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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Qiao Y, Cheng T, Miao Z, Cui Y, Tu J. Recent Innovations and Technical Advances in High-Throughput Parallel Single-Cell Whole-Genome Sequencing Methods. SMALL METHODS 2024:e2400789. [PMID: 38979872 DOI: 10.1002/smtd.202400789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Indexed: 07/10/2024]
Abstract
Single-cell whole-genome sequencing (scWGS) detects cell heterogeneity at the aspect of genomic variations, which are inheritable and play an important role in life processes such as aging and cancer progression. The recent explosive development of high-throughput single-cell sequencing methods has enabled high-performance heterogeneity detection through a vast number of novel strategies. Despite the limitation on total cost, technical advances in high-throughput single-cell whole-genome sequencing methods are made for higher genome coverage, parallel throughput, and level of integration. This review highlights the technical advancements in high-throughput scWGS in the aspects of strategies design, data efficiency, parallel handling platforms, and their applications on human genome. The experimental innovations, remaining challenges, and perspectives are summarized and discussed.
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Affiliation(s)
- Yi Qiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tianguang Cheng
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Zikun Miao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yue Cui
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jing Tu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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Sashittal P, Chen V, Pasarkar A, Raphael BJ. Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. Bioinformatics 2024; 40:i218-i227. [PMID: 38940122 PMCID: PMC11211840 DOI: 10.1093/bioinformatics/btae231] [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] [Indexed: 06/29/2024] Open
Abstract
MOTIVATION Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model "heteroplasmy," which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree. RESULTS We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods. AVAILABILITY AND IMPLEMENTATION https://github.com/raphael-group/MERLIN.
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Affiliation(s)
- Palash Sashittal
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States
| | - Viola Chen
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States
| | - Amey Pasarkar
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ 08540, United States
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Ding Y, Peng YY, Li S, Tang C, Gao J, Wang HY, Long ZY, Lu XM, Wang YT. Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases. Cell Biochem Biophys 2023:10.1007/s12013-023-01207-3. [PMID: 38133792 DOI: 10.1007/s12013-023-01207-3] [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: 08/21/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The mammalian central nervous system consists of a large number of cells, which contain not only different types of neurons, but also a large number of glial cells, such as astrocytes, oligodendrocytes, and microglia. These cells are capable of performing highly refined electrophysiological activities and providing the brain with functions such as nutritional support, information transmission and pathogen defense. The diversity of cell types and individual differences between cells have brought inspiration to the study of the mechanism of central nervous system diseases. In order to explore the role of different cells, a new technology, single-cell sequencing technology has emerged to perform specific analysis of high-throughput cell populations, and has been continuously developed. Single-cell sequencing technology can accurately analyze single-cell expression in mixed-cell populations and collect cells from different spatial locations, time stages and types. By using single-cell sequencing technology to compare gene expression profiles of normal and diseased cells, it is possible to discover cell subsets associated with specific diseases and their associated genes. Therefore, scientists can understand the development process, related functions and disease state of the nervous system from an unprecedented depth. In conclusion, single-cell sequencing technology provides a powerful technology for the discovery of novel therapeutic targets for central nervous system diseases.
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Affiliation(s)
- Yang Ding
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yu-Yuan Peng
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Sen Li
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Can Tang
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jie Gao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Yong-Tang Wang
- State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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Lynch C, Armstrong E, Charitou M, Gordon T, Griffin D. Investigation of the risk of paternal cell contamination in PGT and the necessity of intracytoplasmic sperm injection. HUM FERTIL 2023; 26:958-963. [PMID: 35535579 DOI: 10.1080/14647273.2022.2026498] [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: 08/31/2020] [Accepted: 05/05/2021] [Indexed: 11/04/2022]
Abstract
ICSI is widely recommended for patients undergoing preimplantation genetic testing (PGT), but are sperm a potential source of paternal cell contamination in PGT? Semen samples were obtained from five normozoospermic men consenting to research. From each sample 1, 2, 4, 8 and 10 sperm were collected in PCR tubes and whole genome amplification according to PGT-A and PGT-SR processing protocols was undertaken. None of the 25 samples submitted (a total of 125 sperm) showed evidence of DNA amplification. Thus, paternal cell contamination resulting from using conventional in vitro fertilization (IVF) as the insemination method, carries a low risk of an adverse event or misdiagnosis in PGT-A. Due to the higher risk incurred with PGT-SR, clinics may wish to exercise increased caution and continue using ICSI, while PGT-M involves different processing protocols, presenting a different risk profile.
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Affiliation(s)
- Colleen Lynch
- CooperSugical Fertility Solutions, London, UK
- School of Biosciences, University of Kent, Canterbury, UK
| | | | | | - Tony Gordon
- CooperSugical Fertility Solutions, London, UK
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury, UK
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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7
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Amemiya K, Hirotsu Y, Mochizuki H, Higuchi R, Nakagomi T, Goto T, Oyama T, Kondo T, Omata M. Deep targeted sequencing of cytological tumor cells using whole genome amplification. Cancer Cytopathol 2023; 131:58-68. [PMID: 36219530 DOI: 10.1002/cncy.22653] [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: 07/06/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND Genomic profiling in lung cancer is essential for precision medicine. Cytological specimens provide an alternative to formalin-fixed paraffin-embedded (FFPE) samples for comprehensive genomic analysis. However, this approach remains challenging when a limited number of tumor cells are available. We applied whole genome amplification (WGA) to cytology specimens to overcome this limitation. METHODS Using a lung cancer panel targeting 58 genes, we performed next-generation sequencing of whole genome-amplified DNA extracted from cytological specimens containing 10-20 tumor cells (cyto-WGA) and DNA from corresponding FFPE tumor tissue. We compared sequencing data from cyto-WGA and FFPE samples to examine the detection accuracy of copy number variations and oncogenic and drug-matched variants. RESULTS The DNA quality and quantity from cyto-WGA were higher than those from FFPE samples (p < .0005 and p < .05, respectively). Sequencing metrics of cyto-WGA and FFPE tissues showed no difference in the number of mapped reads and mean coverage depth, but there were significant differences in the on-target rate (p < .05) and uniformity (p < .0005). Copy number variations in cyto-WGA samples (n = 211) were higher than in FFPE samples (n = 9) (p < .0001). Fourty nine oncogenic variants were detected in cyto-WGA and 39 in FFPE. Of these variants, 34 (63%) were present in both samples. In addition, all 16 drug-matched variants were detected in FFPE and cyto-WGA samples with 100% concordance. CONCLUSION Cyto-WGA can be a feasible and alternative method to detect oncogenic and drug-matched variants.
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Affiliation(s)
- Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,Department of Pathology, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Rumi Higuchi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Takahiro Nakagomi
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Taichiro Goto
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Toshio Oyama
- Pathology Division, Laboratory Department, Yamanashi Prefectural Central Hospital, Kofu, Yamanashi, Japan
| | - Tetsuo Kondo
- Department of Pathology, School of Medicine, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Yamanashi, Japan.,The University of Tokyo, Tokyo, Japan
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Chimera: The spoiler in multiple displacement amplification. Comput Struct Biotechnol J 2023; 21:1688-1696. [PMID: 36879882 PMCID: PMC9984789 DOI: 10.1016/j.csbj.2023.02.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/18/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Multiple displacement amplification (MDA) based on isothermal random priming and high fidelity phi29 DNA polymerase-mediated processive extension has revolutionized the field of whole genome amplification by enabling the amplification of minute amounts of DNA, such as from a single cell, generating vast amounts of DNA with high genome coverage. Despite its advantages, MDA has its own challenges, one of the grandest being the formation of chimeric sequences (chimeras), which presents in all MDA products and seriously disturbs the downstream analysis. In this review, we provide a comprehensive overview of current research on MDA chimeras. We first reviewed the mechanisms of chimera formation and chimera detection methods. We then systematically summarized the characteristics of chimeras, including overlap, chimeric distance, chimeric density, and chimeric rate, as found in independently published sequencing data. Finally, we reviewed the methods used to process chimeric sequences and their impacts on the improvement of data utilization efficiency. The information presented in this review will be useful for those interested in understanding the challenges with MDA and in improving its performance.
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Jing X, Gong Y, Xu T, Davison PA, MacGregor-Chatwin C, Hunter CN, Xu L, Meng Y, Ji Y, Ma B, Xu J, Huang WE. Revealing CO 2-Fixing SAR11 Bacteria in the Ocean by Raman-Based Single-Cell Metabolic Profiling and Genomics. BIODESIGN RESEARCH 2022; 2022:9782712. [PMID: 37850122 PMCID: PMC10521720 DOI: 10.34133/2022/9782712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/26/2022] [Indexed: 10/19/2023] Open
Abstract
The majority of marine microbes remain uncultured, which hinders the identification and mining of CO2-fixing genes, pathways, and chassis from the oceans. Here, we investigated CO2-fixing microbes in seawater from the euphotic zone of the Yellow Sea of China by detecting and tracking their 13C-bicarbonate (13C-HCO3-) intake via single-cell Raman spectra (SCRS) analysis. The target cells were then isolated by Raman-activated Gravity-driven Encapsulation (RAGE), and their genomes were amplified and sequenced at one-cell resolution. The single-cell metabolism, phenotype and genome are consistent. We identified a not-yet-cultured Pelagibacter spp., which actively assimilates 13C-HCO3-, and also possesses most of the genes encoding enzymes of the Calvin-Benson cycle for CO2 fixation, a complete gene set for a rhodopsin-based light-harvesting system, and the full genes necessary for carotenoid synthesis. The four proteorhodopsin (PR) genes identified in the Pelagibacter spp. were confirmed by heterologous expression in E. coli. These results suggest that hitherto uncultured Pelagibacter spp. uses light-powered metabolism to contribute to global carbon cycling.
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Affiliation(s)
- Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Paul A. Davison
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Craig MacGregor-Chatwin
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C. Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - La Xu
- Disease and Fishery Drugs Research Center, Marine Biology Institute of Shandong Province, Qingdao, ShandongChina
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Single-Cell Biotechnology, Ltd, Qingdao, ShandongChina
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Institute of Energy Research, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ Oxford, UK
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Next generation biosecurity: Towards genome based identification to prevent spread of agronomic pests and pathogens using nanopore sequencing. PLoS One 2022; 17:e0270897. [PMID: 35877652 PMCID: PMC9312391 DOI: 10.1371/journal.pone.0270897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/19/2022] [Indexed: 11/19/2022] Open
Abstract
The unintentional movement of agronomic pests and pathogens is steadily increasing due to the intensification of global trade. Being able to identify accurately and rapidly early stages of an invasion is critical for developing successful eradication or management strategies. For most invasive organisms, molecular diagnostics is today the method of choice for species identification. However, the currently implemented tools are often developed for certain taxa and need to be adapted for new species, making them ill-suited to cope with the current constant increase in new invasive species. To alleviate this impediment, we developed a fast and accurate sequencing tool allowing to modularly obtain genetic information at different taxonomical levels. Using whole genome amplification (WGA) followed by Oxford nanopore MinION sequencing, our workflow does not require any a priori knowledge on the investigated species and its classification. While mainly focusing on harmful plant pathogenic insects, we also demonstrate the suitability of our workflow for the molecular identification of bacteria (Erwinia amylovora and Escherichia coli), fungi (Cladosporium herbarum, Colletotrichum salicis, Neofabraea alba) and nematodes (Globodera rostochiensis). On average, the pairwise identity between the generated consensus sequences and best GenBank BLAST matches was 99.6 ± 0.6%. Additionally, assessing the generated insect genomic dataset, the potential power of the workflow to detect pesticide resistance genes, as well as arthropod-infecting viruses and endosymbiotic bacteria is demonstrated.
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11
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Jäger R. New Perspectives for Whole Genome Amplification in Forensic STR Analysis. Int J Mol Sci 2022; 23:ijms23137090. [PMID: 35806097 PMCID: PMC9267064 DOI: 10.3390/ijms23137090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Modern PCR-based analytical techniques have reached sensitivity levels that allow for obtaining complete forensic DNA profiles from even tiny traces containing genomic DNA amounts as small as 125 pg. Yet these techniques have reached their limits when it comes to the analysis of traces such as fingerprints or single cells. One suggestion to overcome these limits has been the usage of whole genome amplification (WGA) methods. These methods aim at increasing the copy number of genomic DNA and by this means generate more template DNA for subsequent analyses. Their application in forensic contexts has so far remained mostly an academic exercise, and results have not shown significant improvements and even have raised additional analytical problems. Until very recently, based on these disappointments, the forensic application of WGA seems to have largely been abandoned. In the meantime, however, novel improved methods are pointing towards a perspective for WGA in specific forensic applications. This review article tries to summarize current knowledge about WGA in forensics and suggests the forensic analysis of single-donor bioparticles and of single cells as promising applications.
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Affiliation(s)
- Richard Jäger
- Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany;
- Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
- Institute of Safety and Security Research, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
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12
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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13
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Whole Genome Amplification in Preimplantation Genetic Testing in the Era of Massively Parallel Sequencing. Int J Mol Sci 2022; 23:ijms23094819. [PMID: 35563216 PMCID: PMC9102663 DOI: 10.3390/ijms23094819] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/16/2022] Open
Abstract
Successful whole genome amplification (WGA) is a cornerstone of contemporary preimplantation genetic testing (PGT). Choosing the most suitable WGA technique for PGT can be particularly challenging because each WGA technique performs differently in combination with different downstream processing and detection methods. The aim of this review is to provide insight into the performance and drawbacks of DOP-PCR, MDA and MALBAC, as well as the hybrid WGA techniques most widely used in PGT. As the field of PGT is moving towards a wide adaptation of comprehensive massively parallel sequencing (MPS)-based approaches, we especially focus our review on MPS parameters and detection opportunities of WGA-amplified material, i.e., mappability of reads, uniformity of coverage and its influence on copy number variation analysis, and genomic coverage and its influence on single nucleotide variation calling. The ability of MDA-based WGA solutions to better cover the targeted genome and the ability of PCR-based solutions to provide better uniformity of coverage are highlighted. While numerous comprehensive PGT solutions exploiting different WGA types and adjusted bioinformatic pipelines to detect copy number and single nucleotide changes are available, the ones exploiting MDA appear more advantageous. The opportunity to fully analyse the targeted genome is influenced by the MPS parameters themselves rather than the solely chosen WGA.
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14
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Redavid I, Conserva MR, Anelli L, Zagaria A, Specchia G, Musto P, Albano F. Single-Cell Sequencing: Ariadne’s Thread in the Maze of Acute Myeloid Leukemia. Diagnostics (Basel) 2022; 12:diagnostics12040996. [PMID: 35454044 PMCID: PMC9024495 DOI: 10.3390/diagnostics12040996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 02/01/2023] Open
Abstract
Acute myeloid leukemia (AML) is a haematological neoplasm resulting from the accumulation of genetic and epigenetic alterations. Patients’ prognoses vary with AML genetic heterogeneity, which hampers successful treatments. Single-cell approaches have provided new insights of the clonal architecture of AML, revealing the mutational history from diagnosis, during treatment and to relapse. In this review, we imagine single-cell technologies as the Ariadne’s thread that will guide us out of the AML maze, provide a precise identikit of the leukemic cell at single-cell resolution and explore genomic, transcriptomic, epigenetic and proteomic levels.
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Affiliation(s)
- Immacolata Redavid
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Maria Rosa Conserva
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Luisa Anelli
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Antonella Zagaria
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Giorgina Specchia
- School of Medicine, University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
| | - Pellegrino Musto
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
| | - Francesco Albano
- Hematology Section, Department of Emergency and Organ Transplantation (D.E.T.O.), University of Bari ‘Aldo Moro’, 70124 Bari, Italy; (I.R.); (M.R.C.); (L.A.); (A.Z.); (P.M.)
- Correspondence:
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15
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Liao F, Liu Q, Xiao C, Yi S, Huang D. Assessment of Multiple Annealing and Looping-Based Amplification Cycle-Based Whole-Genome Amplification for Short Tandem Repeat Genotyping of Low Copy Number-DNA. Genet Test Mol Biomarkers 2022; 26:191-197. [PMID: 35394799 DOI: 10.1089/gtmb.2021.0268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Aim: A common problem in forensic practice is the lack of sufficient amounts of good quality genomic DNA. A possible solution is the amplification of the available genomic DNA before locus-specific polymerase chain reaction (PCR) analysis. The aim of this study was to evaluate multiple annealing and looping-based amplification cycle (MALBAC)-based whole-genome amplification (WGA) for short tandem repeat (STR) genotyping of low copy number DNA (LCN-DNA). Materials and Methods: DNA isolated from five blood samples was quantified and diluted to 250, 150, 100, 50, 25, and 5 pg/μL. After preamplification with MALBAC, WGA products were quantified. PCR-STR genotyping was performed in triplicate using dilution or purification-treated WGA products for each level of DNA. STR profiles were analyzed and compared with that from non-WGA DNA. Results: The purification treatment performed better than dilution of the MALBAC-based WGA products. Compared with the non-WGA DNA, both the average number and peak heights of correct alleles were significantly improved after preamplification with the MALBAC-based WGA at DNA inputs of ≤50 pg. Like other WGA methods, allele dropout and allele drop-in were observed in the profiling results for many samples. Conclusions: MALBAC shows great potential in LCN-DNA analysis and could find broader application in the fields of forensics and genetics.
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Affiliation(s)
- Fei Liao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Quan Liu
- Hubei Key Laboratory of Forensic Science (Hubei University of Police), Wuhan, China
| | - Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Metcalfe CJ, Li J, Zheng B, Stiller J, Healey A, Piperidis N, Aitken KS. Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1279-1292. [PMID: 35275251 DOI: 10.1007/s00122-022-04030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci.
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Affiliation(s)
- Cushla J Metcalfe
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Jingchuan Li
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Bangyou Zheng
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Jiri Stiller
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Karen S Aitken
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia.
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17
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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18
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Dong Z, Wang Y, Yin D, Hang X, Pu L, Zhang J, Geng J, Chang L. Advanced techniques for gene heterogeneity research: Single‐cell sequencing and on‐chip gene analysis systems. VIEW 2022. [DOI: 10.1002/viw.20210011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Zaizai Dong
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Yu Wang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Dedong Yin
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Xinxin Hang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Lei Pu
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jianfu Zhang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jia Geng
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Lingqian Chang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
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Bahonar S, Montazeri H. Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV. Methods Mol Biol 2022; 2493:267-277. [PMID: 35751821 DOI: 10.1007/978-1-0716-2293-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
SCAN-SNV is a recent computational tool for somatic single-nucleotide variant (SNV) identification from the single-cell DNA sequencing data. The workflow of the SCAN-SNV package is as follows. First, candidate somatic SNVs and credible heterozygous single-nucleotide polymorphisms (hSNP) are obtained by analyzing single-cell and matched bulk sequencing data, respectively. Subsequently, SCAN-SNV estimates genome-wide allele-specific amplification balance (AB) at any position of DNA sequencing data using a probabilistic spatial statistical model. Finally, candidate somatic SNVs that are likely artifacts according to the AB predictions are further removed to obtain putative mutations. This chapter provides a step-by-step practical guide of the package by explaining how to install and use the variance caller in a real-world example.
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Affiliation(s)
- Sajedeh Bahonar
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Hesam Montazeri
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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20
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O'Grady CJ, Dhandapani V, Colbourne JK, Frisch D. Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs. Mol Ecol Resour 2021; 22:946-961. [PMID: 34672105 DOI: 10.1111/1755-0998.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.
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Affiliation(s)
- Christopher James O'Grady
- School of Life Sciences, University of Warwick, Coventry, UK.,Cell and Gene Therapy Catapult, London, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Dagmar Frisch
- School of Biosciences, University of Birmingham, Birmingham, UK.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
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21
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Parikh FR, Athalye AS, Kulkarni DK, Sanap RR, Dhumal SB, Warang DJ, Naik DJ, Madon PF. Evolution and Utility of Preimplantation Genetic Testing for Monogenic Disorders in Assisted Reproduction - A Narrative Review. J Hum Reprod Sci 2021; 14:329-339. [PMID: 35197677 PMCID: PMC8812395 DOI: 10.4103/jhrs.jhrs_148_21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/20/2021] [Accepted: 11/20/2021] [Indexed: 11/04/2022] Open
Abstract
Preimplantation genetic testing (PGT) for monogenic disorders and assisted reproductive technology have evolved and progressed in tandem. PGT started with single-cell polymerase chain reaction (PCR) followed by fluorescent in situ hybridisation for a limited number of chromosomes, later called 'preimplantation genetic diagnosis (PGD) version 1'. This review highlights the various molecular genetic techniques that have evolved to detect specific inherited monogenic disorders in the preimplantation embryo. Literature review in English was performed in PubMed from 1990 to 2021, using the term 'preimplantation genetic diagnosis'. With whole-genome amplification, multiple copies of embryonic DNA were created. This helped in avoiding misdiagnosis caused by allele dropout. Multiplex fluorescent PCR analysed informative short tandem repeats (STR) and detected mutations simultaneously on automated capillary electrophoresis sequencers by mini-sequencing. Comparative genomic hybridisation (CGH) and array CGH were used for 24 chromosome aneuploidy screening. Subsequently, aneuploidies were detected by next-generation sequencing using single-nucleotide polymorphism arrays, while STR markers were used for haplotyping. 'PGD version 2' included accurate marker-based diagnosis of most monogenic disorders and detection of aneuploidy of all chromosomes. Human leukocyte antigen matching of embryos has important implications in diagnosis and cure of haemoglobinopathies and immunodeficiencies in children by means of matched related haematopoietic stem cell transplantation from an unaffected 'saviour sibling' obtained by PGT.
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Affiliation(s)
- Firuza R. Parikh
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Arundhati S. Athalye
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhananjaya K. Kulkarni
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Rupesh R. Sanap
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Suresh B. Dhumal
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dhanashree J. Warang
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Dattatray J. Naik
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
| | - Prochi F. Madon
- Department of Assisted Reproduction and Genetics, Jaslok-FertilTree International Fertility Centre, Jaslok Hospital and Research Centre, Mumbai, Maharashtra, India
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22
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scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:346-357. [PMID: 34280548 PMCID: PMC8864190 DOI: 10.1016/j.gpb.2021.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 12/10/2020] [Accepted: 03/06/2021] [Indexed: 11/28/2022]
Abstract
Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution. Unfortunately, classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification. We developed a single-cell DNA library preparation method without preamplification in nanolitre scale (scDPN) to address these issues. The method achieved a throughput of up to 1800 cells per run for copy number variation (CNV) detection. Also, our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification (MDA) method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation. We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma (HCC). We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome. Furthermore, we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q, 10q, and 14q developed into the dominant clone in the recurrent tumor, indicating clonal selection during recurrence in HCC. Overall, this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution
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23
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Khoshkhoo S, Lal D, Walsh CA. Application of single cell genomics to focal epilepsies: A call to action. Brain Pathol 2021; 31:e12958. [PMID: 34196990 PMCID: PMC8412079 DOI: 10.1111/bpa.12958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Focal epilepsies are the largest epilepsy subtype and associated with significant morbidity. Somatic variation is a newly recognized genetic mechanism underlying a subset of focal epilepsies, but little is known about the processes through which somatic mosaicism causes seizures, the cell types carrying the pathogenic variants, or their developmental origin. Meanwhile, the inception of single cell biology has completely revolutionized the study of neurological diseases and has the potential to answer some of these key questions. Focusing on single cell genomics, transcriptomics, and epigenomics in focal epilepsy research, circumvents the averaging artifact associated with studying bulk brain tissue and offers the kind of granularity that is needed for investigating the consequences of somatic mosaicism. Here we have provided a brief overview of some of the most developed single cell techniques and the major considerations around applying them to focal epilepsy research.
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Affiliation(s)
- Sattar Khoshkhoo
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dennis Lal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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24
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Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA. Sci Rep 2021; 11:12820. [PMID: 34140556 PMCID: PMC8211769 DOI: 10.1038/s41598-021-92092-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/28/2021] [Indexed: 11/08/2022] Open
Abstract
The macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.
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25
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Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan. Sci Rep 2021; 11:12222. [PMID: 34108585 PMCID: PMC8190148 DOI: 10.1038/s41598-021-91615-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 05/27/2021] [Indexed: 11/09/2022] Open
Abstract
Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data ( http://marine-meta.healthscience.sci.waseda.ac.jp/omd/ ), which provides a three-dimensional bird's-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.
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26
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Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A 2021; 118:2024176118. [PMID: 34099548 PMCID: PMC8214697 DOI: 10.1073/pnas.2024176118] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
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27
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Long N, Qiao Y, Xu Z, Tu J, Lu Z. Recent advances and application in whole-genome multiple displacement amplification. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0217-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Genomic surveillance of Plasmodium falciparum and Plasmodium vivax cases at the University Hospital in Tegucigalpa, Honduras. Sci Rep 2020; 10:20975. [PMID: 33262482 PMCID: PMC7708478 DOI: 10.1038/s41598-020-78103-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/09/2020] [Indexed: 11/09/2022] Open
Abstract
Malaria continues to be an important health problem in Honduras despite major progress achieved reducing its incidence in the last two decades. In a context of case reduction, continuing surveillance of parasite diversity and drug resistance is an important component to assist effective malaria control strategies and support risk assessments. In this study, we employed next generation sequencing on collected Plasmodium vivax and P. falciparum samples from the Hospital Escuela (University Hospital) in Honduras between 2005 and 2017. Hospital Escuela is the main public health hospital in Honduras and receives suspected malaria cases from endemic regions within the country. The resulting sequencing data was used to assess complexity of infections, parasite population structure, parasite diversity and drug resistance profiling. All P. vivax samples and all autochtonous P. falciparum samples were monoclonal and presented a low intra population diversity (π = 0.25 and 0.07, respectively). Genotyping of drug resistance markers showed that three P. falciparum samples presented the chloroquine resistant haplotype SVMNT on pfcrtr (positions 72-76). Epidemiological data suggested that two of these samples were imported cases from Africa whereas the third one was a local case. Three suspected imported cases (two of which were also pfcrt mutants) presented the pfmdr1 86Y mutation that further enhances the CQ resistant genotype. No evidence was found for kelch13 artemisinin resistance associated mutations nor parasite genetic background mutations. Discriminant analysis of principal components and phylogenetic analysis showed two P. vivax and two P. falciparum parasite sub-populations with limited recombination between them. It also confirmed the closer relationship of the three imported cases with African strains. Our findings showed that local Honduras P. falciparum strains do not hold CQ resistance polymorphisms which aligns with clinical data reported by the country and supports the continuity of CQ based treatment in Honduras. In addition, our findings highlight the need of using genomic approaches to provide key information about parasite biology including drug resistance, population structure and HRP2/HRP3 deletions which are becoming relevant as the country move towards elimination.
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29
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Luo C, Fernie AR, Yan J. Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants. TRENDS IN PLANT SCIENCE 2020; 25:1030-1040. [PMID: 32532595 DOI: 10.1016/j.tplants.2020.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
The development of genomics and epigenomics has allowed rapid advances in our understanding of plant biology. However, conventional bulk analysis dilutes cell-specific information by providing only average information, thereby limiting the resolution of genomic and functional genomic studies. Recent advances in single-cell sequencing technology concerning genomics and epigenomics open new avenues to dissect cell heterogeneity in multiple biological processes. Recent applications of these approaches to plants have provided exciting insights into diverse biological questions. We highlight the methodologies underlying the current techniques of single-cell genomics and epigenomics before covering their recent applications, potential significance, and future perspectives in plant biology.
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Affiliation(s)
- Cheng Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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30
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Spider Silk Fibroin Protein Heterologously Produced in Rice Seeds Reduce Diabetes and Hypercholesterolemia in Mice. PLANTS 2020; 9:plants9101282. [PMID: 32998453 PMCID: PMC7650732 DOI: 10.3390/plants9101282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 11/16/2022]
Abstract
Silk fibroin proteins are biomaterials with diverse applications. These spider and silkworm proteins have specific biological effects when consumed by mammals; in addition to reducing blood pressure and blood glucose and cholesterol levels, they have anti-human immunodeficiency virus activity. In the present study, rice (Oryza sativa) was engineered to produce the C-terminus of the major ampullate spidroin protein from the spider Araneus ventricosus under the control of a Prolamin promoter. Homozygous transgenic rice lines were identified, and the therapeutic effect of this spider silk fibroin protein on the lipid and glucose metabolism was analyzed in a mouse model. Feeding fat-fed mice, the transgenic rice seeds for four weeks reduced serum concentrations of triglycerides, total cholesterol, low-density lipoprotein cholesterol, glutamic oxaloacetic transaminase, and glutamic pyruvic transaminase, and lowered blood glucose levels. This is the first study to investigate the effects of consumption of rice seeds heterologously expressing spider silk fibroin protein in a mammalian model. Our findings suggest that functional foods containing spider silk fibroin protein might be useful as potential pharmaceutical materials for preventing and treating diabetes, hyperlipidemia, and hypercholesterolemia.
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31
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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. RICE (NEW YORK, N.Y.) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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32
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Mishra A, Dhali A, Reddy IJ, Kolte AP. Sexing of pre-implantation ovine embryos through polymerase chain reaction-based amplification of GAPDH, SRY and AMEL genes. Reprod Domest Anim 2020; 55:885-892. [PMID: 32379910 DOI: 10.1111/rda.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.
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Affiliation(s)
- Ashish Mishra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Arindam Dhali
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Ippala J Reddy
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Atul P Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
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33
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Popovic M, Dhaenens L, Boel A, Menten B, Heindryckx B. Chromosomal mosaicism in human blastocysts: the ultimate diagnostic dilemma. Hum Reprod Update 2020; 26:313-334. [DOI: 10.1093/humupd/dmz050] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Abstract
BACKGROUND
Trophectoderm (TE) biopsy and next generation sequencing (NGS) are currently the preferred techniques for preimplantation genetic testing for aneuploidies (PGT-A). Although this approach delivered important improvements over previous testing strategies, increased sensitivity has also prompted a rise in diagnoses of uncertain clinical significance. This includes reports of chromosomal mosaicism, suggesting the presence of karyotypically distinct cells within a single TE biopsy. Given that PGT-A relies on the chromosomal constitution of the biopsied cells being representative of the entire embryo, the prevalence and clinical implications of blastocyst mosaicism continue to generate considerable controversy.
OBJECTIVE AND RATIONALE
The objective of this review was to evaluate existing scientific evidence regarding the prevalence and impact of chromosomal mosaicism in human blastocysts. We discuss insights from a biological, technical and clinical perspective to examine the implications of this diagnostic dilemma for PGT-A.
SEARCH METHODS
The PubMed and Google Scholar databases were used to search peer-reviewed publications using the following terms: ‘chromosomal mosaicism’, ‘human’, ‘embryo’, ‘blastocyst’, ‘implantation’, ‘next generation sequencing’ and ‘clinical management’ in combination with other keywords related to the subject area. Relevant articles in the English language, published until October 2019 were critically discussed.
OUTCOMES
Chromosomal mosaicism predominately results from errors in mitosis following fertilization. Although it appears to be less pervasive at later developmental stages, establishing the true prevalence of mosaicism in human blastocysts remains exceedingly challenging. In a clinical context, blastocyst mosaicism can only be reported based on a single TE biopsy and has been ascribed to 2–13% of embryos tested using NGS. Conversely, data from NGS studies disaggregating whole embryos suggests that mosaicism may be present in up to ~50% of blastocysts. However, differences in testing and reporting strategies, analysis platforms and the number of cells sampled inherently overshadow current data, while added uncertainties emanate from technical artefacts. Moreover, laboratory factors and aspects of in vitro culture generate further variability. Outcome data following the transfer of blastocysts diagnosed as mosaic remain limited. Current studies suggest that the transfer of putative mosaic embryos may lead to healthy live births, but also results in significantly reduced ongoing pregnancy rates compared to the transfer of euploid blastocysts. Observations that a subset of mosaic blastocysts has the capacity to develop normally have sparked discussions regarding the ability of embryos to self-correct. However, there is currently no direct evidence to support this assumption. Nevertheless, the exclusion of mosaic blastocysts results in fewer embryos available for transfer, which may inevitably compromise treatment outcomes.
WIDER IMPLICATIONS
Chromosomal mosaicism in human blastocysts remains a perpetual diagnostic and clinical dilemma in the context of PGT-A. This review offers an important scientific resource, informing about the challenges, risks and value of diagnosing mosaicism. Elucidating these uncertainties will ultimately pave the way towards improved clinical and patient management.
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Affiliation(s)
- Mina Popovic
- Ghent-Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lien Dhaenens
- Ghent-Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Annekatrien Boel
- Ghent-Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FAST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
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Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CSO, Aparicio S, Baaijens J, Balvert M, Barbanson BD, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder JD, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Eleven grand challenges in single-cell data science. Genome Biol 2020; 21:31. [PMID: 32033589 PMCID: PMC7007675 DOI: 10.1186/s13059-020-1926-6] [Citation(s) in RCA: 562] [Impact Index Per Article: 140.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/02/2020] [Indexed: 02/08/2023] Open
Abstract
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
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Affiliation(s)
- David Lähnemann
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Paediatric Oncology, Haematology and Immunology, Medical Faculty, Heinrich Heine University, University Hospital, Düsseldorf, Germany
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johannes Köster
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Ewa Szczurek
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, Australia
- Melbourne Integrative Genomics, School of BioSciences–School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD USA
| | - Mark D. Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Catalina A. Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- The Alan Turing Institute, British Library, London, UK
| | - Kieran R. Campbell
- Department of Statistics, University of British Columbia, Vancouver, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
- Data Science Institute, University of British Columbia, Vancouver, Canada
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Charlestown, USA
- Department of Pathology, Harvard Medical School, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jasmijn Baaijens
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Marleen Balvert
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Buys de Barbanson
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
| | - Antonio Cappuccio
- Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Florescu
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rens Holmer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Thamar Jessurun Lobo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Emma M. Keizer
- Biometris, Wageningen University & Research, Wageningen, The Netherlands
| | - Indu Khatri
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M. Kielbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alexey M. Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Boudewijn P.F. Lelieveldt
- PRB lab, Delft University of Technology, Delft, The Netherlands
- Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ion I. Mandoiu
- Computer Science & Engineering Department, University of Connecticut, Storrs, USA
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Felix Mölder
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amir Niknejad
- Computation molecular design, Zuse Institute Berlin, Berlin, Germany
- Mathematics Department, Mount Saint Vincent, New York, USA
| | - Alicja Rączkowska
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Marcel Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Antonios Somarakis
- Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center–DKFZ, Heidelberg, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research–LACDR–Leiden University, Leiden, The Netherlands
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alice C. McHardy
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Sohrab P. Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Alexander Schönhuth
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
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35
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Louhelainen J, Miller D. Forensic Investigation of a Shawl Linked to the "Jack the Ripper" Murders. J Forensic Sci 2020; 65:295-303. [PMID: 30859587 DOI: 10.1111/1556-4029.14038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 11/28/2022]
Abstract
A set of historic murders, known as the "Jack the Ripper murders," started in London in August 1888. The killer's identity has remained a mystery to date. Here, we describe the investigation of, to our knowledge, the only remaining physical evidence linked to these murders, recovered from one of the victims at the scene of the crime. We applied novel, minimally destructive techniques for sample recovery from forensically relevant stains on the evidence and separated single cells linked to the suspect, followed by phenotypic analysis. The mtDNA profiles of both the victim and the suspect matched the corresponding reference samples, fortifying the link of the evidence to the crime scene. Genomic DNA from single cells recovered from the evidence was amplified, and the phenotypic information acquired matched the only witness statement regarded as reliable. To our knowledge, this is the most advanced study to date regarding this case.
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Affiliation(s)
- Jari Louhelainen
- Pharmacy and Biomolecular Sciences, James Parsons Building Byrom Street, Room 10.06, Liverpool, L3 3AF, UK
| | - David Miller
- Reproduction and Early Development Group, Institute of Genetics, Health and Therapeutics, University of Leeds, Clarendon Way, Leeds, LS2 9JT, UK
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36
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Hu WE, Zhang X, Guo QF, Yang JW, Yang Y, Wei SC, Su XD. HeLa-CCL2 cell heterogeneity studied by single-cell DNA and RNA sequencing. PLoS One 2019; 14:e0225466. [PMID: 31790455 PMCID: PMC6886862 DOI: 10.1371/journal.pone.0225466] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/05/2019] [Indexed: 12/18/2022] Open
Abstract
The HeLa cells are the earliest and mostly used laboratory human cells for biomedical particularly cancer research. They were derived from a patient's cervical cancerous tissue, and are known for their heterogeneous cellular origin and variable genomic landscapes. Single-cell sequencing techniques with faithful linear and uniformly amplified genomes (DNA) and transcriptomes (RNA) may facilitate the study of cellular differences at the individual cell level. In this work, we have performed single-cell DNA and RNA sequencing with HeLa-CCL2 cells to study their heterogeneity. We have studied the complexity of copy number variations (CNVs) of HeLa-CCL2 genome at the single cell level, and revealed the transcriptomic heterogeneity of HeLa-CCL2. We also analyzed the relationship between genome and transcriptome at the single-cell level, and found overall correlation between CNV and transcriptome expression patterns. Finally, we concluded that although single-cell sequencing techniques are applicable to study heterogeneous cells such as HeLa-CCL2, the data analyses need to be more careful and well controlled.
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Affiliation(s)
- Wan-er Hu
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing, China
- Biomedical Pioneering Innovation Center (BIOPIC), and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xin Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Qiu-fang Guo
- Biomedical Pioneering Innovation Center (BIOPIC), and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Jing-wei Yang
- Biomedical Pioneering Innovation Center (BIOPIC), and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Yuan Yang
- Clinical Research Center, Guizhou Medical University Hospital, Guiyang, China
| | - Shi-cheng Wei
- Academy for Advanced Interdisciplinary Studies (AAIS), Peking University, Beijing, China
- * E-mail: (S-CW); (X-DS)
| | - Xiao-dong Su
- Biomedical Pioneering Innovation Center (BIOPIC), and State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
- * E-mail: (S-CW); (X-DS)
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37
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Machida M, Kibayashi K. Investigation of the efficiency of whole genome amplification prior to short tandem repeat analysis using degraded DNA. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Diakité SAS, Traoré K, Sanogo I, Clark TG, Campino S, Sangaré M, Dabitao D, Dara A, Konaté DS, Doucouré F, Cissé A, Keita B, Doumbouya M, Guindo MA, Toure MB, Sogoba N, Doumbia S, Awandare GA, Diakité M. A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. Malar J 2019; 18:361. [PMID: 31718631 PMCID: PMC6849310 DOI: 10.1186/s12936-019-2986-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drug resistance is one of the greatest challenges of malaria control programme in Mali. Recent advances in next-generation sequencing (NGS) technologies provide new and effective ways of tracking drug-resistant malaria parasites in Africa. The diversity and the prevalence of Plasmodium falciparum drug-resistance molecular markers were assessed in Dangassa and Nioro-du-Sahel in Mali, two sites with distinct malaria transmission patterns. Dangassa has an intense seasonal malaria transmission, whereas Nioro-du-Sahel has an unstable and short seasonal malaria transmission. METHODS Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from P. falciparum positive patients in 2016. Samples were analysed on the Agena MassARRAY® iPLEX platform. Specific codons were targeted in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease and Pfmdr2 genes. The Sanger's 101-SNPs-barcode method was used to assess the genetic diversity of P. falciparum and to determine the parasite species. RESULTS The Pfcrt_76T chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in Nioro-du-Sahel (p = 0.025). The Pfdhfr_51I-59R-108N pyrimethamine-resistance genotype was 14.1% and 19.6%, respectively in Dangassa and Nioro-du-Sahel. Mutations in the Pfdhps_S436-A437-K540-A581-613A sulfadoxine-resistance gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (p = 0.035). Up to 17.8% of the isolates from Dangassa vs 7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype. The amodiaquine-resistance Pfmdr1_N86Y mutation was identified in only three samples (two in Dangassa and one in Nioro-du-Sahel). The lumefantrine-reduced susceptibility Pfmdr1_Y184F mutation was found in 39.9% and 48.2% of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance Exo_E415G mutation was found in Dangassa, while no artemisinin resistance genetic-background were identified. A high P. falciparum diversity was observed, but no clear genetic aggregation was found at either study sites. Higher multiplicity of infection was observed in Dangassa with both COIL (p = 0.04) and Real McCOIL (p = 0.02) methods relative to Nioro-du-Sahel. CONCLUSIONS This study reveals high prevalence of chloroquine and pyrimethamine-resistance markers as well as high codon substitution rate in the sulfadoxine-resistance gene. High genetic diversity of P. falciparum was observed. These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.
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Affiliation(s)
- Seidina A S Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali.
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ibrahim Sanogo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Modibo Sangaré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa S Konaté
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fousseyni Doucouré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Cissé
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourama Keita
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mory Doumbouya
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Merepen A Guindo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamoudou B Toure
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
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39
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Muriuki JM, Mentzer AJ, Band G, Gilchrist JJ, Carstensen T, Lule SA, Goheen MM, Joof F, Kimita W, Mogire R, Cutland CL, Diarra A, Rautanen A, Pomilla C, Gurdasani D, Rockett K, Mturi N, Ndungu FM, Scott JAG, Sirima SB, Morovat A, Prentice AM, Madhi SA, Webb EL, Elliott AM, Bejon P, Sandhu MS, Hill AVS, Kwiatkowski DP, Williams TN, Cerami C, Atkinson SH. The ferroportin Q248H mutation protects from anemia, but not malaria or bacteremia. SCIENCE ADVANCES 2019; 5:eaaw0109. [PMID: 31517041 PMCID: PMC6726445 DOI: 10.1126/sciadv.aaw0109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Iron acquisition is critical for life. Ferroportin (FPN) exports iron from mature erythrocytes, and deletion of the Fpn gene results in hemolytic anemia and increased fatality in malaria-infected mice. The FPN Q248H mutation (glutamine to histidine at position 248) renders FPN partially resistant to hepcidin-induced degradation and was associated with protection from malaria in human studies of limited size. Using data from cohorts including over 18,000 African children, we show that the Q248H mutation is associated with modest protection against anemia, hemolysis, and iron deficiency, but we found little evidence of protection against severe malaria or bacteremia. We additionally observed no excess Plasmodium growth in Q248H erythrocytes ex vivo, nor evidence of selection driven by malaria exposure, suggesting that the Q248H mutation does not protect from malaria and is unlikely to deprive malaria parasites of iron essential for their growth.
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Affiliation(s)
- John Muthii Muriuki
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gavin Band
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James J. Gilchrist
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Swaib A. Lule
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Morgan M. Goheen
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
- University of North Carolina School of Medicine, CB 7435, Chapel Hill, North Carolina USA
| | - Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Wandia Kimita
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Reagan Mogire
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Clare L. Cutland
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Centre de Recherche Action en Sante (GRAS), 06 BP 10248, Ouagadougou 06, Burkina Faso
| | - Anna Rautanen
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Kirk Rockett
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Neema Mturi
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - Francis M. Ndungu
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
| | - J. Anthony G. Scott
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- London School of Hygiene and Tropical Medicine, London, UK
| | - Sodiomon B. Sirima
- Centre de Recherche Action en Sante (GRAS), 06 BP 10248, Ouagadougou 06, Burkina Faso
| | - Alireza Morovat
- Department of Clinical Biochemistry, Oxford University Hospitals, Oxford, UK
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Emily L. Webb
- London School of Hygiene and Tropical Medicine, London, UK
| | - Alison M. Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Philip Bejon
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Clinical Vaccinology and Tropical Medicine and the Jenner Institute Laboratories, University of Oxford, Oxford, UK
| | - Dominic P. Kwiatkowski
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Thomas N. Williams
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Medicine, Imperial College, London, UK
| | - Carla Cerami
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Sarah H. Atkinson
- Kenya Medical Research Institute (KEMRI) Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Paediatrics, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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40
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Wang C, Yan Y, Chen X, Al‐Farraj SA, El‐Serehy HA, Gao F. Further analyses on the evolutionary “key‐protist”
Halteria
(Protista, Ciliophora) based on transcriptomic data. ZOOL SCR 2019. [DOI: 10.1111/zsc.12380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chundi Wang
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Ying Yan
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
| | - Xiao Chen
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
- Department of Genetics and Development Columbia University Medical Center New York NY USA
| | - Saleh A. Al‐Farraj
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Hamed A. El‐Serehy
- Zoology Department, College of Science King Saud University Riyadh Saudi Arabia
| | - Feng Gao
- Institute of Evolution & Marine Biodiversity Ocean University of China Qingdao China
- Key Laboratory of Mariculture (Ocean University of China) Ministry of Education Qingdao China
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41
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Liu Y, Yao J, Walther-Antonio M. Whole genome amplification of single epithelial cells dissociated from snap-frozen tissue samples in microfluidic platform. BIOMICROFLUIDICS 2019; 13:034109. [PMID: 31149320 PMCID: PMC6520095 DOI: 10.1063/1.5090235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/28/2019] [Indexed: 05/04/2023]
Abstract
Single cell sequencing is a technology capable of analyzing the genome of a single cell within a population. This technology is mostly integrated with microfluidics for precise cell manipulation and fluid handling. So far, most of the microfluidic-based single cell genomic studies have been focused on lab-cultured species or cell lines that are relatively easy to handle following standard microfluidic-based protocols without additional adjustments. The major challenges for performing single cell sequencing on clinical samples is the complex nature of the samples which requires additional sample processing steps to obtain intact single cells of interest without using amplification-inhibitive agents. Fluorescent-activated cell sorting is a common option to obtain single cells from clinical samples for single cell applications but requires >100 000 viable cells in suspension and the need for specialized laboratory and personnel. In this work, we present a protocol that can be used to obtain intact epithelial cells from snap-frozen postsurgical human endometrial tissues for single cell whole genome amplification. Our protocol includes sample thawing, cell dissociation, and labeling for genome amplification of targeted cells. Between 80% and 100% of single cell replicates lead to >25 ng of DNA after amplification with no measurable contamination, sufficient for downstream sequencing.
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42
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Hinch AG, Zhang G, Becker PW, Moralli D, Hinch R, Davies B, Bowden R, Donnelly P. Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm. Science 2019; 363:eaau8861. [PMID: 30898902 PMCID: PMC6445350 DOI: 10.1126/science.aau8861] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023]
Abstract
Recombination is critical to meiosis and evolution, yet many aspects of the physical exchange of DNA via crossovers remain poorly understood. We report an approach for single-cell whole-genome DNA sequencing by which we sequenced 217 individual hybrid mouse sperm, providing a kilobase-resolution genome-wide map of crossovers. Combining this map with molecular assays measuring stages of recombination, we identified factors that affect crossover probability, including PRDM9 binding on the non-initiating template homolog and telomere proximity. These factors also influence the time for sites of recombination-initiating DNA double-strand breaks to find and engage their homologs, with rapidly engaging sites more likely to form crossovers. We show that chromatin environment on the template homolog affects positioning of crossover breakpoints. Our results also offer insights into recombination in the pseudoautosomal region.
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Affiliation(s)
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Robert Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Statistics, University of Oxford, Oxford, UK
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43
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Öztaş DY, Altunbek M, Uzunoglu D, Yılmaz H, Çetin D, Suludere Z, Çulha M. Tracing Size and Surface Chemistry-Dependent Endosomal Uptake of Gold Nanoparticles Using Surface-Enhanced Raman Scattering. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4020-4028. [PMID: 30773019 DOI: 10.1021/acs.langmuir.8b03988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based single-cell analysis is an emerging approach to obtain molecular level information from molecular dynamics in a living cell. In this study, endosomal biochemical dynamics was investigated based on size and surface chemistry-dependent uptake of gold nanoparticles (AuNPs) on single cells over time using SERS. MDA-MB-231 breast cancer cells were exposed to 13 and 50 nm AuNPs and their polyadenine oligonucleotide-modified forms by controlling the order and combination of AuNPs. The average spectra obtained from 20 single cells were analyzed to study the nature of the biochemical species or processes taking place on the AuNP surfaces. The spectral changes, especially from proteins and lipids of endosomal vesicles, were observed depending on the size, surface chemistry, and combination as well as the duration of the AuNP treatment. The results demonstrate that SERS spectra are sensitive to trace biochemical changes not only the size, surface chemistry, and aggregation status of AuNPs but also the endosomal maturation steps over time, which can be simple and fast way for understanding the AuNP behavior in single cell and useful for the assisting and controlling of AuNP-based gene or drug delivery applications.
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Affiliation(s)
- Deniz Yaşar Öztaş
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Mine Altunbek
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Deniz Uzunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | - Hülya Yılmaz
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
| | | | | | - Mustafa Çulha
- Department of Genetics and Bioengineering, Faculty of Engineering , Yeditepe University , Ataşehir, Istanbul 34755 , Turkey
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44
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Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE. The Impact of Heterogeneity on Single-Cell Sequencing. Front Genet 2019; 10:8. [PMID: 30881372 PMCID: PMC6405636 DOI: 10.3389/fgene.2019.00008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/09/2019] [Indexed: 12/28/2022] Open
Abstract
The importance of diversity and cellular specialization is clear for many reasons, from population-level diversification, to improved resiliency to unforeseen stresses, to unique functions within metazoan organisms during development and differentiation. However, the level of cellular heterogeneity is just now becoming clear through the integration of genome-wide analyses and more cost effective Next Generation Sequencing (NGS). With easy access to single-cell NGS (scNGS), new opportunities exist to examine different levels of gene expression and somatic mutational heterogeneity, but these assays can generate yottabyte scale data. Here, we model the importance of heterogeneity for large-scale analysis of scNGS data, with a focus on the utilization in oncology and other diseases, providing a guide to aid in sample size and experimental design.
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Affiliation(s)
- Samantha L Goldman
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Shuxiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China.,Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States.,The Feil Family Brain and Mind Research Institute, New York, NY, United States
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45
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Garavello M, Cuenca J, Dreissig S, Fuchs J, Houben A, Aleza P. Assessing Ploidy Level Analysis and Single Pollen Genotyping of Diploid and Euploid Citrus Genotypes by Fluorescence-Activated Cell Sorting and Whole-Genome Amplification. FRONTIERS IN PLANT SCIENCE 2019; 10:1174. [PMID: 31611896 PMCID: PMC6769063 DOI: 10.3389/fpls.2019.01174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/27/2019] [Indexed: 05/06/2023]
Abstract
Flow cytometry is widely used to determine genome size and ploidy level in plants. This technique, when coupled with fluorescence-activated cell sorting (FACS), whole genome amplification and genotyping (WGA), opens up new opportunities for genetic studies of individualized nuclei. This strategy was used to analyze the genetic composition of single pollen nuclei of different citrus species. The flow cytometry and microscope observations allowed us to differentiate the populations of pollen nuclei present in the diploid and euploid genotypes analyzed, showing that citrus has binuclear pollen. We have identified in the "CSO" tangor an additional nuclei population composed by the vegetative plus generative nuclei. Genotyping of this nuclei population revealed that vegetative and generative nuclei show the same genetic configuration. In addition, we have demonstrated the presence of unreduced gametes in the diploid genotype "Mexican lime." Genomic amplification is a robust method for haploid nuclei genotyping with several molecular markers, whereas in diploid nuclei using heterozygous markers showed a bias towards one of the two alleles, limiting the use of this tool in this type of nuclei. We further discuss the importance and applications of single pollen genotyping in citrus genetic studies.
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Affiliation(s)
- Miguel Garavello
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- INTA, Concordia Agricultural Experiment Station, Concordia, Argentina
| | - José Cuenca
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
| | - Steven Dreissig
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jörg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Houben
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Valencia, Spain
- *Correspondence: Pablo Aleza,
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Laser-Based Microdissection of Single Cells from Tissue Sections and PCR Analysis of Rearranged Immunoglobulin Genes from Isolated Normal and Malignant Human B Cells. Methods Mol Biol 2019; 1956:61-75. [PMID: 30779030 DOI: 10.1007/978-1-4939-9151-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Normal and malignant B cells carry rearranged immunoglobulin (Ig) variable region genes, which due to their practically limitless diversity represent ideal clonal markers for these cells. We describe here an approach to isolate single cells from frozen tissue sections by microdissection using a laser-based method. From the isolated cells, rearranged IgH and Igκ genes are amplified in a semi-nested PCR approach, using a collection of V gene subgroup-specific primers recognizing nearly all V genes together with primers for the J genes. By sequence analysis of V region genes from distinct cells, the clonal relationship of the B lineage cells can unequivocally be determined and related to the histological distribution of the cells. The approach is also useful to determine V, D, and J gene usage. Moreover, the presence and pattern of somatic Ig V gene mutations give valuable insight into the stage of differentiation of the B cells.
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47
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Dewasurendra RL, Jeffreys A, Gunawardena SA, Chandrasekharan NV, Rockett K, Kwiatkowski D, Karunaweera ND. Host genetic polymorphisms and serological response against malaria in a selected population in Sri Lanka. Malar J 2018; 17:473. [PMID: 30558622 PMCID: PMC6296029 DOI: 10.1186/s12936-018-2622-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/11/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Antibodies against the merozoite surface protein 1-19 (MSP1-19) and the apical membrane antigen 1 (AMA1) of the malaria parasite (Plasmodium vivax) are proven to be important in protection against clinical disease. Differences in the production/maintenance of antibodies may be due to many factors including host genetics. This paper discusses the association of 4 anti-malarial antibodies with selected host genetic markers. METHODS Blood was collected from individuals (n = 242) with a history of malaria within past 15 years for DNA and serum. ELISA was carried out for serum to determine the concentration of anti-malarial antibodies MSP1-19 and AMA1 for both vivax and falciparum malaria. 170 SNPs related to malaria were genotyped. Associations between seropositivity, antibody levels and genetic, non-genetic factors were determined. RESULTS Age ranged 13-74 years (mean age = 40.21 years). Majority were females. Over 90% individuals possessed either one or more type(s) of anti-malarial antibodies. Five SNPs were significantly associated with seropositivity. One SNP was associated with MSP1-19_Pv(rs739718); 4 SNPs with MSP1-19_Pf (rs6874639, rs2706379, rs2706381 and rs2075820) and1 with AMA1_Pv (rs2075820). Eleven and 7 genotypes (out of 15) were significantly associated with either presence or absence of antibodies. Three SNPs were found to be significantly associated with the antibody levels viz. rs17411697 with MSP1-19_Pv, rs2227491 with AMA1_Pv and rs229587 with AMA1_Pf. Linkage of the markers in the two groups was similar, but lower LOD scores were observed in seropositives compared to seronegatives. DISCUSSION AND CONCLUSIONS The study suggests that several SNPs in the human genome that exist in Sri Lankan populations are significantly associated with anti-malarial antibodies, either with generation and/or maintenance of antibodies for longer periods, which can be due to either individual polymorphisms or most probably a combined effect of the markers.
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Affiliation(s)
- Rajika L Dewasurendra
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka
| | - Anna Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sharmini A Gunawardena
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka
| | | | - Kirk Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Nadira D Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo 8, Sri Lanka.
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48
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Burbulis IE, Wierman MB, Wolpert M, Haakenson M, Lopes MB, Schiff D, Hicks J, Loe J, Ratan A, McConnell MJ. Improved molecular karyotyping in glioblastoma. Mutat Res 2018; 811:16-26. [PMID: 30055482 DOI: 10.1016/j.mrfmmm.2018.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 06/08/2023]
Abstract
Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.
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Affiliation(s)
- Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Matt Wolpert
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Mark Haakenson
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - David Schiff
- Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - James Hicks
- Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Justin Loe
- Full Genomes Corp, Inc., Rockville, MD, United States
| | - Aakrosh Ratan
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States.
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49
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Volozonoka L, Perminov D, Korņejeva L, Alkšere B, Novikova N, Pīmane EJ, Blumberga A, Kempa I, Miskova A, Gailīte L, Fodina V. Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing. J Assist Reprod Genet 2018; 35:1457-1472. [PMID: 29687370 PMCID: PMC6086788 DOI: 10.1007/s10815-018-1187-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
PURPOSE To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. METHODS Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out. A total of 62 embryos were retrieved from nine couples with a confirmed single gene disorder being transmitted in their family with various inheritance traits-autosomal dominant (genes-ACTA2, HTT, KRT14), autosomal recessive (genes-ALOX12B, TPP1, GLB1) and X-linked (genes-MTM1, DMD). Whole genome amplification (WGA) for the day 5 embryo trophectoderm single biopsies was carried out by multiple displacement amplification (MDA) or polymerase chain reaction (PCR)-based technology OmniPlex and was used for direct (Sanger sequencing, fragment size analysis, SNaPshot) and indirect mutation assessment (STR marker haplotyping), and embryo aneuploidy testing by array comparative genome hybridization (aCGH). RESULTS Family haplotyping revealed informative/semi-informative microsatellite markers for all clinical cases for all types of inheritance. Indirect testing gave a persuasive conclusion for all embryos assessed, which was confirmed through direct testing. The overall allele dropout (ADO) rate was higher for PCR-based WGA, and MDA shows a better genomic recovery scale. Five euploid embryos were subjected to elective single embryo transfer (eSET), which resulted in four clinical pregnancies and birth of two healthy children, which proved free of disease causative variants running in the family postnataly. CONCLUSIONS A developed multifactor PGT protocol can be adapted and applied to virtually any genetic condition and is capable of improving single gene disorder preimplantation genetic testing in a patient-tailored manner thus increasing pregnancy rates, saving costs and increasing patient reliability.
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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia.
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia.
| | - Dmitry Perminov
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
- Department of Molecular Biology, "E. Gulbja Laboratory", Riga, LV-1006, Latvia
| | - Liene Korņejeva
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Baiba Alkšere
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Natālija Novikova
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
- Faculty of Medicine, University of Latvia, Riga, LV-1586, Latvia
| | - Evija Jokste Pīmane
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Arita Blumberga
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
| | - Inga Kempa
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Anna Miskova
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, LV-1007, Latvia
| | - Linda Gailīte
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Dzirciema street 16, Riga, LV-1007, Latvia
| | - Violeta Fodina
- Centre of Genetics, "IVF Riga" Reproductive Genetics Clinic, Riga, LV-1010, Latvia
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The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms. MICROMACHINES 2018; 9:mi9080367. [PMID: 30424300 PMCID: PMC6187716 DOI: 10.3390/mi9080367] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/13/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022]
Abstract
Single-cell sequencing is a powerful technology that provides the capability of analyzing a single cell within a population. This technology is mostly coupled with microfluidic systems for controlled cell manipulation and precise fluid handling to shed light on the genomes of a wide range of cells. So far, single-cell sequencing has been focused mostly on human cells due to the ease of lysing the cells for genome amplification. The major challenges that bacterial species pose to genome amplification from single cells include the rigid bacterial cell walls and the need for an effective lysis protocol compatible with microfluidic platforms. In this work, we present a lysis protocol that can be used to extract genomic DNA from both gram-positive and gram-negative species without interfering with the amplification chemistry. Corynebacterium glutamicum was chosen as a typical gram-positive model and Nostoc sp. as a gram-negative model due to major challenges reported in previous studies. Our protocol is based on thermal and chemical lysis. We consider 80% of single-cell replicates that lead to >5 ng DNA after amplification as successful attempts. The protocol was directly applied to Gloeocapsa sp. and the single cells of the eukaryotic Sphaerocystis sp. and achieved a 100% success rate.
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