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Pinto AM, Ariani F, Bianciardi L, Daga S, Renieri A. Exploiting the potential of next-generation sequencing in genomic medicine. Expert Rev Mol Diagn 2017; 16:1037-47. [PMID: 27574853 DOI: 10.1080/14737159.2016.1224181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol 2017; 17:194. [PMID: 28903732 PMCID: PMC5598039 DOI: 10.1186/s12866-017-1101-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies. Electronic supplementary material The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imane Allali
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.,Laboratory of Biochemistry & Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Belen Cadenas
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Natasha Butz
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Hosni M Hassan
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Matthew Koci
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Anne Ballou
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Mendoza
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rizwana Ali
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.
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Yuan Y, Bayer PE, Batley J, Edwards D. Improvements in Genomic Technologies: Application to Crop Genomics. Trends Biotechnol 2017; 35:547-558. [DOI: 10.1016/j.tibtech.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/13/2022]
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Chen CW, Chang CY. Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope. J Vis Exp 2017. [PMID: 28362368 DOI: 10.3791/55417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The identification of an antigenic epitope by the immune system allows for the understanding of the protective mechanism of neutralizing antibodies that may facilitate the development of vaccines and peptide drugs. Peptide scanning is a simple and efficient method that straightforwardly maps the linear epitope recognized by a monoclonal antibody (mAb). Here, the authors present an epitope determination methodology involving serially truncated recombinant proteins, synthetic peptide design, and dot-blot hybridization for the antigenic recognition of nervous necrosis virus coat protein using a neutralizing mAb. This technique relies on the dot-blot hybridization of synthetic peptides and mAbs on a polyvinylidene fluoride (PVDF) membrane. The minimum antigenic region of a viral coat protein recognized by the RG-M56 mAb can be narrowed down by step-by-step trimmed peptide mapping onto a 6-mer peptide epitope. In addition, alanine scanning mutagenesis and residue substitution can be performed to characterize the binding significance of each amino acid residue making up the epitope. The residues flanking the epitope site were found to play critical roles in peptide conformation regulation. The identified epitope peptide may be used to form crystals of epitope peptide-antibody complexes for an x-ray diffraction study and functional competition, or for therapeutics.
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Affiliation(s)
- Chien-Wen Chen
- Institute of Cellular and Organismic Biology, Academia Sinica
| | - Chi-Yao Chang
- Institute of Cellular and Organismic Biology, Academia Sinica;
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Pu D, Pan R, Liu W, Xiao P. Quantitative analysis of single-nucleotide polymorphisms by pyrosequencing with di-base addition. Electrophoresis 2017; 38:876-885. [PMID: 27957738 DOI: 10.1002/elps.201600430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 02/06/2023]
Abstract
We have developed and validated a novel method for quantitative detection of SNPs by using pyrosequencing with di-base addition (PDBA). Based on the principle that the signal intensity is proportional to the template concentration within a linear concentration range, linear formula (Y = AX + B) for each genotype is established, and the relationship between two genotypes of a single SNP can be resolved by corresponding linear formulas. Here, PDBA assays were developed to detect variants rs6717546 and rs4148324, and the linear formulas for each genotype of rs6717546 and rs4148324 were established. The method allowed to quantitatively determine each genotype and showed 100% accordant results against a panel of defined mixtures. A set of 24 template fragments containing variants rs6717546 or rs4148324 was tested to evaluate the method. Our results showed that allele frequency of each genotype was accurately quantified, with results comparable to those of conventional pyrosequencing. Furthermore, this method was capable of detecting alleles with frequencies as low as 3%, which was more sensitive than ∼5 to ∼7% level detected by conventional pyrosequencing. This method offers high sensitivity, reproducibility, and relatively low costs, and thus could provide a much-needed approach for quantitative analysis of SNPs in clinical samples.
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Affiliation(s)
- Dan Pu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China.,School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, P. R. China
| | - Rongfang Pan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Wenbin Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, P. R. China
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Hoffman DJ, Campos-Ponce M, Taddei CR, Doak CM. Microbiome, growth retardation and metabolism: are they related? Ann Hum Biol 2017; 44:201-207. [PMID: 27927018 DOI: 10.1080/03014460.2016.1267261] [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] [Indexed: 02/08/2023]
Abstract
CONTEXT Despite an improvement in food security and the delivery of nutritional supplements to children living in impoverished parts of the world, poor growth is still highly prevalent. Given that the microbiome is related to both nutrient absorption, as well as overweight/obesity, it may play a central role in limiting or modifying normal growth processes while contributing to chronic disease risks. OBJECTIVE The objective of this paper is to describe normal growth processes, the role of the microbiome in supporting or disrupting normal growth processes, and its potential impact on long-term health. METHODS A literature search of relevant human and laboratory research on growth, microbiome and the relationship between poor growth and chronic diseases was conducted. This review focuses on potential mechanisms that implicate the microbiome as a mediator of poor growth and later metabolic outcomes. In this relationship, attention was given to the potential for gastrointestinal infections to disrupt the microbiome. RESULTS Based on the studies reviewed, it is clear that exposure to infections disturbs both intestinal functioning as well as normal growth and changes in the microbiome may influence micronutrient availability and metabolic processes. CONCLUSIONS The microbiome may play a significant role in limiting human growth, but little is known about changes in the microbiome during periods of undernutrition. Thus, it is of great scientific and public health importance to improve the understanding of how the microbiome changes during nutrient deprivation. To best address the issue of the double burden and poor growth in low-income countries, research is warranted to advance the knowledge of the long-term role of the microbiome in the health of children exposed to undernutrition.
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Affiliation(s)
- Daniel J Hoffman
- a Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition, and Health , Rutgers, the State University of New Jersey , New Brunswick , NJ , USA
| | - Maiza Campos-Ponce
- b Department of Health Sciences , VU University , Amsterdam , The Netherlands
| | - Carla R Taddei
- c Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences , University of São Paulo , São Paulo, SP , Brazil.,d School of Arts, Science and Humanities , University of São Paulo , São Paulo, SP , Brazil
| | - Colleen M Doak
- b Department of Health Sciences , VU University , Amsterdam , The Netherlands
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Abstract
Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.
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60
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Pranavchand R, Reddy BM. Genomics era and complex disorders: Implications of GWAS with special reference to coronary artery disease, type 2 diabetes mellitus, and cancers. J Postgrad Med 2016; 62:188-98. [PMID: 27424552 PMCID: PMC4970347 DOI: 10.4103/0022-3859.186390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Human Genome Project (HGP) has identified millions of single nucleotide polymorphisms (SNPs) and their association with several diseases, apart from successfully characterizing the Mendelian/monogenic diseases. However, the dissection of precise etiology of complex genetic disorders still poses a challenge for human geneticists. This review outlines the landmark results of genome-wide association studies (GWAS) with respect to major complex diseases - Coronary artery disease (CAD), type 2 diabetes mellitus (T2DM), and predominant cancers. A brief account on the current Indian scenario is also given. All the relevant publications till mid-2015 were accessed through web databases such as PubMed and Google. Several databases providing genetic information related to these diseases were tabulated and in particular, the list of the most significant SNPs identified through GWAS was made, which may be useful for designing studies in functional validation. Post-GWAS implications and emerging concepts such as epigenomics and pharmacogenomics were also discussed.
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Affiliation(s)
- R Pranavchand
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Andhra Pradesh, India
| | - B M Reddy
- Molecular Anthropology Group, Biological Anthropology Unit, Indian Statistical Institute, Hyderabad, Andhra Pradesh, India
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Ambardar S, Gupta R, Trakroo D, Lal R, Vakhlu J. High Throughput Sequencing: An Overview of Sequencing Chemistry. Indian J Microbiol 2016; 56:394-404. [PMID: 27784934 PMCID: PMC5061697 DOI: 10.1007/s12088-016-0606-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/22/2016] [Indexed: 01/19/2023] Open
Abstract
In the present century sequencing is to the DNA science, what gel electrophoresis was to it in the last century. From 1977 to 2016 three generation of the sequencing technologies of various types have been developed. Second and third generation sequencing technologies referred commonly to as next generation sequencing technology, has evolved significantly with increase in sequencing speed, decrease in sequencing cost, since its inception in 2004. GS FLX by 454 Life Sciences/Roche diagnostics, Genome Analyzer, HiSeq, MiSeq and NextSeq by Illumina, Inc., SOLiD by ABI, Ion Torrent by Life Technologies are various type of the sequencing platforms available for second generation sequencing. The platforms available for the third generation sequencing are Helicos™ Genetic Analysis System by SeqLL, LLC, SMRT Sequencing by Pacific Biosciences, Nanopore sequencing by Oxford Nanopore's, Complete Genomics by Beijing Genomics Institute and GnuBIO by BioRad, to name few. The present article is an overview of the principle and the sequencing chemistry of these high throughput sequencing technologies along with brief comparison of various types of sequencing platforms available.
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Affiliation(s)
- Sheetal Ambardar
- Metagenomics Laboratory, School of Biotechnology, University of Jammu, Jammu, J&K India
- Centre for Cellular and Molecular Platform, National Centre for Biological Sciences, TIFR Bangalore, Bangalore, India
- Institute of Trans-Disciplinary Health Sciences and Technology, Trans-Disciplinary University, Bangalore, 560064 India
| | - Rikita Gupta
- Metagenomics Laboratory, School of Biotechnology, University of Jammu, Jammu, J&K India
| | - Deepika Trakroo
- Metagenomics Laboratory, School of Biotechnology, University of Jammu, Jammu, J&K India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, South Campus, University of Delhi, Delhi, India
| | - Jyoti Vakhlu
- Metagenomics Laboratory, School of Biotechnology, University of Jammu, Jammu, J&K India
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Kremer FS, Eslabão MR, Dellagostin OA, Pinto LDS. Genix: a new online automated pipeline for bacterial genome annotation. FEMS Microbiol Lett 2016; 363:fnw263. [DOI: 10.1093/femsle/fnw263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/30/2016] [Accepted: 11/15/2016] [Indexed: 12/23/2022] Open
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Manook A, Hiergeist A, Rupprecht R, Baghai TC. Dickdarmmikrobiom und Depression. DER NERVENARZT 2016; 87:1227-1240. [DOI: 10.1007/s00115-016-0230-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Alhagamhmad MH, Day AS, Lemberg DA, Leach ST. An overview of the bacterial contribution to Crohn disease pathogenesis. J Med Microbiol 2016; 65:1049-1059. [PMID: 27501828 DOI: 10.1099/jmm.0.000331] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Crohn disease (CD) is a chronic inflammatory condition primarily affecting the gastro-intestinal tract and is characterized by reduced bacterial diversity. The exact cause of disease is unknown; however, evidence suggests that several components, including microbiota, may contribute to the underlying pathology and disease development. Perturbation of the host-microbe commensal relationship is considered the main driving force of tissue destruction and pathological changes seen in CD. Several putative bacterial pathogens including species from Mycobacterium, Campylobacter and Helicobacter are postulated in the aetiology of CD. However, to date, no strong evidence supports a single bacterium contributing overall to CD pathogenesis. Alternatively, dysbiosis or bacterial imbalance is more widely accepted as a leading factor in the disrupted host-immune system cross-talk resulting in subsequent intestinal inflammation. Depletion of symbiont microbes including Firmicutes, Bifidobacterium and Clostridia, in conjunction with an increase in pathobiont microbes from Bacteroidetes and Enterobacteria, is a striking feature observed in CD. No single factor has been identified as driving this dysbiosis, although diet, antibiotic exposure and possible early life events in presence of underlying genetic susceptibility may contribute. The aim of this review is to highlight the current accumulating literature on the proposed role of bacteria in the pathogenesis of CD.
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Affiliation(s)
- Moftah H Alhagamhmad
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Andrew S Day
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Department of Paediatrics, University of Otago, Christchurch, New Zealand
| | - Daniel A Lemberg
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- Department of Gastroenterology, Sydney Children's Hospital, Randwick, Sydney, NSW, Australia
| | - Steven T Leach
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
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Nanoelectronic three-dimensional (3D) nanotip sensing array for real-time, sensitive, label-free sequence specific detection of nucleic acids. Biomed Microdevices 2016; 18:7. [PMID: 26780442 DOI: 10.1007/s10544-016-0032-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high level of sensitivity has been yet stunted due to two factors: one, slow binding kinetics caused by the lack of probe molecules on the sensors and two, limited mass transport due to the planar structure (two-dimensional) of the current biosensors. Here we present a novel three-dimensional (3D), highly sensitive, real-time, inexpensive and label-free nanotip array as a rapid and direct platform to sequence-specific DNA screening. Our nanotip sensors are designed to have a nano sized thin film as their sensing area (~ 20 nm), sandwiched between two sensing electrodes. The tip is then conjugated to a DNA oligonucleotide complementary to the sequence of interest, which is electrochemically detected in real-time via impedance changes upon the formation of a double-stranded helix at the sensor interface. This 3D configuration is specifically designed to improve the biomolecular hit rate and the detection speed. We demonstrate that our nanotip array effectively detects oligonucleotides in a sequence-specific and highly sensitive manner, yielding concentration-dependent impedance change measurements with a target concentration as low as 10 pM and discrimination against even a single mismatch. Notably, our nanotip sensors achieve this accurate, sensitive detection without relying on signal indicators or enhancing molecules like fluorophores. It can also easily be scaled for highly multiplxed detection with up to 5000 sensors/square centimeter, and integrated into microfluidic devices. The versatile, rapid, and sensitive performance of the nanotip array makes it an excellent candidate for point-of-care diagnostics, and high-throughput DNA analysis applications.
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Abou Tayoun AN, Krock B, Spinner NB. Sequencing-based diagnostics for pediatric genetic diseases: progress and potential. Expert Rev Mol Diagn 2016; 16:987-99. [PMID: 27388938 DOI: 10.1080/14737159.2016.1209411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease. We discuss the challenges of genomic sequencing including incomplete current knowledge of variants, lack of data about certain genomic regions, mosaicism, and the presence of regions with high homology. Expert commentary: NGS has been a transformative technology and the gap between the research and clinical communities has never been so narrow. Therapeutic interventions are emerging based on genomic findings and the applications of NGS are progressing to prenatal genetics, epigenomics and transcriptomics.
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Affiliation(s)
- Ahmad N Abou Tayoun
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Bryan Krock
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
| | - Nancy B Spinner
- a Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine , The Children's Hospital of Philadelphia , Philadelphia , PA , USA.,b The Perelman School of Medicine , The University of Pennsylvania , Philadelphia , PA , USA
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Ong Q, Nguyen P, Thao NP, Le L. Bioinformatics Approach in Plant Genomic Research. Curr Genomics 2016; 17:368-78. [PMID: 27499685 PMCID: PMC4955030 DOI: 10.2174/1389202917666160331202956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/11/2015] [Accepted: 09/18/2015] [Indexed: 11/22/2022] Open
Abstract
The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity.
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Affiliation(s)
- Quang Ong
- Plant Abiotic Stress Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuc Nguyen
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
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Shields CW, Ohiri KA, Szott LM, López GP. Translating microfluidics: Cell separation technologies and their barriers to commercialization. CYTOMETRY PART B-CLINICAL CYTOMETRY 2016; 92:115-125. [PMID: 27282966 DOI: 10.1002/cyto.b.21388] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 01/09/2023]
Abstract
Advances in microfluidic cell sorting have revolutionized the ways in which cell-containing fluids are processed, now providing performances comparable to, or exceeding, traditional systems, but in a vastly miniaturized format. These technologies exploit a wide variety of physical phenomena to manipulate cells and fluid flow, such as magnetic traps, sound waves and flow-altering micropatterns, and they can evaluate single cells by immobilizing them onto surfaces for chemotherapeutic assessment, encapsulate cells into picoliter droplets for toxicity screenings and examine the interactions between pairs of cells in response to new, experimental drugs. However, despite the massive surge of innovation in these high-performance lab-on-a-chip devices, few have undergone successful commercialization, and no device has been translated to a widely distributed clinical commodity to date. Persistent challenges such as an increasingly saturated patent landscape as well as complex user interfaces are among several factors that may contribute to their slowed progress. In this article, we identify several of the leading microfluidic technologies for sorting cells that are poised for clinical translation; we examine the principal barriers preventing their routine clinical use; finally, we provide a prospectus to elucidate the key criteria that must be met to overcome those barriers. Once established, these tools may soon transform how clinical labs study various ailments and diseases by separating cells for downstream sequencing and enabling other forms of advanced cellular or sub-cellular analysis. © 2016 International Clinical Cytometry Society.
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Affiliation(s)
- C Wyatt Shields
- NSF Research Triangle Materials Research Science and Engineering Center, Duke University, Durham, North Carolina, 27708.,Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
| | - Korine A Ohiri
- NSF Research Triangle Materials Research Science and Engineering Center, Duke University, Durham, North Carolina, 27708.,Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708
| | - Luisa M Szott
- NSF Research Triangle Materials Research Science and Engineering Center, Duke University, Durham, North Carolina, 27708.,Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708
| | - Gabriel P López
- NSF Research Triangle Materials Research Science and Engineering Center, Duke University, Durham, North Carolina, 27708.,Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708.,Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708.,Center for Biomedical Engineering, Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico, 87131
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Hiergeist A, Gläsner J, Reischl U, Gessner A. Analyses of Intestinal Microbiota: Culture versus Sequencing. ILAR J 2016; 56:228-40. [PMID: 26323632 DOI: 10.1093/ilar/ilv017] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Analyzing human as well as animal microbiota composition has gained growing interest because structural components and metabolites of microorganisms fundamentally influence all aspects of host physiology. Originally dominated by culture-dependent methods for exploring these ecosystems, the development of molecular techniques such as high throughput sequencing has dramatically increased our knowledge. Because many studies of the microbiota are based on the bacterial 16S ribosomal RNA (rRNA) gene targets, they can, at least in principle, be compared to determine the role of the microbiome composition for developmental processes, host metabolism, and physiology as well as different diseases. In our review, we will summarize differences and pitfalls in current experimental protocols, including all steps from nucleic acid extraction to bioinformatical analysis which may produce variation that outweighs subtle biological differences. Future developments, such as integration of metabolomic, transcriptomic, and metagenomic data sets and standardization of the procedures, will be discussed.
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Affiliation(s)
- Andreas Hiergeist
- Andreas Hiergeist, PhD, and Joachim Gläsner, PhD, are senior scientists at the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany. Udo Reischl, PhD, is Head of Molecular Diagnostics and an associate professor for Medical Microbiology; and André Gessner, MD, PhD, is Director of the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
| | - Joachim Gläsner
- Andreas Hiergeist, PhD, and Joachim Gläsner, PhD, are senior scientists at the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany. Udo Reischl, PhD, is Head of Molecular Diagnostics and an associate professor for Medical Microbiology; and André Gessner, MD, PhD, is Director of the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
| | - Udo Reischl
- Andreas Hiergeist, PhD, and Joachim Gläsner, PhD, are senior scientists at the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany. Udo Reischl, PhD, is Head of Molecular Diagnostics and an associate professor for Medical Microbiology; and André Gessner, MD, PhD, is Director of the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
| | - André Gessner
- Andreas Hiergeist, PhD, and Joachim Gläsner, PhD, are senior scientists at the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany. Udo Reischl, PhD, is Head of Molecular Diagnostics and an associate professor for Medical Microbiology; and André Gessner, MD, PhD, is Director of the Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
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70
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Gallagher IJ, Jacobi C, Tardif N, Rooyackers O, Fearon K. Omics/systems biology and cancer cachexia. Semin Cell Dev Biol 2016; 54:92-103. [DOI: 10.1016/j.semcdb.2015.12.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
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71
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Establishment of A Rapid and Inexpensive Identification Method for HLA-B*58: 01 Genotype. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60930-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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72
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Pereira FL, Soares SC, Dorella FA, Leal CA, Figueiredo HC. Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes. Genomics 2016; 107:189-98. [DOI: 10.1016/j.ygeno.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/01/2016] [Accepted: 03/17/2016] [Indexed: 11/28/2022]
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73
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Mariano DCB, Sousa TDJ, Pereira FL, Aburjaile F, Barh D, Rocha F, Pinto AC, Hassan SS, Saraiva TDL, Dorella FA, de Carvalho AF, Leal CAG, Figueiredo HCP, Silva A, Ramos RTJ, Azevedo VAC. Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002. BMC Genomics 2016; 17:315. [PMID: 27129708 PMCID: PMC4851793 DOI: 10.1186/s12864-016-2673-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/22/2016] [Indexed: 12/13/2022] Open
Abstract
Background Studies have detected mis-assemblies in genomes of the species Corynebacterium pseudotuberculosis. These new discover have been possible due to the evolution of the Next-Generation Sequencing platforms, which have provided sequencing with accuracy and reduced costs. In addition, the improving of techniques for construction of high accuracy genomic maps, for example, Whole-genome mapping (WGM) (OpGen Inc), have allow high-resolution assembly that can detect large rearrangements. Results In this work, we present the resequencing of Corynebacterium pseudotuberculosis strain 1002 (Cp1002). Cp1002 was the first strain of this species sequenced in Brazil, and its genome has been used as model for several studies in silico of caseous lymphadenitis disease. The sequencing was performed using the platform Ion PGM and fragment library (200 bp kit). A restriction map was constructed, using the technique of WGM with the enzyme KpnI. After the new assembly process, using WGM as scaffolder, we detected a large inversion with size bigger than one-half of genome. A specific analysis using BLAST and NR database shows that the inversion occurs between two homology RNA ribosomal regions. Conclusion In conclusion, the results showed by WGM could be used to detect mismatches in assemblies, providing genomic maps with high resolution and allow assemblies with more accuracy and completeness. The new assembly of C. pseudotuberculosis was deposited in GenBank under the accession no. CP012837. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2673-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diego César Batista Mariano
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Felipe Luiz Pereira
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, 721172, India
| | - Flávia Rocha
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Anne Cybelle Pinto
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Syed Shah Hassan
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Tessália Diniz Luerce Saraiva
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda Alves Dorella
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Alex Fiorini de Carvalho
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Augusto Gomes Leal
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Henrique César Pereira Figueiredo
- National Reference Laboratory for Aquatic Animal Diseases of Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Vasco Ariston Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, CEP 31270-901, Belo Horizonte, Minas Gerais, Brazil.
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Zhirnov V, Zadegan RM, Sandhu GS, Church GM, Hughes WL. Nucleic acid memory. NATURE MATERIALS 2016; 15:366-70. [PMID: 27005909 PMCID: PMC6361517 DOI: 10.1038/nmat4594] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Nucleic acid memory has a retention time far exceeding electronic memory. As an alternative storage media, DNA surpasses the information density and energy of operation offered by flash memory.
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Affiliation(s)
- Victor Zhirnov
- Semiconductor Research Corporation, 1101 Slater Road, Durham, North Carolina 27703, USA
| | - Reza M Zadegan
- Department of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725-2090, USA
| | - Gurtej S Sandhu
- Micron Technology, Inc., PO Box 6, 8000 South Federal Way, Boise, Idaho 83707-0006, USA
| | - George M Church
- Department of Genetics, Harvard University, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - William L Hughes
- Department of Materials Science and Engineering, Boise State University, 1910 University Drive, Boise, Idaho 83725-2090, USA
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75
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Guimarães LC, Florczak-Wyspianska J, de Jesus LB, Viana MVC, Silva A, Ramos RTJ, Soares SDC, Soares SDC. Inside the Pan-genome - Methods and Software Overview. Curr Genomics 2016; 16:245-52. [PMID: 27006628 PMCID: PMC4765519 DOI: 10.2174/1389202916666150423002311] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 12/11/2022] Open
Abstract
The number of genomes that have been deposited in databases has increased exponentially
after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence
data; this circumstance has demanded the development of new bioinformatics software and the creation
of new areas, such as comparative genomics. In comparative genomics, the genetic content of an
organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences,
identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative
genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome
size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the
genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number
of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory
or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be
“open” as long as new genes are added significantly to the total repertoire for each new additional genome and “closed”
when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform
all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous
gene identification.
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Affiliation(s)
- Luis Carlos Guimarães
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil;; Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | | | - Leandro Benevides de Jesus
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil
| | - Marcus Vinícius Canário Viana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Avenue Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Rommel Thiago Jucá Ramos
- Department of Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
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76
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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77
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Microbial Whole-Genome Sequencing: Applications in Clinical Microbiology and Public Health. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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78
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Zeron-Medina J, Ochoa de Olza M, Braña I, Rodon J. The Personalization of Therapy: Molecular Profiling Technologies and Their Application. Semin Oncol 2015; 42:775-87. [DOI: 10.1053/j.seminoncol.2015.09.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.
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Affiliation(s)
- Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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80
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Uptmoor AC, Freudenberg J, Schwäbel ST, Paulus F, Rominger F, Hinkel F, Bunz UHF. Reverse Engineering of Conjugated Microporous Polymers: Defect Structures of Tetrakis(4‐ethynylphenyl)stannane Networks. Angew Chem Int Ed Engl 2015; 54:14673-6. [DOI: 10.1002/anie.201506905] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/11/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Andrea C. Uptmoor
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
| | - Jan Freudenberg
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
| | - S. Thimon Schwäbel
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
| | - Fabian Paulus
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
| | - Frank Rominger
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
| | - Felix Hinkel
- Centre of Advanced Materials (CAM), Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 225, 69120 Heidelberg (Germany)
| | - Uwe H. F. Bunz
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany)
- Centre of Advanced Materials (CAM), Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 225, 69120 Heidelberg (Germany)
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81
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Uptmoor AC, Freudenberg J, Schwäbel ST, Paulus F, Rominger F, Hinkel F, Bunz UHF. “Sequenzanalyse” konjugierter, mikroporöser Polymere (CMPs): Defektstrukturen eines Tetrakis(4‐ethinylphenyl)stannan‐Netzwerks. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrea C. Uptmoor
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
| | - Jan Freudenberg
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
| | - S. Thimon Schwäbel
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
| | - Fabian Paulus
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
| | - Frank Rominger
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
| | - Felix Hinkel
- Centre of Advanced Materials (CAM), Ruprecht‐Karls‐Universität Heidelberg (Deutschland)
| | - Uwe H. F. Bunz
- Organisch‐Chemisches Institut, Ruprecht‐Karls‐Universität, Im Neuenheimer Feld 270, 69120 Heidelberg (Deutschland)
- Centre of Advanced Materials (CAM), Ruprecht‐Karls‐Universität Heidelberg (Deutschland)
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McQueen CM, Dindot SV, Foster MJ, Cohen ND. Genetic Susceptibility to Rhodococcus equi. J Vet Intern Med 2015; 29:1648-59. [PMID: 26340305 PMCID: PMC4895676 DOI: 10.1111/jvim.13616] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/29/2015] [Accepted: 08/10/2015] [Indexed: 02/02/2023] Open
Abstract
Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).
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Affiliation(s)
- C M McQueen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
| | - S V Dindot
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - M J Foster
- Medical Sciences Library, Texas A&M University, College Station, TX
| | - N D Cohen
- Department of Large Animal Clinical Sciences, Texas A&M University, College Station, TX
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83
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Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
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Omondi D, Masiga DK, Ajamma YU, Fielding BC, Njoroge L, Villinger J. Unraveling Host-Vector-Arbovirus Interactions by Two-Gene High Resolution Melting Mosquito Bloodmeal Analysis in a Kenyan Wildlife-Livestock Interface. PLoS One 2015; 10:e0134375. [PMID: 26230507 PMCID: PMC4521840 DOI: 10.1371/journal.pone.0134375] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/08/2015] [Indexed: 11/23/2022] Open
Abstract
The blood-feeding patterns of mosquitoes are directly linked to the spread of pathogens that they transmit. Efficient identification of arthropod vector bloodmeal hosts can identify the diversity of vertebrate species potentially involved in disease transmission cycles. While molecular bloodmeal analyses rely on sequencing of cytochrome b (cyt b) or cytochrome oxidase 1 gene PCR products, recently developed bloodmeal host identification based on high resolution melting (HRM) analyses of cyt b PCR products is more cost-effective. To resolve the diverse vertebrate hosts that mosquitoes may potentially feed on in sub-Saharan Africa, we utilized HRM profiles of both cyt b and 16S ribosomal RNA genes. Among 445 blood-fed Aedeomyia, Aedes, Anopheles, Culex, Mansonia, and Mimomyia mosquitoes from Kenya’s Lake Victoria and Lake Baringo regions where many mosquito-transmitted pathogens are endemic, we identified 33 bloodmeal hosts including humans, eight domestic animal species, six peridomestic animal species and 18 wildlife species. This resolution of vertebrate host species was only possible by comparing profiles of both cyt b and 16S markers, as melting profiles of some pairs of species were similar for either marker but not both. We identified mixed bloodmeals in a Culex pipiens from Mbita that had fed on a goat and a human and in two Mansonia africana mosquitoes from Baringo that each had fed on a rodent (Arvicanthis niloticus) in addition to a human or baboon. We further detected Sindbis and Bunyamwera viruses in blood-fed mosquito homogenates by Vero cell culture and RT-PCR in Culex, Aedeomyia, Anopheles and Mansonia mosquitoes from Baringo that had fed on humans and livestock. The observed mosquito feeding on both arbovirus amplifying hosts (including sheep and goats) and possible arbovirus reservoirs (birds, porcupine, baboons, rodents) informs arbovirus disease epidemiology and vector control strategies.
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Affiliation(s)
- David Omondi
- Martin Lüscher Emerging Infectious Disease (ML-EID) Laboratory, International Centre for Insect Physiology and Ecology, P. O Box 30772-00100, Nairobi, Kenya
- Molecular Biology and Virology Laboratory, Department of Medical Biosciences, University of Western Cape, Private Bag X17, Bellville, 7535, South Africa
- Biochemistry and Molecular Biology Department, Egerton University, P.O Box 536, Egerton, 20115, Kenya
| | - Daniel K. Masiga
- Martin Lüscher Emerging Infectious Disease (ML-EID) Laboratory, International Centre for Insect Physiology and Ecology, P. O Box 30772-00100, Nairobi, Kenya
| | - Yvonne Ukamaka Ajamma
- Martin Lüscher Emerging Infectious Disease (ML-EID) Laboratory, International Centre for Insect Physiology and Ecology, P. O Box 30772-00100, Nairobi, Kenya
| | - Burtram C. Fielding
- Molecular Biology and Virology Laboratory, Department of Medical Biosciences, University of Western Cape, Private Bag X17, Bellville, 7535, South Africa
| | - Laban Njoroge
- Invertebrates Zoology Section, Zoology Department, National Museums of Kenya, P.O. Box 40658-00100, Nairobi, Kenya
| | - Jandouwe Villinger
- Martin Lüscher Emerging Infectious Disease (ML-EID) Laboratory, International Centre for Insect Physiology and Ecology, P. O Box 30772-00100, Nairobi, Kenya
- * E-mail:
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85
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Karki R, Pandya D, Elston RC, Ferlini C. Defining "mutation" and "polymorphism" in the era of personal genomics. BMC Med Genomics 2015; 8:37. [PMID: 26173390 PMCID: PMC4502642 DOI: 10.1186/s12920-015-0115-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 07/06/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The growing advances in DNA sequencing tools have made analyzing the human genome cheaper and faster. While such analyses are intended to identify complex variants, related to disease susceptibility and efficacy of drug responses, they have blurred the definitions of mutation and polymorphism. DISCUSSION In the era of personal genomics, it is critical to establish clear guidelines regarding the use of a reference genome. Nowadays DNA variants are called as differences in comparison to a reference. In a sequencing project Single Nucleotide Polymorphisms (SNPs) and DNA mutations are defined as DNA variants detectable in >1 % or <1 % of the population, respectively. The alternative use of the two terms mutation or polymorphism for the same event (a difference as compared with a reference) can lead to problems of classification. These problems can impact the accuracy of the interpretation and the functional relationship between a disease state and a genomic sequence. We propose to solve this nomenclature dilemma by defining mutations as DNA variants obtained in a paired sequencing project including the germline DNA of the same individual as a reference. Moreover, the term mutation should be accompanied by a qualifying prefix indicating whether the mutation occurs only in somatic cells (somatic mutation) or also in the germline (germline mutation). We believe this distinction in definition will help avoid confusion among researchers and support the practice of sequencing the germline and somatic tissues in parallel to classify the DNA variants thus defined as mutations.
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Affiliation(s)
- Roshan Karki
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA
| | - Deep Pandya
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA
| | - Robert C Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Cristiano Ferlini
- Danbury Hospital Research Institute, Western Connecticut Health Network, 131 West Street, Danbury, CT, 06810, USA.
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86
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Rovigatti U. Cancer modelling in the NGS era - Part I: Emerging technology and initial modelling. Crit Rev Oncol Hematol 2015; 96:274-307. [PMID: 26427785 DOI: 10.1016/j.critrevonc.2015.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/14/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
It is today indisputable that great progresses have been made in our molecular understanding of cancer cells, but an effective implementation of such knowledge into dramatic cancer-cures is still belated and yet desperately needed. This review gives a snapshot at where we stand today in this search for cancer understanding and definitive treatments, how far we have progressed and what are the major obstacles we will have to overcome both technologically and for disease modelling. In the first part, promising 3rd/4th Generation Sequencing Technologies will be summarized (particularly IonTorrent and OxfordNanopore technologies). Cancer modelling will be then reviewed from its origin in XIX Century Germany to today's NGS applications for cancer understanding and therapeutic interventions. Developments after Molecular Biology revolution (1953) are discussed as successions of three phases. The first, PH1, labelled "Clonal Outgrowth" (from 1960s to mid 1980s) was characterized by discoveries in cytogenetics (Nowell, Rowley) and viral oncology (Dulbecco, Bishop, Varmus), which demonstrated clonality. Treatments were consequently dominated by a "cytotoxic eradication" strategy with chemotherapeutic agents. In PH2, (from the mid 1980s to our days) the description of cancer as "Gene Networks" led to targeted-gene-therapies (TGTs). TGTs are the focus of Section 3: in view of their apparent failing (Ephemeral Therapies), alternative strategies will be discussed in review part II (particularly cancer immunotherapy, CIT). Additional Pitfalls impinge on the concepts of tumour heterogeneity (inter/intra; ITH). The described pitfalls set the basis for a new phase, PH3, which is called "NGS Era" and will be also discussed with ten emerging cancer models in the Review 2nd part.
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Affiliation(s)
- Ugo Rovigatti
- University of Pisa Medical School, Oncology Department, via Roma 55, 56127 Pisa, Italy.
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87
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Abstract
The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.
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Pollastro C, Ziviello C, Costa V, Ciccodicola A. Pharmacogenomics of Drug Response in Type 2 Diabetes: Toward the Definition of Tailored Therapies? PPAR Res 2015; 2015:415149. [PMID: 26161088 PMCID: PMC4486250 DOI: 10.1155/2015/415149] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/24/2015] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes is one of the major causes of mortality with rapidly increasing prevalence. Pharmacological treatment is the first recommended approach after failure in lifestyle changes. However, a significant number of patients shows-or develops along time and disease progression-drug resistance. In addition, not all type 2 diabetic patients have the same responsiveness to drug treatment. Despite the presence of nongenetic factors (hepatic, renal, and intestinal), most of such variability is due to genetic causes. Pharmacogenomics studies have described association between single nucleotide variations and drug resistance, even though there are still conflicting results. To date, the most reliable approach to investigate allelic variants is Next-Generation Sequencing that allows the simultaneous analysis, on a genome-wide scale, of nucleotide variants and gene expression. Here, we review the relationship between drug responsiveness and polymorphisms in genes involved in drug metabolism (CYP2C9) and insulin signaling (ABCC8, KCNJ11, and PPARG). We also highlight the advancements in sequencing technologies that to date enable researchers to perform comprehensive pharmacogenomics studies. The identification of allelic variants associated with drug resistance will constitute a solid basis to establish tailored therapeutic approaches in the treatment of type 2 diabetes.
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Affiliation(s)
- Carla Pollastro
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
- DiST, Department of Science and Technology, “Parthenope” University of Naples, Centro Direzionale, Isola C4, 80143 Naples, Italy
| | - Carmela Ziviello
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alfredo Ciccodicola
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
- DiST, Department of Science and Technology, “Parthenope” University of Naples, Centro Direzionale, Isola C4, 80143 Naples, Italy
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89
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Blackburn HL, Schroeder B, Turner C, Shriver CD, Ellsworth DL, Ellsworth RE. Management of Incidental Findings in the Era of Next-generation Sequencing. Curr Genomics 2015; 16:159-74. [PMID: 26069456 PMCID: PMC4460220 DOI: 10.2174/1389202916666150317232930] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/23/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings (IF)- genetic alterations associated with conditions or diseases unrelated to the patient's present condition for which current tests are being performed- may have important clinical ramifications. The current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed - actionable mutations, variants of unknown significance, or all IF? Policies for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric, and adult patients.
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Affiliation(s)
| | - Bradley Schroeder
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | - Clesson Turner
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Craig D. Shriver
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Rachel E. Ellsworth
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
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90
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Abstract
Inherited arrhythmia syndromes are collectively associated with substantial morbidity, yet our understanding of the genetic architecture of these conditions remains limited. Recent technological advances in DNA sequencing have led to the commercialization of genetic testing now widely available in clinical practice. In particular, next-generation sequencing allows the large-scale and rapid assessment of entire genomes. Although next-generation sequencing represents a major technological advance, it has introduced numerous challenges with respect to the interpretation of genetic variation and has opened a veritable floodgate of biological data of unknown clinical significance to practitioners. In this review, we discuss current genetic testing indications for inherited arrhythmia syndromes, broadly outline characteristics of next-generation sequencing techniques, and highlight challenges associated with such testing. We further summarize future directions that will be necessary to address to enable the widespread adoption of next-generation sequencing in the routine management of patients with inherited arrhythmia syndromes.
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Affiliation(s)
- Steven A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, and Medical and Population Genetics Program, The Broad Institute, Cambridge, Massachusetts.
| | - Patrick T Ellinor
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, and Medical and Population Genetics Program, The Broad Institute, Cambridge, Massachusetts
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91
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Jiang W, Liang P, Wang B, Fang J, Lang J, Tian G, Jiang J, Zhu TF. Optimized DNA extraction and metagenomic sequencing of airborne microbial communities. Nat Protoc 2015; 10:768-79. [PMID: 25906115 PMCID: PMC7086576 DOI: 10.1038/nprot.2015.046] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2-3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.
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Affiliation(s)
- Wenjun Jiang
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Peng Liang
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
| | - Buying Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Tsinghua University, Beijing, China
| | - Jianhuo Fang
- Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jidong Lang
- Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China
| | - Geng Tian
- Center of Biomedical Analysis, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jingkun Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, State Environmental Protection Key Laboratory of Sources and Control of Air Pollution Complex, Tsinghua University, Beijing, China
| | - Ting F Zhu
- School of Life Sciences, Center for Synthetic and Systems Biology, Ministry of Education Key Laboratory of Bioinformatics, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, China
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92
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Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DGB, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Arch Pathol Lab Med 2015; 139:481-93. [DOI: 10.5858/arpa.2014-0250-cp] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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93
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Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J, Cogulu O. Evolution of genetic techniques: past, present, and beyond. BIOMED RESEARCH INTERNATIONAL 2015; 2015:461524. [PMID: 25874212 PMCID: PMC4385642 DOI: 10.1155/2015/461524] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 12/05/2022]
Abstract
Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.
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Affiliation(s)
- Asude Alpman Durmaz
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology, Warsaw University Faculty of Medicine, 61 02-091 Warsaw, Poland
| | - Gokce Toruner
- Institute of Genomic Medicine, UMDNJ-NJ Medical School, Newark, NJ 07103, USA
| | - Jacqueline Schoumans
- Department of Medical Genetics, Cancer Cytogenetic Unit, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ozgur Cogulu
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
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94
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Borland KM, AbdulSalam SF, Solivio MJ, Burke MP, Wolfkiel PR, Lawson SM, Stockman CA, Andersen JM, Smith S, Tolstolutskaya JN, Gurjar PN, Bercz AP, Merino EJ, Litosh VA. Base-modified thymidines capable of terminating DNA synthesis are novel bioactive compounds with activity in cancer cells. Bioorg Med Chem 2015; 23:1869-81. [PMID: 25778768 DOI: 10.1016/j.bmc.2015.01.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/22/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Current FDA-approved chemotherapeutic antimetabolites elicit severe side effects that warrant their improvement; therefore, we designed compounds with mechanisms of action focusing on inhibiting DNA replication rather than targeting multiple pathways. We previously discovered that 5-(α-substituted-2-nitrobenzyloxy)methyluridine-5'-triphosphates were exquisite DNA synthesis terminators; therefore, we synthesized a library of 35 thymidine analogs and evaluated their activity using an MTT cell viability assay of MCF7 breast cancer cells chosen for their vulnerability to these nucleoside derivatives. Compound 3a, having an α-tert-butyl-2-nitro-4-(phenyl)alkynylbenzyloxy group, showed an IC50 of 9±1μM. The compound is more selective for cancer cells than for fibroblast cells compared with 5-fluorouracil. Treatment of MCF7 cells with 3a elicits the DNA damage response as indicated by phosphorylation of γ-H2A. A primer extension assay of the 5'-triphosphate of 3a revealed that 3aTP is more likely to inhibit DNA polymerase than to lead to termination events upon incorporation into the DNA replication fork.
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Affiliation(s)
- Kayla M Borland
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Safnas F AbdulSalam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Morwena J Solivio
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Matthew P Burke
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Patrick R Wolfkiel
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Sean M Lawson
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Courtney A Stockman
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Joel M Andersen
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Skyler Smith
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Julia N Tolstolutskaya
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Purujit N Gurjar
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Aron P Bercz
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Edward J Merino
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA
| | - Vladislav A Litosh
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct. ML 0172, Cincinnati, OH 45221-0172, USA.
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95
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Borisov OV, Alvarez M, Carroll JA, Brown PW. Sequence Variants and Sequence Variant Analysis in Biotherapeutic Proteins. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Oleg V. Borisov
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Melissa Alvarez
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - James A. Carroll
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Paul W. Brown
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
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Abstract
Activating mutation of KRAS plays a significant role in the pathogenesis of common human malignancies and molecular testing of KRAS mutation has emerged as an essential biomarker in the current practice of clinical oncology. The presence of KRAS mutation is generally associated with clinical aggressiveness of the cancer and reduced survival of the patient. Therapeutically, KRAS mutation testing has maximum utility in stratifying metastatic colorectal carcinoma and lung cancer patients for treatment with targeted therapy. Diagnostically, KRAS mutation testing is useful in the workup of pancreaticobiliary and thyroid cancers, particularly using cytological specimens. In the era of precision medicine, the role of KRAS mutation testing is poised to expand, likely in a setting of combinatorial therapeutic strategy and requiring additional mutation testing of its upstream and/or downstream effectors.
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Affiliation(s)
- Sudhir Perincheri
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520-8023, USA
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97
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Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
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98
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XING XQ, CHU YN, XIANG Z, SONG QX, ZHOU GH. Establishment of Cloning and Sequencing Method for High-Resolution HLA-B Genotype Assay. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2014. [DOI: 10.1016/s1872-2040(14)60779-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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99
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Diekstra A, Bosgoed E, Rikken A, van Lier B, Kamsteeg EJ, Tychon M, Derks RC, van Soest RA, Mensenkamp AR, Scheffer H, Neveling K, Nelen MR. Translating sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing. Clin Chem 2014; 61:154-62. [PMID: 25274553 DOI: 10.1373/clinchem.2014.225250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic laboratories, enabling the sequencing of large targeted gene panels or exomes. The development of benchtop NGS instruments now allows the analysis of single genes or small gene panels, making these platforms increasingly competitive with Sanger sequencing. METHODS We developed a generic automated ion semiconductor sequencing work flow that can be used in a clinical setting and can serve as a substitute for Sanger sequencing. Standard amplicon-based enrichment remained identical to PCR for Sanger sequencing. A novel postenrichment pooling strategy was developed, limiting the number of library preparations and reducing sequencing costs up to 70% compared to Sanger sequencing. RESULTS A total of 1224 known pathogenic variants were analyzed, yielding an analytical sensitivity of 99.92% and specificity of 99.99%. In a second experiment, a total of 100 patient-derived DNA samples were analyzed using a blind analysis. The results showed an analytical sensitivity of 99.60% and specificity of 99.98%, comparable to Sanger sequencing. CONCLUSIONS Ion semiconductor sequencing can be a first choice mutation scanning technique, independent of the genes analyzed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Hans Scheffer
- Department of Human Genetics and Donders Center for Neurosciences, Radboud university medical center, Nijmegen, the Netherlands
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Abstract
The introduction of next generation sequencing (NGS) has led to an exponential increase of elucidated genetic causes in both extremely rare diseases and common but heterogeneous disorders. It can be applied to the whole or to selected parts of the genome (genome or exome sequencing, gene panels). NGS is not only useful in large extended families with linkage information, but may also be applied to detect de novo mutations or mosaicism in sporadic patients without a prior hypothesis about the mutated gene. Currently, NGS is applied in both research and clinical settings, and there is a rapid transition of research findings to diagnostic applications. These developments may greatly help to minimize the "diagnostic odyssey" for patients as whole-genome analysis can be performed in a few days at reasonable costs compared with gene-by-gene analysis based on Sanger sequencing following diverse clinical tests. Despite the enthusiasm about NGS, one has to keep in mind its limitations, such as a coverage and accuracy of < 100%, resulting in missing variants and false positive findings. In addition, variant interpretation is challenging as there is usually more than one candidate variant found. Therefore, there is an urgent need to define standards for NGS with respect to run quality and variant interpretation, as well as mechanisms of quality control. Further, there are ethical challenges including incidental findings and how to guide unaffected probands seeking direct-to-customer testing. However, taken together, the application of NGS in research and diagnostics provides a tremendous opportunity to better serve our patients.
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Affiliation(s)
- Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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