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Tierno D, Grassi G, Scomersi S, Bortul M, Generali D, Zanconati F, Scaggiante B. Next-Generation Sequencing and Triple-Negative Breast Cancer: Insights and Applications. Int J Mol Sci 2023; 24:ijms24119688. [PMID: 37298642 DOI: 10.3390/ijms24119688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
The poor survival of triple-negative breast cancer (TNBC) is due to its aggressive behavior, large heterogeneity, and high risk of recurrence. A comprehensive molecular investigation of this type of breast cancer using high-throughput next-generation sequencing (NGS) methods may help to elucidate its potential progression and discover biomarkers related to patient survival. In this review, the NGS applications in TNBC research are described. Many NGS studies point to TP53 mutations, immunocheckpoint response genes, and aberrations in the PIK3CA and DNA repair pathways as recurrent pathogenic alterations in TNBC. Beyond their diagnostic and predictive/prognostic value, these findings suggest potential personalized treatments in PD -L1-positive TNBC or in TNBC with a homologous recombination deficit. Moreover, the comprehensive sequencing of large genomes with NGS has enabled the identification of novel markers with clinical value in TNBC, such as AURKA, MYC, and JARID2 mutations. In addition, NGS investigations to explore ethnicity-specific alterations have pointed to EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation as possible molecular signatures of African and African American TNBC. Finally, the development of long-read sequencing methods and their combination with optimized short-read techniques promise to improve the efficiency of NGS approaches for future massive clinical use.
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Affiliation(s)
- Domenico Tierno
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Gabriele Grassi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Serena Scomersi
- Breast Unit-Azienda Sanitaria Universitaria Integrata Giuliano Isontina ASUGI, University of Trieste, 34149 Trieste, Italy
| | - Marina Bortul
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Daniele Generali
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Azienda Socio-Sanitaria Territoriale di Cremona-ASST, Breast Cancer Unit and Translational Research Unit, 26100 Cremona, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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2
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Reconstruction of evolving gene variants and fitness from short sequencing reads. Nat Chem Biol 2021; 17:1188-1198. [PMID: 34635842 PMCID: PMC8551035 DOI: 10.1038/s41589-021-00876-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
Directed evolution can generate proteins with tailor-made activities. However, full-length genotypes, their frequencies and fitnesses are difficult to measure for evolving gene-length biomolecules using most high-throughput DNA sequencing methods, as short read lengths can lose mutation linkages in haplotypes. Here we present Evoracle, a machine learning method that accurately reconstructs full-length genotypes (R2 = 0.94) and fitness using short-read data from directed evolution experiments, with substantial improvements over related methods. We validate Evoracle on phage-assisted continuous evolution (PACE) and phage-assisted non-continuous evolution (PANCE) of adenine base editors and OrthoRep evolution of drug-resistant enzymes. Evoracle retains strong performance (R2 = 0.86) on data with complete linkage loss between neighboring nucleotides and large measurement noise, such as pooled Sanger sequencing data (~US$10 per timepoint), and broadens the accessibility of training machine learning models on gene variant fitnesses. Evoracle can also identify high-fitness variants, including low-frequency 'rising stars', well before they are identifiable from consensus mutations.
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Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. ACTA ACUST UNITED AC 2019; 122:e59. [PMID: 29851291 DOI: 10.1002/cpmb.59] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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5
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Yan S, Li X, Zhang P, Wang Y, Chen HY, Huang S, Yu H. Direct sequencing of 2'-deoxy-2'-fluoroarabinonucleic acid (FANA) using nanopore-induced phase-shift sequencing (NIPSS). Chem Sci 2019; 10:3110-3117. [PMID: 30996894 PMCID: PMC6429604 DOI: 10.1039/c8sc05228j] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 01/23/2019] [Indexed: 12/21/2022] Open
Abstract
2'-deoxy-2'-fluoroarabinonucleic acid (FANA), which is one type of xeno-nucleic acid (XNA), has been intensively studied in molecular medicine and synthetic biology because of its superior gene-silencing and catalytic activities. Although urgently required, FANA cannot be directly sequenced by any existing platform. Nanopore sequencing, which identifies a single molecule analyte directly from its physical and chemical properties, shows promise for direct XNA sequencing. As a proof of concept, different FANA homopolymers show well-distinguished pore blockage signals in a Mycobacterium smegmatis porin A (MspA) nanopore. By ligating FANA with a DNA drive-strand, direct FANA sequencing has been demonstrated using phi29 DNA polymerase by Nanopore-Induced Phase Shift Sequencing (NIPSS). When bound with an FANA template, the phi29 DNA polymerase shows unexpected reverse transcriptase activity when monitored in a single molecule assay. Following further investigations into the ensemble, phi29 DNA polymerase is shown to be a previously unknown reverse transcriptase for FANA that operates at room temperature, and is potentially ideal for nanopore sequencing. These results represent the first direct sequencing of a sugar-modified XNA and suggest that phi29 DNA polymerase could act as a promising enzyme for sustained sequencing of a wide variety of XNAs.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- School of Chemistry and Chemical Engineering
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Xintong Li
- Department of Biomedical Engineering
, College of Engineering and Applied Sciences
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- Collaborative Innovation Centre of Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- School of Chemistry and Chemical Engineering
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- School of Chemistry and Chemical Engineering
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- Collaborative Innovation Centre of Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- School of Chemistry and Chemical Engineering
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- Collaborative Innovation Centre of Chemistry for Life Sciences
, Nanjing University
,
210023
, Nanjing
, China
- School of Chemistry and Chemical Engineering
, Nanjing University
,
210023
, Nanjing
, China
.
| | - Hanyang Yu
- Department of Biomedical Engineering
, College of Engineering and Applied Sciences
, Nanjing University
,
210023
, Nanjing
, China
.
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6
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Taskova M, Uhd J, Miotke L, Kubit M, Bell J, Ji HP, Astakhova K. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence. Anal Chem 2017; 89:4363-4366. [PMID: 28382823 DOI: 10.1021/acs.analchem.7b00646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New approaches for genomic DNA/RNA detection are in high demand in order to provide controls for existing enzymatic technologies and to create alternatives for emerging applications. In particular, there is an unmet need in rapid, reliable detection of short RNA regions which could open up new opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA followed by click assembly and analysis of the read sequence by various techniques. As we demonstrate in this paper, using our new approach, a viral RNA sequence can be detected in less than 2 h without the need for cDNA synthesis or any other enzymatic reactions and with a sensitivity of <10 pM target RNA.
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Affiliation(s)
- Maria Taskova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Jesper Uhd
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - Matthew Kubit
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States
| | - John Bell
- Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University , 269 Campus Drive, Stanford, California 94305, United States.,Stanford Genome Technology Center, Stanford University , 3165 Porter Drive, Palo Alto, California 94304, United States
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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Wu CH, Holden MT, Smith LM. Enzymatic fabrication of high-density RNA arrays. Angew Chem Int Ed Engl 2014; 53:13514-7. [PMID: 25339581 DOI: 10.1002/anie.201408747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/28/2023]
Abstract
A powerful new strategy for the fabrication of high-density RNA arrays is described. A high-density DNA array is fabricated by standard photolithographic methods, the surface-bound DNA molecules are enzymatically copied into their RNA complements from a surface-bound RNA primer, and the DNA templates are enzymatically destroyed, leaving behind the desired RNA array. The strategy is compatible with 2'-fluoro-modified (2'F) ribonucleoside triphosphates (rNTPs), which may be included in the polymerase extension reaction to impart nuclease resistance and other desirable characteristics to the synthesized RNAs. The use and fidelity of the arrays are explored with DNA hybridization, DNAzyme cleavage, and nuclease digestion experiments.
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Affiliation(s)
- Cheng-Hsien Wu
- Department of Chemistry, University of Wisconsin at Madison, 1101 University Avenue, Madison, WI 53706 (USA)
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Yadav NK, Shukla P, Omer A, Pareek S, Singh RK. Next generation sequencing: potential and application in drug discovery. ScientificWorldJournal 2014; 2014:802437. [PMID: 24688432 PMCID: PMC3933208 DOI: 10.1155/2014/802437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/18/2013] [Indexed: 01/07/2023] Open
Abstract
The world has now entered into a new era of genomics because of the continued advancements in the next generation high throughput sequencing technologies, which includes sequencing by synthesis-fluorescent in situ sequencing (FISSEQ), pyrosequencing, sequencing by ligation using polony amplification, supported oligonucleotide detection (SOLiD), sequencing by hybridization along with sequencing by ligation, and nanopore technology. Great impacts of these methods can be seen for solving the genome related problems of plant and animal kingdom that will open the door of a new era of genomics. This may ultimately overcome the Sanger sequencing that ruled for 30 years. NGS is expected to advance and make the drug discovery process more rapid.
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Affiliation(s)
- Navneet Kumar Yadav
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
| | - Pooja Shukla
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
| | - Ankur Omer
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
| | - Shruti Pareek
- Jaipur National University, Jaipur, Rajasthan 302017, India
| | - R. K. Singh
- Hematological Facility, Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research, New Delhi 110 001, India
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10
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An integer programming approach to DNA sequence assembly. Comput Biol Chem 2011; 35:251-8. [PMID: 21864794 DOI: 10.1016/j.compbiolchem.2011.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 05/11/2011] [Accepted: 06/06/2011] [Indexed: 11/20/2022]
Abstract
De novo sequence assembly is a ubiquitous combinatorial problem in all DNA sequencing technologies. In the presence of errors in the experimental data, the assembly problem is computationally challenging, and its solution may not lead to a unique reconstruct. The enumeration of all alternative solutions is important in drawing a reliable conclusion on the target sequence, and is often overlooked in the heuristic approaches that are currently available. In this paper, we develop an integer programming formulation and global optimization solution strategy to solve the sequence assembly problem with errors in the data. We also propose an efficient technique to identify all alternative reconstructs. When applied to examples of sequencing-by-hybridization, our approach dramatically increases the length of DNA sequences that can be handled with global optimality certificate to over 10,000, which is more than 10 times longer than previously reported. For some problem instances, alternative solutions exhibited a wide range of different ability in reproducing the target DNA sequence. Therefore, it is important to utilize the methodology proposed in this paper in order to obtain all alternative solutions to reliably infer the true reconstruct. These alternative solutions can be used to refine the obtained results and guide the design of further experiments to correctly reconstruct the target DNA sequence.
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11
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Obermayer B, Krammer H, Braun D, Gerland U. Emergence of information transmission in a prebiotic RNA reactor. PHYSICAL REVIEW LETTERS 2011; 107:018101. [PMID: 21797574 DOI: 10.1103/physrevlett.107.018101] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 05/31/2023]
Abstract
A poorly understood step in the transition from a chemical to a biological world is the emergence of self-replicating molecular systems. We study how a precursor for such a replicator might arise in a hydrothermal RNA reactor, which accumulates longer sequences from unbiased monomer influx and random ligation. In the reactor, intra- and intermolecular base pairing locally protects from random cleavage. By analyzing stochastic simulations, we find temporal sequence correlations that constitute a signature of information transmission, weaker but of the same form as in a true replicator.
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Affiliation(s)
- Benedikt Obermayer
- Arnold-Sommerfeld-Center für Theoretische Physik and Center for NanoScience, Ludwig-Maximilians-Universität München, Germany
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12
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Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol 2010; 21:439-76. [PMID: 20561776 PMCID: PMC3121537 DOI: 10.1016/j.copbio.2010.05.002] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/03/2010] [Accepted: 05/06/2010] [Indexed: 12/29/2022]
Abstract
Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.
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Affiliation(s)
- Sheereen Majd
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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Affiliation(s)
- Bertrand Jordan
- Marseille-Nice Génopole, case 901, Parc Scientifique de Luminy, 13288 Marseille Cedex 9, France.
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14
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Hsu AP, Fleisher TA, Niemela JE. Mutation analysis in primary immunodeficiency diseases: case studies. Curr Opin Allergy Clin Immunol 2009; 9:517-24. [PMID: 19841577 PMCID: PMC2774237 DOI: 10.1097/aci.0b013e3283328f59] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The application of mutation analysis is becoming an integral part of the complete evaluation of patients with primary immunodeficiencies, and as such, clinicians caring for these patients must develop a better understanding of the utility and challenges of this important laboratory technology. RECENT FINDINGS Genomic DNA sequencing is currently the standard approach used to characterize a possible gene mutation causing a specific primary immunodeficiency. There are clinical situations in which this approach is revealing of a genetic defect and other circumstances in which this generates a false-positive or false-negative result. One case study is presented that reviews a straightforward analysis that clarifies the genetic basis of a primary immunodeficiency, and four cases are presented that required additional studies to clarify the underlying basis of the immunodeficiency. In the latter circumstances, the rationale for additional studies is outlined and the outcome of these is presented. SUMMARY The identification of a gene mutation as the underlying basis of a primary immunodeficiency begins with the evaluation of the clinical presentation focusing on the infection history so as to develop a differential diagnosis including potential genetic causes. The next step is to obtain specific laboratory studies, including immunologic function evaluation, and, based on these findings, to proceed with DNA sequencing of one or several selected candidate genes. Genomic DNA sequencing has certain limitations, and alternative follow-up approaches may be necessary to establish the molecular basis of the primary immunodeficiency in a given patient.
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MESH Headings
- Autoimmune Lymphoproliferative Syndrome/diagnosis
- Autoimmune Lymphoproliferative Syndrome/genetics
- Autoimmune Lymphoproliferative Syndrome/immunology
- Autoimmune Lymphoproliferative Syndrome/physiopathology
- Bacterial Infections/immunology
- CD40 Ligand/genetics
- Child
- DNA Mutational Analysis
- Diagnostic Errors
- Ectodermal Dysplasia 1, Anhidrotic/diagnosis
- Ectodermal Dysplasia 1, Anhidrotic/genetics
- Ectodermal Dysplasia 1, Anhidrotic/immunology
- Female
- Humans
- Hyper-IgM Immunodeficiency Syndrome, Type 1/diagnosis
- Hyper-IgM Immunodeficiency Syndrome, Type 1/genetics
- Hyper-IgM Immunodeficiency Syndrome, Type 1/immunology
- Hyper-IgM Immunodeficiency Syndrome, Type 1/physiopathology
- I-kappa B Kinase/genetics
- Infant
- Interleukin Receptor Common gamma Subunit/genetics
- Interleukin-1 Receptor-Associated Kinases/genetics
- Lymphatic Diseases
- Male
- Mutation
- Purpura, Thrombocytopenic, Idiopathic/diagnosis
- Purpura, Thrombocytopenic, Idiopathic/genetics
- Purpura, Thrombocytopenic, Idiopathic/immunology
- Purpura, Thrombocytopenic, Idiopathic/physiopathology
- Severe Combined Immunodeficiency/diagnosis
- Severe Combined Immunodeficiency/genetics
- Severe Combined Immunodeficiency/immunology
- Severe Combined Immunodeficiency/physiopathology
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Affiliation(s)
- Amy P. Hsu
- Laboratory of Clinical Infectious Disease, NIAID, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas A. Fleisher
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Julie E. Niemela
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Booty MG, Chae JJ, Masters SL, Remmers EF, Barham B, Le JM, Barron KS, Holland SM, Kastner DL, Aksentijevich I. Familial Mediterranean fever with a single MEFV mutation: where is the second hit? ACTA ACUST UNITED AC 2009; 60:1851-61. [PMID: 19479870 DOI: 10.1002/art.24569] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Familial Mediterranean fever (FMF) has traditionally been considered an autosomal-recessive disease; however, it has been observed that a substantial number of patients with clinical FMF possess only 1 demonstrable MEFV mutation. The purpose of this study was to perform an extensive search for a second MEFV mutation in 46 patients diagnosed clinically as having FMF and carrying only 1 high-penetrance FMF mutation. METHODS MEFV and other candidate genes were sequenced by standard capillary electrophoresis. In 10 patients, the entire 15-kb MEFV genomic region was resequenced using hybridization-based chip technology. MEFV gene expression levels were determined by quantitative reverse transcription-polymerase chain reaction. Pyrin protein levels were examined by Western blotting. RESULTS A second MEFV mutation was not identified in any of the patients who were screened. Haplotype analysis did not identify a common haplotype that might be associated with the transmission of a second FMF allele. Western blots did not demonstrate a significant difference in pyrin levels between patients with a single mutation and those with a double mutation; however, FMF patients of both types showed higher protein expression as compared with controls and with non-FMF patients with active inflammation. Screening of genes encoding pyrin-interacting proteins identified rare mutations in a small number of patients, suggesting the possibility of digenic inheritance. CONCLUSION Our data underscore the existence of a significant subset of FMF patients who are carriers of only 1 MEFV mutation and demonstrate that complete MEFV sequencing is not likely to yield a second mutation. Screening for the set of the most common mutations and detection of a single mutation appears to be sufficient in the presence of clinical symptoms for the diagnosis of FMF and the initiation of a trial of colchicine.
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Affiliation(s)
- Matthew G Booty
- Genetics and Genomics Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland 20892-1820, USA
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16
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Branton D, Deamer DW, Marziali A, Bayley H, Benner SA, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, Jovanovich SB, Krstic PS, Lindsay S, Ling XS, Mastrangelo CH, Meller A, Oliver JS, Pershin YV, Ramsey JM, Riehn R, Soni GV, Tabard-Cossa V, Wanunu M, Wiggin M, Schloss JA. The potential and challenges of nanopore sequencing. Nat Biotechnol 2008; 26:1146-53. [PMID: 18846088 DOI: 10.1038/nbt.1495] [Citation(s) in RCA: 1581] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for approximately $1,000 in approximately 24 h.
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Affiliation(s)
- Daniel Branton
- Department of Molecular and Cell Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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17
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Chen YJ, Huang X. DNA sequencing by denaturation: principle and thermodynamic simulations. Anal Biochem 2008; 384:170-9. [PMID: 18930015 DOI: 10.1016/j.ab.2008.09.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 09/12/2008] [Accepted: 09/27/2008] [Indexed: 11/16/2022]
Abstract
We describe a new DNA sequencing method called sequencing by denaturation (SBD). A Sanger dideoxy sequencing reaction is performed on the templates on a solid surface to generate a ladder of DNA fragments randomly terminated by fluorescently labeled dideoxyribonucleotides. The labeled DNA fragments are sequentially denatured from the templates and the process is monitored by measuring the change in fluorescence intensities from the surface. By analyzing the denaturation profiles, the base sequence of the template can be determined. Using thermodynamic principles, we simulated the denaturation profiles of a series of oligonucleotides ranging from 12 to 32 bases and developed a base-calling algorithm to decode the sequences. These simulations demonstrate that DNA molecules up to 20 bases can be sequenced by SBD. Experimental measurements of the melting profiles of DNA fragments in solution confirm that DNA sequences can be determined by SBD. The potential limitations and advantages of SBD are discussed. With SBD, millions of sequencing reactions can be performed on a small area on a surface in parallel with a very small amount of sequencing reagents. Therefore, DNA sequencing by SBD could potentially result in a significant increase in speed and reduction in cost in large-scale genome resequencing.
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Affiliation(s)
- Ying-Ja Chen
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
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Haslam NJ, Whiteford NE, Weber G, Prügel-Bennett A, Essex JW, Neylon C. Optimal probe length varies for targets with high sequence variation: implications for probe library design for resequencing highly variable genes. PLoS One 2008; 3:e2500. [PMID: 18563203 PMCID: PMC2430613 DOI: 10.1371/journal.pone.0002500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 04/30/2008] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Sequencing by hybridisation is an effective method for obtaining large amounts of DNA sequence information at low cost. The efficiency of SBH depends on the design of the probe library to provide the maximum information for minimum cost. Long probes provide a higher probability of non-repeated sequences but lead to an increase in the number of probes required whereas short probes may not provide unique sequence information due to repeated sequences. We have investigated the effect of probe length, use of reference sequences, and thermal filtering on the design of probe libraries for several highly variable target DNA sequences. RESULTS We designed overlapping probe libraries for a range of highly variable drug target genes based on known sequence information and develop a formal terminology to describe probe library design. We find that for some targets these libraries can provide good coverage of a previously unseen target whereas for others the coverage is less than 30%. The optimal probe length varies from as short at 12 nt to as large as 19 nt and depends on the sequence, its variability, and the stringency of thermal filtering. It cannot be determined from inspection of an example gene sequence. CONCLUSIONS Optimal probe length and the optimal number of reference sequences used to design a probe library are highly target specific for highly variable sequencing targets. The optimum design cannot be determined simply by inspection of input sequences or of alignments but only by detailed analysis of the each specific target. For highly variable sequences, shorter probes can in some cases provide better information than longer probes. Probe library design would benefit from a general purpose tool for analysing these issues. The formal terminology developed here and the analysis approaches it is used to describe will contribute to the development of such tools.
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Affiliation(s)
- Niall J Haslam
- School of Chemistry, University of Southampton, Southhampton, United Kingdom.
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Chetta M, Drmanac A, Santacroce R, Grandone E, Surrey S, Fortina P, Margaglione M. Identification of FVIII gene mutations in patients with hemophilia A using new combinatorial sequencing by hybridization. INDIAN JOURNAL OF HUMAN GENETICS 2008; 14:55-64. [PMID: 20300295 PMCID: PMC2840789 DOI: 10.4103/0971-6866.44106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND: Standard methods of mutation detection are time consuming in Hemophilia A (HA) rendering their application unavailable in some analysis such as prenatal diagnosis. OBJECTIVES: To evaluate the feasibility of combinatorial sequencing-by-hybridization (cSBH) as an alternative and reliable tool for mutation detection in FVIII gene. PATIENTS/METHODS: We have applied a new method of cSBH that uses two different colors for detection of multiple point mutations in the FVIII gene. The 26 exons encompassing the HA gene were analyzed in 7 newly diagnosed Italian patients and in 19 previously characterized individuals with FVIII deficiency. RESULTS: Data show that, when solution-phase TAMRA and QUASAR labeled 5-mer oligonucleotide sets mixed with unlabeled target PCR templates are co-hybridized in the presence of DNA ligase to universal 6-mer oligonucleotide probe-based arrays, a number of mutations can be successfully detected. The technique was reliable also in identifying a mutant FVIII allele in an obligate heterozygote. A novel missense mutation (Leu1843Thr) in exon 16 and three novel neutral polymorphisms are presented with an updated protocol for 2-color cSBH. CONCLUSIONS: cSBH is a reliable tool for mutation detection in FVIII gene and may represent a complementary method for the genetic screening of HA patients.
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Kricka LJ, Master SR. Validation and Quality Control of Protein Microarray-based Analytical Methods. Mol Biotechnol 2007; 38:19-31. [DOI: 10.1007/s12033-007-0066-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 07/06/2007] [Indexed: 01/20/2023]
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Peltonen J, Welsh JA, Vähäkangas KH. Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene? Hum Exp Toxicol 2007; 26:9-18. [PMID: 17334176 DOI: 10.1177/0960327107071918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Mutation analysis methods have increased in variety during the past years. High-throughput microarray methods have especially increased in popularity. However, new methods require reference points, and not all of the methods are equal in sensitivity and specificity. Furthermore, the detection of unknown missense mutations, such as unknown TP53 mutations in human tumors, for clinical purposes requires great accuracy, which may be difficult to acquire with the current high-throughput methods. For these reasons, the classical methods, such as PCR-manual sequencing and PCR-SSCP, are still valuable and necessary.
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Affiliation(s)
- J Peltonen
- Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
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22
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Yao F, Zhang R, Zhu Z, Xia K, Liu C. MutScreener: primer design tool for PCR-direct sequencing. Nucleic Acids Res 2006; 34:W660-4. [PMID: 16845093 PMCID: PMC1538803 DOI: 10.1093/nar/gkl168] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In searching for susceptibility genes, both positional cloning and candidate gene strategies have been helpful. Mutation screening is one of the many technologies that have been implemented in order to identify mutations or polymorphisms in candidate genes or genomic regions. Since human genome sequence is available, PCR-direct sequencing is one of the major methods for mutation screening or resequencing. Unfortunately, assay design can be laborious if multiple genes or large regions need to be investigated. To solve this conundrum a web-based application, MutScreener, has been developed. MutScreener assists in the analysis of human gene structure and design of PCR/sequencing primer. This application supports batch assay design based on either existing public gene annotation or custom gene annotation. The optional universal tagged primers can support high throughput resequencing processes. MutScreener is available for public use at .
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Affiliation(s)
| | | | | | | | - Chunyu Liu
- Department of Psychiatry, University of ChicagoChicago, IL, USA
- To whom correspondence should be addressed. Tel: 773 834 3604; Fax: 773 834 2970;
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23
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Whiteford N, Haslam N, Weber G, Prügel-Bennett A, Essex JW, Roach PL, Bradley M, Neylon C. An analysis of the feasibility of short read sequencing. Nucleic Acids Res 2005; 33:e171. [PMID: 16275781 PMCID: PMC1278949 DOI: 10.1093/nar/gni170] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20–30 nt, and that reads of 50 nt can provide reconstructed contigs (a contiguous fragment of sequence data) of 1000 nt and greater that cover 80% of human chromosome 1.
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Affiliation(s)
| | | | | | - Adam Prügel-Bennett
- School of Electronics and Computer Science, University of SouthamptonSouthampton SO17 1BJ, UK
| | | | | | - Mark Bradley
- School of Chemistry, University of EdinburghEdinburgh EH9 3JJ, UK
| | - Cameron Neylon
- To whom correspondence should be addressed. Tel: +44 23 8059 4164; Fax: +44 23 8059 6805;
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Li K, Zhang J, Chen L, Sommer SS. Superb nucleotide discrimination by a novel on/off switch for DNA polymerization and its applications. Mol Biotechnol 2005; 29:93-100. [PMID: 15699566 DOI: 10.1385/mb:29:2:093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
With the use of polymerases having 3' to 5' exonuclease activity and 3' phosphorothioate-modified allele-specific primers, we recently devised a SNP-operated on/off switch controlling DNA polymerization. One advantage of this novel on/off switch is its adaptability to arrayed primer extension. To further expand its application in genetic analysis, this new on/off switch was evaluated in discrimination of the match/mismatch status of single nucleotides upstream from the primer 3' terminal. A set of seven amplicons was developed with the templates differing from each other by a single nucleotide. Using this set of amplicons, the new on/off switch was shown to be able to efficiently discriminate single nucleotide polymorphisms from the primer 3' terminus to the -6 position from the primer 3' terminus. These data, illustrating the broad single nucleotide discrimination ability of this novel on/off switch, explain why the SNP-operated on/off switch is powerful in SNP analysis, and also indicate useful applications to genetic analysis additional to SNP assay. First, these data broaden the application of the novel on/off switch in the analysis of mutations other than SNPs. Second, it raises a nucleotide-walking algorithm suitable for de novo array-based sequencing analysis.
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Affiliation(s)
- Kai Li
- SNP Institute, Hengyang, Hunan, China.
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Wong CW, Albert TJ, Vega VB, Norton JE, Cutler DJ, Richmond TA, Stanton LW, Liu ET, Miller LD. Tracking the evolution of the SARS coronavirus using high-throughput, high-density resequencing arrays. Genome Res 2004; 14:398-405. [PMID: 14993206 PMCID: PMC353227 DOI: 10.1101/gr.2141004] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the development and validation of an oligonucleotide resequencing array for interrogating the entire 30-kb SARS-CoV genome in a rapid, cost-effective fashion. Using this platform, we sequenced SARS-CoV genomes from Vero cell culture isolates of 12 patients and directly from four patient tissues. The sequence obtained from the array is highly reproducible, accurate (>99.99% accuracy) and capable of identifying known and novel variants of SARS-CoV. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable, and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale, making this an ideal platform for the global monitoring of SARS-CoV and other small-genome pathogens.
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Pe'er I, Arbili N, Liu Y, Enck C, Gelfand CA, Shamir R. Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays. Nucleic Acids Res 2003; 31:5667-75. [PMID: 14500830 PMCID: PMC206457 DOI: 10.1093/nar/gkg757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally determining a polynucleotide sequence from its oligonucleotide content. We present here new methods that use such arrays for re-sequencing. Our methods are applied to data obtained by the polymerase signaling assay, which arrays single-based primer extension reactions for either universal or partial arrays of pentanucleotides. The computational analysis uses the spectrum alignment algorithm, which is refined and enhanced here in order to overcome noise incurred by the use of such short primers. We present accurate re-sequencing results for both synthetic and amplified DNA molecules.
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Affiliation(s)
- Itsik Pe'er
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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