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Kumar KR, Cowley MJ, Davis RL. Next-Generation Sequencing and Emerging Technologies. Semin Thromb Hemost 2024. [PMID: 38692283 DOI: 10.1055/s-0044-1786397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.
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Affiliation(s)
- Kishore R Kumar
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
| | - Mark J Cowley
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
| | - Ryan L Davis
- Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
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2
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Antunes J, Walichiewicz P, Forouzmand E, Barta R, Didier M, Han Y, Perez JC, Snedecor J, Zlatkov C, Padmabandu G, Devesse L, Radecke S, Holt CL, Kumar SA, Budowle B, Stephens KM. Developmental validation of the ForenSeq® Kintelligence kit, MiSeq FGx® sequencing system and ForenSeq Universal Analysis Software. Forensic Sci Int Genet 2024; 71:103055. [PMID: 38762965 DOI: 10.1016/j.fsigen.2024.103055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/21/2024]
Abstract
Forensic Investigative Genetic Genealogy, a recent sub discipline of forensic genomics, leverages the high throughput and sensitivity of detection of next generation sequencing and established genetic and genealogical approaches to support the identification of human remains from missing persons investigations and investigative lead generation in violent crimes. To facilitate forensic DNA evidence analysis, the ForenSeq® Kintelligence multiplex, consisting of 10,230 SNPs, was developed. Design of the ForenSeq Kintelligence Kit, the MiSeq FGx® Sequencing System and the ForenSeq Universal Analysis Software is described. Developmental validation in accordance with SWGDAM guidelines and forensic quality assurance standards, using single source samples, is reported for the end-to-end workflow from library preparation to data interpretation. Performance metrics support the conclusion that more genetic information can be obtained from challenging samples compared to other commercially available forensic targeted DNA assays developed for capillary electrophoresis (CE) or other current next generation sequencing (NGS) kits due to the higher number of markers, the overall shorter amplicon sizes (97.8% <150 bp), and kit design. Data indicate that the multiplex is robust and fit for purpose for a wide range of quantity and quality samples. The ForenSeq Kintelligence Kit and the Universal Analysis Software allow transfer of the genetic component of forensic investigative genetic genealogy to the operational forensic laboratory.
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Affiliation(s)
- Joana Antunes
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Paulina Walichiewicz
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Elmira Forouzmand
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Richelle Barta
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Meghan Didier
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Yonmee Han
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Juan Carlos Perez
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - June Snedecor
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Clare Zlatkov
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Gothami Padmabandu
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Laurence Devesse
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Sarah Radecke
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Cydne L Holt
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Swathi A Kumar
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bruce Budowle
- University of Helsinki, Department of Forensic Medicine, Haartmaninkatu 8, P.O. Box 63, Helsinki 00014, Finland; Forensic Science Institute, Radford University, Radford, VA 24142, USA
| | - Kathryn M Stephens
- Verogen, Inc., now a QIAGEN company, 11111 Flintkote Ave., San Diego, CA 92121, USA.
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3
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Salava H, Deák T, Czepe C, Maghuly F. Sample and Library Preparation for PacBio Long-Read Sequencing in Grapevine. Methods Mol Biol 2024; 2787:183-197. [PMID: 38656490 DOI: 10.1007/978-1-0716-3778-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
PacBio long-read sequencing is a third-generation technology that generates long reads up to 20 kilobases (kb), unlike short-read sequencing instruments that produce up to 600 bases. Long-read sequencing is particularly advantageous in higher organisms, such as humans and plants, where repetitive regions in the genome are more abundant. The PacBio long-read sequencing uses a single molecule, real-time approach where the SMRT cells contain several zero-mode waveguides (ZMWs). Each ZMW contains a single DNA molecule bound by a DNA polymerase. All ZMWs are flushed with deoxy nucleotides with a fluorophore specific to each nucleotide. As the sequencing proceeds, the detector detects the wavelength of the fluorescence and the nucleotides are read in real-time. This chapter describes the sample and library preparation for PacBio long-read sequencing for grapevine.
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Affiliation(s)
- Hymavathi Salava
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Tamás Deák
- Institute of Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences (MATE), Budapest, Hungary
| | - Carmen Czepe
- Next Generation Sequencing Unit, Vienna Biocenter Core Facilities (VBCF), Vienna, Austria
| | - Fatemeh Maghuly
- Plant Functional Genomics Lab, Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Soikkeli M, Murros A, Rantala A, Txoperena O, Kilpi OP, Kainlauri M, Sovanto K, Maestre A, Centeno A, Tukkiniemi K, Gomes Martins D, Zurutuza A, Arpiainen S, Prunnila M. Wafer-Scale Graphene Field-Effect Transistor Biosensor Arrays with Monolithic CMOS Readout. ACS APPLIED ELECTRONIC MATERIALS 2023; 5:4925-4932. [PMID: 37779890 PMCID: PMC10536967 DOI: 10.1021/acsaelm.3c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
The reliability of analysis is becoming increasingly important as point-of-care diagnostics are transitioning from single-analyte detection toward multiplexed multianalyte detection. Multianalyte detection benefits greatly from complementary metal-oxide semiconductor (CMOS) integrated sensing solutions, offering miniaturized multiplexed sensing arrays with integrated readout electronics and extremely large sensor counts. The development of CMOS back end of line integration compatible graphene field-effect transistor (GFET)-based biosensing has been rapid during the past few years, in terms of both the fabrication scale-up and functionalization toward biorecognition from real sample matrices. The next steps in industrialization relate to improving reliability and require increased statistics. Regarding functionalization toward truly quantitative sensors, on-chip bioassays with improved statistics require sensor arrays with reduced variability in functionalization. Such multiplexed bioassays, whether based on graphene or on other sensitive nanomaterials, are among the most promising technologies for label-free electrical biosensing. As an important step toward that, we report wafer-scale fabrication of CMOS-integrated GFET arrays with high yield and uniformity, designed especially for biosensing applications. We demonstrate the operation of the sensing platform array with 512 GFETs in simultaneous detection for the sodium chloride concentration series. This platform offers a truly statistical approach on GFET-based biosensing and further to quantitative and multianalyte sensing. The reported techniques can also be applied to other fields relying on functionalized GFETs, such as gas or chemical sensing or infrared imaging.
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Affiliation(s)
- Miika Soikkeli
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Anton Murros
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Arto Rantala
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Oihana Txoperena
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Olli-Pekka Kilpi
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Markku Kainlauri
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Kuura Sovanto
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Arantxa Maestre
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Alba Centeno
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Kari Tukkiniemi
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - David Gomes Martins
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Amaia Zurutuza
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Sanna Arpiainen
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Mika Prunnila
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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Chen S, Bashir R. Advances in field-effect biosensors towards point-of-use. NANOTECHNOLOGY 2023; 34:492002. [PMID: 37625391 PMCID: PMC10523595 DOI: 10.1088/1361-6528/acf3f0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 08/25/2023] [Indexed: 08/27/2023]
Abstract
The future of medical diagnostics calls for portable biosensors at the point of care, aiming to improve healthcare by reducing costs, improving access, and increasing quality-what is called the 'triple aim'. Developing point-of-care sensors that provide high sensitivity, detect multiple analytes, and provide real time measurements can expand access to medical diagnostics for all. Field-effect transistor (FET)-based biosensors have several advantages, including ultrahigh sensitivity, label-free and amplification-free detection, reduced cost and complexity, portability, and large-scale multiplexing. They can also be integrated into wearable or implantable devices and provide continuous, real-time monitoring of analytesin vivo, enabling early detection of biomarkers for disease diagnosis and management. This review analyzes advances in the sensitivity, parallelization, and reusability of FET biosensors, benchmarks the limit of detection of the state of the art, and discusses the challenges and opportunities of FET biosensors for future healthcare applications.
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Affiliation(s)
- Sihan Chen
- Holonyak Micro and Nanotechnology Laboratory, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Rashid Bashir
- Holonyak Micro and Nanotechnology Laboratory, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
- Department of Bioengineering, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
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6
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Budowle B, Arnette A, Sajantila A. A cost-benefit analysis for use of large SNP panels and high throughput typing for forensic investigative genetic genealogy. Int J Legal Med 2023; 137:1595-1614. [PMID: 37341834 PMCID: PMC10421786 DOI: 10.1007/s00414-023-03029-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/16/2023] [Indexed: 06/22/2023]
Abstract
Next-generation sequencing (NGS), also known as massively sequencing, enables large dense SNP panel analyses which generate the genetic component of forensic investigative genetic genealogy (FIGG). While the costs of implementing large SNP panel analyses into the laboratory system may seem high and daunting, the benefits of the technology may more than justify the investment. To determine if an infrastructural investment in public laboratories and using large SNP panel analyses would reap substantial benefits to society, a cost-benefit analysis (CBA) was performed. This CBA applied the logic that an increase of DNA profile uploads to a DNA database due to a sheer increase in number of markers and a greater sensitivity of detection afforded with NGS and a higher hit/association rate due to large SNP/kinship resolution and genealogy will increase investigative leads, will be more effective for identifying recidivists which in turn reduces future victims of crime, and will bring greater safety and security to communities. Analyses were performed for worst case/best case scenarios as well as by simulation sampling the range spaces with multiple input values simultaneously to generate best estimate summary statistics. This study shows that the benefits, both tangible and intangible, over the lifetime of an advanced database system would be huge and can be projected to be for less than $1 billion per year (over a 10-year period) investment can reap on average > $4.8 billion in tangible and intangible cost-benefits per year. More importantly, on average > 50,000 individuals need not become victims if FIGG were employed, assuming investigative associations generated were acted upon. The benefit to society is immense making the laboratory investment a nominal cost. The benefits likely are underestimated herein. There is latitude in the estimated costs, and even if they were doubled or tripled, there would still be substantial benefits gained with a FIGG-based approach. While the data used in this CBA are US centric (primarily because data were readily accessible), the model is generalizable and could be used by other jurisdictions to perform relevant and representative CBAs.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
- Radford University Forensic Science Institute, Radford University, Radford, VA, USA.
| | - Andrew Arnette
- Department of Business Information Technology, Virginia Tech, Blacksburg, VA, USA
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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7
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Shin W, Yun J, Han K, Park DG. Comparison of genetic variation between primary colorectal cancer and metastatic peritoneal cancer. Genes Genomics 2023:10.1007/s13258-023-01408-3. [PMID: 37277571 DOI: 10.1007/s13258-023-01408-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
BACKGROUND Among cancer metastases by primary colorectal cancer (CRC), peritoneal metastasis is the second most common metastatic lesion after liver metastasis. In treating metastatic CRC, it is very important to differentiate targeted-therapy and chemotherapy according to the characteristics of each lesion because the genetic variation of the primary and metastatic lesions are different. However, there are few studies of genetic characteristics on peritoneal metastasis caused by primary CRC, so molecular-level studies are continuously required. OBJECTIVE We propose an appropriate peritoneal metastasis treatment policy by identifying the genetic characteristics between primary CRC and synchronous peritoneal metastatic lesions. METHODS Primary CRC and synchronous peritoneal metastasis samples were analyzed in pairs from six patients using Comprehensive Cancer Panel (409 cancer-related genes, Thermo Fisher Scientific, USA) and next-generation sequencing (NGS). RESULTS The mutations were commonly found on the KMT2C and THBS1 genes in both primary CRC and peritoneal metastasis. The PDE4DIP gene was mutated in all cases except for on a sample of peritoneal metastasis. As a result of analysis using the mutation database, we confirmed that the gene mutations of primary CRC and the peritoneal metastasis derived from it showed the same tendency, although we did not accompany the gene expression level or epigenetic study. CONCLUSION It is thought that the treatment policy through molecular genetic testing of primary CRC can also be applied to peritoneal metastasis treatment. Our study is expected to be the basis for further peritoneal metastasis research.
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Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, Republic of Korea
| | - Jeongseok Yun
- Department of Surgery, Dankook University College of Medicine, Cheonan, Republic of Korea
| | - Kyudong Han
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, Republic of Korea.
- Department of Microbiology, Dankook University, Cheonan, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea.
- R&D Center, HuNbiome Co., Ltd, Seoul, Republic of Korea.
| | - Dong-Guk Park
- NGS Clinical Laboratory, Dankook University Hospital, Cheonan, Republic of Korea.
- Department of Surgery, Dankook University College of Medicine, Cheonan, Republic of Korea.
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Stephens KM, Barta R, Fleming K, Perez JC, Wu SF, Snedecor J, Holt CL, LaRue B, Budowle B. Developmental validation of the ForenSeq MainstAY kit, MiSeq FGx sequencing system and ForenSeq Universal Analysis Software. Forensic Sci Int Genet 2023; 64:102851. [PMID: 36907074 DOI: 10.1016/j.fsigen.2023.102851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
For human identification purposes, forensic genetics has primarily relied upon a core set of autosomal (and to a lesser extent Y chromosome) short tandem repeat (STR) markers that are enriched by amplification using the polymerase chain reaction (PCR) that are subsequently separated and detected using capillary electrophoresis (CE). While STR typing conducted in this manner is well-developed and robust, advances in molecular biology that have occurred over the last 15 years, in particular massively parallel sequencing (MPS) [1-7], offer certain advantages as compared to CE-based typing. First and foremost is the high throughput capacity of MPS. Current bench top high throughput sequencers enable larger batteries of markers to be multiplexed and multiple samples to be sequenced simultaneously (e.g., millions to billions of nucleotides can be sequenced in one run). Second, compared to the length-based CE approach, sequencing STRs increases discrimination power, enhances sensitivity of detection, reduces noise due to instrumentation, and improves mixture interpretation [4,8-23]. Third, since detection of STRs is based on sequence and not fluorescence, amplicons can be designed that are shorter in length and of similar lengths among loci, where possible, which can improve amplification efficiency and analysis of degraded samples. Lastly, MPS offers a single format approach that can be applied to analysis of a wide variety of genetic markers of forensic interest (e.g., STRs, mitochondrial DNA, single nucleotide polymorphisms, insertion/deletions). These features make MPS a desirable technology for casework [14,15,24,25-48]. The developmental validation of the ForenSeq MainstAY library preparation kit with the MiSeq FGx Sequencing System and ForenSeq Universal Software is reported here to assist with validation of this MPS system for casework [49]. The results show that the system is sensitive, accurate and precise, specific, and performs well with mixtures and mock case-type samples.
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Affiliation(s)
| | - Richelle Barta
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Keenan Fleming
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | | | - Shan-Fu Wu
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - June Snedecor
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Cydne L Holt
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bobby LaRue
- Verogen, Inc., 11111 Flintkote Ave., San Diego, CA 92121, USA
| | - Bruce Budowle
- University of Helsinki, Department of Forensic Medicine, Haartmaninkatu 8, P.O. Box 63, Helsinki 00014, Finland
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9
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Optimizing Molecular Minimal Residual Disease Analysis in Adult Acute Lymphoblastic Leukemia. Cancers (Basel) 2023; 15:cancers15020374. [PMID: 36672325 PMCID: PMC9856386 DOI: 10.3390/cancers15020374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Minimal/measurable residual disease (MRD) evaluation has resulted in a fundamental instrument to guide patient management in acute lymphoblastic leukemia (ALL). From a methodological standpoint, MRD is defined as any approach aimed at detecting and possibly quantifying residual neoplastic cells beyond the sensitivity level of cytomorphology. The molecular methods to study MRD in ALL are polymerase chain reaction (PCR) amplification-based approaches and are the most standardized techniques. However, there are some limitations, and emerging technologies, such as digital droplet PCR (ddPCR) and next-generation sequencing (NGS), seem to have advantages that could improve MRD analysis in ALL patients. Furthermore, other blood components, namely cell-free DNA (cfDNA), appear promising and are also being investigated for their potential role in monitoring tumor burden and response to treatment in hematologic malignancies. Based on the review of the literature and on our own data, we hereby discuss how emerging molecular technologies are helping to refine the molecular monitoring of MRD in ALL and may help to overcome some of the limitations of standard approaches, providing a benefit for the care of patients.
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10
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Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
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Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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11
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Benz S, Mitra S. From Genomics to Metagenomics in the Era of Recent Sequencing Technologies. Methods Mol Biol 2023; 2649:1-20. [PMID: 37258855 DOI: 10.1007/978-1-0716-3072-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.
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Affiliation(s)
- Saskia Benz
- School of medicine, University of Leeds, Leeds, UK
| | - Suparna Mitra
- Leeds Institute of Medical Research, University of Leeds, Leeds General Infirmary, Leeds, UK.
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12
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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13
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A Review of Next Generation Sequencing Methods and its Applications in Laboratory Diagnosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing (NGS) is a new technology used to detect the sequence of DNA and RNA and to detect mutations or variations of significance. NGS generates large quantities of sequence data within a short time duration. The various types of sequencing includes Sanger Sequencing, Pyrosequencing, Sequencing by Synthesis (Illumina), Ligation (SoLID), Single molecule Fluorescent Sequencing (Helicos), Single molecule Real time Sequencing (Pacbio), Semiconductor sequencing (Ion torrent technology), Nanopore sequencing and fourth generation sequencing. These methods of sequencing have been modified and improved over the years such that it has become cost effective and accessible to diagnostic laboratories. Management of Outbreaks, rapid identification of bacteria, molecular case finding, taxonomy, detection of the zoonotic agents and guiding prevention strategies in HIV outbreaks are just a few of the many applications of Next Generation sequencing in clinical microbiology.
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14
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Genetic Alterations, DNA Methylation, Alloantibodies and Phenotypic Heterogeneity in Type III von Willebrand Disease. Genes (Basel) 2022; 13:genes13060971. [PMID: 35741733 PMCID: PMC9222927 DOI: 10.3390/genes13060971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Type III von Willebrand disease is present in the Punjab province of Pakistan along with other inherited bleeding disorders like hemophilia. Cousin marriages are very common in Pakistan so genetic studies help to establish protocols for screening, especially at the antenatal level. Factors behind the phenotypic variation of the severity of bleeding in type III vWD are largely unknown. The study was conducted to determine Mutations/genetic alterations in type III von Willebrand disease and also to determine the association of different mutations, methylation status, ITGA2B/B3 mutations and alloimmunization with the severity of type III vWD. After informed consent and detailed history of the patients, routine tests and DNA extraction from blood, mutational analysis was performed by Next Generation Sequencing on Ion Torrent PGM. DNA methylation status was also checked with the help of PCR. In our cohort, 55 cases were detected with pathogenic mutations. A total of 27 different mutations were identified in 55 solved cases; 16 (59.2%) were novel. The mean bleeding score in truncating mutations and essential splice site mutations was relatively higher than weak and strong missense mutations. The mean bleeding score showed insignificant variation for different DNA methylation statuses of the VWF gene at the cg23551979 CpG site. Mutations in exons 7,10, 25, 28, 31, 43, and intron 41 splice site account for 75% of the mutations.
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15
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van Bladel DAG, van der Last-Kempkes JLM, Scheijen B, Groenen PJTA. Next-Generation Sequencing-Based Clonality Detection of Immunoglobulin Gene Rearrangements in B-Cell Lymphoma. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:7-42. [PMID: 35622318 DOI: 10.1007/978-1-0716-2115-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Immunoglobulin (IG) clonality assessment is a widely used supplementary test for the diagnosis of suspected lymphoid malignancies. The specific rearrangements of the immunoglobulin (IG) heavy and light chain genes act as a unique hallmark of a B-cell lymphoma, a feature that is used in clonality assessment. The widely used BIOMED-2/EuroClonality IG clonality assay, visualized by GeneScanning or heteroduplex analysis, has an unprecedented high detection rate because of the complementarity of this approach. However, the BIOMED-2/EuroClonality clonality assays have been developed for the assessment of specimens with optimal DNA quality. Further improvements for the assessment of samples with suboptimal DNA quality, such as from formalin-fixed paraffin-embedded (FFPE) specimens or specimens with a limited tumor burden, are required. The EuroClonality-NGS Working Group recently developed a next-generation sequencing (NGS)-based clonality assay for the detection of the IG heavy and kappa light chain rearrangements, using the same complementary approach as in the conventional assay. By employing next-generation sequencing, both the sensitivity and specificity of the clonality assay have increased, which not only is very useful for diagnostic clonality testing but also allows robust comparison of clonality patterns in a patient with multiple lymphoma's that have suboptimal DNA quality. Here, we describe the protocols for IG-NGS clonality assessment that are compatible for Ion Torrent and Illumina sequencing platforms including pre-analytical DNA isolation, the analytical phase, and the post-analytical data analysis.
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Affiliation(s)
- Diede A G van Bladel
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Blanca Scheijen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:jpm12050750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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17
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Yang J, Liu H, Pan W, Song M, Lu Y, Wang-Ngai Chow F, Hang-Mei Leung P, Deng Y, Hori M, He N, Li S. Recent Advances of Human Leukocyte Antigen (HLA) Typing Technology Based on High-Throughput Sequencing. J Biomed Nanotechnol 2022; 18:617-639. [PMID: 35715925 DOI: 10.1166/jbn.2022.3280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The major histocompatibility complex (MHC) in humans is a genetic region consisting of cell surface proteins located on the short arm of chromosome 6. This is also known as the human leukocyte antigen (HLA) region. The HLA region consists of genes that exhibit complex genetic polymorphisms, and are extensively involved in immune responses. Each individual has a unique set of HLAs. Donor-recipient HLA allele matching is an important factor for organ transplantation. Therefore, an established rapid and accurate HLA typing technology is instrumental to preventing graft-verses-host disease (GVHD) in organ recipients. As of recent, high-throughput sequencing has allowed for an increase read length and higher accuracy and throughput, thus achieving complete and high-resolution full-length typing. With more advanced nanotechnology used in high-throughput sequencing, HLA typing is more widely used in third-generation single-molecule sequencing. This review article summarizes some of the most widely used sequencing typing platforms and evaluates the latest developments in HLA typing kits and their clinical applications.
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Affiliation(s)
- Jin Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Mengru Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Yutong Lu
- School of Electrical and Information Engineering, Hunan University, Changsha 410012, Hunan, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Masahi Hori
- 2-16-5 Edagawa, Koto-Ku, Tokyo, 135-0051, Japan
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, Hunan, China
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18
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Bahuguna S, Atilano M, Glittenberg M, Lee D, Arora S, Wang L, Zhou J, Redhai S, Boutros M, Ligoxygakis P. Bacterial recognition by PGRP-SA and downstream signalling by Toll/DIF sustain commensal gut bacteria in Drosophila. PLoS Genet 2022; 18:e1009992. [PMID: 35007276 PMCID: PMC8782595 DOI: 10.1371/journal.pgen.1009992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
The gut sets the immune and metabolic parameters for the survival of commensal bacteria. We report that in Drosophila, deficiency in bacterial recognition upstream of Toll/NF-κB signalling resulted in reduced density and diversity of gut bacteria. Translational regulation factor 4E-BP, a transcriptional target of Toll/NF-κB, mediated this host-bacteriome interaction. In healthy flies, Toll activated 4E-BP, which enabled fat catabolism, which resulted in sustaining of the bacteriome. The presence of gut bacteria kept Toll signalling activity thus ensuring the feedback loop of their own preservation. When Toll activity was absent, TOR-mediated suppression of 4E-BP made fat resources inaccessible and this correlated with loss of intestinal bacterial density. This could be overcome by genetic or pharmacological inhibition of TOR, which restored bacterial density. Our results give insights into how an animal integrates immune sensing and metabolism to maintain indigenous bacteria in a healthy gut.
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Affiliation(s)
- Shivohum Bahuguna
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Magda Atilano
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Marcus Glittenberg
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Dohun Lee
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Srishti Arora
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Lihui Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jun Zhou
- German Cancer Research Centre (DKFZ), Division Signalling and Functional Genomics, BioQuant and Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Siamak Redhai
- German Cancer Research Centre (DKFZ), Division Signalling and Functional Genomics, BioQuant and Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Centre (DKFZ), Division Signalling and Functional Genomics, BioQuant and Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Petros Ligoxygakis
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Shojaei Baghini M, Vilouras A, Dahiya R. Ultra-Thin Chips With ISFET Array for Continuous Monitoring of Body Fluids Ph. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2021; 15:1174-1185. [PMID: 35007198 DOI: 10.1109/tbcas.2022.3141553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper presents ISFET array based pH-sensing system-on-ultra-thin-chip (SoUTC) designed and fabricated in 350 nm CMOS technology. The SoUTC with the proposed current-mode active-pixel ISFET circuit array is desined to operate at 2 V and consumes 6.28 μW per-pixel. The presented SoUTC exhibits low sensitivity to process, voltage, temperature and strain-induced (PVTS) variations. The silicon area occupancy of each active-pixel is 44.9 × 33.5 µm2 with an ion-sensing area of 576 µm2. The design of presented ISFET device is analysed with finite element modeling in COMSOL Multiphysics using compact model parameters of MOSFET in 350 nm CMOS technology. Owing to thin (∼30 µm) Si-substrate the presented SoUTC can conform to curvilinear surfaces, allowing intimate contact necessary for reliable data for monitoring of analytes in body fluids such as sweat. Further, it can operate either in a rolling shutter fashion or in a pseudo-random pixel selection mode allowing the simultaneous detection of pH from different skin regions. Finally, the circuits have been tested in aqueous Dulbecco's Modified Eagle Medium (DMEM) culture media with 5-9 pH values, which mimics cellular environments, to demonstrate their potential use for continuous monitoring of body-fluids pH.
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20
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The storm of NGS in NSCLC diagnostic-therapeutic pathway: How to sun the real clinical practice. Crit Rev Oncol Hematol 2021; 169:103561. [PMID: 34856311 DOI: 10.1016/j.critrevonc.2021.103561] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
The increasing number of approved drugs along with next generation sequencing (NGS) technologies look out as potential revolution of biomolecular characterization of non-small-cell lung cancer (NSCLC). Nevertheless, several aspects impact on success rate of NGS in clinical practice: a multidisciplinary approach and thorough knowledge of strengths and limits of each technologic diagnostic tool are required. Crucial preliminary step is the selection of the best available sample before testing, aware of clinical condition and setting of disease. Genomic data should be than integrated in the clinical context and matched with available therapeutic options; Molecular Tumor Boards (MTB) are worldwide emerging interdisciplinary groups implemented to transfer the impact of precision medicine in clinical practice. In order to guarantee equity in treatment, these considerations should find their application widely and rapidly. Aim of this review is offering an overview of emerging biomarkers, relative upcoming targeted drugs, and new diagnostic chances with an authors' perspective about a real-life diagnostic-therapeutic algorithm useful for daily clinical practice.
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21
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Hasan N, Kansakar U, Sherer E, DeCoster MA, Radadia AD. Ion-Selective Membrane-Coated Graphene-Hexagonal Boron Nitride Heterostructures for Field-Effect Ion Sensing. ACS OMEGA 2021; 6:30281-30291. [PMID: 34805660 PMCID: PMC8600519 DOI: 10.1021/acsomega.1c02222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/12/2021] [Indexed: 06/13/2023]
Abstract
An intrinsic ion sensitivity exceeding the Nernst-Boltzmann limit and an sp 2 -hybridized carbon structure make graphene a promising channel material for realizing ion-sensitive field-effect transistors with a stable solid-liquid interface under biased conditions in buffered salt solutions. Here, we examine the performance of graphene field-effect transistors coated with ion-selective membranes as a tool to selectively detect changes in concentrations of Ca2+, K+, and Na+ in individual salt solutions as well as in buffered Locke's solution. Both the shift in the Dirac point and transconductance could be measured as a function of ion concentration with repeatability exceeding 99.5% and reproducibility exceeding 98% over 60 days. However, an enhancement of selectivity, by about an order magnitude or more, was observed using transconductance as the indicator when compared to Dirac voltage, which is the only factor reported to date. Fabricating a hexagonal boron nitride multilayer between graphene and oxide further increased the ion sensitivity and selectivity of transconductance. These findings incite investigating ion sensitivity of transconductance in alternative architectures as well as urge the exploration of graphene transistor arrays for biomedical applications.
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Affiliation(s)
- Nowzesh Hasan
- Institute
for Micromanufacturing, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
- Center
for Biomedical Engineering and Rehabilitation Sciences, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
| | - Urna Kansakar
- Institute
for Micromanufacturing, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
- Center
for Biomedical Engineering and Rehabilitation Sciences, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
| | - Eric Sherer
- Chemical
Engineering, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
| | - Mark A. DeCoster
- Institute
for Micromanufacturing, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
- Center
for Biomedical Engineering and Rehabilitation Sciences, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
| | - Adarsh D. Radadia
- Institute
for Micromanufacturing, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
- Center
for Biomedical Engineering and Rehabilitation Sciences, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
- Chemical
Engineering, Louisiana Tech University, 911 Hergot Avenue, Ruston, Louisiana 71272, United States
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22
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Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. Funct Integr Genomics 2021; 22:3-26. [PMID: 34657989 DOI: 10.1007/s10142-021-00810-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/25/2021] [Accepted: 10/03/2021] [Indexed: 10/20/2022]
Abstract
This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the "metagenome."
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23
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Zhang Y, Ma L. Application of high-throughput sequencing technology in HIV drug resistance detection. BIOSAFETY AND HEALTH 2021. [DOI: 10.1016/j.bsheal.2021.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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24
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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26
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An ISFET Microarray Sensor System for Detecting the DNA Base Pairing. MICROMACHINES 2021; 12:mi12070731. [PMID: 34206209 PMCID: PMC8305849 DOI: 10.3390/mi12070731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 01/15/2023]
Abstract
Deoxyribonucleic acid (DNA) sequencing technology provides important data for the disclosure of genetic information and plays an important role in gene diagnosis and gene therapy. Conventional sequencing devices are expensive and require large and bulky optical structures and additional fluorescent labeling steps. Sequencing equipment based on a semiconductor chip has the advantages of fast sequencing speed, low cost and small size. The detection of DNA base pairing is the most important step in gene sequencing. In this study, a large-scale ion-sensitive field-effect transistor (ISFET) array chip with more than 13 million sensitive units is successfully designed for detecting the DNA base pairing. DNA base pairing is successfully detected by the sensor system, which includes the ISFET microarray chip, microfluidic system, and test platform. The chip achieves a high resolution of at least 0.5 mV, thus enabling the recognition of the change of 0.01 pH value. This complementary metal-oxide semiconductor (CMOS) compatible and cost-efficient sensor array chip, together with other specially designed components, can form a complete DNA sequencing system with potential application in the molecular biology fields.
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Scatena C, Murtas D, Tomei S. Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. Front Oncol 2021; 11:635488. [PMID: 34123788 PMCID: PMC8193952 DOI: 10.3389/fonc.2021.635488] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine.
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Affiliation(s)
- Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department, Sidra Medicine, Doha, Qatar
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QTL Analysis of Adult Plant Resistance to Stripe Rust in a Winter Wheat Recombinant Inbred Population. PLANTS 2021; 10:plants10030572. [PMID: 33803625 PMCID: PMC8002966 DOI: 10.3390/plants10030572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022]
Abstract
Stripe rust, caused by the fungus Puccinia striiformis f. sp. tritici, is a worldwide disease of wheat that causes devastating crop losses. Resistant cultivars have been developed over the last 40 years that have significantly reduced the economic impact of the disease on growers, but in heavy infection years it is mostly controlled through the intensive application of fungicides. The Pacific Northwest of the United States has an ideal climate for stripe rust and has one of the most diverse race compositions in the country. This has resulted in many waves of epidemics that have overcome most of the resistance genes traditionally used in elite germplasm. The best way to prevent high yield losses, reduce production costs to growers, and reduce the heavy application of fungicides is to pyramid multiple stripe rust resistance genes into new cultivars. Using genotyping-by-sequencing, we identified 4662 high quality variant positions in a recombinant inbred line population of 196 individuals derived from a cross between Skiles, a highly resistant winter wheat cultivar, and Goetze, a moderately to highly susceptible winter wheat cultivar, both developed at Oregon State University. A subsequent genome wide association study identified two quantitative trait loci (QTL) on chromosomes 3B and 3D within the predicted locations of stripe rust resistance genes. Resistance QTL, when combined together, conferred high levels of stripe rust resistance above the level of Skiles in some locations, indicating that these QTL would be important additions to future breeding efforts of Pacific Northwest winter wheat cultivars.
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Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: An overview. Hum Immunol 2021; 82:801-811. [PMID: 33745759 DOI: 10.1016/j.humimm.2021.02.012] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
Since the days of Sanger sequencing, next-generation sequencing technologies have significantly evolved to provide increased data output, efficiencies, and applications. These next generations of technologies can be categorized based on read length. This review provides an overview of these technologies as two paradigms: short-read, or "second-generation," technologies, and long-read, or "third-generation," technologies. Herein, short-read sequencing approaches are represented by the most prevalent technologies, Illumina and Ion Torrent, and long-read sequencing approaches are represented by Pacific Biosciences and Oxford Nanopore technologies. All technologies are reviewed along with reported advantages and disadvantages. Until recently, short-read sequencing was thought to provide high accuracy limited by read-length, while long-read technologies afforded much longer read-lengths at the expense of accuracy. Emerging developments for third-generation technologies hold promise for the next wave of sequencing evolution, with the co-existence of longer read lengths and high accuracy.
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Affiliation(s)
- Taishan Hu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Nilesh Chitnis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Anh Dinh
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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30
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Nam JH, Cho YS, Rackerby B, Goddik L, Park SH. Shifts of microbiota during cheese production: impact on production and quality. Appl Microbiol Biotechnol 2021; 105:2307-2318. [PMID: 33661344 DOI: 10.1007/s00253-021-11201-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/12/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023]
Abstract
The high-throughput DNA sequencing (HTS) method is used to identify microbes in cheese and their potential functional properties. The technique can be applied to the microbiota of the cheese processing environment, raw milk, curd, whey, and starter cultures, and be used to improve the quality, safety, and other physicochemical properties of the final product. The HTS method is also utilized to study the microbiota shift of different types of cheeses during processing, as the composition and functional properties of the microbiome provide unique characteristics to different cheeses. Although there are several reviews that focused on microbiota of various types of cheeses, this review focuses on evaluating the microbiota shift of different types of cheese production and highlights key bacteria in each step of the processing as well as microbiota of various types of cheeses. KEY POINTS: • High-throughput sequencing can be applied to identify microbiota in cheese. • Microbiota in cheese is changed during making process and aging. • Starter culture plays an important role to establish microbiota in cheese.
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Affiliation(s)
- Jun Haeng Nam
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Yong Sun Cho
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
- Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Bryna Rackerby
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Lisbeth Goddik
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, 3051 SW Campus Way, Corvallis, OR, 97331, USA.
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Pisapia P, Pepe F, Iaccarino A, Sgariglia R, Nacchio M, Conticelli F, Salatiello M, Tufano R, Russo G, Gragnano G, Girolami I, Eccher A, Malapelle U, Troncone G. Next Generation Sequencing in Cytopathology: Focus on Non-Small Cell Lung Cancer. Front Med (Lausanne) 2021; 8:633923. [PMID: 33644101 PMCID: PMC7904874 DOI: 10.3389/fmed.2021.633923] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular cytopathology is a rapidly evolving field embracing both conventional microscopy and molecular pathology. Its growing popularity stems from the fact that in many types of advanced cancers, including non small cell lung cancer (NSCLC), cytological samples often constitute the only available specimens for morphomolecular analysis. Indeed, non formalin fixed and paraffin embedded (FFPE) cytological samples feature a higher quality of extracted nucleic acids than histological specimens. However, because of the growing complexity of molecular testing, several efforts should be made to validate the analytical performance of the wide array of currently available molecular technologies, including next generation sequencing (NGS). This technology has the terrific advantage of allowing simultaneous detection of scores of predictive biomarkers even in low-input DNA/RNA specimens. Here, we briefly review the role of the modern cytopathologist in the morphomolecular diagnosing of advanced stage NSCLC and the adoption of NGS in conventional cytopreparations (cell blocks, direct smears, and liquid-based cytology) and supernatants.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Floriana Conticelli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Salatiello
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Ilaria Girolami
- Division of Pathology, Central Hospital Bolzano, Bolzano, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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32
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Combining Chemical Functionalization and FinFET Geometry for Field Effect Sensors as Accessible Technology to Optimize pH Sensing. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9020020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Field Effect Transistors (FETs) have led the progress of applications measuring the acidity in aqueous solutions thanks to their accuracy, ease of miniaturization and capacity of multiplexing. The signal-to-noise ratio and linearity of the sensors are two of the most relevant figures of merit that can facilitate the improvements of these devices. In this work we present the functionalization with aminopropyltriethoxysilane (APTES) of a promising new FET design consisting of a high height-to-width aspect ratio with an efficient 2D gating architecture that improves both factors. We measured the transistor transfer and output characteristics before and after APTES functionalization, obtaining an improved sensitivity and linearity in both responses. We also compared the experimental results with a site-biding model of the surface buffering capacity of the APTES functionalized layers.
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33
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Siddika T, Heinemann IU. Bringing MicroRNAs to Light: Methods for MicroRNA Quantification and Visualization in Live Cells. Front Bioeng Biotechnol 2021; 8:619583. [PMID: 33537295 PMCID: PMC7848212 DOI: 10.3389/fbioe.2020.619583] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
MiRNAs are small non-coding RNAs that interact with their target mRNAs for posttranscriptional gene regulation. Finely controlled miRNA biogenesis, target recognition and degradation indicate that maintaining miRNA homeostasis is essential for regulating cell proliferation, growth, differentiation and apoptosis. Increasingly, miRNAs have been recognized as a potential biomarker for disease diagnosis. MiRNAs can be found in blood, plasma, and tissues, and miRNA expression and activity differ in developmental stages, tissues and in response to external stimuli. MiRNA transcripts are matured from pri-miRNA over pre-miRNA to mature miRNA, a process that includes multiple steps and enzymes. Many tools are available to identify and quantify specific miRNAs, ranging from measuring total miRNA, specific miRNA activity, miRNA arrays and miRNA localization. The various miRNA assays differ in accuracy, cost, efficiency and convenience of monitoring miRNA dynamics. To acknowledge the significance and increasing research interest in miRNAs, we summarize the traditional as well as novel methods of miRNA quantification with strengths and limitations of various techniques in biochemical and medical research.
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Affiliation(s)
| | - Ilka U. Heinemann
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
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34
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Sharma P, Sharma BS, Verma RJ. A Guide to RNAseq Data Analysis Using Bioinformatics Approaches. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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35
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Teske D, Peters A, Möllers A, Fischer M. Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14323-14333. [PMID: 32917087 DOI: 10.1021/acs.jafc.0c03001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.
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Affiliation(s)
- Doreen Teske
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alina Peters
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alexander Möllers
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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36
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Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic Acids Analysis. Sci China Chem 2020; 64:171-203. [PMID: 33293939 PMCID: PMC7716629 DOI: 10.1007/s11426-020-9864-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, 710049 China
| | - Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Jinqi Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Changlong Hao
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fujian Huang
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Yanyi Huang
- College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Hua Kuang
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Zhenyu Lin
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Dingbin Liu
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin, 300071 China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Libing Liu
- Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chunhua Lu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Fang Luo
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jiashu Sun
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190 China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014 China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing, 100084 China
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Shu Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada
| | - Lingling Wu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108 China
| | - Fan Xia
- Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan, 430074 China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, 214122 China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Bi-Feng Yuan
- Department of Chemistry, Wuhan University, Wuhan, 430072 China
| | - Quan Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005 China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Huanghao Yang
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou, 350116 China
| | - Weihong Tan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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37
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Lee N, Park MJ, Song W, Jeon K, Jeong S. Currently Applied Molecular Assays for Identifying ESR1 Mutations in Patients with Advanced Breast Cancer. Int J Mol Sci 2020; 21:ijms21228807. [PMID: 33233830 PMCID: PMC7699999 DOI: 10.3390/ijms21228807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Approximately 70% of breast cancers, the leading cause of cancer-related mortality worldwide, are positive for the estrogen receptor (ER). Treatment of patients with luminal subtypes is mainly based on endocrine therapy. However, ER positivity is reduced and ESR1 mutations play an important role in resistance to endocrine therapy, leading to advanced breast cancer. Various methodologies for the detection of ESR1 mutations have been developed, and the most commonly used method is next-generation sequencing (NGS)-based assays (50.0%) followed by droplet digital PCR (ddPCR) (45.5%). Regarding the sample type, tissue (50.0%) was more frequently used than plasma (27.3%). However, plasma (46.2%) became the most used method in 2016-2019, in contrast to 2012-2015 (22.2%). In 2016-2019, ddPCR (61.5%), rather than NGS (30.8%), became a more popular method than it was in 2012-2015. The easy accessibility, non-invasiveness, and demonstrated usefulness with high sensitivity of ddPCR using plasma have changed the trends. When using these assays, there should be a comprehensive understanding of the principles, advantages, vulnerability, and precautions for interpretation. In the future, advanced NGS platforms and modified ddPCR will benefit patients by facilitating treatment decisions efficiently based on information regarding ESR1 mutations.
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Affiliation(s)
- Nuri Lee
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Min-Jeong Park
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Wonkeun Song
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
| | - Kibum Jeon
- Department of Laboratory Medicine, Hangang Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea;
| | - Seri Jeong
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07440, Korea; (N.L.); (M.-J.P.); (W.S.)
- Correspondence: ; Tel.: +82-845-5305
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Kim KD, Kang Y, Kim C. Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1454. [PMID: 33126607 PMCID: PMC7694055 DOI: 10.3390/plants9111454] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/11/2023]
Abstract
Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.
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Affiliation(s)
- Kyung Do Kim
- Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea;
| | - Yuna Kang
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
| | - Changsoo Kim
- Department of Crop Science, Chungnam National University, Daejeon 34134, Korea;
- Department of Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Korea
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Abstract
Reducing the risk of (cross-)contamination, improving the chain of custody, providing fast analysis times and options of direct analysis at crime scenes: these requirements within forensic DNA analysis can be met upon using microfluidic devices. To become generally applied in forensics, the most important requirements for microfluidic devices are: analysis time, method of DNA detection and biocompatibility of used materials. In this work an overview is provided about biosensing of DNA, by DNA profiling via standard short tandem repeat (STR) analysis or by next generation sequencing. The material of which a forensic microfluidic device is made is crucial: it should for example not inhibit DNA amplification and its thermal conductivity and optical transparency should be suitable for achieving fast analysis. The characteristics of three materials frequently used materials, i.e., glass, silicon and PDMS, are given, in addition to a promising alternative, viz. cyclic olefin copolymer (COC). New experimental findings are presented about the biocompatibility of COC and the use of COC chips for multiple displacement amplification and real-time monitoring of DNA amplification.
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40
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A ten-minute, single step, label-free, sample-to-answer assay for qualitative detection of cytokines in serum at femtomolar levels. Biomed Microdevices 2020; 22:73. [PMID: 33037941 DOI: 10.1007/s10544-020-00525-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Label-free electronic affinity based immuno-sensing is an attractive candidate as a platform technology for analyzing biomarkers due to the ease of miniaturization and minimal use of reagents. Electronic based sensing approaches, however, have lagged behind their optical counterparts in terms of detection limit, selectivity, and reliability. Also, the matrix dependent nature of electronic sensing modalities makes difficult the analysis of biomarkers in high salt concentration samples such as serum due to charge screening. We present a novel sensing platform, the micro-well sensor, that works by functionalizing nanoscale volume wells with antibodies and monitoring the impedance change inside the wells due binding of target protein. This detection modality is advantageous to many label-free electronic sensors in that signal power scales with increase in salt concentration, thus improving the sensitivity of the platform. We demonstrate rapid label-free qualitative detection of cytokines within ten minutes at femtoMolar concentrations and a dynamic range of 3 orders of magnitude in serum samples. We describe the design, fabrication, and characterization of the micro-well sensor in serum samples using inflammatory protein biomarkers.
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Manderstedt E, Nilsson R, Ljung R, Lind‐Halldén C, Astermark J, Halldén C. Detection of mosaics in hemophilia A by deep Ion Torrent sequencing and droplet digital PCR. Res Pract Thromb Haemost 2020; 4:1121-1130. [PMID: 33134778 PMCID: PMC7590296 DOI: 10.1002/rth2.12425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The occurrence of mosaicism in hemophilia A (HA) has been investigated in several studies using different detection methods. OBJECTIVES To characterize and compare the ability of AmpliSeq/Ion Torrent sequencing and droplet digital polymerase chain reaction (ddPCR) for mosaic detection in HA. METHODS Ion Torrent sequencing and ddPCR were used to analyze 20 healthy males and 16 mothers of sporadic HA patients. RESULTS An error-rate map over all coding positions and all positions reported as mutated in the F8-specific mutation database was produced. The sequencing produced a mean read depth of >1500X where >97% of positions were covered by >100 reads. Higher error frequencies were observed in positions with A or T as reference allele and in positions surrounded on both sides with C or G. Seventeen of 9319 positions had a mean substitution error frequency >1%. The ability to identify low-level mosaicism was determined primarily by read depth and error rate of each specific position. Limit of detection (LOD) was <1% for 97% of positions with substitutions and 90% of indel positions. The positions with LOD >1% require repeated testing and mononucleotide repeats with more than four repeat units need an alternative analysis strategy. Mosaicism was detected in 1 of 16 mothers and confirmed using ddPCR. CONCLUSIONS Deep sequencing using an AmpliSeq/Ion Torrent strategy allows for simultaneous identification of disease-causing mutations in patients and mosaicism in mothers. ddPCR has high sensitivity but is hampered by the need for mutation-specific design.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Rosanna Nilsson
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Rolf Ljung
- Department of Clinical Sciences‐Pediatrics, Lund and Malmö Center for Thrombosis and HemostasisLund UniversitySkåne University HospitalMalmöSweden
| | - Christina Lind‐Halldén
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Jan Astermark
- Department for Hematology, Oncology and Radiation PhysicsCenter for Thrombosis and HemostasisSkåne University HospitalMalmöSweden
| | - Christer Halldén
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
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Shokrof M, Abouelhoda M. IonCRAM: a reference-based compression tool for ion torrent sequence files. BMC Bioinformatics 2020; 21:397. [PMID: 32907531 PMCID: PMC7487613 DOI: 10.1186/s12859-020-03726-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/31/2020] [Indexed: 12/29/2022] Open
Abstract
Background Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. However, the tools for generating the CRAM formats are not designed to handle the flow signals. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving. Results In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%. Conclusions Reducing the space consumption of NGS data reduces the cost of storage and data transfer. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest; as it ultimately contributes to the overall cost reduction of the clinical test. The space saving achieved by our tool is a practical step in this direction. The tool is open source and available at Code Ocean, github, and http://ioncram.saudigenomeproject.com.
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Affiliation(s)
- Moustafa Shokrof
- Faculty of Computer Science, University of California at Davis, Davis, CA, USA
| | - Mohamed Abouelhoda
- King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia. .,Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, University Square, Giza, Egypt.
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Siu RHP, Liu Y, Chan KHY, Ridzewski C, Slaughter LS, Wu AR. Optimization of on-bead emulsion polymerase chain reaction based on single particle analysis. Talanta 2020; 221:121593. [PMID: 33076127 DOI: 10.1016/j.talanta.2020.121593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
Emulsion polymerase chain reaction (ePCR) enables parallel amplification of millions of different DNA molecules while avoiding bias and chimeric byproducts, essential criteria for applications including next generation sequencing, aptamer selection, and protein-DNA interaction studies. Despite these advantages, ePCR remains underused due to the lack of optimal starting conditions, straightforward methods to evaluate success, and guidelines for tuning the reaction. This knowledge has been elusive for bulk emulsion generation methods, such as stirring and vortexing, the only methods that can emulsify libraries of ≥108 sequences within minutes, because these emulsions have not been characterized in ways that preserve the heterogeneity that defines successful ePCR. Our study quantifies the outcome of ePCR from conditions specified in the literature using single particle analysis, which preserves this heterogeneity. We combine ePCR with magnetic microbeads and quantify the amplification yield via qPCR and the proportion of clonal and saturated beads via flow cytometry. Our single particle level analysis of thousands of beads resolves two key criteria that define the success of ePCR: 1) whether the target fraction of 20% clonal beads predicted by the Poisson distribution is achieved, and 2) whether those beads are partially or maximally covered by amplified DNA. We found that among the two concentrations of polymerase tested, only the higher one, which is 20-fold more than the concentration recommended for conventional PCR, could yield sufficient PCR products. Dramatic increases in the concentrations of reverse primer and nucleotides recommended in literature gave no measurable change in outcome. We thus provide evidence-based starting conditions for effective and economical ePCR for real DNA libraries and a straightforward workflow for evaluating the success of tuning ePCR prior to downstream applications.
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Affiliation(s)
- Ryan H P Siu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Yang Liu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Kaitlin H Y Chan
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Clara Ridzewski
- Natural and Environmental Sciences, Zittau/Görlitz University of Applied Sciences, Germany
| | - Liane Siu Slaughter
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong.
| | - Angela R Wu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong; Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong.
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Latorre-Pérez A, Pascual J, Porcar M, Vilanova C. A lab in the field: applications of real-time, in situ metagenomic sequencing. Biol Methods Protoc 2020; 5:bpaa016. [PMID: 33134552 PMCID: PMC7585387 DOI: 10.1093/biomethods/bpaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 01/18/2023] Open
Abstract
High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.
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Affiliation(s)
| | | | - Manuel Porcar
- Darwin Bioprospecting Excellence SL, Valencia, Spain
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Valencia, Spain
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45
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Gao G, Smith DI. Clinical Massively Parallel Sequencing. Clin Chem 2020; 66:77-88. [PMID: 31811004 DOI: 10.1373/clinchem.2019.303305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.
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Affiliation(s)
- Ge Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - David I Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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Kuan DH, Huang NT. Recent advancements in microfluidics that integrate electrical sensors for whole blood analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3318-3332. [PMID: 32930218 DOI: 10.1039/d0ay00413h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Whole blood analysis reveals crucial information about various physiological and pathological conditions, including cancer metastasis, infection, and immune status, among others. Despite this rich information, the complex composition of whole blood usually required multiple sample preparation steps to purify targeted analytes. Traditionally, whole blood preparation processes, including centrifugation, lysis, dilution, or staining, are usually manually operated by well-trained technicians using bench-top instruments. This preparation can require a large blood volume and cannot be directly integrated with detection systems. Recently, various studies have integrated microfluidics with electrical sensors for whole blood analysis, with a focus on cell-based analysis, such as cell type, number, morphology, phenotype, and secreted molecules. These miniaturized systems require less sample and shorter reaction times. Besides, the sample processing and analysis can be fully integrated and automated with minimal operations. We believe these systems can transfer the current whole blood analysis from hospitals or laboratories into clinics or home settings to enable real-time and continuous health condition monitoring in point-of-care settings.
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Affiliation(s)
- Da-Han Kuan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taiwan.
| | - Nien-Tsu Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taiwan.
- Department of Electrical Engineering, National Taiwan University, Taiwan
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47
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Matern BM, Olieslagers TI, Groeneweg M, Duygu B, Wieten L, Tilanus MGJ, Voorter CEM. Long-Read Nanopore Sequencing Validated for Human Leukocyte Antigen Class I Typing in Routine Diagnostics. J Mol Diagn 2020; 22:912-919. [PMID: 32302780 DOI: 10.1016/j.jmoldx.2020.04.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/03/2020] [Accepted: 04/02/2020] [Indexed: 01/23/2023] Open
Abstract
Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution DNA sequence analysis is the gold standard for determining compatibility between patient and donor for hematopoietic stem cell transplantation. Single-molecule sequencing (PacBio or MinION) is a newest (third) generation sequencing approach. MinION is a nanopore sequencing platform, which provides long targeted DNA sequences. The long reads provide unambiguous phasing, but the initial high error profile prevented its use in high-impact applications, such as HLA typing for HLA matching of donor and recipient in the transplantation setting. Ongoing developments on instrumentation and basecalling software have improved the per-base accuracy of 1D2 nanopore reads tremendously. In the current study, two validation panels of samples covering 70 of the 71 known HLA class I allele groups were used to compare third field sequences obtained by MinION, with Sanger sequence-based typing showing a 100% concordance between both data sets. In addition, the first validation panel was used to set the acceptance criteria for the use of MinION in a routine setting. The acceptance criteria were subsequently confirmed with the second validation panel. In summary, the present study describes validation and implementation of nanopore sequencing HLA class I typing method and illustrates that nanopore sequencing technology has advanced to a point where it can be used in routine diagnostics with high accuracy.
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Affiliation(s)
- Benedict M Matern
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Timo I Olieslagers
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Mathijs Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Burcu Duygu
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lotte Wieten
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Marcel G J Tilanus
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Christina E M Voorter
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands.
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Adapting SureSelect enrichment protocol to the Ion Torrent S5 platform in molecular diagnostics of craniosynostosis. Sci Rep 2020; 10:4159. [PMID: 32139749 PMCID: PMC7058001 DOI: 10.1038/s41598-020-61048-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Obtaining reliable and high fidelity next-generation sequencing (NGS) data requires to choose a suitable sequencing platform and a library preparation approach, which both have their inherent assay-specific limitations. Here, we present the results of successful adaptation of SureSelect hybridisation-based target enrichment protocol for the sequencing on the Ion Torrent S5 platform, which is designed to work preferably with amplicon-based panels. In our study, we applied a custom NGS panel to screen a cohort of 16 unrelated patients affected by premature fusion of the cranial sutures, i.e. craniosynostosis (CS). CS occurs either as an isolated malformation or in a syndromic form, representing a genetically heterogeneous and clinically variable group of disorders. The approach presented here allowed us to achieve high quality NGS data and confirmed molecular diagnosis in 19% of cases, reaching the diagnostic yield similar to some of the published research reports. In conclusion, we demonstrated that an alternative enrichment strategy for library preparations can be successfully applied prior to sequencing on the Ion Torrent S5 platform. Also, we proved that the custom NGS panel designed by us represents a useful and effective tool in the molecular diagnostics of patients with CS.
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49
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Olgac A, Öztoprak Ü, Kasapkara ÇS, Kılıç M, Yüksel D, Derinkuyu EB, Taşçı Yıldız Y, Ceylaner S, Ezgu FS. A rare case of primary coenzyme Q10 deficiency due to COQ9 mutation. J Pediatr Endocrinol Metab 2020; 33:165-170. [PMID: 31821167 DOI: 10.1515/jpem-2019-0245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/21/2019] [Indexed: 11/15/2022]
Abstract
Background Coenzyme Q10 (CoQ10) serves as a shuttle for electrons from complexes I and II to complex III in the respiratory chain, and has important functions within the mitochondria. Primary CoQ10 deficiency is a mitochondrial disorder which has devastating effects, and which may be partially treated with exogenous CoQ10 supplementation. Case presentation A 9-month-old girl patient was referred to our clinic due to growth retardation, microcephaly and seizures. She was the third child of consanguineous parents (first-degree cousins) of Pakistani origin, born at 38 weeks gestation, weighing 2000 g after an uncomplicated pregnancy, and was hospitalized for 3 days due to respiratory distress. She had sustained clonic seizures when she was 4 months old. Physical examination showed microcephaly, truncal hypotonia and dysmorphic features. Metabolic tests were inconclusive. Abdominal ultrasonography revealed cystic appearance of the kidneys. Non-compaction of the left ventricle was detected in echocardiography. Cranial magnetic resonance imaging (MRI) showed hypoplasia of the cerebellar vermis and brain stem, corpus callosum agenesis, and cortical atrophy. A panel testing of 450 genes involved in inborn errors of metabolism (IEM) was performed that showed a novel frameshift c.384delG (Gly129Valfs*17) homozygous mutation in COQ9. A treatment of 5 mg/kg/day exogenous CoQ10 was started when she was 10 months old, and the dosage was increased to 50 mg/kg/day after the exact diagnosis. No objective neurological improvement could be observed after the adjustment of the drug dosage. Conclusions We report a case of CoQ10 deficiency due to a novel COQ9 gene mutation that adds clinical data from a newly diagnosed patient. Our case also outlines the importance of genetic panels used for specific diseases including IEM.
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Affiliation(s)
- Asburce Olgac
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Metabolism, Ankara, Turkey
| | - Ülkühan Öztoprak
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Neurology, Ankara, Turkey
| | - Çiğdem Seher Kasapkara
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Metabolism, Ankara, Turkey
| | - Mustafa Kılıç
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Metabolism, Ankara, Turkey
| | - Deniz Yüksel
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Neurology, Ankara, Turkey
| | - Emine Betül Derinkuyu
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Radiology, Ankara, Turkey
| | - Yasemin Taşçı Yıldız
- University of Health Sciences, Dr. Sami Ulus Maternity and Children's Research and Education Hospital, Department of Pediatric Radiology, Ankara, Turkey
| | | | - Fatih Süheyl Ezgu
- Gazi University Hospital, Department of Pediatric Metabolism and Nutrition, Ankara, Turkey
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50
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Murphy TW, Hsieh YP, Zhu B, Naler LB, Lu C. Microfluidic Platform for Next-Generation Sequencing Library Preparation with Low-Input Samples. Anal Chem 2020; 92:2519-2526. [PMID: 31894965 DOI: 10.1021/acs.analchem.9b04086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Advances in next-generation sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here, we present a microfluidic droplet-based system for NGS library preparation, capable of reducing the number of pipetting steps significantly, reducing reagent consumption by 10×, and automating much of the process, while supporting an extremely low DNA input requirement (10 pg per library). This semiautomated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch-to-batch variation and operator hands-on time.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Bohan Zhu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Lynette B Naler
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Chang Lu
- Department of Chemical Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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