SBH) of determining the order in which nucleotides should occur on a DNA string is still under discussion for enhancements on computational intelligence although the next generation of DNA sequencing has come into existence. In the last decade, many works related to graph theory-based DNA sequencing have been carried out in the literature. This paper proposes a method for SBH by integrating hypergraph with genetic algorithm (HGGA) for designing a novel analytic technique to obtain DNA sequence from its spectrum. The paper represents elements of the spectrum and its relation as hypergraph and applies the unimodular property to ensure the compatibility of relations between l-mers. The hypergraph representation and unimodular property are bound with the genetic algorithm that has been customized with a novel selection and crossover operator reducing the computational complexity with accelerated convergence. Subsequently, upon determining the primary strand, an anti-homomorphism is invoked to find the reverse complement of the sequence. The proposed algorithm is implemented in the GenBank BioServer datasets, and the results are found to prove the efficiency of the algorithm. The HGGA is a non-classical algorithm with significant advantages and computationally attractive complexity reductions ranging to [Formula: see text] with improved accuracy that makes it prominent for applications other than DNA sequencing like image processing, task scheduling and big data processing.
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Affiliation(s)
- V Swaminathan
- Discrete Mathematics Research Laboratory, Srinivasa Ramanujan Centre, SASTRA University, Thanjavur, India.,School of Humanities and Sciences, SASTRA University, Thanjavur, India
| | - Gangothri Rajaram
- School of Computing, SASTRA University, Thanjavur, Tamilnadu, India. .,School of Humanities and Sciences, SASTRA University, Thanjavur, India.
| | - V Abhishek
- School of Computing, SASTRA University, Thanjavur, Tamilnadu, India.,School of Humanities and Sciences, SASTRA University, Thanjavur, India
| | - Boosi Shashank Reddy
- School of Computing, SASTRA University, Thanjavur, Tamilnadu, India.,School of Humanities and Sciences, SASTRA University, Thanjavur, India
| | - K Kannan
- Discrete Mathematics Research Laboratory, Srinivasa Ramanujan Centre, SASTRA University, Thanjavur, India. .,School of Computing, SASTRA University, Thanjavur, Tamilnadu, India. .,School of Humanities and Sciences, SASTRA University, Thanjavur, India.
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Majlessi L, Sayes F, Bureau JF, Pawlik A, Michel V, Jouvion G, Huerre M, Severgnini M, Consolandi C, Peano C, Brosch R, Touati E, Leclerc C. Colonization with Helicobacter is concomitant with modified gut microbiota and drastic failure of the immune control of Mycobacterium tuberculosis. Mucosal Immunol 2017; 10:1178-1189. [PMID: 28145441 DOI: 10.1038/mi.2016.140] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/28/2016] [Indexed: 02/04/2023]
Abstract
Epidemiological and experimental observations suggest that chronic microbial colonization can impact the immune control of other unrelated pathogens contracted in a concomitant or sequential manner. Possible interactions between Mycobacterium tuberculosis infection and persistence of other bacteria have scarcely been investigated. Here we demonstrated that natural colonization of the digestive tract with Helicobacter hepaticus in mice is concomitant with modification of the gut microbiota, subclinical inflammation, and drastic impairment of immune control of the growth of subsequently administered M. tuberculosis, which results in severe lung tissue injury. Our results provided insights upon the fact that this prior H. hepaticus colonization leads to failures in the mechanisms that could prevent the otherwise balanced cross-talk between M. tuberculosis and the immune system. Such disequilibrium ultimately leads to the inhibition of control of mycobacterial growth, outbreak of inflammation, and lung pathology. Among the dysregulated immune signatures, we noticed a correlation between the detrimental lung injury and the accumulation of activated T-lymphocytes. Our findings suggest that the impact of prior Helicobacter spp. colonization and subsequent M. tuberculosis parasitism might be greater than previously thought, which is a key point given that both species are among the most frequent invasive bacteria in human populations.
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Affiliation(s)
- L Majlessi
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, Paris, France.,Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France.,INSERM U1041, Paris, France
| | - F Sayes
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, Paris, France.,Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France.,INSERM U1041, Paris, France
| | - J-F Bureau
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
| | - A Pawlik
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, Paris, France
| | - V Michel
- Institut Pasteur, Unité de Pathogenèse de Helicobacter, Paris, France.,CNRS ERL3526, Paris, France
| | - G Jouvion
- Institut Pasteur, Unité d'Histopathologie Humaine et Modèles Animaux, Paris, France.,Institut Pasteur, URE Histotechnologie et Pathologie, Paris, France
| | - M Huerre
- Institut Pasteur, URE Histotechnologie et Pathologie, Paris, France.,Institut Curie, Département de Pathologie, Paris, France
| | - M Severgnini
- Institute of Biomedical Technologies, CNR, Segrate, Milan, Italy
| | - C Consolandi
- Institute of Biomedical Technologies, CNR, Segrate, Milan, Italy
| | - C Peano
- Institute of Biomedical Technologies, CNR, Segrate, Milan, Italy
| | - R Brosch
- Institut Pasteur, Unité de Pathogénomique Mycobactérienne Intégrée, Paris, France
| | - E Touati
- Institut Pasteur, Unité de Pathogenèse de Helicobacter, Paris, France.,CNRS ERL3526, Paris, France
| | - C Leclerc
- Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Paris, France.,INSERM U1041, Paris, France
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33
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Bozan M, Akyol Ç, Ince O, Aydin S, Ince B. Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass. Appl Microbiol Biotechnol 2017; 101:6849-6864. [PMID: 28779289 DOI: 10.1007/s00253-017-8438-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.
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Affiliation(s)
- Mahir Bozan
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Çağrı Akyol
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Sevcan Aydin
- Department of Genetics and Bioengineering, Nişantaşı University, Maslak, 34469, Istanbul, Turkey.
| | - Bahar Ince
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
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34
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Taskova M, Uhd J, Miotke L, Kubit M, Bell J, Ji HP, Astakhova K. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. Anal Chem 2017; 89:4363-4366. [PMID: 28382823 DOI: 10.1021/acs.analchem.7b00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New approaches for genomic DNA/RNA detection are in high demand in order to provide controls for existing enzymatic technologies and to create alternatives for emerging applications. In particular, there is an unmet need in rapid, reliable detection of short RNA regions which could open up new opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA followed by click assembly and analysis of the read sequence by various techniques. As we demonstrate in this paper, using our new approach, a viral RNA sequence can be detected in less than 2 h without the need for cDNA synthesis or any other enzymatic reactions and with a sensitivity of <10 pM target RNA.
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Affiliation(s)
- Maria Taskova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Uhd
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - Matthew Kubit
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - John Bell
- Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States.,Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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35
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Kaskova ZM, Dörr FA, Petushkov VN, Purtov KV, Tsarkova AS, Rodionova NS, Mineev KS, Guglya EB, Kotlobay A, Baleeva NS, Baranov MS, Arseniev AS, Gitelson JI, Lukyanov S, Suzuki Y, Kanie S, Pinto E, Di Mascio P, Waldenmaier HE, Pereira TA, Carvalho RP, Oliveira AG, Oba Y, Bastos EL, Stevani CV, Yampolsky IV. Mechanism and color modulation of fungal bioluminescence. SCIENCE ADVANCES 2017; 3:e1602847. [PMID: 28508049 PMCID: PMC5406138 DOI: 10.1126/sciadv.1602847] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/01/2017] [Indexed: 05/16/2023]
Abstract
Bioluminescent fungi are spread throughout the globe, but details on their mechanism of light emission are still scarce. Usually, the process involves three key components: an oxidizable luciferin substrate, a luciferase enzyme, and a light emitter, typically oxidized luciferin, and called oxyluciferin. We report the structure of fungal oxyluciferin, investigate the mechanism of fungal bioluminescence, and describe the use of simple synthetic α-pyrones as luciferins to produce multicolor enzymatic chemiluminescence. A high-energy endoperoxide is proposed as an intermediate of the oxidation of the native luciferin to the oxyluciferin, which is a pyruvic acid adduct of caffeic acid. Luciferase promiscuity allows the use of simple α-pyrones as chemiluminescent substrates.
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Affiliation(s)
- Zinaida M. Kaskova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Felipe A. Dörr
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508-900, Brazil
| | - Valentin N. Petushkov
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Konstantin V. Purtov
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Aleksandra S. Tsarkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Natalja S. Rodionova
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Konstantin S. Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elena B. Guglya
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexey Kotlobay
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S. Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Josef I. Gitelson
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
| | - Sergey Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Yoshiki Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Shusei Kanie
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Ernani Pinto
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, 05508-900, Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Hans E. Waldenmaier
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Tatiana A. Pereira
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Rodrigo P. Carvalho
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Anderson G. Oliveira
- Departamento de Oceanografia Física, Química e Geológica, Instituto Oceanográfico, Universidade de São Paulo, 05508-120, Brazil
| | - Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan
| | - Erick L. Bastos
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Cassius V. Stevani
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Ilia V. Yampolsky
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences (SB RAS), Federal Research Center “Krasnoyarsk Science Center SB RAS,” Akademgorodok, Krasnoyarsk 660036, Russia
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Lee HS, Kim WH, Kwak Y, Koh J, Bae JM, Kim KM, Chang MS, Han HS, Kim JM, Kim HW, Chang HK, Choi YH, Park JY, Gu MJ, Lhee MJ, Kim JY, Kim HS, Cho MY. Molecular Testing for Gastrointestinal Cancer. J Pathol Transl Med 2017; 51:103-121. [PMID: 28219002 PMCID: PMC5357760 DOI: 10.4132/jptm.2017.01.24] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 12/20/2022] Open
Abstract
With recent advances in molecular diagnostic methods and targeted cancer therapies, several molecular tests have been recommended for gastric cancer (GC) and colorectal cancer (CRC). Microsatellite instability analysis of gastrointestinal cancers is performed to screen for Lynch syndrome, predict favorable prognosis, and screen patients for immunotherapy. The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor has been approved in metastatic CRCs with wildtype RAS (KRAS and NRAS exon 2-4). A BRAF mutation is required for predicting poor prognosis. Additionally, amplification of human epidermal growth factor receptor 2 (HER2) and MET is also associated with resistance to EGFR inhibitor in metastatic CRC patients. The BRAF V600E mutation is found in sporadic microsatellite unstable CRCs, and thus is helpful for ruling out Lynch syndrome. In addition, the KRAS mutation is a prognostic biomarker and the PIK3CA mutation is a molecular biomarker predicting response to phosphoinositide 3-kinase/AKT/mammalian target of rapamycin inhibitors and response to aspirin therapy in CRC patients. Additionally, HER2 testing should be performed in all recurrent or metastatic GCs. If the results of HER2 immunohistochemistry are equivocal, HER2 silver or fluorescence in situ hybridization testing are essential for confirmative determination of HER2 status. Epstein-Barr virus-positive GCs have distinct characteristics, including heavy lymphoid stroma, hypermethylation phenotype, and high expression of immune modulators. Recent advances in next-generation sequencing technologies enable us to examine various genetic alterations using a single test. Pathologists play a crucial role in ensuring reliable molecular testing and they should also take an integral role between molecular laboratories and clinicians.
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Affiliation(s)
- Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yoonjin Kwak
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jiwon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Kyoung-Mee Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mee Soo Chang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Hye Seung Han
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Joon Mee Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Hwal Woong Kim
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
| | - Hee Kyung Chang
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
| | - Young Hee Choi
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
| | - Ji Y. Park
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Mi Jin Gu
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
| | - Min Jin Lhee
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
| | - Jung Yeon Kim
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
| | - Hee Sung Kim
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Mee-Yon Cho
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Gastrointestinal Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
- Department of Pathology, Seegene Medical Foundation, Busan, Korea
- Department of Pathology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Korea
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea
- Department of Pathology, Catholic University of Daegu School of Medicine, Daegu, Korea
- Department of Pathology, Yeungnam University College of Medicine, Daegu, Korea
- Department of Pathology, Seoul Red Cross Hospital, Seoul, Korea
- Department of Pathology, Inje University Sanggye Paik Hospital, Seoul, Korea
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
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Abbadi M, Marciano S, Tosi F, De Battisti C, Panzarin V, Arcangeli G, Cattoli G. Species identification of bivalve molluscs by pyrosequencing. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:512-519. [PMID: 27068666 DOI: 10.1002/jsfa.7754] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/23/2016] [Accepted: 04/05/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The increase in seafood consumption and the presence of different species of bivalves on the global markets has given rise to several commercial frauds based on species substitution. To prevent and detect wilful or unintentional frauds, reliable and rapid techniques are required to identify seafood species in different products. In the present work, a pyrosequencing-based technology has been used for the molecular identification of bivalve species. RESULTS Processed and unprocessed samples of 15 species belonging to the bivalve families Pectinidae, Mytilidae, Donacidae, Ostreidae, Pharide and Veneridae were analysed and correctly identified by the developed pyrosequencing-based method according to the homology between query sequences of the 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase I (COI) genes and their correspondent reference libraries. This technique exhibits great potential in automated and high-throughput processing systems, allowing the simultaneous analysis of 96 samples in shorter execution and turnaround times. CONCLUSIONS The correct identification of all the species shows how useful this technique may prove to differentiate species from different products, providing an alternative, simple, rapid and economical tool to detect seafood substitution frauds. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Miriam Abbadi
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Sabrina Marciano
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Federica Tosi
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Cristian De Battisti
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Valentina Panzarin
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
| | - Giuseppe Arcangeli
- National Reference Laboratory for Fish, Molluscs and Crustacean Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, 45011 Adria, Rovigo, Italy
| | - Giovanni Cattoli
- Research and Innovation Department, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Legnaro, Padova, Italy
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38
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Pu D, Xiao P. A real-time decoding sequencing technology—new possibility for high throughput sequencing. RSC Adv 2017. [DOI: 10.1039/c7ra06202h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The challenges and corresponding solutions for a decoding sequencing to be compatible with high throughput sequencing (HTS) technologies are provided.
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Affiliation(s)
- Dan Pu
- School of Bioinformatics
- Chongqing University of Posts and Telecommunications
- Chongqing
- China
- State Key Laboratory of Bioelectronics
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
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Thanchomnang T, Tantrawatpan C, Intapan PM, Sanpool O, Lulitanond V, Tourtip S, Yamasaki H, Maleewong W. Rapid identification of nine species of diphyllobothriidean tapeworms by pyrosequencing. Sci Rep 2016; 6:37228. [PMID: 27853295 PMCID: PMC5112553 DOI: 10.1038/srep37228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
The identification of diphyllobothriidean tapeworms (Cestoda: Diphyllobothriidea) that infect humans and intermediate/paratenic hosts is extremely difficult due to their morphological similarities, particularly in the case of Diphyllobothrium and Spirometra species. A pyrosequencing method for the molecular identification of pathogenic agents has recently been developed, but as of yet there have been no reports of pyrosequencing approaches that are able to discriminate among diphyllobothriidean species. This study, therefore, set out to establish a pyrosequencing method for differentiating among nine diphyllobothriidean species, Diphyllobothrium dendriticum, Diphyllobothrium ditremum, Diphyllobothrium latum, Diphyllobothrium nihonkaiense, Diphyllobothrium stemmacephalum, Diplogonoporus balaenopterae, Adenocephalus pacificus, Spirometra decipiens and Sparganum proliferum, based on the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as a molecular marker. A region of 41 nucleotides in the cox1 gene served as a target, and variations in this region were used for identification using PCR plus pyrosequencing. This region contains nucleotide variations at 12 positions, which is enough for the identification of the selected nine species of diphyllobothriidean tapeworms. This method was found to be a reliable tool not only for species identification of diphyllobothriids, but also for epidemiological studies of cestodiasis caused by diphyllobothriidean tapeworms at public health units in endemic areas.
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Affiliation(s)
- Tongjit Thanchomnang
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chairat Tantrawatpan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Division of Cell Biology, Department of Preclinical Sciences, Faculty of Medicine, Thammasat University, Rangsit Campus, Pathum Thani, 12120, Thailand
| | - Pewpan M Intapan
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Oranuch Sanpool
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Viraphong Lulitanond
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Somjintana Tourtip
- Faculty of Medicine, Mahasarakham University, Mahasarakham, 44000, Thailand
| | - Hiroshi Yamasaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Wanchai Maleewong
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand.,Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
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40
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Park JH, Choi O, Lee TH, Kim H, Sang BI. Pyrosequencing analysis of microbial communities in hollow fiber-membrane biofilm reactors system for treating high-strength nitrogen wastewater. CHEMOSPHERE 2016; 163:192-201. [PMID: 27529383 DOI: 10.1016/j.chemosphere.2016.07.099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
Wastewaters from swine farms, nitrogen-dealing industries or side-stream processes of a wastewater treatment plant (e.g., anaerobic digesters, sludge thickening processes, etc.) are characterized by low C/N ratios and not easily treatable. In this study, a hollow fiber-membrane biofilm reactors (HF-MBfR) system consisting of an O2-based HF-MBfR and an H2-based HF-MBfR was applied for treating high-strength wastewater. The reactors were continuously operated with low supply of O2 and H2 and without any supply of organic carbon for 250 d. Gradual increase of ammonium and nitrate concentration in the influent showed stable and high nitrogen removal efficiency, and the maximum ammonium and nitrate removal rates were 0.48 kg NH4(+)-N m(-3) d(-1) and 0.55 kg NO3(-)-N m(-3) d(-1), respectively. The analysis of the microbial communities using pyrosequencing analysis indicated that Nitrosospira multiformis, ammonium-oxidizing bacteria, and Nitrobacter winogradskyi and Nitrobacter vulgaris, nitrite-oxidizing bacteria were highly enriched in the O2-based HF-MBfR. In the H2-based HF-MBfR, hydrogenotrophic denitrifying bacteria belonging to the family of Thiobacillus and Comamonadaceae were initially dominant, but were replaced to heterotrophic denitrifiers belonging to Rhodocyclaceae and Rhodobacteraceae utilizing by-products induced from autotrophic denitrifying bacteria. The pyrosequencing analysis of microbial communities indicates that the autotrophic HF-MBfRs system well developed autotrophic nitrifying and denitrifying bacteria within a relatively short period to accomplish almost complete nitrogen removal.
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Affiliation(s)
- Jung-Hun Park
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Okkyoung Choi
- The Research Institute of Industrial Science, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Tae-Ho Lee
- The Research Institute of Industrial Science, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea
| | - Hyunook Kim
- Department of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-Ku, Seoul 02504, South Korea.
| | - Byoung-In Sang
- Department of Chemical Engineering, Hanyang University, 222 Wangshimni-Ro, Seongdong-Ku, Seoul 04763, South Korea.
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41
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Min KW, Kim WS, Jang SJ, Choi YD, Chang S, Jung SH, Kim L, Roh MS, Lee CS, Shim JW, Kim MJ, Lee GK. MassARRAY, pyrosequencing, and PNA clamping for EGFR mutation detection in lung cancer tissue and cytological samples: a multicenter study. J Cancer Res Clin Oncol 2016; 142:2209-16. [PMID: 27535566 DOI: 10.1007/s00432-016-2211-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/25/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Testing for epidermal growth factor receptor (EGFR) mutation is an important process in the therapeutic plan of patients with lung cancer. Recently, MassARRAY, based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, has been shown to be a useful method for somatic mutation analysis with pyrosequencing and peptide nucleic acid clamping (PNAc). METHODS A total of 107 tissues and 67 cytological samples, which were confirmed to have lung adenocarcinoma at nine hospitals in Korea, were collected. Among the MassARRAY, pyrosequencing, and PNAc, the concordance rates and sensitivity of EGFR mutation detection were analyzed and validated in comparative tissue and cytological specimens. RESULTS The concordance rate between pyrosequencing and PNAc was higher than that between MassARRAY and either of the pyrosequencing and PNAc in both tissue and cytological samples. In a comparison of diagnostic performance, MassARRAY (sensitivity: 85.7 %) was higher than pyrosequencing (74.3 %) and PNAc (70 %) in tissue, although pyrosequencing (80.5 %) was more highly sensitive, compared to MassARRAY (70.7 %) and PNAc (70.7 %) in terms of cytology. Unexpectedly, use of MassARRAY resulted in a significantly different EGFR mutation detection rate between tissue and cytological samples. CONCLUSIONS When used for the detection of EGFR mutations, MassARRAY was more sensitive than pyrosequencing or PNA clamping in tissue, but not in cytological samples. In EGFR mutation detection between tissues and cytology, PNAc showed relatively higher concordance than MassARRAY or pyrosequencing.
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Affiliation(s)
- Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, 153, Gyeongchun-ro, Guri-si, Gyeonggi-do, 11923, South Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, 120-1, Neungdong-ro, Gwangjin-gu, Seoul, 05030, South Korea.
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olymphic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Yoo Duk Choi
- Department of Pathology, Chonnam National University Hospital, Chonnam National University Medical School, 160, Baekseo-ro, Dong-gu, Gwangju, 61469, South Korea
| | - Sunhee Chang
- Department of Pathology, Inje Unversity Ilsan Paik Hospital, Inje University School of Medicine, 170, Juhwa-ro, Ilsanseo-gu, Goyang-si, Gyeonggi-do, 10380, South Korea
| | - Soon Hee Jung
- Department of Pathology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, 20, Ilsan-ro, Wonju-si, Gangwon-do, 26426, South Korea
| | - Lucia Kim
- Department of Pathology, Inha University Hospital, Inha University School of Medicine, 27, Inhang-ro, Jung-gu, Incheon, 22332, South Korea
| | - Mee-Sook Roh
- Department of Pathology, Dong-A University Hospital, Dong-A University College of Medicine, 26, Daesingongwon-ro, Seo-gu, Busan, 49201, South Korea
| | - Choong Sik Lee
- Department of Pathology, Chungnam National University Hospital, Chungnam National University College of Medicine, 282, Munhwa-ro, Jung-gu, Daejeon, 35015, South Korea
| | - Jung Weon Shim
- Department of Pathology, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, 7, Keunjaebong-gil, Hwaseong-si, Gyeonggi-do, 18450, South Korea
| | - Mi Jin Kim
- Department of Pathology, Yeungnam University Medical Center, Yeungnam University College of Medicine, 170, Hyeonchung-ro, Nam-gu, Daegu, 42415, South Korea
| | - Geon Kook Lee
- Department of Pathology, National Cancer Center, 323, Ilsan-ro, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10408, South Korea
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42
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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43
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The A, C, G, and T of Genome Assembly. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6329217. [PMID: 27247941 PMCID: PMC4877455 DOI: 10.1155/2016/6329217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/22/2015] [Indexed: 11/18/2022]
Abstract
Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.
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44
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Forte VA, Barrak DK, Elhodaky M, Tung L, Snow A, Lang JE. The potential for liquid biopsies in the precision medical treatment of breast cancer. Cancer Biol Med 2016; 13:19-40. [PMID: 27144060 PMCID: PMC4850125 DOI: 10.28092/j.issn.2095-3941.2016.0007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Currently the clinical management of breast cancer relies on relatively few prognostic/predictive clinical markers (estrogen receptor, progesterone receptor, HER2), based on primary tumor biology. Circulating biomarkers, such as circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs) may enhance our treatment options by focusing on the very cells that are the direct precursors of distant metastatic disease, and probably inherently different than the primary tumor's biology. To shift the current clinical paradigm, assessing tumor biology in real time by molecularly profiling CTCs or ctDNA may serve to discover therapeutic targets, detect minimal residual disease and predict response to treatment. This review serves to elucidate the detection, characterization, and clinical application of CTCs and ctDNA with the goal of precision treatment of breast cancer.
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Affiliation(s)
- Victoria A Forte
- Department of Medicine, Division of Medical Oncology, University of Southern California (USC), Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Dany K Barrak
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
| | - Mostafa Elhodaky
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Stem Cell and Regenerative Medicine, USC, Los Angeles, CA 90033, USA
| | - Lily Tung
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
| | - Anson Snow
- Department of Medicine, Division of Medical Oncology, University of Southern California (USC), Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Julie E Lang
- USC Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Surgery, Division of Breast, Endocrine and Soft Tissue Surgery, USC, Los Angeles, CA 90033, USA
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45
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How-Kit A, Tost J. Pyrosequencing®-Based Identification of Low-Frequency Mutations Enriched Through Enhanced-ice-COLD-PCR. Methods Mol Biol 2016; 1315:83-101. [PMID: 26103893 DOI: 10.1007/978-1-4939-2715-9_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A number of molecular diagnostic assays have been developed in the last years for mutation detection. Although these methods have become increasingly sensitive, most of them are incompatible with a sequencing-based readout and require prior knowledge of the mutation present in the sample. Consequently, coamplification at low denaturation (COLD)-PCR-based methods have been developed and combine a high analytical sensitivity due to mutation enrichment in the sample with the identification of known or unknown mutations by downstream sequencing experiments. Among these methods, the recently developed Enhanced-ice-COLD-PCR appeared as the most powerful method as it outperformed the other COLD-PCR-based methods in terms of the mutation enrichment and due to the simplicity of the experimental setup of the assay. Indeed, E-ice-COLD-PCR is very versatile as it can be used on all types of PCR platforms and is applicable to different types of samples including fresh frozen, FFPE, and plasma samples. The technique relies on the incorporation of an LNA containing blocker probe in the PCR reaction followed by selective heteroduplex denaturation enabling amplification of the mutant allele while amplification of the wild-type allele is prevented. Combined with Pyrosequencing(®), which is a very quantitative high-resolution sequencing technology, E-ice-COLD-PCR can detect and identify mutations with a limit of detection down to 0.01 %.
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Affiliation(s)
- Alexandre How-Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset-CEPH, 27 rue Juliette Dodu, 75010, Paris, France
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46
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Moison C, Assemat F, Daunay A, Arimondo PB, Tost J. DNA Methylation Analysis of ChIP Products at Single Nucleotide Resolution by Pyrosequencing®. Methods Mol Biol 2016; 1315:315-33. [PMID: 26103908 DOI: 10.1007/978-1-4939-2715-9_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction and co-occurrence of protein and DNA-based epigenetic modifications have become a topic of interest for many fundamental and biomedical questions. We describe within this chapter a protocol that combines two techniques in order to determine the methylation status of the DNA specifically associated with a protein of interest. First, DNA that directly interacts with the selected protein (such as a specific histone modification, a transcription factor, or any other DNA-associated protein) is purified by standard chromatin immunoprecipitation (ChIP). Second, the level of DNA methylation of this immunoprecipitated DNA is measured by bisulfite conversion and Pyrosequencing, a quantitative sequencing-by-synthesis method. This procedure allows determining the methylation status of genomic DNA associated to a specific protein at single nucleotide resolution.
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Affiliation(s)
- Céline Moison
- Unité de Service et de Recherche CNRS-Pierre Fabre n°3388, Epigenetic Targeting of Cancer (ETaC), Toulouse, France
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Abstract
We demonstrate the use of open-surface microfluidics to sequence DNA by pyrosequencing at the plain hydrophobically coated surface of a microscope glass cover slip. This method offers significant advantages in terms of instrument size, simplicity, disposability, and functional integration, particularly when combined with the broad and flexible capabilities of open-surface microfluidics. The DNA was incubated on superparamagnetic particles and placed on a hydrophobically coated glass substrate. The particles with bound DNA were moved using magnetic force through microliter-sized droplets covered with mineral oil to prevent water evaporation from the droplets. These droplets served as reaction "stations" performing pyrosequencing as well as washing stations. The resequencing protocol with 34-mer single-stranded DNA (ssDNA) was used to determine the reaction performance. The de novo sequencing was performed with 51-mer and 81-mer ssDNA. The method can be integrated with previously shown sample preparation and PCR into a single sample-to-answer system on a plain glass surface.
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Affiliation(s)
- Ana V Almeida
- KIST-Europe, Microfluidics Group, Campus E7.1, 66111 Saarbrücken, Germany.
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Pu D, Mao C, Cui L, Shi Z, Xiao P. Pyrosequencing with di-base addition for single nucleotide polymorphism genotyping. Anal Bioanal Chem 2016; 408:3113-23. [PMID: 26935928 DOI: 10.1007/s00216-016-9359-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/16/2016] [Accepted: 01/22/2016] [Indexed: 12/13/2022]
Abstract
We develop color code-based pyrosequencing with di-base addition for analysis of single nucleotide polymorphisms (SNPs). When a di-base is added into the polymerization, one or several two-color code(s) containing the type and the number of incorporated nucleotides will be produced. The code information obtained in a single run is useful to genotype SNPs as each allelic variant will give a specific pattern compared to the two other variants. Special care has to be taken while designing the di-base dispensation order. Here, we present a detailed protocol for establishing sequence-specific di-base addition to avoid nonsynchronous extension at the SNP sites. By using this technology, as few as 50 copies of DNA templates were accurately sequenced. Higher signals were produced and thus a relatively lower sample amount was required. Furthermore, the read length of per flow was increased, making simultaneous identification of multiple SNPs in a single sequencing run possible. Validation of the method was performed by using templates with two SNPs covering 37 bp and with three SNPs covering 58 bp as well as 82 bp. These SNPs were successfully genotyped by using only a sequencing primer in a single PCR/sequencing run. Our results demonstrated that this technology could be potentially developed into a powerful methodology to accurately determine SNPs so as to diagnose clinical settings.
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Affiliation(s)
- Dan Pu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Chengguang Mao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Lunbiao Cui
- Key Laboratory of Enteric Pathogenic Microbiology (NHFPC), Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, 210009, China
| | - Zhiyang Shi
- Key Laboratory of Enteric Pathogenic Microbiology (NHFPC), Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, 210009, China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
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Grasso C, Trevisan M, Fiano V, Tarallo V, De Marco L, Sacerdote C, Richiardi L, Merletti F, Gillio-Tos A. Performance of Different Analytical Software Packages in Quantification of DNA Methylation by Pyrosequencing. PLoS One 2016; 11:e0150483. [PMID: 26934703 PMCID: PMC4775062 DOI: 10.1371/journal.pone.0150483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/14/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pyrosequencing has emerged as an alternative method of nucleic acid sequencing, well suited for many applications which aim to characterize single nucleotide polymorphisms, mutations, microbial types and CpG methylation in the target DNA. The commercially available pyrosequencing systems can harbor two different types of software which allow analysis in AQ or CpG mode, respectively, both widely employed for DNA methylation analysis. OBJECTIVE Aim of the study was to assess the performance for DNA methylation analysis at CpG sites of the two pyrosequencing software which allow analysis in AQ or CpG mode, respectively. Despite CpG mode having been specifically generated for CpG methylation quantification, many investigations on this topic have been carried out with AQ mode. As proof of equivalent performance of the two software for this type of analysis is not available, the focus of this paper was to evaluate if the two modes currently used for CpG methylation assessment by pyrosequencing may give overlapping results. METHODS We compared the performance of the two software in quantifying DNA methylation in the promoter of selected genes (GSTP1, MGMT, LINE-1) by testing two case series which include DNA from paraffin embedded prostate cancer tissues (PC study, N = 36) and DNA from blood fractions of healthy people (DD study, N = 28), respectively. RESULTS We found discrepancy in the two pyrosequencing software-based quality assignment of DNA methylation assays. Compared to the software for analysis in the AQ mode, less permissive criteria are supported by the Pyro Q-CpG software, which enables analysis in CpG mode. CpG mode warns the operators about potential unsatisfactory performance of the assay and ensures a more accurate quantitative evaluation of DNA methylation at CpG sites. CONCLUSION The implementation of CpG mode is strongly advisable in order to improve the reliability of the methylation analysis results achievable by pyrosequencing.
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Affiliation(s)
- Chiara Grasso
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Morena Trevisan
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Tarallo
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura De Marco
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Carlotta Sacerdote
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Franco Merletti
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- Cancer Epidemiology Unit, Department of Medical Sciences, City of Health and Science Hospital, Turin, Italy
| | - Anna Gillio-Tos
- Cancer Epidemiology Unit – C.E.R.M.S, Department of Medical Sciences, University of Turin, Turin, Italy
- * E-mail:
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Min KW, Kim WS, Jang SJ, Choi YD, Chang S, Jung SH, Kim L, Roh MS, Lee CS, Shim JW, Kim MJ, Lee GK. Comparison of EGFR mutation detection between the tissue and cytology using direct sequencing, pyrosequencing and peptide nucleic acid clamping in lung adenocarcinoma: Korean multicentre study. QJM 2016; 109:167-73. [PMID: 26031706 DOI: 10.1093/qjmed/hcv103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The importance of sensitive methods for the detection of epidermal growth factor receptor (EGFR) mutation is emphasized. The aim of this study is to perform comparative and concordance analyses of direct sequencing, pyrosequencing and peptide nucleic acid (PNA) clamping for detecting EGFR gene mutations using archived tissue and cytology specimens. METHODS Samples from a total of 112 cases, which were diagnosed with adenocarcinoma of the lung at nine hospitals in Korea were collected. Using the above three methods, the concordance rates of EGFR mutations in exons 18, 19, 20 and 21 were analysed and validated in comparative tissue and cytology specimens. RESULTS Comparison of EGFR mutation detection between the tissue and cytology had a high concordance rate. The diagnostic performance of pyrosequencing and PNA clamping in tissue was higher than that of direct sequencing as well as cytology. Additionally, among some of the patients who had EGFR wild type by single method, EGFR mutations were detected by other methods. Cytology specimens had a diagnostic performance for the detection of EGFR mutations. CONCLUSIONS Cytology specimens had a diagnostic performance for the detection of EGFR mutations that was comparable to that of tissues. For detecting EGFR mutations, pyrosequencing or PNA clamping was more sensitive than direct sequencing. In EGFR mutation negative patients who are difficult to obtain tissue, repeating test using pyrosequencing or PNA clamping is recommended to improve the detection rate of EGFR mutation than only one, especially in cytology.
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Affiliation(s)
- Kyueng-Whan Min
- From the Department of Pathology, Konkuk University School of Medicine, Seoul
| | - Wan-Seop Kim
- From the Department of Pathology, Konkuk University School of Medicine, Seoul,
| | - Se Jin Jang
- Asan Medical Center, University of Ulsan, College of Medicine, Seoul
| | - Yoo Duk Choi
- Chonnam National University Medical School, Gwangju
| | | | | | - Lucia Kim
- Inha University School of Medicine, Incheon
| | | | - Choong Sik Lee
- Chungnam National University College of Medicine, Daejeon
| | | | - Mi Jin Kim
- Yeungnam University College of Medicine, Daegu, and
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