1
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Sund KL, Liu J, Lee J, Garbe J, Abdelhamed Z, Maag C, Hallinan B, Wu SW, Sperry E, Deshpande A, Stottmann R, Smolarek TA, Dyer LM, Hestand MS. Long-read sequencing and optical genome mapping identify causative gene disruptions in noncoding sequence in two patients with neurologic disease and known chromosome abnormalities. Am J Med Genet A 2024:e63818. [PMID: 39041659 DOI: 10.1002/ajmg.a.63818] [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: 03/07/2024] [Revised: 06/12/2024] [Accepted: 07/07/2024] [Indexed: 07/24/2024]
Abstract
Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long-read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease-causing genes with relevant neurologic phenotypes (MBD5, NKX2-1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.
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Affiliation(s)
- Kristen L Sund
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, California, USA
| | - John Garbe
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zakia Abdelhamed
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Chelsey Maag
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Barbara Hallinan
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Steven W Wu
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ethan Sperry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Archana Deshpande
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rolf Stottmann
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Lisa M Dyer
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Matthew S Hestand
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
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2
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Junjun R, Zhengqian Z, Ying W, Jialiang W, Yongzhuang L. A comprehensive review of deep learning-based variant calling methods. Brief Funct Genomics 2024; 23:303-313. [PMID: 38366908 DOI: 10.1093/bfgp/elae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/14/2024] [Accepted: 01/18/2023] [Indexed: 02/18/2024] Open
Abstract
Genome sequencing data have become increasingly important in the field of personalized medicine and diagnosis. However, accurately detecting genomic variations remains a challenging task. Traditional variation detection methods rely on manual inspection or predefined rules, which can be time-consuming and prone to errors. Consequently, deep learning-based approaches for variation detection have gained attention due to their ability to automatically learn genomic features that distinguish between variants. In our review, we discuss the recent advancements in deep learning-based algorithms for detecting small variations and structural variations in genomic data, as well as their advantages and limitations.
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Affiliation(s)
- Ren Junjun
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin 150001, China
| | - Zhang Zhengqian
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin 150001, China
| | - Wu Ying
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin 150001, China
| | - Wang Jialiang
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin 150001, China
| | - Liu Yongzhuang
- Harbin Institute of Technology, School of Computer Science and Technology, Harbin 150001, China
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3
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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4
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Chen K, He Y, Wang W, Yuan X, Carbone DP, Yang F. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing) 2024; 69:1556-1568. [PMID: 38641511 DOI: 10.1016/j.scib.2024.03.062] [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: 09/25/2023] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.
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Affiliation(s)
- Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing 100191, China
| | - David P Carbone
- Thoracic Oncology Center, Ohio State University, Columbus 43026, USA.
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China.
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5
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Williams CM, O'Connell J, Freyman WA, Gignoux CR, Ramachandran S, Williams AL. Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin classification of variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592816. [PMID: 38766004 PMCID: PMC11100733 DOI: 10.1101/2024.05.06.592816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Haplotype phasing, the process of determining which genetic variants are physically located on the same chromosome, is crucial for various genetic analyses. In this study, we first benchmark SHAPEIT and Beagle, two state-of-the-art phasing methods, on two large datasets: > 8 million diverse, research-consented 23andMe, Inc. customers and the UK Biobank (UKB). We find that both perform exceptionally well. Beagle's median switch error rate (SER) (after excluding single SNP switches) in white British trios from UKB is 0.026% compared to 0.00% for European ancestry 23andMe research participants; 55.6% of European ancestry 23andMe research participants have zero non-single SNP switches, compared to 42.4% of white British trios. South Asian ancestry 23andMe research participants have the highest median SER amongst the 23andMe populations, but it is still remarkably low at 0.46%. We also investigate the relationship between identity-by-descent (IBD) and SER, finding that switch errors tend to occur in regions of little or no IBD segment coverage. SHAPEIT and Beagle excel at 'intra-chromosomal' phasing, but lack the ability to phase across chromosomes, motivating us to develop an inter-chromosomal phasing method, called HAPTIC ( HAP lotype TI ling and C lustering), that assigns paternal and maternal variants discretely genome-wide. Our approach uses identity-by-descent (IBD) segments to phase blocks of variants on different chromosomes. HAPTIC represents the segments a focal individual shares with their relatives as nodes in a signed graph and performs bipartite clustering on the signed graph using spectral clustering. We test HAPTIC on 1022 UKB trios, yielding a median phase error of 0.08% in regions covered by IBD segments (33.5% of sites). We also ran HAPTIC in the 23andMe database and found a median phase error rate (the rate of mismatching alleles between the inferred and true phase) of 0.92% in Europeans (93.8% of sites) and 0.09% in admixed Africans (92.7% of sites). HAPTIC's precision depends heavily on data from relatives, so will increase as datasets grow larger and more diverse. HAPTIC enables analyses that require the parent-of-origin of variants, such as association studies and ancestry inference of untyped parents.
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6
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Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024; 14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.
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Affiliation(s)
- Carmela Scarano
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosa Redenta De Simone
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gennaro Di Bonito
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
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7
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Schlotter T, Kloter T, Hengsteler J, Yang K, Zhan L, Ragavan S, Hu H, Zhang X, Duru J, Vörös J, Zambelli T, Nakatsuka N. Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection. ACS NANO 2024; 18:6286-6297. [PMID: 38355286 PMCID: PMC10906075 DOI: 10.1021/acsnano.3c10679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer-target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.
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Affiliation(s)
- Tilman Schlotter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tom Kloter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Kyungae Yang
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Lijian Zhan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Sujeni Ragavan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Haiying Hu
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Xinyu Zhang
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Jens Duru
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - János Vörös
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tomaso Zambelli
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
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8
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Algharagholy L, García-Suárez VM, Abaas SS. Selective Sensing of DNA Nucleobases with Angular Discrimination. ACS OMEGA 2024; 9:3240-3249. [PMID: 38284083 PMCID: PMC10809688 DOI: 10.1021/acsomega.3c04945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024]
Abstract
The fast and precise selective sensing of DNA nucleobases is a long-pursued method that can lead to huge advances in the field of genomics and have an impact on aspects such as the prevention of diseases, health enhancement, and, in general, all types of medical treatments. We present here a new type of nanoscale sensor based on carbon nanotubes with a specific geometry that can discriminate the type of nucleobase and also its angle of orientation. The proper differentiation of nucleobases is essential to clearly sequence DNA chains, while angular discrimination is key to improving the sensing selectivity. We perform first-principle and quantum transport simulations to calculate the transmission, conductance, and current of the nanotube-based nanoscale sensor in the presence of the four nucleotides (A, C, G, and T), each of them rotated 0, 90, 180, or 270°. Our results show that this system is able to effectively discriminate between the four nucleotides and their angle of orientation. We explain these findings in terms of the interaction between the phosphate group of the nucleotide and the nanotube wall. The phosphate specifically distorts the electronic structure of the nanotube depending on the distance and the orientation and leads to nontrivial changes in the transmission. This work provides a method for finer and more precise sequential DNA chains.
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Affiliation(s)
- Laith
A. Algharagholy
- Department
of Physics, College of Science, University
of Sumer, Al-Rifai, 64005 Thi-Qar, Iraq
| | | | - Sawsan S. Abaas
- Nasiriyah
Directorate of Education, Ministry of Education, Nasiriyah, 64001 Thi-Qar, Iraq
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9
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Li H, Sun L, Qiao H, Sun Z, Wang P, Xie C, Hu X, Nie T, Yang X, Li G, Zhang Y, Wang X, Li Z, Jiang J, Li C, You X. Polymyxin resistance caused by large-scale genomic inversion due to IS 26 intramolecular translocation in Klebsiella pneumoniae. Acta Pharm Sin B 2023; 13:3678-3693. [PMID: 37719365 PMCID: PMC10501869 DOI: 10.1016/j.apsb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 09/19/2023] Open
Abstract
Polymyxin B and polymyxin E (colistin) are presently considered the last line of defense against human infections caused by multidrug-resistant Gram-negative organisms such as carbapenemase-producer Enterobacterales, Acinetobacter baumannii, and Klebsiella pneumoniae. Yet resistance to this last-line drugs is a major public health threat and is rapidly increasing. Polymyxin S2 (S2) is a polymyxin B analogue previously synthesized in our institute with obviously high antibacterial activity and lower toxicity than polymyxin B and colistin. To predict the possible resistant mechanism of S2 for wide clinical application, we experimentally induced bacterial resistant mutants and studied the preliminary resistance mechanisms. Mut-S, a resistant mutant of K. pneumoniae ATCC BAA-2146 (Kpn2146) induced by S2, was analyzed by whole genome sequencing, transcriptomics, mass spectrometry and complementation experiment. Surprisingly, large-scale genomic inversion (LSGI) of approximately 1.1 Mbp in the chromosome caused by IS26 mediated intramolecular transposition was found in Mut-S, which led to mgrB truncation, lipid A modification and hence S2 resistance. The resistance can be complemented by plasmid carrying intact mgrB. The same mechanism was also found in polymyxin B and colistin induced drug-resistant mutants of Kpn2146 (Mut-B and Mut-E, respectively). This is the first report of polymyxin resistance caused by IS26 intramolecular transposition mediated mgrB truncation in chromosome in K. pneumoniae. The findings broaden our scope of knowledge for polymyxin resistance and enriched our understanding of how bacteria can manage to survive in the presence of antibiotics.
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Affiliation(s)
- Haibin Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lang Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Han Qiao
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zongti Sun
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Penghe Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Chunyang Xie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinxin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Tongying Nie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guoqing Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Youwen Zhang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiukun Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhuorong Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Jiandong Jiang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Science & Peking Union Medical College, Beijing 100050, China
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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10
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Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A. Long-read whole-genome analysis of human single cells. Nat Commun 2023; 14:5164. [PMID: 37620373 PMCID: PMC10449900 DOI: 10.1038/s41467-023-40898-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.
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Affiliation(s)
- Joanna Hård
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- ETH AI Center, ETH Zurich, Zurich, Switzerland.
| | - Jeff E Mold
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Susana Häggqvist
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | | | - Jessica Nordlund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lars Feuk
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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11
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Machado HE, Øbro NF, Williams N, Tan S, Boukerrou AZ, Davies M, Belmonte M, Mitchell E, Baxter EJ, Mende N, Clay A, Ancliff P, Köglmeier J, Killick SB, Kulasekararaj A, Meyer S, Laurenti E, Campbell PJ, Kent DG, Nangalia J, Warren AJ. Convergent somatic evolution commences in utero in a germline ribosomopathy. Nat Commun 2023; 14:5092. [PMID: 37608017 PMCID: PMC10444798 DOI: 10.1038/s41467-023-40896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 08/14/2023] [Indexed: 08/24/2023] Open
Abstract
Clonal tracking of cells using somatic mutations permits exploration of clonal dynamics in human disease. Here, we perform whole genome sequencing of 323 haematopoietic colonies from 10 individuals with the inherited ribosomopathy Shwachman-Diamond syndrome to reconstruct haematopoietic phylogenies. In ~30% of colonies, we identify mutually exclusive mutations in TP53, EIF6, RPL5, RPL22, PRPF8, plus chromosome 7 and 15 aberrations that increase SBDS and EFL1 gene dosage, respectively. Target gene mutations commence in utero, resulting in a profusion of clonal expansions, with only a few haematopoietic stem cell lineages (mean 8, range 1-24) contributing ~50% of haematopoietic colonies across 8 individuals (range 4-100% clonality) by young adulthood. Rapid clonal expansion during disease transformation is associated with biallelic TP53 mutations and increased mutation burden. Our study highlights how convergent somatic mutation of the p53-dependent nucleolar surveillance pathway offsets the deleterious effects of germline ribosomopathy but increases opportunity for TP53-mutated cancer evolution.
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Affiliation(s)
| | - Nina F Øbro
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | - Shengjiang Tan
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK
| | - Ahmed Z Boukerrou
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK
| | - Megan Davies
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Emily Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - E Joanna Baxter
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Nicole Mende
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anna Clay
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Philip Ancliff
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jutta Köglmeier
- Department of Haematology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sally B Killick
- University Hospitals Dorset NHS Foundation Trust, The Royal Bournemouth Hospital, Bournemouth, UK
| | - Austin Kulasekararaj
- Department of Haematological Medicine, King's College Hospital NHS Foundation Trust and King's College London, London, UK
| | - Stefan Meyer
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Road, Manchester, UK
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester Foundation Trust, Manchester, Oxford Road, Manchester, UK
- Teenage and Adolescent Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
| | - Elisa Laurenti
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - David G Kent
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- York Biomedical Research Institute, Department of Biology, University of York, York, UK.
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Alan J Warren
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge, UK.
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12
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Yu L, Kang X, Li F, Mehrafrooz B, Makhamreh A, Fallahi A, Foster JC, Aksimentiev A, Chen M, Wanunu M. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol 2023; 41:1130-1139. [PMID: 36624148 PMCID: PMC10329728 DOI: 10.1038/s41587-022-01598-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/02/2022] [Indexed: 01/10/2023]
Abstract
The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is ~1.4 nm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.
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Affiliation(s)
- Luning Yu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Fanjun Li
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Behzad Mehrafrooz
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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13
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Tan DZJ, Fung V, Sun T, Tian K, Li Z, Zhou K. Developing a Nanopore Sequencing Workflow for Protein Engineering Applications. ACS Synth Biol 2023; 12:2041-2050. [PMID: 37403232 DOI: 10.1021/acssynbio.3c00087] [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: 07/06/2023]
Abstract
Sequencing plays a critical role in protein engineering, where the genetic information encoding for a desired mutation can be identified. We evaluated the performance of two commercially available NGS technologies (Illumina NGS and nanopore sequencing) on the available mutant libraries that were either previously constructed for other protein engineering projects or constructed in-house for this study. The sequencing results from Illumina sequencing indicated that a substantial proportion of the reads exhibited strand exchange, which mixed information of different mutants. When nanopore sequencing was used, the occurrence of strand exchange was substantially reduced compared with that of Illumina sequencing. We then developed a new library preparation workflow for nanopore sequencing and were successful in further reducing the incidence of strand exchange. The optimized workflow was successfully used to aid selection of improved alcohol dehydrogenase mutants in cells where their activities were coupled with the cell growth rate. The workflow quantified the enrichment fold change of most mutants in the library (size = 1728) in the growth-based selection passaging. A mutant that was >500% more active than its parent variant was identified based on the fold change data but not with the absolute abundance data (random sampling of the passaged cells), highlighting the usefulness of this rapid and affordable sequencing workflow in protein engineering.
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Affiliation(s)
- Daniel Zhi Jun Tan
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Vincent Fung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Tao Sun
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kaiyuan Tian
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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14
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Petrone JR, Rios Glusberger P, George CD, Milletich PL, Ahrens AP, Roesch LFW, Triplett EW. RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing. Front Microbiol 2023; 14:1201064. [PMID: 37547696 PMCID: PMC10402275 DOI: 10.3389/fmicb.2023.1201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.
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15
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Zhong J, Liu Y, Luo N, Wei Q, Su Q, Zou J, Wu X, Huang X, Jiang Y, Liang L, Li H, Lin J. Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome. Ann Clin Microbiol Antimicrob 2023; 22:57. [PMID: 37430367 DOI: 10.1186/s12941-023-00608-9] [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: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens. RESULTS This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People's Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS. CONCLUSIONS In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.
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Affiliation(s)
- Juan Zhong
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China.
| | - Yanfen Liu
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Na Luo
- NanNing Center for Disease Control and Prevention, Nanning, China
| | - Qiu Wei
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | - Qisi Su
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Jun Zou
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Xiaozhong Wu
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | | | - Yuting Jiang
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | - Lijuan Liang
- Nanning Yunju Biotechnology Co., Ltd, Nanning, China
| | - Hongmian Li
- The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| | - Jianyan Lin
- The First People's Hospital of Nanning, Nanning, China.
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16
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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17
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Yee R, Simner PJ. Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results. Clin Lab Med 2022; 42:557-572. [PMID: 36368782 DOI: 10.1016/j.cll.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rebecca Yee
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Meyer B1-193, 600 North Wolfe Street, Baltimore, MD 21287-7093, USA.
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18
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Scott ER, Yang Y, Botton MR, Seki Y, Hoshitsuki K, Harting J, Baybayan P, Cody N, Nicoletti P, Moriyama T, Chakraborty S, Yang JJ, Edelmann L, Schadt EE, Korlach J, Scott SA. Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery. Hum Mutat 2022; 43:1557-1566. [PMID: 36057977 PMCID: PMC9875722 DOI: 10.1002/humu.24457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.-121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.
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Affiliation(s)
- Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Yoshinori Seki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pennsylvania, Pittsburgh, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Neal Cody
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
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19
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Ko BJ, Lee C, Kim J, Rhie A, Yoo DA, Howe K, Wood J, Cho S, Brown S, Formenti G, Jarvis ED, Kim H. Widespread false gene gains caused by duplication errors in genome assemblies. Genome Biol 2022; 23:205. [PMID: 36167596 PMCID: PMC9516828 DOI: 10.1186/s13059-022-02764-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/02/2022] [Indexed: 12/22/2022] Open
Abstract
Background False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna’s Hummingbird, and their new counterparts of the same species generated by the Vertebrate Genomes Project, of which the Vertebrate Genomes Project pipeline attempted to eliminate false duplications through haplotype phasing and purging. These assemblies are among the first generated by the Vertebrate Genomes Project where there was a prior chromosomal level reference assembly to compare with. Results Whole genome alignments revealed that 4 to 16% of the sequences are falsely duplicated in the previous assemblies, impacting hundreds to thousands of genes. These lead to overestimated gene family expansions. The main source of the false duplications is heterotype duplications, where the haplotype sequences were relatively more divergent than other parts of the genome leading the assembly algorithms to classify them as separate genes or genomic regions. A minor source is sequencing errors. Ancient ATP nucleotide binding gene families have a higher prevalence of false duplications compared to other gene families. Although present in a smaller proportion, we observe false duplications remaining in the Vertebrate Genomes Project assemblies that can be identified and purged. Conclusions This study highlights the need for more advanced assembly methods that better separate haplotypes and sequence errors, and the need for cautious analyses on gene gains. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02764-1.
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Affiliation(s)
- Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Juwan Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Dong Ahn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | | | | | - Seoae Cho
- eGnome, Inc, Seoul, Republic of Korea
| | - Samara Brown
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Giulio Formenti
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Laboratory of the Neurogenetics of Language, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea. .,eGnome, Inc, Seoul, Republic of Korea.
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20
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Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
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Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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21
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Meggendorfer M, Jobanputra V, Wrzeszczynski KO, Roepman P, de Bruijn E, Cuppen E, Buttner R, Caldas C, Grimmond S, Mullighan CG, Elemento O, Rosenquist R, Schuh A, Haferlach T. Analytical demands to use whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:16-22. [PMID: 34119643 DOI: 10.1016/j.semcancer.2021.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Interrogating the tumor genome in its entirety by whole-genome sequencing (WGS) offers an unprecedented insight into the biology and pathogenesis of cancer, with potential impact on diagnostics, prognostication and therapy selection. WGS is able to detect sequence as well as structural variants and thereby combines central domains of cytogenetics and molecular genetics. Given the potential of WGS in directing targeted therapeutics and clinical decision-making, we envision a gradual transition of the method from research to clinical routine. This review is one out of three within this issue aimed at facilitating this effort, by discussing in-depth analytical validation, clinical interpretation and clinical utility of WGS. The review highlights the requirements for implementing, validating and maintaining a clinical WGS pipeline to obtain high-quality patient-specific data in accordance with the local regulatory landscape. Every step of the WGS pipeline, which includes DNA extraction, library preparation, sequencing, bioinformatics analysis, and data storage, is considered with respect to its logistics, necessities, potential pitfalls, and the required quality management. WGS is likely to drive clinical diagnostics and patient care forward, if requirements and challenges of the technique are recognized and met.
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Affiliation(s)
| | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, USA; Columbia University Medical Center, 650 W 168th St, New York, USA
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, USA
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
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22
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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23
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Xuhui L, Weiwei C, Siqi L, Junteng F, Hang Z, Xiangbo Z, Yongwen Q. Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage. BMC PLANT BIOLOGY 2022; 22:398. [PMID: 35963989 PMCID: PMC9375949 DOI: 10.1186/s12870-022-03787-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND As maize originated in tropical or subtropical zones, most maize germplasm is extremely sensitive to low temperatures during the seedling stage. Clarifying the molecular mechanism of cold acclimation would facilitate the breeding of cold tolerant maize varieties, which is one of the major sustainability factors for crop production. To meet this goal, we investigated two maize inbred lines with contrasting levels of cold tolerance at the seedling stage (IL85, a cold tolerant line; B73, a cold sensitive line), and performed full-length transcriptome sequencing on the root tips of seedlings before and after 24 h of cold treatment. RESULTS We identified 152,263 transcripts, including 20,993 novel transcripts, and determined per-transcript expression levels. A total of 1,475 transcripts were specifically up-regulated in the cold tolerant line IL85 under cold stress. GO enrichment analysis revealed that 25 transcripts were involved in reactive oxygen species (ROS) metabolic processes and 15 transcripts were related to the response to heat. Eight genes showed specific differential alternative splicing (DAS) in IL85 under cold stress, and were mainly involved in amine metabolism. A total of 1,111 lncRNAs were further identified, 62 of which were up-regulated in IL85 or B73 under cold stress, and their corresponding target genes were enriched in protein phosphorylation. CONCLUSIONS These results provide new insights into the molecular mechanism of cold acclimation during the seedling stage in maize, and will facilitate the development of cultivars with improved cold stress tolerance.
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Affiliation(s)
- Li Xuhui
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Chen Weiwei
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Lu Siqi
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China
| | - Fang Junteng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China
| | - Zhu Hang
- College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhang Xiangbo
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China
| | - Qi Yongwen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, Guangdong, China.
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510325, Guangdong, China.
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24
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Reis AL, Hammond JH, Stevanovski I, Arnold JC, McGregor IS, Deveson IW, Gururajan A. Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition. iScience 2022; 25:104861. [PMID: 36039298 PMCID: PMC9418440 DOI: 10.1016/j.isci.2022.104861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/03/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
Our understanding of the molecular pathology of posttraumatic stress disorder (PTSD) is evolving due to advances in sequencing technologies. With the recent emergence of Oxford Nanopore direct RNA-seq (dRNA-seq), it is now also possible to interrogate diverse RNA modifications, collectively known as the “epitranscriptome.”. Here, we present our analyses of the male and female mouse amygdala transcriptome and epitranscriptome, obtained using parallel Illumina RNA-seq and Oxford Nanopore dRNA-seq, associated with the acquisition of PTSD-like fear induced by Pavlovian cued-fear conditioning. We report significant sex-specific differences in the amygdala transcriptional response during fear acquisition and a range of shared and dimorphic epitranscriptomic signatures. Differential RNA modifications are enriched among mRNA transcripts associated with neurotransmitter regulation and mitochondrial function, many of which have been previously implicated in PTSD. Very few differentially modified transcripts are also differentially expressed, suggesting an influential, expression-independent role for epitranscriptional regulation in PTSD-like fear acquisition. PTSD-like trauma has sexually dimorphic effects on the amygdala transcriptome Most RNA modifications identified adhere to the known patterns associated with m6A There was enrichment of RNA modifications in neurological/PTSD-related genes There was little overlap between transcriptomic and epitranscriptomic signatures
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25
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Schaal W, Ameur A, Olsson-Strömberg U, Hermanson M, Cavelier L, Spjuth O. Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening. Cancer Inform 2022; 21:11769351221110872. [PMID: 35860345 PMCID: PMC9290162 DOI: 10.1177/11769351221110872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/22/2022] [Indexed: 11/15/2022] Open
Abstract
Objective The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia. Materials and Methods Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp. Results The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application. Conclusions Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.
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Affiliation(s)
- Wesley Schaal
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Pincer Bio AB, Uppsala, Sweden
| | - Adam Ameur
- Pincer Bio AB, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Monica Hermanson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden.,Pincer Bio AB, Uppsala, Sweden
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26
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Makhoul M, Chawla HS, Wittkop B, Stahl A, Voss-Fels KP, Zetzsche H, Snowdon RJ, Obermeier C. Long-Amplicon Single-Molecule Sequencing Reveals Novel, Trait-Associated Variants of VERNALIZATION1 Homoeologs in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:942461. [PMID: 36420025 PMCID: PMC9676936 DOI: 10.3389/fpls.2022.942461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/03/2022] [Indexed: 05/26/2023]
Abstract
The gene VERNALIZATION1 (VRN1) is a key controller of vernalization requirement in wheat. The genome of hexaploid wheat (Triticum aestivum) harbors three homoeologous VRN1 loci on chromosomes 5A, 5B, and 5D. Structural sequence variants including small and large deletions and insertions and single nucleotide polymorphisms (SNPs) in the three homoeologous VRN1 genes not only play an important role in the control of vernalization requirement, but also have been reported to be associated with other yield related traits of wheat. Here we used single-molecule sequencing of barcoded long-amplicons to assay the full-length sequences (∼13 kbp plus 700 bp from the promoter sequence) of the three homoeologous VRN1 genes in a panel of 192 predominantly European winter wheat cultivars. Long read sequences revealed previously undetected duplications, insertions and single-nucleotide polymorphisms in the three homoeologous VRN1 genes. All the polymorphisms were confirmed by Sanger sequencing. Sequence analysis showed the predominance of the winter alleles vrn-A1, vrn-B1, and vrn-D1 across the investigated cultivars. Associations of SNPs and structural variations within the three VRN1 genes with 20 economically relevant traits including yield, nodal root-angle index and quality related traits were evaluated at the levels of alleles, haplotypes, and copy number variants. Cultivars carrying structural variants within VRN1 genes showed lower grain yield, protein yield and biomass compared to those with intact genes. Cultivars carrying a single vrn-A1 copy and a unique haplotype with a high number of SNPs were found to have elevated grain yield, kernels per spike and kernels per m2 along with lower grain sedimentation values. In addition, we detected a novel SNP polymorphism within the G-quadruplex region of the promoter of vrn-A1 that was associated with deeper roots in winter wheat. Our findings show that multiplex, single-molecule long-amplicon sequencing is a useful tool for detecting variants in target genes within large plant populations, and can be used to simultaneously assay sequence variants among target multiple gene homoeologs in polyploid crops. Numerous novel VRN1 haplotypes and alleles were identified that showed significantly associations to economically important traits. These polymorphisms were converted into PCR or KASP assays for use in marker-assisted breeding.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet S. Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Kai Peter Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
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27
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Huang AY, Lee EA. Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data. FRONTIERS IN AGING 2022; 2:800380. [PMID: 35822012 PMCID: PMC9261417 DOI: 10.3389/fragi.2021.800380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
Abstract
Somatic mutations are DNA variants that occur after the fertilization of zygotes and accumulate during the developmental and aging processes in the human lifespan. Somatic mutations have long been known to cause cancer, and more recently have been implicated in a variety of non-cancer diseases. The patterns of somatic mutations, or mutational signatures, also shed light on the underlying mechanisms of the mutational process. Advances in next-generation sequencing over the decades have enabled genome-wide profiling of DNA variants in a high-throughput manner; however, unlike germline mutations, somatic mutations are carried only by a subset of the cell population. Thus, sensitive bioinformatic methods are required to distinguish mutant alleles from sequencing and base calling errors in bulk tissue samples. An alternative way to study somatic mutations, especially those present in an extremely small number of cells or even in a single cell, is to sequence single-cell genomes after whole-genome amplification (WGA); however, it is critical and technically challenging to exclude numerous technical artifacts arising during error-prone and uneven genome amplification in current WGA methods. To address these challenges, multiple bioinformatic tools have been developed. In this review, we summarize the latest progress in methods for identification of somatic mutations and the challenges that remain to be addressed in the future.
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Affiliation(s)
- August Yue Huang
- Division of Genetics and Genomics, Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, United States, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, United States, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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28
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New Developments and Possibilities in Reanalysis and Reinterpretation of Whole Exome Sequencing Datasets for Unsolved Rare Diseases Using Machine Learning Approaches. Int J Mol Sci 2022; 23:ijms23126792. [PMID: 35743235 PMCID: PMC9224427 DOI: 10.3390/ijms23126792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/21/2022] Open
Abstract
Rare diseases impact the lives of 300 million people in the world. Rapid advances in bioinformatics and genomic technologies have enabled the discovery of causes of 20–30% of rare diseases. However, most rare diseases have remained as unsolved enigmas to date. Newer tools and availability of high throughput sequencing data have enabled the reanalysis of previously undiagnosed patients. In this review, we have systematically compiled the latest developments in the discovery of the genetic causes of rare diseases using machine learning methods. Importantly, we have detailed methods available to reanalyze existing whole exome sequencing data of unsolved rare diseases. We have identified different reanalysis methodologies to solve problems associated with sequence alterations/mutations, variation re-annotation, protein stability, splice isoform malfunctions and oligogenic analysis. In addition, we give an overview of new developments in the field of rare disease research using whole genome sequencing data and other omics.
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29
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Zhai Q, van der Lee M, van Gelder T, Swen JJ. Why We Need to Take a Closer Look at Genetic Contributions to CYP3A Activity. Front Pharmacol 2022; 13:912618. [PMID: 35784699 PMCID: PMC9243486 DOI: 10.3389/fphar.2022.912618] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Cytochrome P450 3A (CYP3A) subfamily enzymes are involved in the metabolism of 40% of drugs in clinical use. Twin studies have indicated that 66% of the variability in CYP3A4 activity is hereditary. Yet, the complexity of the CYP3A locus and the lack of distinct drug metabolizer phenotypes has limited the identification and clinical application of CYP3A genetic variants compared to other Cytochrome P450 enzymes. In recent years evidence has emerged indicating that a substantial part of the missing heritability is caused by low frequency genetic variation. In this review, we outline the current pharmacogenomics knowledge of CYP3A activity and discuss potential future directions to improve our genetic knowledge and ability to explain CYP3A variability.
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30
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Hanxiao D, Luming S, Songchang C, Jingmin Y, Yueping Z, Shuo Z, Hongyan C, Ning J, Daru L. Noninvasive prenatal prediction of fetal haplotype with Spearman rank correlation analysis model. Mol Genet Genomic Med 2022; 10:e1988. [PMID: 35644943 PMCID: PMC9356545 DOI: 10.1002/mgg3.1988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/29/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Background Noninvasive prenatal testing (NIPT) has been widely used clinically to detect fetal chromosomal aneuploidy with high accuracy rates, gradually replacing traditional serological screening. However, the application of NIPT for monogenic diseases is still in an immature stage of exploration. The detection of mutations in peripheral blood of pregnant women requires precise qualitative and quantitative techniques, which limits its application. The bioinformatic strategies based on the SNP (single nucleotide polymorphism) linkage analysis are more practical, which can be divided into two types depending on whether proband information is needed. Hidden Markov Mode (HMM) and Sequential probability ratio test (SPRT) are suitable for families with probands. In contrast, methods based on databases and population demographic information are suitable for families without probands. Methods In this study, we proposed a Spearman rank correlation analysis method to infer the fetal haplotypes based on core family information. Allele frequencies of SNPs that were used to construct parental haplotypes were calculated as sets of nonparametric variables, in contrast to their theoretical values represented by a fetal fraction (FF). The effects on the calculation of the fetal concentration of two DNA enrichment methods, multiple‐PCR amplification, and targeted hybrid capture, were compared, and the heterozygosity distribution of SNPs within pedigrees was analyzed to reveal the best conditions for the model application. Results Predictions of the paternal haplotype inheritance were in line with expectations for both DNA library construction methods, while for maternal haplotype inheritance prediction, the rates were 96.55% for method multiple‐PCR amplification and 95.8% for method targeted hybrid capture. Conclusion Positive prediction rates showed that the maternal haplotype prediction was not as accurate as paternal one, due to the large amount of maternal noise in the mother's peripheral blood. Although this model is relatively immature, it provides a new perspective for noninvasive prenatal clinical tests of monogenic diseases.
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Affiliation(s)
- Du Hanxiao
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Sun Luming
- Department of Fetal Medicine & Prenatal Diagnosis CenterShanghai First Maternity and Infant Hospital, Tongji University School of MedicineShanghaiChina
| | - Chen Songchang
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Yang Jingmin
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Key Laboratory of Birth Defects and Reproductive Health of National Health and NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research InstituteChongqingChina
- Shanghai WeHealth BioMedical Technology Co., Ltd.ShanghaiChina
| | - Zhang Yueping
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Zhang Shuo
- Obstetrics and Gynecology Hospital, Fudan UniversityShanghaiChina
| | - Chen Hongyan
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Jiang Ning
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
| | - Lu Daru
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Key Laboratory of Birth Defects and Reproductive Health of National Health and NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research InstituteChongqingChina
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31
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Bhat GR, Sethi I, Rah B, Kumar R, Afroze D. Innovative in Silico Approaches for Characterization of Genes and Proteins. Front Genet 2022; 13:865182. [PMID: 35664302 PMCID: PMC9159363 DOI: 10.3389/fgene.2022.865182] [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: 01/29/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bioinformatics is an amalgamation of biology, mathematics and computer science. It is a science which gathers the information from biology in terms of molecules and applies the informatic techniques to the gathered information for understanding and organizing the data in a useful manner. With the help of bioinformatics, the experimental data generated is stored in several databases available online like nucleotide database, protein databases, GENBANK and others. The data stored in these databases is used as reference for experimental evaluation and validation. Till now several online tools have been developed to analyze the genomic, transcriptomic, proteomics, epigenomics and metabolomics data. Some of them include Human Splicing Finder (HSF), Exonic Splicing Enhancer Mutation taster, and others. A number of SNPs are observed in the non-coding, intronic regions and play a role in the regulation of genes, which may or may not directly impose an effect on the protein expression. Many mutations are thought to influence the splicing mechanism by affecting the existing splice sites or creating a new sites. To predict the effect of mutation (SNP) on splicing mechanism/signal, HSF was developed. Thus, the tool is helpful in predicting the effect of mutations on splicing signals and can provide data even for better understanding of the intronic mutations that can be further validated experimentally. Additionally, rapid advancement in proteomics have steered researchers to organize the study of protein structure, function, relationships, and dynamics in space and time. Thus the effective integration of all of these technological interventions will eventually lead to steering up of next-generation systems biology, which will provide valuable biological insights in the field of research, diagnostic, therapeutic and development of personalized medicine.
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Affiliation(s)
- Gh. Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu, India
| | - Bilal Rah
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Dil Afroze
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
- *Correspondence: Dil Afroze,
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32
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Gomez K. Advances in the diagnosis of heritable platelet disorders. Blood Rev 2022; 56:100972. [PMID: 35595614 DOI: 10.1016/j.blre.2022.100972] [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: 04/20/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
The last decade has seen large increases in the number of patients registered with heritable platelet disorders in national databases of bleeding disorders. Although individually rare, collectively they are a relatively common cause of heritable bleeding. This revolution has come about through the application of high-throughput sequencing strategies and efforts to standardize diagnostic testing. There is renewed interest in established parameters such as platelet volume and utilising simple tools such as blood smears. The diagnostic yield from peripheral blood smears can be improved with new microscopy techniques that could potentially assist in determining which patients need to be referred to tertiary centres for specialist testing. A better understanding of the other clinical features that can accompany abnormalities of platelet number or function, can lead to better clinical management and prevention of serious complications. There are challenges for clinicians who need to be aware of these developments, understand the limitations of new diagnostic techniques and keep abreast of strategies for incorporation into clinical practice. This review discusses some of these approaches, the limitations that clinicians need to be aware of and techniques that may enter clinical use in the future.
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Affiliation(s)
- Keith Gomez
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.
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33
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Fang L, Liu Q, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biol 2022; 23:108. [PMID: 35484600 PMCID: PMC9052667 DOI: 10.1186/s13059-022-02670-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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Affiliation(s)
- Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,School of Life Sciences, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA. .,Nevada Institute of Personalized Medicine, College of Science, University of Nevada, Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA.
| | - Alex Mas Monteys
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pedro Gonzalez-Alegre
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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34
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Chauhan N, Saxena K, Jain U. Single molecule detection; from microscopy to sensors. Int J Biol Macromol 2022; 209:1389-1401. [PMID: 35413320 DOI: 10.1016/j.ijbiomac.2022.04.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/31/2022] [Accepted: 04/05/2022] [Indexed: 01/31/2023]
Abstract
Single molecule detection is necessary to find out physical, chemical properties and their mechanism involved in the normal functioning of body cells. In this way, they can provide a new direction to the healthcare system. Various techniques have been developed and employed for their successful detection. Herein, we have emphasized various traditional methods as well as biosensing technology which offer single molecule sensitivity. The various methods including plasmonic resonance, nanopores, whispering gallery mode, Simoa assay and recognition tunneling are discussed in the initial part which has been followed by a discussion about biosensor-based detection. Plasmonic, SERS, CRISPR/Cas, and other types of biosensors are focused in this review and found to be highly sensitive for single molecule detection. This review provides an overview of progression in different techniques employed for single molecule detection.
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Affiliation(s)
- Nidhi Chauhan
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Kirti Saxena
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India
| | - Utkarsh Jain
- Amity Institute of Nanotechnology (AINT), Amity University Uttar Pradesh (AUUP), Noida 201313, U.P., India.
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35
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Review of the use of nanodevices to detect single molecules. Anal Biochem 2022; 654:114645. [DOI: 10.1016/j.ab.2022.114645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/21/2022]
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Li W, Zhou J, Maccaferri N, Krahne R, Wang K, Garoli D. Enhanced Optical Spectroscopy for Multiplexed DNA and Protein-Sequencing with Plasmonic Nanopores: Challenges and Prospects. Anal Chem 2022; 94:503-514. [PMID: 34974704 PMCID: PMC8771637 DOI: 10.1021/acs.analchem.1c04459] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Wang Li
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Juan Zhou
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Nicolò Maccaferri
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511 Luxembourg, Luxembourg
- Department
of Physics, Umeå University, Linnaeus väg 20, SE-90736 Umeå, Sweden
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
| | - Kang Wang
- State
Key Laboratory of Analytical Chemistry for Life Science School of
Chemistry and Chemical Engineering, Nanjing
University, Nanjing 210023, P. R. China
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, Optoelectronics
Research Line, Morego
30, I-16163 Genova, Italy
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Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle. THE PHARMACOGENOMICS JOURNAL 2022; 22:75-81. [PMID: 34741133 PMCID: PMC8794781 DOI: 10.1038/s41397-021-00259-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of pharmacogenomics in clinical practice is becoming standard of care. However, due to the complex genetic makeup of pharmacogenes, not all genetic variation is currently accounted for. Here, we show the utility of long-read sequencing to resolve complex pharmacogenes by analyzing a well-characterised sample. This data consists of long reads that were processed to resolve phased haploblocks. 73% of pharmacogenes were fully covered in one phased haploblock, including 9/15 genes that are 100% complex. Variant calling accuracy in the pharmacogenes was high, with 99.8% recall and 100% precision for SNVs and 98.7% precision and 98.0% recall for Indels. For the majority of gene-drug interactions in the DPWG and CPIC guidelines, the associated genes could be fully resolved (62% and 63% respectively). Together, these findings suggest that long-read sequencing data offers promising opportunities in elucidating complex pharmacogenes and haplotype phasing while maintaining accurate variant calling.
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38
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Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel) 2021; 12:life12010030. [PMID: 35054423 PMCID: PMC8780579 DOI: 10.3390/life12010030] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications.
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Hanson RL, Lazalde E, Knob R, Harris DH, Akuoko Y, Nielsen JB, Woolley AT. Multilabel hybridization probes for sequence-specific detection of sepsis-related drug resistance genes in plasmids. TALANTA OPEN 2021; 3. [PMID: 34950926 DOI: 10.1016/j.talo.2021.100034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Emerging antimicrobial drug resistance is increasing the complexity involved in treating critical conditions such as bacterial induced sepsis. Methods for diagnosing specific drug resistance tend to be rapid or sensitive, but not both. Detection methods like sequence-specific single-molecule analysis could address this concern if they could be adapted to work on smaller targets similar to those produced in traditional clinical situations. In this work we demonstrate that a 120 bp double stranded polynucleotide with an overhanging single stranded 25 bp probe sequence can be created by immobilizing DNA with a biotin/streptavidin magnetic bead system, labeling with SYBR Gold, and rinsing the excess away while the probe retains multiple fluorophores. These probes with multiple fluorophores can then be used to label a bacterial plasmid target in a sequence-specific manner. These probes enabled the detection of 1 pM plasmid samples containing a portion of an antibiotic resistance gene sequence. This system shows the possibility of improving capture and fluorescence labeling of small nucleic acid fragments, generating lower limits of detection for clinically relevant samples while maintaining rapid processing times.
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Affiliation(s)
- Robert L Hanson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Elaine Lazalde
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Radim Knob
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - David H Harris
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Yesman Akuoko
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
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40
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Piriyapongsa J, Sukritha C, Kaewprommal P, Intarat C, Triparn K, Phornsiricharoenphant K, Chaosrikul C, Shaw PJ, Chantratita W, Mahasirimongkol S, Tongsima S. PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation. J Pers Med 2021; 11:1230. [PMID: 34834582 PMCID: PMC8618518 DOI: 10.3390/jpm11111230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/17/2021] [Accepted: 11/16/2021] [Indexed: 11/29/2022] Open
Abstract
The increasing availability of next generation sequencing (NGS) for personal genomics could promote pharmacogenomics (PGx) discovery and application. However, current tools for analysis and interpretation of pharmacogenomic variants from NGS data are inadequate, as none offer comprehensive analytic functions in a simple, web-based platform. In addition, no tools exist to analyze human leukocyte antigen (HLA) genes for determining potential risks of immune-mediated adverse drug reaction (IM-ADR). We describe PharmVIP, a web-based PGx tool, for one-stop comprehensive analysis and interpretation of genome-wide variants obtained from NGS platforms. PharmVIP comprises three main interpretation modules covering analyses of pharmacogenes involved in pharmacokinetics, pharmacodynamics and IM-ADR. The Guideline module provides Clinical Pharmacogenetics Implementation Consortium (CPIC) drug guideline recommendations based on the translation of genotypic data in genes having guidelines. The HLA module reports HLA genotypes, potential adverse drug reactions, and the relevant drug guidelines. The Pharmacogenes module is employed for prioritizing variants according to variant effect on gene function. Detailed, customizable reports are provided as exportable files and as an interactive web version. PharmVIP is a new integrated NGS workflow for the PGx community to facilitate discovery and clinical application.
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Affiliation(s)
- Jittima Piriyapongsa
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chanathip Sukritha
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Pavita Kaewprommal
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chalermpong Intarat
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Kwankom Triparn
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Krittin Phornsiricharoenphant
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Chadapohn Chaosrikul
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
| | - Philip J. Shaw
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Phayathai, Bangkok 10400, Thailand;
| | - Surakameth Mahasirimongkol
- Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Klong Luang, Pathum Thani 12120, Thailand; (C.S.); (P.K.); (C.I.); (K.T.); (K.P.); (C.C.); (S.T.)
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41
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Kuo MC, Liu SCH, Hsu YF, Wu RM. The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways. J Biomed Sci 2021; 28:78. [PMID: 34794432 PMCID: PMC8603508 DOI: 10.1186/s12929-021-00775-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson's disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson's disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.
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Affiliation(s)
- Ming-Che Kuo
- Department of Medicine, Section of Neurology, Cancer Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sam Chi-Hao Liu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ruey-Meei Wu
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
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42
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Yang ZW, Men Y, Zhang J, Liu ZH, Luo JY, Wang YH, Li WJ, Xie Q. Evaluation of Sample Preservation Approaches for Better Insect Microbiome Research According to Next-Generation and Third-Generation Sequencing. MICROBIAL ECOLOGY 2021; 82:971-980. [PMID: 33709229 DOI: 10.1007/s00248-021-01727-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/24/2021] [Indexed: 05/13/2023]
Abstract
The microbial communities associated with insects play critical roles in many physiological functions such as digestion, nutrition, and defense. Meanwhile, with the development of sequencing technology, more and more studies begin to focus on broader biodiversity of insects and the corresponding mechanisms of insect microbial symbiosis, which need longer time collecting in the field. However, few studies have evaluated the effect of insect microbiome sample preservation approaches especially in different time durations or have assessed whether these approaches are appropriate for both next-generation sequencing (NGS) and third-generation sequencing (TGS) technologies. Here, we used Tessaratoma papillosa (Hemiptera: Tessaratomidae), an important litchi pest, as the model insect and adopted two sequencing technologies to evaluate the effect of four different preservation approaches (cetyltrimethylammonium bromide (CTAB), ethanol, air dried, and RNAlater). We found the samples treated by air dried method, which entomologists adopted for morphological observation and classical taxonomy, would get worse soon. RNAlater as the most expensive approaches for insect microbiome sample preservation did not suit for field works longer than 1 month. We recommended CTAB and ethanol as better preservatives in longer time field work for their effectiveness and low cost. Comparing with the full-length 16S rRNA gene sequenced by TGS, the V4 region of 16S rRNA gene sequenced by NGS has a lower resolution trait and may misestimate the composition of microbial communities. Our results provided recommendations for suitable preservation approaches applied to insect microbiome studies based on two sequencing technologies, which can help researchers properly preserve samples in field works.
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Affiliation(s)
- Zi-Wen Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Yu Men
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Jing Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Zhi-Hui Liu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Jiu-Yang Luo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yan-Hui Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Qiang Xie
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
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43
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Takai N, Shoji K, Maki T, Kawano R. Simple Fabrication of Solid-State Nanopores on a Carbon Film. MICROMACHINES 2021; 12:mi12091135. [PMID: 34577778 PMCID: PMC8469253 DOI: 10.3390/mi12091135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 01/12/2023]
Abstract
Solid-state nanopores are widely used as a platform for stochastic nanopore sensing because they can provide better robustness, controllable pore size, and higher integrability than biological nanopores. However, the fabrication procedures, including thin film preparation and nanopore formation, require advanced micro-and nano-fabrication techniques. Here, we describe the simple fabrication of solid-state nanopores in a commercially available material: a flat thin carbon film-coated micro-grid for a transmission electron microscope (TEM). We attempted two general methods for nanopore fabrication in the carbon film. The first method was a scanning TEM (STEM) electron beam method. Nanopores were fabricated by irradiating a focused electron beam on the carbon membrane on micro-grids, resulting in the production of nanopores with pore diameters ranging from 2 to 135 nm. The second attempt was a dielectric breakdown method. In this method, nanopores were fabricated by applying a transmembrane voltage of 10 or 30 V through the carbon film on micro-grids. As a result, nanopores with pore diameters ranging from 3.7 to 1345 nm were obtained. Since these nanopores were successfully fabricated in the commercially available carbon thin film using readily available devices, we believe that these solid-state nanopores offer great utility in the field of nanopore research.
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Affiliation(s)
- Natsumi Takai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (N.T.); (T.M.)
| | - Kan Shoji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (N.T.); (T.M.)
- Department of Mechanical Engineering, Nagaoka University of Technology, Niigata 940-2188, Japan
- Correspondence: (K.S.); (R.K.)
| | - Tei Maki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (N.T.); (T.M.)
- JEOL Ltd., Tokyo 196-8558, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan; (N.T.); (T.M.)
- Correspondence: (K.S.); (R.K.)
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44
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Ahsan MU, Liu Q, Fang L, Wang K. NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks. Genome Biol 2021; 22:261. [PMID: 34488830 PMCID: PMC8419925 DOI: 10.1186/s13059-021-02472-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 08/19/2021] [Indexed: 11/24/2022] Open
Abstract
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs using long-range haplotype information, then phases long reads with called SNPs and calls indels with local realignment. Evaluation on 8 human genomes demonstrates that NanoCaller generally achieves better performance than competing approaches. We experimentally validate 41 novel variants in a widely used benchmarking genome, which could not be reliably detected previously. In summary, NanoCaller facilitates the discovery of novel variants in complex genomic regions from long-read sequencing.
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Affiliation(s)
- Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Zhang P, Ganesamoorthy D, Nguyen SH, Au R, Coin LJ, Tey SK. Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. J Immunother Cancer 2021; 8:jitc-2019-000299. [PMID: 32527930 PMCID: PMC7292043 DOI: 10.1136/jitc-2019-000299] [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] [Accepted: 03/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes. Current short-read next-generation sequencing methods require specialized instruments and large batch runs. Methods We used nanopore sequencing to analyze the vector integration sites of T cells transduced by the gammaretroviral vector, SFG.iCasp9.2A.ΔCD19. DNA from oligoclonal cell lines and polyclonal clinical samples were restriction enzyme digested with two 6-cutters, NcoI and BspHI; and the flanking genomic DNA amplified by inverse PCR or cassette ligation PCR. Following nested PCR and barcoding, the amplicons were sequenced on the Oxford Nanopore platform. Reads were filtered for quality, trimmed, and aligned. Custom tool was developed to cluster reads and merge overlapping clusters. Results Both inverse PCR and cassette ligation PCR could successfully amplify flanking genomic DNA, with cassette ligation PCR showing less bias. The 4.8 million raw reads were grouped into 12,186 clusters and 6410 clones. The 3′long terminal repeat (LTR)-genome junction could be resolved within a 5-nucleotide span for a majority of clusters and within one nucleotide span for clusters with ≥5 reads. The chromosomal distributions of the insertional sites and their predilection for regions proximate to transcription start sites were consistent with previous reports for gammaretroviral vector integrants as analyzed by short-read next-generation sequencing. Conclusion Our study shows that it is feasible to use nanopore sequencing to map polyclonal vector integration sites. The assay is scalable and requires minimum capital, which together enable cost-effective and timely analysis. Further refinement is required to reduce amplification bias and improve single nucleotide resolution.
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Affiliation(s)
- Ping Zhang
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Raymond Au
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Disease, Imperial College London, London, London, UK
| | - Siok-Keen Tey
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia .,Department of Haematology and Bone Marrow Transplantation, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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Popitsch N, Preuner S, Lion T. Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data. Bioinformatics 2021; 37:4620-4625. [PMID: 34270680 DOI: 10.1093/bioinformatics/btab526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/15/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Clinical decision making is increasingly guided by accurate and recurrent determination of presence and frequency of (somatic) variants and their haplotype through panel sequencing of disease-relevant genomic regions. Haplotype calling (phasing), however, is difficult and error prone unless variants are located on the same read which limits the ability of short-read sequencing to detect, e.g., co-occurrence of drug-resistance variants. Long-read panel sequencing enables direct phasing of amplicon variants besides having multiple other benefits, however, high error rates of current technologies prevented their applicability in the past. RESULTS We have developed Nanopanel2, a variant caller for Nanopore panel sequencing data. Nanopanel2 works directly on base-called FAST5 files and uses allele probability distributions and several other filters to robustly separate true from false positive (FP) calls. It effectively calls SNVs and INDELs with variant allele frequencies as low as 1% and 5% respectively and produces only few low-frequency false-positive calls (∼1 FP call with VAF¡5% per kb amplicon). Haplotype compositions are then determined by direct phasing. Nanopanel2 is the first somatic variant caller for Nanopore data, enabling accurate, fast (turnaround <48h) and cheap (sequencing costs ∼10$/sample) diagnostic workflows. AVAILABILITY The data for this study have been deposited at zenodo.org under DOIs accession numbers 4110691 and 4110698. Nanopanel2 is open source and available at https://github.com/popitsch/nanopanel2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Niko Popitsch
- Children's Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Sandra Preuner
- Children's Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria.,Department of Pediatrics, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
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Reyes CJ, Laabs BH, Schaake S, Lüth T, Ardicoglu R, Rakovic A, Grütz K, Alvarez-Fischer D, Jamora RD, Rosales RL, Weyers I, König IR, Brüggemann N, Klein C, Dobricic V, Westenberger A, Trinh J. Brain Regional Differences in Hexanucleotide Repeat Length in X-Linked Dystonia-Parkinsonism Using Nanopore Sequencing. NEUROLOGY-GENETICS 2021; 7:e608. [PMID: 34250228 PMCID: PMC8265576 DOI: 10.1212/nxg.0000000000000608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022]
Abstract
Objective Our study investigated the presence of regional differences in hexanucleotide repeat number in postmortem brain tissues of 2 patients with X-linked dystonia-parkinsonism (XDP), a combined dystonia-parkinsonism syndrome modified by a (CCCTCT)n repeat within the causal SINE-VNTR-Alu retrotransposon insertion in the TAF1 gene. Methods Genomic DNA was extracted from blood and postmortem brain samples, including the basal ganglia and cortex from both patients and from the cerebellum, midbrain, and pituitary gland from 1 patient. Repeat sizing was performed using fragment analysis, small-pool PCR-based Southern blotting, and Oxford nanopore sequencing. Results The basal ganglia (p < 0.001) and cerebellum (p < 0.001) showed higher median repeat numbers and higher degrees of repeat instability compared with blood. Conclusions Somatic repeat instability may predominate in brain regions selectively affected in XDP, thereby hinting at its potential role in disease manifestation and modification.
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Affiliation(s)
- Charles Jourdan Reyes
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Björn-Hergen Laabs
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Theresa Lüth
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Raphaela Ardicoglu
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Aleksandar Rakovic
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Karen Grütz
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Daniel Alvarez-Fischer
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Roland Dominic Jamora
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Raymond L Rosales
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Imke Weyers
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Inke R König
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Norbert Brüggemann
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Valerija Dobricic
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Ana Westenberger
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
| | - Joanne Trinh
- Institute of Neurogenetics (C.J.R., S.S., T.L., R.A., A.R., K.G., D.A.-F., N.B., C.K., V.D., A.W., J.T.), University of Lübeck, and Institute of Medical Biometry and Statistics (B.-H.L., I.R.K.), University of Lübeck, Germany; Department of Neurosciences (R.D.J.), College of Medicine-Philippine General Hospital, University of the Philippines Manila; Department of Neurology and Psychiatry (R.L.R.), University of Santo Tomas Hospital, Manila, Philippines; Institute of Anatomy (I.W.), Department of Neurology (N.B.), and Lübeck Interdisciplinary Platform for Genome Analytics (V.D.), University of Lübeck, Germany
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Lin B, Hui J, Mao H. Nanopore Technology and Its Applications in Gene Sequencing. BIOSENSORS-BASEL 2021; 11:bios11070214. [PMID: 34208844 PMCID: PMC8301755 DOI: 10.3390/bios11070214] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022]
Abstract
In recent years, nanopore technology has become increasingly important in the field of life science and biomedical research. By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules. One of the most successful applications of nanopore technology, the Oxford Nanopore Technology, marks the beginning of the fourth generation of gene sequencing technology. In this review, the operational principle and the technology for signal processing of the nanopore gene sequencing are documented. Moreover, this review focuses on the applications using nanopore gene sequencing technology, including the diagnosis of cancer, detection of viruses and other microbes, and the assembly of genomes. These applications show that nanopore technology is promising in the field of biological and biomedical sensing.
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Affiliation(s)
- Bo Lin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianan Hui
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-21-62511070-8707
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Reynaud L, Bouchet-Spinelli A, Janot JM, Buhot A, Balme S, Raillon C. Discrimination of α-Thrombin and γ-Thrombin Using Aptamer-Functionalized Nanopore Sensing. Anal Chem 2021; 93:7889-7897. [PMID: 34038092 DOI: 10.1021/acs.analchem.1c00461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein detection and identification at the single-molecule level are major challenges in many biotechnological fields. Solid-state nanopores have raised attention as label-free biosensors with high sensitivity. Here, we use solid-state nanopore sensing to discriminate two closely related proteins, α-thrombin and γ-thrombin. We show that aptamer functionalization improves protein discrimination thanks to a significant difference in the relative current blockade amplitude. To enhance discrimination, we postprocessed the signals using machine learning and training algorithms and we were able to reach an accuracy of 98.8% using seven features and ensemble methods.
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Affiliation(s)
- Lucile Reynaud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | | | - Jean-Marc Janot
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
| | - Sébastien Balme
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, Montpellier F-34095, France
| | - Camille Raillon
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, SyMMES, Grenoble F-38054, France
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50
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Cho SY, Gong X, Koman VB, Kuehne M, Moon SJ, Son M, Lew TTS, Gordiichuk P, Jin X, Sikes HD, Strano MS. Cellular lensing and near infrared fluorescent nanosensor arrays to enable chemical efflux cytometry. Nat Commun 2021; 12:3079. [PMID: 34035262 PMCID: PMC8149711 DOI: 10.1038/s41467-021-23416-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nanosensors have proven to be powerful tools to monitor single cells, achieving spatiotemporal precision even at molecular level. However, there has not been way of extending this approach to statistically relevant numbers of living cells. Herein, we design and fabricate nanosensor array in microfluidics that addresses this limitation, creating a Nanosensor Chemical Cytometry (NCC). nIR fluorescent carbon nanotube array is integrated along microfluidic channel through which flowing cells is guided. We can utilize the flowing cell itself as highly informative Gaussian lenses projecting nIR profiles and extract rich information. This unique biophotonic waveguide allows for quantified cross-correlation of biomolecular information with various physical properties and creates label-free chemical cytometer for cellular heterogeneity measurement. As an example, the NCC can profile the immune heterogeneities of human monocyte populations at attomolar sensitivity in completely non-destructive and real-time manner with rate of ~600 cells/hr, highest range demonstrated to date for state-of-the-art chemical cytometry.
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Affiliation(s)
- Soo-Yeon Cho
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manki Son
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tedrick Thomas Salim Lew
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pavlo Gordiichuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiaojia Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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