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Betschart RO, Riccio C, Aguilera-Garcia D, Blankenberg S, Guo L, Moch H, Seidl D, Solleder H, Thalén F, Thiéry A, Twerenbold R, Zeller T, Zoche M, Ziegler A. Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control. Biom J 2024; 66:e202300278. [PMID: 38988195 DOI: 10.1002/bimj.202300278] [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: 10/09/2023] [Revised: 03/21/2024] [Accepted: 05/14/2024] [Indexed: 07/12/2024]
Abstract
Rapid advances in high-throughput DNA sequencing technologies have enabled large-scale whole genome sequencing (WGS) studies. Before performing association analysis between phenotypes and genotypes, preprocessing and quality control (QC) of the raw sequence data need to be performed. Because many biostatisticians have not been working with WGS data so far, we first sketch Illumina's short-read sequencing technology. Second, we explain the general preprocessing pipeline for WGS studies. Third, we provide an overview of important QC metrics, which are applied to WGS data: on the raw data, after mapping and alignment, after variant calling, and after multisample variant calling. Fourth, we illustrate the QC with the data from the GENEtic SequencIng Study Hamburg-Davos (GENESIS-HD), a study involving more than 9000 human whole genomes. All samples were sequenced on an Illumina NovaSeq 6000 with an average coverage of 35× using a PCR-free protocol. For QC, one genome in a bottle (GIAB) trio was sequenced in four replicates, and one GIAB sample was successfully sequenced 70 times in different runs. Fifth, we provide empirical data on the compression of raw data using the DRAGEN original read archive (ORA). The most important quality metrics in the application were genetic similarity, sample cross-contamination, deviations from the expected Het/Hom ratio, relatedness, and coverage. The compression ratio of the raw files using DRAGEN ORA was 5.6:1, and compression time was linear by genome coverage. In summary, the preprocessing, joint calling, and QC of large WGS studies are feasible within a reasonable time, and efficient QC procedures are readily available.
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Affiliation(s)
| | | | - Domingo Aguilera-Garcia
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Blankenberg
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linlin Guo
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Moch
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Dagmar Seidl
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Hugo Solleder
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
| | - Felix Thalén
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
| | | | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Tanja Zeller
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Martin Zoche
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Andreas Ziegler
- Cardio-CARE, Medizincampus Davos, Davos, Switzerland
- Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Population Health Innovation (POINT), University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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2
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Malapelle U, Leighl N, Addeo A, Hershkovitz D, Hochmair MJ, Khorshid O, Länger F, de Marinis F, Peled N, Sheffield BS, Smit EF, Viteri S, Wolf J, Venturini F, O'Hara RM, Rolfo C. Recommendations for reporting tissue and circulating tumour (ct)DNA next-generation sequencing results in non-small cell lung cancer. Br J Cancer 2024; 131:212-219. [PMID: 38750115 PMCID: PMC11263606 DOI: 10.1038/s41416-024-02709-4] [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] [Received: 01/04/2024] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 07/24/2024] Open
Abstract
Non-small cell lung cancer is a heterogeneous disease and molecular characterisation plays an important role in its clinical management. Next-generation sequencing-based panel testing enables many molecular alterations to be interrogated simultaneously, allowing for comprehensive identification of actionable oncogenic drivers (and co-mutations) and appropriate matching of patients with targeted therapies. Despite consensus in international guidelines on the importance of broad molecular profiling, adoption of next-generation sequencing varies globally. One of the barriers to its successful implementation is a lack of accepted standards and guidelines specifically for the reporting and clinical annotation of next-generation sequencing results. Based on roundtable discussions between pathologists and oncologists, we provide best practice recommendations for the reporting of next-generation sequencing results in non-small cell lung cancer to facilitate its use and enable easy interpretation for physicians. These are intended to complement existing guidelines related to the use of next-generation sequencing (solid and liquid). Here, we discuss next-generation sequencing workflows, the structure of next-generation sequencing reports, and our recommendations for best practice thereof. The aim of these recommendations and considerations is ultimately to ensure that reports are fully interpretable, and that the most appropriate treatment options are selected based on robust molecular profiles in well-defined reports.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Natasha Leighl
- Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Alfredo Addeo
- Oncology Unit, Geneva University Hospital, Geneva, Switzerland
| | | | - Maximilian J Hochmair
- Department of Respiratory & Critical Care Medicine, Karl Landsteiner Institute of Lung Research & Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Ola Khorshid
- National Cancer Institute, Cairo University, Cairo, Egypt
| | - Florian Länger
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Nir Peled
- Helmesely Cancer Center, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Brandon S Sheffield
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON, Canada
| | - Egbert F Smit
- Department of Pulmonary Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - Santiago Viteri
- UOMI Cancer Center, Clínica Mi Tres Torres, Barcelona, Spain
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany
| | | | | | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Medical System & Icahn School of Medicine, New York, NY, USA.
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3
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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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Cooper B, Yang R. An assessment of AcquireX and Compound Discoverer software 3.3 for non-targeted metabolomics. Sci Rep 2024; 14:4841. [PMID: 38418855 PMCID: PMC10902394 DOI: 10.1038/s41598-024-55356-3] [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: 10/20/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
We used the Exploris 240 mass spectrometer for non-targeted metabolomics on Saccharomyces cerevisiae strain BY4741 and tested AcquireX software for increasing the number of detectable compounds and Compound Discoverer 3.3 software for identifying compounds by MS2 spectral library matching. AcquireX increased the number of potentially identifiable compounds by 50% through six iterations of MS2 acquisition. On the basis of high-scoring MS2 matches made by Compound Discoverer, there were 483 compounds putatively identified from nearly 8000 candidate spectra. Comparisons to 20 amino acid standards, however, revealed instances whereby compound matches could be incorrect despite strong scores. Situations included the candidate with the top score not being the correct compound, matching the same compound at two different chromatographic peaks, assigning the highest score to a library compound much heavier than the mass for the parent ion, and grouping MS2 isomers to a single parent ion. Because the software does not calculate false positive and false discovery rates at these multiple levels where such errors can propagate, we conclude that manual examination of findings will be required post software analysis. These results will interest scientists who may use this platform for metabolomics research in diverse disciplines including medical science, environmental science, and agriculture.
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Affiliation(s)
- Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Ronghui Yang
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
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5
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Bridgers J, Alexander K, Karsan A. Operationalizing Quality Assurance for Clinical Illumina Somatic Next-Generation Sequencing Pipelines. J Mol Diagn 2024; 26:96-105. [PMID: 38086510 DOI: 10.1016/j.jmoldx.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 09/01/2023] [Accepted: 11/07/2023] [Indexed: 01/26/2024] Open
Abstract
Quality assurance (QA) is essential for precision oncology workflows, in particular in the clinical setting. However, because of numerous variations in laboratory and bioinformatics pipelines, QA practices remain non-standardized, are often ad hoc, and are lacking longitudinal tracking. A selected review of existing software was performed for quality control of Illumina next-generation sequencing data, focusing specifically on generalizable tools that can be integrated into any bioinformatics workflow to easily develop a QA workflow with longitudinal tracking. Although all implementations need to be integrated, validated, and iterated upon to suit individual operations, providing a base suite of options will enable better validation and use of QA in clinical somatic mutation testing for workflows using Illumina next-generation sequencing and beyond.
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Affiliation(s)
- Joshua Bridgers
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Kenyon Alexander
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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6
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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Parvizpour S, Beyrampour-Basmenj H, Razmara J, Farhadi F, Shamsir MS. Cancer treatment comes to age: from one-size-fits-all to next-generation sequencing (NGS) technologies. BIOIMPACTS : BI 2023; 14:29957. [PMID: 39104623 PMCID: PMC11298019 DOI: 10.34172/bi.2023.29957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 08/07/2024]
Abstract
Cancer is one of the leading causes of death worldwide and one of the greatest challenges in extending life expectancy. The paradigm of one-size-fits-all medicine has already given way to the stratification of patients by disease subtypes, clinical characteristics, and biomarkers (stratified medicine). The introduction of next-generation sequencing (NGS) in clinical oncology has made it possible to tailor cancer patient therapy to their molecular profiles. NGS is expected to lead the transition to precision medicine (PM), where the right therapeutic approach is chosen for each patient based on their characteristics and mutations. Here, we highlight how the NGS technology facilitates cancer treatment. In this regard, first, precision medicine and NGS technology are reviewed, and then, the NGS revolution in precision medicine is described. In the sequel, the role of NGS in oncology and the existing limitations are discussed. The available databases and bioinformatics tools and online servers used in NGS data analysis are also reviewed. The review ends with concluding remarks.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hanieh Beyrampour-Basmenj
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematics, Statistics and Computer Science, University of Tabriz, Tabriz, Iran
| | - Farhad Farhadi
- Food and Drug Administration, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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8
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Zong L, Zhu Y, Jiang Y, Xia Y, Liu Q, Jiang S. A comprehensive assessment of exome capture methods for RNA sequencing of formalin-fixed and paraffin-embedded samples. BMC Genomics 2023; 24:777. [PMID: 38102591 PMCID: PMC10722801 DOI: 10.1186/s12864-023-09886-1] [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] [Received: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
RNA-Seq analysis of Formalin-Fixed and Paraffin-Embedded (FFPE) samples has emerged as a highly effective approach and is increasingly being used in clinical research and drug development. However, the processing and storage of FFPE samples are known to cause extensive degradation of RNAs, which limits the discovery of gene expression or gene fusion-based biomarkers using RNA sequencing, particularly methods reliant on Poly(A) enrichment. Recently, researchers have developed an exome targeted RNA-Seq methodology that utilizes biotinylated oligonucleotide probes to enrich RNA transcripts of interest, which could overcome these limitations. Nevertheless, the standardization of this experimental framework, including probe designs, sample multiplexing, sequencing read length, and bioinformatic pipelines, remains an essential requirement. In this study, we conducted a comprehensive comparison of three main commercially available exome capture kits and evaluated key experimental parameters, to provide the overview of the advantages and limitations associated with the selection of library preparation protocols and sequencing platforms. The results provide valuable insights into the best practices for obtaining high-quality data from FFPE samples.
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Affiliation(s)
- Liang Zong
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
- College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, China
| | - Yabing Zhu
- BGI Tech Solutions Co., Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yuan Jiang
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Ying Xia
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Qun Liu
- Wuhan BGI Technology Service Co., Ltd. BGI-Wuhan, Wuhan, China
| | - Sanjie Jiang
- BGI Tech Solutions Co., Ltd. BGI-Shenzhen, Shenzhen, China.
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Meredith LW, Aboualy M, Ochola R, Okwarah P, Ozel M, Abubakar A, Barakat A. Key aspects defining the development and implementation of a regional genomic surveillance strategy for the Eastern Mediterranean Region. Influenza Other Respir Viruses 2023; 17:e13205. [PMID: 37859974 PMCID: PMC10583647 DOI: 10.1111/irv.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023] Open
Abstract
The COVID-19 pandemic highlighted the critical role of pathogen sequencing in making informed public health decisions. Initially, the Eastern Mediterranean Region faced limitations in sequencing capacity. However, with robust WHO and stakeholder support, the situation significantly improved. By 2022, COVID-19 sequencing was underway in 22 out of 23 regional countries, with varying throughput and capacity. Notably, three genomic hubs were established in Oman, UAE, and Morocco, playing a key role in providing expanded genomics training and support across the region. While primarily for COVID-19 surveillance, this sequencing capacity offers an opportunity to integrate genomic surveillance into existing networks. This integration can enable early detection and response to high-threat pathogens with pandemic potential. To advance this, WHO/EMRO collaborated with stakeholders to formulate the Eastern Mediterranean Regional Genomic Surveillance Strategy for Emerging Pathogens of Pandemic Concern. Consultative meetings with regional and international genomic surveillance experts identified strategy focal points, key partners, priority pathogens, and implementation steps. As the strategy awaits member states' ratification in Q4 2023, this manuscript outlines pivotal facets defined by member states and the strategic document's key deliverables and opportunities. These efforts aim to yield a substantial positive impact within the region.
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Affiliation(s)
- Luke W. Meredith
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mustafa Aboualy
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Rachel Ochola
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Patrick Okwarah
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Mehmet Ozel
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Abdinasir Abubakar
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
| | - Amal Barakat
- Infectious Hazard Management, Department of Health EmergencyWorld Health Organization, Eastern Mediterranean Regional OfficeCairoEgypt
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Sigwart JD, Chen C, Tilic E, Vences M, Riehl T. Why is there no service to support taxonomy? Bioessays 2023; 45:e2300070. [PMID: 37318314 DOI: 10.1002/bies.202300070] [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] [Received: 04/20/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023]
Abstract
Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at 'turbo taxonomy' have been unsatisfactory. We are developing a taxonomic service in the Senckenberg Ocean Species Alliance to provide fundamental data for new species descriptions. This will also function as a hub to connect a global network of taxonomists, assembling an alliance of scientists working on potential new species to tackle both the extinction and inclusion crises we face today. The current rate of new species descriptions is simply too slow; the discipline is often dismissed as old fashioned, and there is a crisis level need for taxonomic descriptions to come to grips with the scale of Anthropocene biodiversity loss. Here, we envision how the process of describing and naming species would benefit from a service supporting the acquisition of descriptive data. Also see the video abstract here: https://youtu.be/E8q3KJor_F8.
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Affiliation(s)
- Julia D Sigwart
- Senckenberg Research Institute and Museum, Marine Zoology Department, Frankfurt, Germany
| | - Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), X-STAR, Yokosuka, Japan
| | - Ekin Tilic
- Senckenberg Research Institute and Museum, Marine Zoology Department, Frankfurt, Germany
| | - Miguel Vences
- Technische Universität Braunschweig, Zoological Institute, Braunschweig, Germany
| | - Torben Riehl
- Senckenberg Research Institute and Museum, Marine Zoology Department, Frankfurt, Germany
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11
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Stanasiuk C, Milting H, Homm S, Persson J, Holtz L, Wittmer A, Fox H, Laser T, Knöll R, Pohl GM, Paluszkiewicz L, Jakob T, Bachmann-Mennenga B, Henzler D, Grautoff S, Veit G, Klingel K, Hori E, Kellner U, Karger B, Schlepper S, Pfeiffer H, Gummert J, Gärtner A, Tiesmeier J. Blood taken immediately after fatal resuscitation attempts yields higher quality DNA for genetic studies as compared to autopsy samples. Int J Legal Med 2023; 137:1569-1581. [PMID: 36773088 PMCID: PMC10421769 DOI: 10.1007/s00414-023-02966-7] [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: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND The out-of-hospital cardiac arrest (OHCA) in the young may be associated with a genetic predisposition which is relevant even for genetic counseling of relatives. The identification of genetic variants depends on the availability of intact genomic DNA. DNA from autopsy may be not available due to low autopsy frequencies or not suitable for high-throughput DNA sequencing (NGS). The emergency medical service (EMS) plays an important role to save biomaterial for subsequent molecular autopsy. It is not known whether the DNA integrity of samples collected by the EMS is better suited for NGS than autopsy specimens. MATERIAL AND METHODS DNA integrity was analyzed by standardized protocols. Fourteen blood samples collected by the EMS and biomaterials from autopsy were compared. We collected 172 autopsy samples from different tissues and blood with postmortem intervals of 14-168 h. For comparison, DNA integrity derived from blood stored under experimental conditions was checked against autopsy blood after different time intervals. RESULTS DNA integrity and extraction yield were higher in EMS blood compared to any autopsy tissue. DNA stability in autopsy specimens was highly variable and had unpredictable quality. In contrast, collecting blood samples by the EMS is feasible and delivered comparably the highest DNA integrity. CONCLUSIONS Isolation yield and DNA integrity from blood samples collected by the EMS is superior in comparison to autopsy specimens. DNA from blood samples collected by the EMS on scene is stable at room temperature or even for days at 4 °C. We conclude that the EMS personnel should always save a blood sample of young fatal OHCA cases died on scene to enable subsequent genetic analysis.
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Affiliation(s)
- Caroline Stanasiuk
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Hendrik Milting
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany.
| | - Sören Homm
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Jan Persson
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Lars Holtz
- Emergency Department, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Axel Wittmer
- Institute for Pathology, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Henrik Fox
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Thorsten Laser
- Center for Congenital Heart Diseases, Heart and Diabetes Center NRW, 32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Ralph Knöll
- Karolinska Institute, University Hospital, Myocardial Genetic, 14157, Huddinge, Sweden
| | - Greta Marie Pohl
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Lech Paluszkiewicz
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Thomas Jakob
- Intensive Care and Emergency Medicine, Herford Hospital, Campus OWL, Ruhr-University Bochum, University Clinic for Anesthesiology, Bochum, Germany
- Present address: Clinic for Anesthesiology, Intensive Care Medicine, Emergency Medicine and Pain Medicine, Bielefeld Hospital, University Hospital Eastern Westphalia-Lippe, Bielefeld University, Bielefeld, Germany
| | - Bernd Bachmann-Mennenga
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Dietrich Henzler
- Intensive Care and Emergency Medicine, Herford Hospital, Campus OWL, Ruhr-University Bochum, University Clinic for Anesthesiology, Bochum, Germany
| | - Steffen Grautoff
- Emergency Department, Herford Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Gunter Veit
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Johannes Wesling Hospital Minden, MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology, University Hospital Tuebingen, D-72076, Tuebingen, Germany
| | - Erika Hori
- Institute for Pathology, Johannes Wesling Hospital Minden, MKK-Hospital, D-32429 Minden, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Udo Kellner
- Institute for Pathology, Johannes Wesling Hospital Minden, MKK-Hospital, D-32429 Minden, Campus OWL, Ruhr-University Bochum, Bochum, Germany
| | - Bernd Karger
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Stefanie Schlepper
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Heidi Pfeiffer
- Institute for Forensic Medicine, University Hospital, Wilhelms-University Muenster, Muenster, Germany
| | - Jan Gummert
- Clinic for Thoracic and Cardiovascular Surgery, Heart- and Diabetes Center NRW, D-32545 Bad Oeynhausen, University Hospital of the Ruhr-University Bochum, Bochum, Germany
| | - Anna Gärtner
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
| | - Jens Tiesmeier
- Erich and Hanna Klessmann-Institute for Cardiovascular Research and Development, Heart- and Diabetes Center NRW, University Hospital of the Ruhr-University Bochum, Georgstr. 11, D-32545, Bad Oeynhausen, Germany
- Institute for Anesthesiology, Intensive Care- and Emergency Medicine, Luebbecke MKK-Hospital, Campus OWL, Ruhr-University Bochum, Bochum, Germany
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12
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Keenum I, Player R, Kralj J, Servetas S, Sussman MD, Russell JA, Stone J, Chandrapati S, Sozhamannan S. Amplicon Sequencing Minimal Information (ASqMI): Quality and Reporting Guidelines for Actionable Calls in Biodefense Applications. J AOAC Int 2023; 106:1424-1430. [PMID: 37067472 PMCID: PMC10472743 DOI: 10.1093/jaoacint/qsad047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/30/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Accurate, high-confidence data is critical for assessing potential biothreat incidents. In a biothreat event, false-negative and -positive results have serious consequences. Worst case scenarios can result in unnecessary shutdowns or fatalities at an exorbitant monetary and psychological cost, respectively. Quantitative PCR assays for agents of interest have been successfully used for routine biosurveillance. Recently, there has been increased impetus for adoption of amplicon sequencing (AS) for biosurveillance because it enables discrimination of true positives from near-neighbor false positives, as well as broad, simultaneous detection of many targets in many pathogens in a high-throughput scheme. However, the high sensitivity of AS can lead to false positives. Appropriate controls and workflow reporting can help address these challenges. OBJECTIVES Data reporting standards are critical to data trustworthiness. The standards presented herein aim to provide a framework for method quality assessment in biodetection. METHODS We present a set of standards, Amplicon Sequencing Minimal Information (ASqMI), developed under the auspices of the AOAC INTERNATIONAL Stakeholder Program on Agent Detection Assays for making actionable calls in biosurveillance applications. In addition to the first minimum information guidelines for AS, we provide a controls checklist and scoring scheme to assure AS run quality and assess potential sample contamination. RESULTS Adoption of the ASqMI guidelines will improve data quality, help track workflow performance, and ultimately provide decision makers confidence to trust the results of this new and powerful technology. CONCLUSION AS workflows can provide robust, confident calls for biodetection; however, due diligence in reporting and controls are needed. The ASqMI guideline is the first AS minimum reporting guidance document that also provides the means for end users to evaluate their workflows to improve confidence. HIGHLIGHTS Standardized reporting guidance for actionable calls is critical to ensuring trustworthy data.
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Affiliation(s)
- Ishi Keenum
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Robert Player
- The Johns Hopkins University, Applied Physics Laboratory, Laurel, MD 20723, USA
- Datirium, LLC, Cincinnati, OH 45526, USA
| | - Jason Kralj
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Stephanie Servetas
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Complex Microbial Systems Group, Gaithersburg, MD 20899, USA
| | - Michael D Sussman
- US Department of Agriculture, Agricultural Analytics Division, Livestock and Poultry Programs, Agricultural Marketing Service, Washington, DC 20250 USA
| | | | | | | | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA
- Joint Research and Development, Inc., Stafford, VA 22556, USA
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13
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Kabbani D, Akika R, Wahid A, Daly AK, Cascorbi I, Zgheib NK. Pharmacogenomics in practice: a review and implementation guide. Front Pharmacol 2023; 14:1189976. [PMID: 37274118 PMCID: PMC10233068 DOI: 10.3389/fphar.2023.1189976] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Considerable efforts have been exerted to implement Pharmacogenomics (PGx), the study of interindividual variations in DNA sequence related to drug response, into routine clinical practice. In this article, we first briefly describe PGx and its role in improving treatment outcomes. We then propose an approach to initiate clinical PGx in the hospital setting. One should first evaluate the available PGx evidence, review the most relevant drugs, and narrow down to the most actionable drug-gene pairs and related variant alleles. This is done based on data curated and evaluated by experts such as the pharmacogenomics knowledge implementation (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC), as well as drug regulatory authorities such as the US Food and Drug Administration (FDA) and European Medicinal Agency (EMA). The next step is to differentiate reactive point of care from preemptive testing and decide on the genotyping strategy being a candidate or panel testing, each of which has its pros and cons, then work out the best way to interpret and report PGx test results with the option of integration into electronic health records and clinical decision support systems. After test authorization or testing requirements by the government or drug regulators, putting the plan into action involves several stakeholders, with the hospital leadership supporting the process and communicating with payers, the pharmacy and therapeutics committee leading the process in collaboration with the hospital laboratory and information technology department, and healthcare providers (HCPs) ordering the test, understanding the results, making the appropriate therapeutic decisions, and explaining them to the patient. We conclude by recommending some strategies to further advance the implementation of PGx in practice, such as the need to educate HCPs and patients, and to push for more tests' reimbursement. We also guide the reader to available PGx resources and examples of PGx implementation programs and initiatives.
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Affiliation(s)
- Danya Kabbani
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Reem Akika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ahmed Wahid
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ann K. Daly
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ingolf Cascorbi
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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14
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Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet 2023; 24:235-250. [PMID: 36476810 PMCID: PMC10204111 DOI: 10.1038/s41576-022-00551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell variation within a cell population. Traditionally, the primary bottleneck in genomic analysis pipelines has been the sequencing itself, which has been much more expensive than the computational analyses that follow. However, an important consequence of the continued drive to expand the throughput of sequencing platforms at lower cost is that often the analytical pipelines are struggling to keep up with the sheer amount of raw data produced. Computational cost and efficiency have thus become of ever increasing importance. Recent methodological advances, such as data sketching, accelerators and domain-specific libraries/languages, promise to address these modern computational challenges. However, despite being more efficient, these innovations come with a new set of trade-offs, both expected, such as accuracy versus memory and expense versus time, and more subtle, including the human expertise needed to use non-standard programming interfaces and set up complex infrastructure. In this Review, we discuss how to navigate these new methodological advances and their trade-offs.
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Affiliation(s)
- Bonnie Berger
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yun William Yu
- Department of Computer and Mathematical Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Tri-Campus Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
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15
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Yanagita E, Yamada H, Kobayashi T, Aimono E, Nakamura K, Hirasawa A, Nishihara H. The DNA integrity number and concentration are useful parameters for successful comprehensive genomic profiling test for cancer using formalin‐fixed paraffin embedded tissue. Pathol Int 2023; 73:198-206. [PMID: 36971494 DOI: 10.1111/pin.13318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023]
Abstract
The acquisition of high-quality biospecimens and the appropriate handling of these materials are indispensable for successful clinical sequencing. We developed a cancer clinical sequencing system targeting 160 cancer genes: PleSSision-Rapid. Through the PleSSision-Rapid system, we have analyzed DNA quality evaluated by DIN (DNA integrity number) with 1329 formalin-fixed paraffin embedded (FFPE) samples including 477 prospectively collected tissues for genomic test (P) and 852 archival samples after routine pathological diagnosis (A1/A2). As a result, the samples with more than DIN 2.1 was 92.0% (439/477) in prospectively collected sample (P), while it was 85.6% (332/388) and 76.7% (356/464) in two types of archival samples (A1/A2). We performed the PleSSision-Rapid sequence using the samples with over DIN 2.1 and DNA concentration >10 ng/μL with which we were able to construct a DNA library, and the probability of sequence success was almost equivalent during all types of specimen processing, at 90.7% (398/439) in (P), 92.5% (307/332) in (A1) and 90.2% (321/356) in (A2), respectively. Our result indicated the clinical benefit to prepare the prospective collection of FFPE materials for indisputable clinical sequence, and that DIN ≥ 2.1 would be a solid parameter for sample preparation of comprehensive genomic profiling tests.
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16
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Lang O, Srivastava D, Pugh BF, Lai WK. GenoPipe: identifying the genotype of origin within (epi)genomic datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532660. [PMID: 36993164 PMCID: PMC10055126 DOI: 10.1101/2023.03.14.532660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e., cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g., indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism’s genome (i.e., epitope insertions, gene deletions, and SNPs).
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17
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Dholariya S, Singh RD, Sonagra A, Yadav D, Vajaria BN, Parchwani D. Integrating Cutting-Edge Methods to Oral Cancer Screening, Analysis, and Prognosis. Crit Rev Oncog 2023; 28:11-44. [PMID: 37830214 DOI: 10.1615/critrevoncog.2023047772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Oral cancer (OC) has become a significant barrier to health worldwide due to its high morbidity and mortality rates. OC is among the most prevalent types of cancer that affect the head and neck region, and the overall survival rate at 5 years is still around 50%. Moreover, it is a multifactorial malignancy instigated by genetic and epigenetic variabilities, and molecular heterogeneity makes it a complex malignancy. Oral potentially malignant disorders (OPMDs) are often the first warning signs of OC, although it is challenging to predict which cases will develop into malignancies. Visual oral examination and histological examination are still the standard initial steps in diagnosing oral lesions; however, these approaches have limitations that might lead to late diagnosis of OC or missed diagnosis of OPMDs in high-risk individuals. The objective of this review is to present a comprehensive overview of the currently used novel techniques viz., liquid biopsy, next-generation sequencing (NGS), microarray, nanotechnology, lab-on-a-chip (LOC) or microfluidics, and artificial intelligence (AI) for the clinical diagnostics and management of this malignancy. The potential of these novel techniques in expanding OC diagnostics and clinical management is also reviewed.
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Affiliation(s)
- Sagar Dholariya
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Ragini D Singh
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Amit Sonagra
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | | | | | - Deepak Parchwani
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
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18
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De Simone C. The authenticity of probiotic foods and dietary supplements: facts and reflections from a court case. CYTA - JOURNAL OF FOOD 2022. [DOI: 10.1080/19476337.2022.2141344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Claudio De Simone
- Infectious Diseases, University of L’Aquila (Italy), L’Aquila, Italy
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19
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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20
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Muñoz-García A, Arbeli Z, Boyacá-Vásquez V, Vanegas J. Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics. MARINE POLLUTION BULLETIN 2022; 184:114204. [PMID: 36219973 DOI: 10.1016/j.marpolbul.2022.114204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.
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Affiliation(s)
- Andrea Muñoz-García
- Pontificia Universidad Javeriana, Bogotá, Colombia; Universidad Antonio Nariño, Sede Circunvalar, Bogotá, Colombia
| | - Ziv Arbeli
- Pontificia Universidad Javeriana, Bogotá, Colombia
| | | | - Javier Vanegas
- Universidad Antonio Nariño, Sede Circunvalar, Bogotá, Colombia.
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21
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Oldoni E, Saunders G, Bietrix F, Garcia Bermejo ML, Niehues A, ’t Hoen PAC, Nordlund J, Hajduch M, Scherer A, Kivinen K, Pitkänen E, Mäkela TP, Gut I, Scollen S, Kozera Ł, Esteller M, Shi L, Ussi A, Andreu AL, van Gool AJ. Tackling the translational challenges of multi-omics research in the realm of European personalised medicine: A workshop report. Front Mol Biosci 2022; 9:974799. [PMID: 36310597 PMCID: PMC9608444 DOI: 10.3389/fmolb.2022.974799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Personalised medicine (PM) presents a great opportunity to improve the future of individualised healthcare. Recent advances in -omics technologies have led to unprecedented efforts characterising the biology and molecular mechanisms that underlie the development and progression of a wide array of complex human diseases, supporting further development of PM. This article reflects the outcome of the 2021 EATRIS-Plus Multi-omics Stakeholder Group workshop organised to 1) outline a global overview of common promises and challenges that key European stakeholders are facing in the field of multi-omics research, 2) assess the potential of new technologies, such as artificial intelligence (AI), and 3) establish an initial dialogue between key initiatives in this space. Our focus is on the alignment of agendas of European initiatives in multi-omics research and the centrality of patients in designing solutions that have the potential to advance PM in long-term healthcare strategies.
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Affiliation(s)
- Emanuela Oldoni
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Gary Saunders
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
- *Correspondence: Gary Saunders, ; Emanuela Oldoni,
| | - Florence Bietrix
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Maria Laura Garcia Bermejo
- Biomarkers and Therapeutic Targets Group, Ramon and Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Anna Niehues
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Peter A. C. ’t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Precision Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Olomouc, Czechia
| | - Andreas Scherer
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Katja Kivinen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Tomi Pekka Mäkela
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | - Łukasz Kozera
- Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC), Graz, Austria
| | - Manel Esteller
- Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Anton Ussi
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Antonio L. Andreu
- European Infrastructure for Translational Medicine (EATRIS), Amsterdam, Netherlands
| | - Alain J. van Gool
- Translational Metabolomic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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22
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Pervez MT, Hasnain MJU, Abbas SH, Moustafa MF, Aslam N, Shah SSM. A Comprehensive Review of Performance of Next-Generation Sequencing Platforms. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3457806. [PMID: 36212714 PMCID: PMC9537002 DOI: 10.1155/2022/3457806] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Background Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results The proposed study, based on previous studies and manufacturers' descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.
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Affiliation(s)
- Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mirza Jawad ul Hasnain
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Syed Hassan Abbas
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Pakistan
| | - Mahmoud F. Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Naeem Aslam
- Department of Computer Science, NFCIET, Khanewal Road, Multan, Pakistan
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Kim MJ, Lee S, Yun H, Cho SI, Kim B, Lee JS, Chae JH, Sun C, Park SS, Seong MW. Consistent count region-copy number variation (CCR-CNV): an expandable and robust tool for clinical diagnosis of copy number variation at the exon level using next-generation sequencing data. Genet Med 2021; 24:663-672. [PMID: 34906491 DOI: 10.1016/j.gim.2021.10.025] [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: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Despite the importance of exonic copy number variations (CNVs) in human genetic diseases, reliable next-generation sequencing-based methods for detecting them are unavailable. We developed an expandable and robust exonic CNV detection tool called consistent count region (CCR)-CNV. METHODS In total, about 1000 samples of the truth set were used for validating CCR-CNV. We compared CCR-CNV performance with 2 well-known CNV tools. Finally, to overcome the limitations of CCR-CNV, we devised a combined approach. RESULTS The mean sensitivity and specificity of CCR-CNV alone were above 95%, which was superior to that of other CNV tools, such as DECoN and Atlas-CNV. However, low covered region and positive predictive value and high false discovery rate act as obstacles to its use in clinical settings. The combined approach showed much improved performance than CCR-CNV alone. CONCLUSION In this study, we present a novel diagnostic tool that allows the identification of exonic CNVs with high confidence using various reagents and clinical next-generation sequencing platforms. We validated this method using the largest multiple ligation-dependent probe amplification-confirmed data set, including sufficient copy normal control data. The approach, combined with existing CNV tools, allows the implementation of CCR-CNV in clinical settings.
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Affiliation(s)
- Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Kim
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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24
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Scherz V, Greub G, Bertelli C. Building up a clinical microbiota profiling: a quality framework proposal. Crit Rev Microbiol 2021; 48:356-375. [PMID: 34752719 DOI: 10.1080/1040841x.2021.1975642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Extensive characterization of the human microbiota has revealed promising relationships between microbial composition and health or disease, generating interest in biomarkers derived from microbiota profiling. However, microbiota complexity and technical challenges strongly influencing the results limit the generalization of microbiota profiling and question its clinical utility. In addition, no quality management scheme has been adapted to the specificities of microbiota profiling, notably due to the heterogeneity in methods and results. In this review, we discuss possible adaptation of classical quality management tools routinely used in diagnostic laboratories to microbiota profiling and propose a specific framework. Multiple quality controls are needed to cover all steps, from sampling to data processing. Standard operating procedures, primarily developed for wet lab analyses, must be adapted to the use of bioinformatic tools. Finally, requirements for test validation and proficiency testing must take into account expected discrepancies in results due to the heterogeneity of the processes. The proposed quality management framework should support the implementation of routine microbiota profiling by clinical laboratories to support patient care. Furthermore, its use in research laboratories would improve publication reproducibility as well as transferability of methods and results to routine practice.
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Affiliation(s)
- Valentin Scherz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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25
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Liu B, Lai J, Wu S, Jiang J, Kuang W. Endophytic bacterial community diversity in two citrus cultivars with different citrus canker disease resistance. Arch Microbiol 2021; 203:5453-5462. [PMID: 34406444 DOI: 10.1007/s00203-021-02530-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/26/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
The selective infection of Xanthomonas citri pv. citri (Xcc) to citrus cultivars is universally known, but the relationship between endophytic bacteria and the resistance of host variety to canker disease remains unclear. In this study, endophytic bacterial populations of two citrus cultivars-the resistant satsuma mandarin and the susceptible Newhall navel orange-were analyzed through high-throughput sequencing. The results showed that endophytic bacterial community of satsuma mandarin was more abundant than that of Newhall navel orange. In addition, bacterial abundance was the highest in the spring samples, followed by that in summer and winter samples, in both the varieties. In all samples, the predominant phyla were Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes; the major genera were Bacillus and Stenotrophomonas, and the main species was Bacillus subtilis. According to the analysis of the predominant bacteria in the two citrus cultivars, B. subtilis with potential antagonistic characteristics against Xcc existed universally in all samples. However, the susceptible Newhall navel oranges were abundant in Bacillus subtilis and had a relatively large number of canker-causing cooperative bacteria such as Stenotrophomonas. The results suggested that endophytic bacterial community of the two citrus cultivars had some differences based on the season or plant tissue, and these differences were mainly in the quantity of bacteria, affecting citrus canker disease occurrence. In conclusion, the differences in endophytic bacteria on citrus cultivars might be related to host resistance or susceptibility to citrus canker disease.
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Affiliation(s)
- Bing Liu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
| | - Jiahao Lai
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Simeng Wu
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Junxi Jiang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Weigang Kuang
- College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China.
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26
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Guenay-Greunke Y, Bohan DA, Traugott M, Wallinger C. Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology. Sci Rep 2021; 11:19510. [PMID: 34593851 PMCID: PMC8484467 DOI: 10.1038/s41598-021-98018-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/30/2021] [Indexed: 01/23/2023] Open
Abstract
High-throughput sequencing platforms are increasingly being used for targeted amplicon sequencing because they enable cost-effective sequencing of large sample sets. For meaningful interpretation of targeted amplicon sequencing data and comparison between studies, it is critical that bioinformatic analyses do not introduce artefacts and rely on detailed protocols to ensure that all methods are properly performed and documented. The analysis of large sample sets and the use of predefined indexes create challenges, such as adjusting the sequencing depth across samples and taking sequencing errors or index hopping into account. However, the potential biases these factors introduce to high-throughput amplicon sequencing data sets and how they may be overcome have rarely been addressed. On the example of a nested metabarcoding analysis of 1920 carabid beetle regurgitates to assess plant feeding, we investigated: (i) the variation in sequencing depth of individually tagged samples and the effect of library preparation on the data output; (ii) the influence of sequencing errors within index regions and its consequences for demultiplexing; and (iii) the effect of index hopping. Our results demonstrate that despite library quantification, large variation in read counts and sequencing depth occurred among samples and that the sequencing error rate in bioinformatic software is essential for accurate adapter/primer trimming and demultiplexing. Moreover, setting an index hopping threshold to avoid incorrect assignment of samples is highly recommended.
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Affiliation(s)
- Yasemin Guenay-Greunke
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria. .,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria.
| | - David A Bohan
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Michael Traugott
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Corinna Wallinger
- Applied Animal Ecology, Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.,Institute of Interdisciplinary Mountain Research, IGF, Austrian Academy of Sciences, Technikerstraße 21a, 6020, Innsbruck, Austria
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Sprang M, Krüger M, Andrade-Navarro MA, Fontaine JF. Statistical guidelines for quality control of next-generation sequencing techniques. Life Sci Alliance 2021; 4:4/11/e202101113. [PMID: 34462322 PMCID: PMC8408346 DOI: 10.26508/lsa.202101113] [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: 05/05/2021] [Revised: 08/17/2021] [Accepted: 08/10/2021] [Indexed: 12/24/2022] Open
Abstract
More and more next-generation sequencing (NGS) data are made available every day. However, the quality of this data is not always guaranteed. Available quality control tools require profound knowledge to correctly interpret the multiplicity of quality features. Moreover, it is usually difficult to know if quality features are relevant in all experimental conditions. Therefore, the NGS community would highly benefit from condition-specific data-driven guidelines derived from many publicly available experiments, which reflect routinely generated NGS data. In this work, we have characterized well-known quality guidelines and related features in big datasets and concluded that they are too limited for assessing the quality of a given NGS file accurately. Therefore, we present new data-driven guidelines derived from the statistical analysis of many public datasets using quality features calculated by common bioinformatics tools. Thanks to this approach, we confirm the high relevance of genome mapping statistics to assess the quality of the data, and we demonstrate the limited scope of some quality features that are not relevant in all conditions. Our guidelines are available at https://cbdm.uni-mainz.de/ngs-guidelines.
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Affiliation(s)
- Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Mainz, Germany
| | - Matteo Krüger
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Mainz, Germany
| | | | - Jean-Fred Fontaine
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Mainz, Germany
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28
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Bartho LA, O'Callaghan JL, Fisher JJ, Cuffe JSM, Kaitu'u-Lino TJ, Hannan NJ, Clifton VL, Perkins AV. Analysis of mitochondrial regulatory transcripts in publicly available datasets with validation in placentae from pre-term, post-term and fetal growth restriction pregnancies. Placenta 2021; 112:162-171. [PMID: 34364121 DOI: 10.1016/j.placenta.2021.07.303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The human placenta has a defined lifespan and placental aging is a key feature as pregnancy progresses. Placental aging and mitochondrial dysfunction are known to play a key role in pregnancy pathophysiology. Premature aging of the placenta has also been linked with placental dysfunction resulting in poor fetal development and premature birth. METHODS The expression of key mitochondrial-related genes were analysed in a series of publicly available databases then expression changes were validated in placental samples collected from term, pre-term, post-term pregnancies and pregnancies complicated by fetal growth restriction (FGR). Gene and protein expression levels of MFN1, MFN2, TFAM, TOMM20, OPA3 and SIRT4 were measured in placental tissues via qPCR and western blotting. RESULTS Initial analysis found that key mitochondrial transcripts related to biogenesis, bioenergetics and mitophagy clustered by pregnancy trimester. A refined list of 13 mitochondrial-related genes were investigated in additional external datasets of pregnancy complications. In the new cohort, protein expression of MFN1 was decreased in FGR and MFN2 is decreased in post-term placenta. Analysis of placental tissues revealed that TOMM20 gene and protein expression was altered in FGR and post-term placenta. DISCUSSION MFN1 and MFN2 play a major role in mitochondrial dynamics, and alterations in these markers have been highlighted in early unexplained miscarriage. TOMM20 is an importer protein that plays a major role in mitophagy and changes have also been identified in age-related diseases. Significant changes in MFN1, MFN2 and TOMM20 indicate that mitochondrial regulators play a critical role in placental aging and placental pathophysiology.
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Affiliation(s)
- Lucy A Bartho
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, Queensland, Australia
| | - Jessica L O'Callaghan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - Joshua J Fisher
- Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - James S M Cuffe
- School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Tu'uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, Dept of Obstetrics and Gynaecology University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Natalie J Hannan
- Translational Obstetrics Group, Dept of Obstetrics and Gynaecology University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Vicki L Clifton
- Pregnancy and Development Group, Mater Research, Translational Research Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Anthony V Perkins
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, Queensland, Australia.
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Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
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Addeo A, Friedlaender A, Banna GL, Weiss GJ. TMB or not TMB as a biomarker: That is the question. Crit Rev Oncol Hematol 2021; 163:103374. [PMID: 34087341 DOI: 10.1016/j.critrevonc.2021.103374] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/29/2021] [Indexed: 12/11/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have revolutionized the landscape of therapeutic options for many cancers. These treatments have demonstrated improved efficacy and often a more favourable toxicity profile compared to standard cytotoxic chemotherapy. There are considerable differences among responders, with some patients experiencing durable long-term disease control and even remission. Given this variability, determining a proper biomarker to select patients for ICI therapy has become increasingly important. The only biomarker proven to be predictive of overall survival benefit with ICI therapy is PD-L1 expression level measured by immunohistochemistry. Several attempts have been made to identify different predictive biomarkers. One of the most intriguing and divisive is tumor mutational burden (TMB). TMB represents the number of mutations per megabase (Mut/Mb) of DNA that were sequenced in a specific cancer. With a higher number of mutations detected, and consequentially an increase in the number neo-epitopes, then it is more likely that one or more of those neo-antigens could be immunogenic and trigger a T cell response. Initially, TMB was identified as a biomarker for ICIs in melanoma and subsequent studies suggested a possible clinical role for TMB in non-small cell lung cancer. The initial data were not confirmed in a prospective study assessing OS as the primary endpoint. Recently, the FDA has approved pembrolizumab in all cancers with a TMB > 10Mut/Mb[12] based on findings from the phase 2 KEYNOTE-158. Much criticism has emerged about this pan-cancer approval, in particular about the use of TMB as biomarker to select patients. Here we review the data about the importance and role of TMB as possible pan-cancer one-size-fits-all biomarker. We highlight the strengths and intrinsic limitations of such a complex biomarker and its adoption in the daily practice.
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Affiliation(s)
- Alfredo Addeo
- Oncology Department, University Hospital of Geneva, Switzerland.
| | - Alex Friedlaender
- Oncology Department, University Hospital of Geneva, Switzerland; Clinique Générale Beaulieu, Geneva, Switzerland
| | | | - Glen J Weiss
- MiRanostics Consulting, Oro Valley, AZ, United States
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Gregory CW. Building a Quality Management System in a Core Facility: A Genomics Core Case Study. J Biomol Tech 2021; 31:57-65. [PMID: 32655325 DOI: 10.7171/jbt.20-3102-004] [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] [Indexed: 11/20/2022]
Abstract
Core facilities are key resources supporting the academic research enterprise, providing access to innovative and essential technologies and expertise. Given the constraints placed on core facilities as recharge centers and the ever-changing research environment, an important competitive differentiator that can support rigorous and reproducible approaches in core labs is the implementation of a quality management system (QMS). This paper describes a systematic approach to building a QMS in a genomics core facility at the University of North Carolina School of Medicine. This model is based on principles of the International Organization for Standardization 9001 system with initiatives focused on process mapping, training (communication, customer service, performance management, development of standard operating procedures, and quality audits), root cause analysis, visual control boards, mock quality audits, and continuous improvement through metrics tracking and "voice of the customer" exercises. The goal of this paper is to share practical step-by-step recommendations and outcomes of this core facility QMS that are generally applicable to academic core facilities, regardless of technical focus. Application of these good laboratory practice principles will foster "competitiveness through compliance" and promote outstanding interdisciplinary research between academic cores and their nonacademic pharmaceutical and federal research partners. Additionally, implementation of the QMS qualified this core to apply for federally funded contracts, thereby diversifying its types of projects and sources of revenue.
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Affiliation(s)
- Christopher W Gregory
- Department of Genetics and Office of Research Technologies, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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Gaille M, Horn R. The ethics of genomic medicine: redefining values and norms in the UK and France. Eur J Hum Genet 2021; 29:780-788. [PMID: 33456054 PMCID: PMC8110530 DOI: 10.1038/s41431-020-00798-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
This paper presents a joint position of the UK-France Genomics and Ethics Network (UK-FR GENE), which has been set up to reflect on the ethical and social issues arising from the integration of genomics into routine clinical care in the UK and France. In 2018, the two countries announced enhanced cooperation between their national strategies, Genomics England and Plan France Médecine Génomique 2025, which offers a unique opportunity to study the impact of genomic medicine and relevant policies in different national contexts. The paper provides first insights into the two national strategies and the norms, values and principles at stake in each country. It discusses the impact of genomic medicine on established relationships and existing regulations, and examines its effects on solidarity and trust in public healthcare systems. Finally, it uses the social contract as an analytical lens to explore and redefine the balance between individual rights and collective duties in the context of genomic medicine. This paper leads to three key observations: (1) despite each country's strategy being at a different stage of implementation, the two countries face similar ethical issues; (2) each country tries to solve these issues by (re-)defining individual rights and collective duties in its own way; (3) the social contract presents a useful tool to analyse the ways the UK and France address the ethical challenges raised by genomics. This overview lays the groundwork for future in-depth comparison, and drive collaborative research, between the UK and France.
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Affiliation(s)
| | - Ruth Horn
- The Ethox Centre and Wellcome Centre for Ethics and Humanities, Nuffield Department of Population Health, University of Oxford, England, UK.
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Kolchanova S, Komissarov A, Kliver S, Mazo-Vargas A, Afanador Y, Velez-Valentín J, de la Rosa RV, Castro-Marquez S, Rivera-Colon I, Majeske AJ, Wolfsberger WW, Hains T, Corvelo A, Martinez-Cruzado JC, Glenn TC, Robinson O, Koepfli KP, Oleksyk TK. Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles. Genes (Basel) 2021; 12:608. [PMID: 33924228 PMCID: PMC8074781 DOI: 10.3390/genes12040608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 01/10/2023] Open
Abstract
Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.
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Affiliation(s)
- Sofiia Kolchanova
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Alexey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 191002 St. Petersburg, Russia;
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 664033 Novosibirsk, Russia;
| | - Anyi Mazo-Vargas
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Yashira Afanador
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Jafet Velez-Valentín
- Conservation Program of the Puerto Rican Parrot, U.S. Fish and Wildlife Service, Rio Grande 00745, Puerto Rico;
| | - Ricardo Valentín de la Rosa
- The Recovery Program of the Puerto Rican Parrot at the Rio Abajo State Forest, Departamento de Recursos Naturales y Ambientales de Puerto Rico, Arecibo 00613, Puerto Rico;
| | - Stephanie Castro-Marquez
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
| | - Israel Rivera-Colon
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Audrey J. Majeske
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
| | - Walter W. Wolfsberger
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
- Department of Biology, Uzhhorod National University, 88000 Uzhhorod, Ukraine
| | - Taylor Hains
- Terra Wildlife Genomics, Washington, DC 20009, USA;
- Environmental Science and Policy, Johns Hopkins University, Washington, DC 20036, USA
| | | | - Juan-Carlos Martinez-Cruzado
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
| | - Travis C. Glenn
- Department of Environmental Health, The University of Georgia, Athens, GA 30602, USA;
| | | | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199034 St. Petersburg, Russia;
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Taras K. Oleksyk
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez 00682, Puerto Rico; (S.K.); (A.M.-V.); (Y.A.); (S.C.-M.); (I.R.-C.); (A.J.M.); (W.W.W.); (J.-C.M.-C.)
- Department of Biological Sciences, Oakland University, Rochester, MI 48307, USA
- Department of Biology, Uzhhorod National University, 88000 Uzhhorod, Ukraine
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Angerilli V, Galuppini F, Pagni F, Fusco N, Malapelle U, Fassan M. The Role of the Pathologist in the Next-Generation Era of Tumor Molecular Characterization. Diagnostics (Basel) 2021; 11:339. [PMID: 33670699 PMCID: PMC7922586 DOI: 10.3390/diagnostics11020339] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Current pathology practice is being shaped by the increasing complexity of modern medicine, in particular of precision oncology, and major technological advances. In the "next-generation technologies era", the pathologist has become the person responsible for the integration and interpretation of morphologic and molecular information and for the delivery of critical answers to diagnostic, prognostic and predictive queries, acquiring a prominent position in the molecular tumor boards.
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Affiliation(s)
- Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Francesca Galuppini
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20122 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138 Naples, Italy;
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
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Kairov U, Molkenov A, Rakhimova S, Kozhamkulov U, Sharip A, Karabayev D, Daniyarov A, H Lee J, D Terwilliger J, Akilzhanova A, Zhumadilov Z. Whole-genome sequencing data of Kazakh individuals. BMC Res Notes 2021; 14:45. [PMID: 33541395 PMCID: PMC7863413 DOI: 10.1186/s13104-021-05464-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/28/2021] [Indexed: 11/22/2022] Open
Abstract
Objectives Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region. Data description Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.
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Affiliation(s)
- Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Aigul Sharip
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Daniyar Karabayev
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Asset Daniyarov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | | | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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Cree IA, Indave Ruiz BI, Zavadil J, McKay J, Olivier M, Kozlakidis Z, Lazar AJ, Hyde C, Holdenrieder S, Hastings R, Rajpoot N, de la Fouchardiere A, Rous B, Zenklusen JC, Normanno N, Schilsky RL. The International Collaboration for Cancer Classification and Research. Int J Cancer 2021; 148:560-571. [PMID: 32818326 PMCID: PMC7756795 DOI: 10.1002/ijc.33260] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3 R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3 R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges.
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Affiliation(s)
- Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | | | - Jiri Zavadil
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - James McKay
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Magali Olivier
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Zisis Kozlakidis
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular PathologyThe University of Texas, MD Anderson Cancer CenterHoustonTexasUSA
| | - Chris Hyde
- Exeter Test GroupCollege of Medicine and Health, University of ExeterExeterUK
| | | | - Ros Hastings
- GenQA (Genomics External Quality Assessment)Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation TrustOxfordUK
| | - Nasir Rajpoot
- Department of Computer ScienceUniversity of WarwickCoventryUK
- Alan Turing InstituteLondonUK
- Department of PathologyUniversity Hospitals Coventry & Warwickshire NHS TrustCoventryUK
| | | | - Brian Rous
- National Cancer Registration Service (Eastern Office), Public Health England, Victoria HouseCambridgeUK
| | - Jean Claude Zenklusen
- Center for Cancer GenomicsNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Nicola Normanno
- Cell Biology and Biotherapy UnitIstituto Nazionale Tumori—IRCCS—“Fondazione G. Pascale,” Via M. SemmolaNaplesItaly
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Fazzini F, Fendt L, Schönherr S, Forer L, Schöpf B, Streiter G, Losso JL, Kloss-Brandstätter A, Kronenberg F, Weissensteiner H. Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking. Int J Mol Sci 2021; 22:ijms22020935. [PMID: 33477827 PMCID: PMC7832847 DOI: 10.3390/ijms22020935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies. However, processes from DNA extraction and library construction to bioinformatic analysis include several varying tasks. Further, there is no validated recommendation for the comprehensive procedure. In this study, we examined potential pitfalls on the sequencing results based on two-person mtDNA mixtures. Therefore, we compared three DNA polymerases, six different variant callers in five mixtures between 50% and 0.5% variant allele frequencies generated with two different amplification protocols. In total, 48 samples were sequenced on Illumina MiSeq. Low-level variant calling at the 1% variant level and below was performed by comparing trimming and PCR duplicate removal as well as six different variant callers. The results indicate that sensitivity, specificity, and precision highly depend on the investigated polymerase but also vary based on the analysis tools. Our data highlight the advantage of prior standardization and validation of the individual laboratory setup with a DNA mixture model. Finally, we provide an artificial heteroplasmy benchmark dataset that can help improve somatic variant callers or pipelines, which may be of great interest for research related to cancer and aging.
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Affiliation(s)
- Federica Fazzini
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Liane Fendt
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Sebastian Schönherr
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Lukas Forer
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Bernd Schöpf
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Gertraud Streiter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Jamie Lee Losso
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Anita Kloss-Brandstätter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Correspondence: ; Tel.: +43-512-9003-70564
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Best practices for reporting individual identification using camera trap photographs. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01294] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Kuwata T, Wakabayashi M, Hatanaka Y, Morii E, Oda Y, Taguchi K, Noguchi M, Ishikawa Y, Nakajima T, Sekine S, Nomura S, Okamoto W, Fujii S, Yoshino T. Impact of DNA integrity on the success rate of tissue-based next-generation sequencing: Lessons from nationwide cancer genome screening project SCRUM-Japan GI-SCREEN. Pathol Int 2020; 70:932-942. [PMID: 33030786 PMCID: PMC7820973 DOI: 10.1111/pin.13029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
In the nationwide cancer genome screening project SCRUM-Japan GI-SCREEN, 2590 archival formalin-fixed paraffin-embedded (FFPE) tumor tissues from 19 institutions were analyzed with two tissue-based next-generation sequencing (NGS) panels at the Clinical Laboratory Improvement Amendments (CLIA)-certified College of American Pathologists (CAP)-accredited central laboratory. The Oncomine Cancer Research Panel (OCP; 143 genes) succeeded in producing validated results for only 68.3% of the samples (%OCP-success). CE-IVD (25 genes) succeeded in 45.9% of the OCP-failed samples, leading to an overall NGS success (%combined-success) rate as high as 82.9%. Among 2573 samples, the DNA-integrity (ΔCt )-high (ΔCt < 4.4, n = 1253) samples showed significantly higher %OCP- and %combined-success rates (90.2% and 97.4%, respectively) than the DNA-integrity-intermediate (4.4 < ΔCt < 6.3, n = 911; 68.9% and 88.7%) and DNA-integrity-low ones (ΔCt > 6.3 or polymerase chain reaction-failed, n = 409; 5.6% and 24.7%). Other factors associated with NGS success included the FFPE-sample storage period (<4 years), the specimen type (surgical) and the primary tumor site (colorectal). Multivariable analysis revealed DNA integrity as the factor with the strongest independent association with NGS success, although it was suggested that other institution-specific factors contribute to the discordance of inter-institutional NGS success rates. Our results emphasize the importance of DNA quality in FFPE samples for NGS tests and the impact of DNA integrity on quality monitoring of pathology specimens for achieving successful NGS.
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Affiliation(s)
- Takeshi Kuwata
- Department of Genetic Medicine and ServicesNational Cancer Center Hospital EastChibaJapan
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
| | - Masashi Wakabayashi
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Yutaka Hatanaka
- Research Division of Genome Companion DiagnosticsHokkaido University HospitalHokkaidoJapan
| | - Eiichi Morii
- Department of PathologyOsaka University Graduate School of MedicineOsakaJapan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Pathological Sciences, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kenichi Taguchi
- Department of PathologyNational Hospital Organization Kyushu Cancer CenterFukuokaJapan
| | - Masayuki Noguchi
- Department of Diagnostic Pathology, Faculty of MedicineUniversity of TsukubaIbarakiJapan
| | - Yuichi Ishikawa
- Department of Pathology, the Cancer InstituteJapanese Foundation for Cancer ResearchTokyoJapan
| | - Takashi Nakajima
- Division of Diagnostic PathologyShizuoka Cancer Center HospitalShizuokaJapan
| | - Shigeki Sekine
- Department of PathologyNational Cancer Center HospitalTokyoJapan
| | - Shogo Nomura
- Clinical Research Support OfficeNational Cancer Center Hospital EastChibaJapan
| | - Wataru Okamoto
- Translational Research Support SectionNational Cancer Center Hospital EastChibaJapan
- Cancer Treatment CenterHiroshima University HospitalHiroshimaJapan
| | - Satoshi Fujii
- Department of Pathology and Clinical LaboratoriesNational Cancer Center Hospital EastChibaJapan
- Department of Molecular PathologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Takayuki Yoshino
- Department of Gastrointestinal OncologyNational Cancer Center Hospital EastChibaJapan
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A novel prognostic two-gene signature for triple negative breast cancer. Mod Pathol 2020; 33:2208-2220. [PMID: 32404959 DOI: 10.1038/s41379-020-0563-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022]
Abstract
The absence of a robust risk stratification tool for triple negative breast cancer (TNBC) underlies imprecise and nonselective treatment of these patients with cytotoxic chemotherapy. This study aimed to interrogate transcriptomes of TNBC resected samples using next generation sequencing to identify novel biomarkers associated with disease outcomes. A subset of cases (n = 112) from a large, well-characterized cohort of primary TNBC (n = 333) were subjected to RNA-sequencing. Reads were aligned to the human reference genome (GRCH38.83) using the STAR aligner and gene expression quantified using HTSEQ. We identified genes associated with distant metastasis-free survival and breast cancer-specific survival by applying supervised artificial neural network analysis with gene selection to the RNA-sequencing data. The prognostic ability of these genes was validated using the Breast Cancer Gene-Expression Miner v4. 0 and Genotype 2 outcome datasets. Multivariate Cox regression analysis identified a prognostic gene signature that was independently associated with poor prognosis. Finally, we corroborated our results from the two-gene prognostic signature by their protein expression using immunohistochemistry. Artificial neural network identified two gene panels that strongly predicted distant metastasis-free survival and breast cancer-specific survival. Univariate Cox regression analysis of 21 genes common to both panels revealed that the expression level of eight genes was independently associated with poor prognosis (p < 0.05). Adjusting for clinicopathological factors including patient's age, grade, nodal stage, tumor size, and lymphovascular invasion using multivariate Cox regression analysis yielded a two-gene prognostic signature (ACSM4 and SPDYC), which was associated with poor prognosis (p < 0.05) independent of other prognostic variables. We validated the protein expression of these two genes, and it was significantly associated with patient outcome in both independent and combined manner (p < 0.05). Our study identifies a prognostic gene signature that can predict prognosis in TNBC patients and could potentially be used to guide the clinical management of TNBC patients.
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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Uelze L, Borowiak M, Bönn M, Brinks E, Deneke C, Hankeln T, Kleta S, Murr L, Stingl K, Szabo K, Tausch SH, Wöhlke A, Malorny B. German-Wide Interlaboratory Study Compares Consistency, Accuracy and Reproducibility of Whole-Genome Short Read Sequencing. Front Microbiol 2020; 11:573972. [PMID: 33013811 PMCID: PMC7516015 DOI: 10.3389/fmicb.2020.573972] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/14/2020] [Indexed: 12/05/2022] Open
Abstract
We compared the consistency, accuracy and reproducibility of next-generation short read sequencing between ten laboratories involved in food safety (research institutes, state laboratories, universities and companies) from Germany and Austria. Participants were asked to sequence six DNA samples of three bacterial species (Campylobacter jejuni, Listeria monocytogenes and Salmonella enterica) in duplicate, according to their routine in-house sequencing protocol. Four different types of Illumina sequencing platforms (MiSeq, NextSeq, iSeq, NovaSeq) and one Ion Torrent sequencing instrument (S5) were involved in the study. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. SNP and cgMLST calling were performed to assess the reproducibility of sequence data collected for individual samples. Overall, we found Illumina short read data to be more accurate (higher base calling accuracy, fewer miss-assemblies) and consistent (little variability between independent sequencing runs within a laboratory) than Ion Torrent sequence data, with little variation between the different Illumina instruments. Two laboratories with Illumina instruments submitted sequence data with lower quality, probably due to the use of a library preparation kit, which shows difficulty in sequencing low GC genome regions. Differences in data quality were more evident after assembling short reads into genome assemblies, with Ion Torrent assemblies featuring a great number of allele differences to Illumina assemblies. Clonality of samples was confirmed through SNP calling, which proved to be a more suitable method for an integrated data analysis of Illumina and Ion Torrent data sets in this study.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Markus Bönn
- Landesamt für Verbraucherschutz Sachsen-Anhalt (LAV), Halle (Saale), Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut (MRI), Kiel, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, AG Molecular Genetics and Genome Analysis, Johannes Gutenberg Universität Mainz, Mainz, Germany
| | - Sylvia Kleta
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Larissa Murr
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kathrin Szabo
- Department 5, Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Anne Wöhlke
- Food and Veterinary Institute, Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Braunschweig, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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44
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Molecular diagnostics for congenital heart disease: a narrative review of the current technologies and applications. JOURNAL OF BIO-X RESEARCH 2020. [DOI: 10.1097/jbr.0000000000000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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45
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Konnick EQ. The regulatory landscape of precision oncology laboratory medicine in the United States - Perspective on the past 5 years and considerations for future regulation. Pract Lab Med 2020; 21:e00172. [PMID: 32509953 PMCID: PMC7261109 DOI: 10.1016/j.plabm.2020.e00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 05/02/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023] Open
Abstract
The regulatory landscape for precision oncology in the United States is complicated, with multiple governmental regulatory agencies with different scopes of jurisdiction. Several regulatory proposals have been introduced since the Food and Drug Administration released a draft guidance to regulate laboratory-developed tests in 2014. Key aspects of the most recent proposals and discussion of central arguments related to the regulation of precision oncology laboratory tests provides insight to stakeholders for future discussions related to regulation of laboratory tests.
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46
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Asalone KC, Ryan KM, Yamadi M, Cohen AL, Farmer WG, George DJ, Joppert C, Kim K, Mughal MF, Said R, Toksoz-Exley M, Bisk E, Bracht JR. Regional sequence expansion or collapse in heterozygous genome assemblies. PLoS Comput Biol 2020; 16:e1008104. [PMID: 32735589 PMCID: PMC7423139 DOI: 10.1371/journal.pcbi.1008104] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 08/12/2020] [Accepted: 06/29/2020] [Indexed: 12/13/2022] Open
Abstract
High levels of heterozygosity present a unique genome assembly challenge and can adversely impact downstream analyses, yet is common in sequencing datasets obtained from non-model organisms. Here we show that by re-assembling a heterozygous dataset with variant parameters and different assembly algorithms, we are able to generate assemblies whose protein annotations are statistically enriched for specific gene ontology categories. While total assembly length was not significantly affected by assembly methodologies tested, the assemblies generated varied widely in fragmentation level and we show local assembly collapse or expansion underlying the enrichment or depletion of specific protein functional groups. We show that these statistically significant deviations in gene ontology groups can occur in seemingly high-quality assemblies, and result from difficult-to-detect local sequence expansion or contractions. Given the unpredictable interplay between assembly algorithm, parameter, and biological sequence data heterozygosity, we highlight the need for better measures of assembly quality than N50 value, including methods for assessing local expansion and collapse. In the genomic era, genomes must be reconstructed from fragments using computational methods, or assemblers. How do we know that a new genome assembly is correct? This is important because errors in assembly can lead to downstream problems in gene predictions and these inaccurate results can contaminate databases, affecting later comparative studies. A particular challenge occurs when a diploid organism inherits two highly divergent genome copies from its parents. While it is widely appreciated that this type of data is difficult for assemblers to handle properly, here we show that the process is prone to more errors than previously appreciated. Specifically, we document examples of regional expansion and collapse, affecting downstream gene prediction accuracy, but without changing the overall genome assembly size or other metrics of accuracy. Our results suggest that assembly evaluation methods should be altered to identify whether regional expansions and collapses are present in the genome assembly.
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Affiliation(s)
- Kathryn C. Asalone
- Biology Department, American University, Washington DC, United States of America
| | - Kara M. Ryan
- Biology Department, American University, Washington DC, United States of America
| | - Maryam Yamadi
- Biology Department, American University, Washington DC, United States of America
| | - Annastelle L. Cohen
- Biology Department, American University, Washington DC, United States of America
| | - William G. Farmer
- Biology Department, American University, Washington DC, United States of America
| | - Deborah J. George
- Biology Department, American University, Washington DC, United States of America
| | - Claudia Joppert
- Biology Department, American University, Washington DC, United States of America
| | - Kaitlyn Kim
- Biology Department, American University, Washington DC, United States of America
| | - Madeeha Froze Mughal
- Biology Department, American University, Washington DC, United States of America
| | - Rana Said
- Biology Department, American University, Washington DC, United States of America
| | - Metin Toksoz-Exley
- Mathematics and Statistics Department, American University, Washington DC, United States of America
| | - Evgeny Bisk
- Office of Information Technology, American University, Washington DC, United States of America
| | - John R. Bracht
- Biology Department, American University, Washington DC, United States of America
- * E-mail:
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Abstract
BACKGROUND During the past decade, breakthroughs in sequencing technology and computational biology have provided the basis for studies of the myriad ways in which microbial communities ("microbiota") in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and replicable profiling of the microbiota for use in diagnostic and therapeutic application. CONTENT This review provides an overview of approaches, challenges, and considerations for diagnostic applications borrowing from other areas of molecular diagnostics, including clinical metagenomics. Methodological considerations and evolving approaches for microbiota profiling from mitochondrially encoded 16S rRNA-based amplicon sequencing to metagenomics and metatranscriptomics are discussed. To improve replicability, at least the most vulnerable steps in testing workflows will need to be standardized and continuous efforts needed to define QC standards. Challenges such as purity of reagents and consumables, improvement of reference databases, and availability of diagnostic-grade data analysis solutions will require joint efforts across disciplines and with manufacturers. SUMMARY The body of literature supporting important links between the microbiota at different anatomic sites with human health and disease is expanding rapidly and therapeutic manipulation of the intestinal microbiota is becoming routine. The next decade will likely see implementation of microbiome diagnostics in diagnostic laboratories to fully capitalize on technological and scientific advances and apply them in routine medical practice.
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Affiliation(s)
- Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT.,IDbyDNA Inc., San Francisco, CA
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48
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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49
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Fujii T, Uchiyama T, Matsuoka M, Myojin T, Sugimoto S, Nitta Y, Okabe F, Sugimoto A, Sekita-Hatakeyama Y, Morita K, Itami H, Hatakeyama K, Ohbayashi C. Evaluation of DNA and RNA quality from archival formalin-fixed paraffin-embedded tissue for next-generation sequencing - Retrospective study in Japanese single institution. Pathol Int 2020; 70:602-611. [PMID: 32542983 DOI: 10.1111/pin.12969] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/21/2022]
Abstract
Genetic analysis on formalin-fixed paraffin-embedded (FFPE) tissue specimens has become a mainstream method, from conventional direct sequencing to comprehensive analysis using next-generation sequencing (NGS). In this study, we evaluated the quality of DNA and RNA extracted from FFPE sections, derived from surgical specimens of different tumor types. Electrophoresis was performed using a 4200 TapeStation to evaluate DNA and RNA fragmentation. DNA Ct values were higher and significantly increased over a period of 4 years compared with those from cell lines or frozen tissues. The RNA integrity number equivalent (RIN) ranged from 1 to 4.1 and DV200 ranged from 7.3 to 81%. Twelve of the 108 cases were analyzed by NGS using the AmpliSeq Cancer HotSpot Panel v2 on a Miniseq system. A sufficient number of reads and coverage were obtained in all cases. Our results revealed that NGS analysis was sufficient for FFPE-derived DNA within 4 years of preservation. Conversely, approximately 20% of the RNA derived from FFPE within 4 years from the collection could be inappropriate for gene analysis based on RIN and DV200. It was suggested that FFPE would be adequate for genetic analysis, although it is desirable to store frozen specimens for the tumor tissues to be subjected to genetic analysis.
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Affiliation(s)
- Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tomoko Uchiyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Minami Matsuoka
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tomoya Myojin
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Sumire Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Yuji Nitta
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Fumi Okabe
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Aya Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Yoko Sekita-Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Kohei Morita
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Hiroe Itami
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Kinta Hatakeyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
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50
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Quality Control of Next-Generation Sequencing-Based HIV-1 Drug Resistance Data in Clinical Laboratory Information Systems Framework. Viruses 2020; 12:v12060645. [PMID: 32545906 PMCID: PMC7354600 DOI: 10.3390/v12060645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/29/2020] [Accepted: 06/11/2020] [Indexed: 01/24/2023] Open
Abstract
Next-generation sequencing (NGS) in HIV drug resistance (HIVDR) testing has the potential to improve both clinical and public health settings, however it challenges the normal operations of quality management systems to be more flexible due to its complexity, massive data generation, and rapidly evolving protocols. While guidelines for quality management in NGS data have previously been outlined, little guidance has been implemented for NGS-based HIVDR testing. This document summarizes quality control procedures for NGS-based HIVDR testing laboratories using a laboratory information systems (LIS) framework. Here, we focus in particular on the quality control measures applied on the final sequencing product aligned with the recommendations from the World Health Organization HIV Drug Resistance Laboratory Network.
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