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Song Z, Lian S, Mak S, Chow MZY, Xu C, Wang W, Keung HY, Lu C, Kebede FT, Gao Y, Cheuk W, Cho WCS, Yang M, Zheng Z. Deep RNA Sequencing Revealed Fusion Junctional Heterogeneity May Predict Crizotinib Treatment Efficacy in ALK-Rearranged NSCLC. J Thorac Oncol 2021; 17:264-276. [PMID: 34626839 DOI: 10.1016/j.jtho.2021.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Gene fusion variants in ALK-rearranged NSCLC may predict patient outcomes, but previous results have been inconclusive. Fusion isoforms coexisting in the same tumor may affect the efficacy of targeted therapy, but they have not been investigated. METHODS Patients with ALK-rearranged NSCLC who received crizotinib treatments were recruited. Precrizotinib tumor tissues were analyzed by the anchored multiplex polymerase chain reaction for targeted RNA sequencing. Kaplan-Meier and Cox regression were used to compare overall and progression-free survivals. RESULTS Of the 51 studied subjects, EML4-ALK variant types v1, v2, v3, and others were detected in 23 (45.1%), five (9.8%), 19 (37.3%), and four patients (7.8%), respectively. Multiple EML4-ALK RNA isoforms were detected in 24 tumors (47.1%), and single isoform in 27 (52.9%). Most of the v3 tumors (16 of 19) harbored both v3a and v3b RNA isoforms. Multiple isoforms were also detected in eight non-v3 tumors (33.3% of all 24 multiple isoforms; five v1, two v5', and one v2). Compared with patients with single isoform, those with multiple isoforms had worse progression-free (hazard ratio and 95% confidence interval: 2.45 [1.06-5.69]) and overall (hazard ratio [95% confidence interval]: 3.74 [1.26-11.13]) survivals after adjusting for potential confounders including variant type. Using the patient-derived H2228 cells known to express v3a and v3b, our single-cell polymerase chain reaction detected either v3a or v3b in most single cells. Treatment of H2228 cells by three ALK inhibitors revealed increased ratios of v3a-to-v3b expression over time. CONCLUSIONS Intratumoral EML4-ALK isoforms may predict the efficacy of targeted therapy in ALK-rearranged NSCLC. Temporal changes of intratumoral fusion isoforms may result from differential selection pressures that a drug might have on one isoform over another. Larger studies on fusion heterogeneity using RNA sequencing are warranted.
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Affiliation(s)
- Zhengbo Song
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, People's Republic of China; Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, People's Republic of China
| | - Shifeng Lian
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Silvia Mak
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Sha Tin, Hong Kong Special Administrative Region of the People's Republic of China
| | - Maggie Zi-Ying Chow
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Sha Tin, Hong Kong Special Administrative Region of the People's Republic of China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, People's Republic of China
| | - Wenxian Wang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, People's Republic of China; Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, People's Republic of China
| | - Hoi Yee Keung
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, People's Republic of China
| | - Chenyu Lu
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China; Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, People's Republic of China
| | - Firaol Tamiru Kebede
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Yanqiu Gao
- Helitec Limited, Shenzhen, People's Republic of China
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China; Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, People's Republic of China
| | - Zongli Zheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Sha Tin, Hong Kong Special Administrative Region of the People's Republic of China; Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region of the People's Republic of China; Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, People's Republic of China.
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Atkins A, Chung CH, Allen AG, Dampier W, Gurrola TE, Sariyer IK, Nonnemacher MR, Wigdahl B. Off-Target Analysis in Gene Editing and Applications for Clinical Translation of CRISPR/Cas9 in HIV-1 Therapy. Front Genome Ed 2021; 3:673022. [PMID: 34713260 PMCID: PMC8525399 DOI: 10.3389/fgeed.2021.673022] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022] Open
Abstract
As genome-editing nucleases move toward broader clinical applications, the need to define the limits of their specificity and efficiency increases. A variety of approaches for nuclease cleavage detection have been developed, allowing a full-genome survey of the targeting landscape and the detection of a variety of repair outcomes for nuclease-induced double-strand breaks. Each approach has advantages and disadvantages relating to the means of target-site capture, target enrichment mechanism, cellular environment, false discovery, and validation of bona fide off-target cleavage sites in cells. This review examines the strengths, limitations, and origins of the different classes of off-target cleavage detection systems including anchored primer enrichment (GUIDE-seq), in situ detection (BLISS), in vitro selection libraries (CIRCLE-seq), chromatin immunoprecipitation (ChIP) (DISCOVER-Seq), translocation sequencing (LAM PCR HTGTS), and in vitro genomic DNA digestion (Digenome-seq and SITE-Seq). Emphasis is placed on the specific modifications that give rise to the enhanced performance of contemporary techniques over their predecessors and the comparative performance of techniques for different applications. The clinical relevance of these techniques is discussed in the context of assessing the safety of novel CRISPR/Cas9 HIV-1 curative strategies. With the recent success of HIV-1 and SIV-1 viral suppression in humanized mice and non-human primates, respectively, using CRISPR/Cas9, rigorous exploration of potential off-target effects is of critical importance. Such analyses would benefit from the application of the techniques discussed in this review.
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Affiliation(s)
- Andrew Atkins
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore E. Gurrola
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, United States,*Correspondence: Brian Wigdahl
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Carøe C, Bohmann K. Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Mol Ecol Resour 2020; 20:1620-1631. [PMID: 32663358 DOI: 10.1111/1755-0998.13227] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) and DNA extracted from bulk specimen samples is a powerful tool in studies of biodiversity, diet and ecological interactions as its inherent labelling of amplicons allows sequencing of taxonomically informative genetic markers from many samples in parallel. However, the occurrence of so-called 'tag-jumps' can cause incorrect assignment of sequences to samples and artificially inflate diversity. Two steps during library preparation of pools of 5' nucleotide-tagged amplicons have been suggested to cause tag-jumps: (a) T4 DNA polymerase blunt-ending in the end-repair step and (b) postligation PCR amplification of amplicon libraries. The discovery of tag-jumps has led to recommendations to only carry out metabarcoding PCR amplifications with primers carrying twin-tags to ensure that tag-jumps cannot result in false assignments of sequences to samples. As this increases both cost and workload, a metabarcoding library preparation protocol which circumvents the two steps that causes tag-jumps is needed. Here, we demonstrate Tagsteady, a PCR-free metabarcoding Illumina library preparation protocol for pools of nucleotide-tagged amplicons that enables efficient and cost-effective generation of metabarcoding data with virtually no tag-jumps. We use pools of twin-tagged amplicons to investigate the effect of T4 DNA polymerase blunt-ending and postligation PCR on the occurrence of tag-jumps and demonstrate that both blunt-ending and postligation PCR, alone or together, can result in detrimental amounts of tag-jumps (here, up to ca. 49% of total sequences), while leaving both steps out (the Tagsteady protocol) results in amounts of sequences carrying new combinations of used tags (tag-jumps) comparable to background contamination.
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Affiliation(s)
- Christian Carøe
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Vu LT, Long NT, Brito B, Stenfeldt C, Phuong NT, Hoang BH, Pauszek SJ, Hartwig EJ, Smoliga GR, Vu PP, Quang LTV, Hung VV, Tho ND, Dong PV, Minh PQ, Bertram M, Fish IH, Rodriguez LL, Dung DH, Arzt J. First detection of foot-and-mouth disease virus O/Ind-2001d in Vietnam. PLoS One 2017; 12:e0177361. [PMID: 28599321 PMCID: PMC5466432 DOI: 10.1371/journal.pone.0177361] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/17/2017] [Indexed: 01/09/2023] Open
Abstract
In recent years, foot-and-mouth disease virus (FMDV) serotype O, topotype Middle East-South Asia (ME-SA), lineage Ind-2001d has spread from the Indian subcontinent to the Middle East, North Africa, and Southeast Asia. In the current report, we describe the first detection of this lineage in Vietnam in May, 2015 in Đắk Nông province. Three subsequent outbreaks caused by genetically related viruses occurred between May–October, 2015 after which the virus was not detected in clinical outbreaks for at least 15 subsequent months. The observed outbreaks affected (in chronological order): cattle in Đắk Nông province, pigs in Đắk Lắk province and Đắk Nông province, and cattle in Ninh Thuận province. The clinical syndromes associated with these outbreaks were consistent with typical FMD in the affected species. Overall attack rate on affected premises was 0.85 in pigs and 0.93 in cattle over the course of the outbreak. Amongst 378 pigs at risk on affected premises, 85 pigs died during the outbreaks; there were no deaths among cattle. The manner in which FMDV/O/ME-SA/Ind-2001d was introduced into Vietnam remains undetermined; however, movement of live cattle is the suspected route. This incursion has substantial implications for epidemiology and control of FMD in Southeast Asia.
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Affiliation(s)
- Le T. Vu
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Ngo T. Long
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Barbara Brito
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Carolina Stenfeldt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Nguyen T. Phuong
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Bui H. Hoang
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Steven J. Pauszek
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
| | - Ethan J. Hartwig
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
| | - George R. Smoliga
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
| | - Pham P. Vu
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Le T. V. Quang
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Vo V. Hung
- Regional Animal Health Office No. 6, Department of Animal Health, Ministry of Agriculture and Rural Development, Ho Chi Minh City, Vietnam
| | - Nguyen D. Tho
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Pham V. Dong
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Phan Q. Minh
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Miranda Bertram
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Ian H. Fish
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
- Oak Ridge Institute for Science and Education, PIADC Research Participation Program, Oak Ridge, TN, United States of America
| | - Luis L. Rodriguez
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
| | - Do H. Dung
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
- * E-mail: (JA); (DHD)
| | - Jonathan Arzt
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, ARS, USDA, Orient Point, NY, United States of America
- * E-mail: (JA); (DHD)
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Chan S, Frasch A, Mandava CS, Ch'ng JH, Quintana MDP, Vesterlund M, Ghorbal M, Joannin N, Franzén O, Lopez-Rubio JJ, Barbieri S, Lanzavecchia A, Sanyal S, Wahlgren M. Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor. Nat Microbiol 2017; 2:17068. [PMID: 28481333 DOI: 10.1038/nmicrobiol.2017.68] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/29/2017] [Indexed: 12/22/2022]
Abstract
Pregnancy-associated malaria commonly involves the binding of Plasmodium falciparum-infected erythrocytes to placental chondroitin sulfate A (CSA) through the PfEMP1-VAR2CSA protein. VAR2CSA is translationally repressed by an upstream open reading frame. In this study, we report that the P. falciparum translation enhancing factor (PTEF) relieves upstream open reading frame repression and thereby facilitates VAR2CSA translation. VAR2CSA protein levels in var2csa-transcribing parasites are dependent on the expression level of PTEF, and the alleviation of upstream open reading frame repression requires the proteolytic processing of PTEF by PfCalpain. Cleavage generates a C-terminal domain that contains a sterile-alpha-motif-like domain. The C-terminal domain is permissive to cytoplasmic shuttling and interacts with ribosomes to facilitate translational derepression of the var2csa coding sequence. It also enhances translation in a heterologous translation system and thus represents the first non-canonical translation enhancing factor to be found in a protozoan. Our results implicate PTEF in regulating placental CSA binding of infected erythrocytes.
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Affiliation(s)
- Sherwin Chan
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Alejandra Frasch
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Jun-Hong Ch'ng
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Department of Microbiology, National University of Singapore 117545, Singapore
| | - Maria Del Pilar Quintana
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden.,Escuela de Medicina y Ciencias de la Salud, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Calle 12C No. 6-25, Bogotá, Colombia
| | - Mattias Vesterlund
- Cancer Proteomics, Department of Oncology-Pathology, Karolinska Institutet, 17176 Stockholm, Sweden
| | - Mehdi Ghorbal
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Nicolas Joannin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
| | - Oscar Franzén
- Department of Genetics and Genomic Sciences, Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Jose-Juan Lopez-Rubio
- University of Montpellier, Faculty of Medicine, Laboratory of Parasitology-Mycology, Montpellier F34090, France.,CNRS - 5290, IRD 224 - University of Montpellier (UMR 'MiVEGEC'), Montpellier, France
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Box-596, 751 24 Uppsala, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Box 280, Nobels väg 16, 171 77 Stockholm, Sweden
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Song H, Ekheden IG, Zheng Z, Ericsson J, Nyrén O, Ye W. Incidence of gastric cancer among patients with gastric precancerous lesions: observational cohort study in a low risk Western population. BMJ 2015; 351:h3867. [PMID: 26215280 PMCID: PMC4516137 DOI: 10.1136/bmj.h3867] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To accurately measure the incidence of gastric cancer among patients with gastric precancerous lesions, and to quantify the excess incidence in comparison with people with normal mucosa on endoscopy and a general population. DESIGN Population based cohort study. SETTING Population of Sweden using data from its national disease registers. PARTICIPANTS 405,172 patients who had gastric biopsy samples taken for non-malignant indications between 1979 and 2011. MAIN OUTCOME MEASURES Incidence of gastric cancer, reported separately for patients with different mucosal changes in biopsy samples. Standardised incidence ratios provided estimation of the relative risk, using the general Swedish population as reference; and hazard ratios were derived from Cox regression modelling for internal comparisons with patients with normal gastric mucosa. RESULTS After excluding the first two years of follow-up, 1599 cases of gastric cancer were identified. The annual crude incidence of gastric cancer was 20 × 10(-5) for those in the normal mucosa group (standardised incidence ratio 1.0), 42 × 10(-5) for those with minor changes (1.5), 59 × 10(-5) for the gastritis group (1.8), 100 × 10(-5) for the atrophic gastritis group (2.8), 129 × 10(-5) for the intestinal metaplasia group (3.4), and 263 × 10(-5) for the dysplasia group (6.5). Cox regression modelling confirmed that excess risks increased monotonically with progressive severity of gastric lesions, with the highest hazard ratio of 10.9 (dysplasia versus normal mucosa, 95% confidence interval 7.7 to 15.4). The increased incidence was stable throughout the follow-up period, and the gaps between cumulative incidence curves grew continuously. CONCLUSIONS Among patients who undergo gastroscopy with biopsy for clinical indications, approximately 1 in 256 with normal mucosa, 1 in 85 with gastritis, 1 in 50 with atrophic gastritis, 1 in 39 with intestinal metaplasia, and 1 in 19 with dysplasia will develop gastric cancer within 20 years. These numbers, along with cost-benefit analyses, should guide future surveillance policies for these particular patient groups.
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Affiliation(s)
- Huan Song
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Isabella Guncha Ekheden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Zongli Zheng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jan Ericsson
- Department of Pathology, Karolinska Hospital, Sweden
| | - Olof Nyrén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
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Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J, Pao W, Engelman JA, Iafrate AJ, Le LP. Anchored multiplex PCR for targeted next-generation sequencing. Nat Med 2014; 20:1479-84. [PMID: 25384085 DOI: 10.1038/nm.3729] [Citation(s) in RCA: 661] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 07/29/2014] [Indexed: 12/13/2022]
Abstract
We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5-100%) and 100% specificity (95% confidence limit: 99.3-100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.
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Affiliation(s)
- Zongli Zheng
- 1] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Liebers
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Boryana Zhelyazkova
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yi Cao
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Divya Panditi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kerry D Lynch
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Juxiang Chen
- 1] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Department of Neurosurgery, Shanghai Changzheng Hospital, Shanghai, China
| | - Hayley E Robinson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Hyo Sup Shim
- 1] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | | | - William Pao
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey A Engelman
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - A John Iafrate
- 1] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Long Phi Le
- 1] Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA. [2] Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
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8
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Hansen MF, Neckmann U, Lavik LAS, Vold T, Gilde B, Toft RK, Sjursen W. A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes. Mol Genet Genomic Med 2014; 2:186-200. [PMID: 24689082 PMCID: PMC3960061 DOI: 10.1002/mgg3.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/21/2013] [Accepted: 12/02/2013] [Indexed: 11/11/2022] Open
Abstract
The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing.
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Affiliation(s)
- Maren F Hansen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Ulrike Neckmann
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Liss A S Lavik
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Trine Vold
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Bodil Gilde
- Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
| | - Ragnhild K Toft
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway
| | - Wenche Sjursen
- Department of Laboratory Medicine, Children and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology Trondheim, Norway ; Department of Pathology and Medical Genetics, St. Olavs Hospital Trondheim, Norway
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9
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Džunková M, Garcia-Garcerà M, Martínez-Priego L, D’Auria G, Calafell F, Moya A. Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate. PLoS One 2014; 9:e97379. [PMID: 24887077 PMCID: PMC4041646 DOI: 10.1371/journal.pone.0097379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/17/2014] [Indexed: 02/07/2023] Open
Abstract
The large amount of DNA needed to prepare a library in next generation sequencing protocols hinders direct sequencing of small DNA samples. This limitation is usually overcome by the enrichment of such samples with whole genome amplification (WGA), mostly by multiple displacement amplification (MDA) based on φ29 polymerase. However, this technique can be biased by the GC content of the sample and is prone to the development of chimeras as well as contamination during enrichment, which contributes to undesired noise during sequence data analysis, and also hampers the proper functional and/or taxonomic assignments. An alternative to MDA is direct DNA sequencing (DS), which represents the theoretical gold standard in genome sequencing. In this work, we explore the possibility of sequencing the genome of Escherichia coli fs 24 from the minimum number of DNA molecules required for pyrosequencing, according to the notion of one-bead-one-molecule. Using an optimized protocol for DS, we constructed a shotgun library containing the minimum number of DNA molecules needed to fill a selected region of a picotiterplate. We gathered most of the reference genome extension with uniform coverage. We compared the DS method with MDA applied to the same amount of starting DNA. As expected, MDA yielded a sparse and biased read distribution, with a very high amount of unassigned and unspecific DNA amplifications. The optimized DS protocol allows unbiased sequencing to be performed from samples with a very small amount of DNA.
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Affiliation(s)
- Mária Džunková
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Marc Garcia-Garcerà
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Llúcia Martínez-Priego
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
| | - Giussepe D’Auria
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
| | - Francesc Calafell
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Andrés Moya
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO-Salud Pública), Valencia, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública (CIBEResp), Madrid, Spain
- * E-mail:
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10
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Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. mBio 2013; 4:e00569-12. [PMID: 23716574 PMCID: PMC3663571 DOI: 10.1128/mbio.00569-12] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The verrucomicrobial subdivision 2 class Spartobacteria is one of the most abundant bacterial lineages in soil and has recently also been found to be ubiquitous in aquatic environments. A 16S rRNA gene study from samples spanning the entire salinity range of the Baltic Sea indicated that, in the pelagic brackish water, a phylotype of the Spartobacteria is one of the dominating bacteria during summer. Phylogenetic analyses of related 16S rRNA genes indicate that a purely aquatic lineage within the Spartobacteria exists. Since no aquatic representative from the Spartobacteria has been cultured or sequenced, the metabolic capacity and ecological role of this lineage are yet unknown. In this study, we reconstructed the genome and metabolic potential of the abundant Baltic Sea Spartobacteria phylotype by metagenomics. Binning of genome fragments by nucleotide composition and a self-organizing map recovered the near-complete genome of the organism, the gene content of which suggests an aerobic heterotrophic metabolism. Notably, we found 23 glycoside hydrolases that likely allow the use of a variety of carbohydrates, like cellulose, mannan, xylan, chitin, and starch, as carbon sources. In addition, a complete pathway for sulfate utilization was found, indicating catabolic processing of sulfated polysaccharides, commonly found in aquatic phytoplankton. The high frequency of glycoside hydrolase genes implies an important role of this organism in the aquatic carbon cycle. Spatiotemporal data of the phylotype’s distribution within the Baltic Sea indicate a connection to Cyanobacteria that may be the main source of the polysaccharide substrates. The ecosystem roles of many phylogenetic lineages are not yet well understood. One such lineage is the class Spartobacteria within the Verrucomicrobia that, despite being abundant in soil and aquatic systems, is relatively poorly studied. Here we circumvented the difficulties of growing aquatic Verrucomicrobia by applying shotgun metagenomic sequencing on a water sample from the Baltic Sea. By using a method based on sequence signatures, we were able to in silico isolate genome fragments belonging to a phylotype of the Spartobacteria. The genome, which represents the first aquatic representative of this clade, encodes a diversity of glycoside hydrolases that likely allow degradation of various complex carbohydrates. Since the phylotype cooccurs with Cyanobacteria, these may be the primary producers of the carbohydrate substrates. The phylotype, which is highly abundant in the Baltic Sea during summer, may thus play an important role in the carbon cycle of this ecosystem.
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11
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Abstract
MOTIVATION Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the estimation of diversity and composition of a sample. To date, there are several tools that aim to remove both sequencing noise and duplicates. Nevertheless, duplicate removal is often based on nucleotide sequences rather than on the underlying flow values, which contain additional information. RESULTS With the novel tool JATAC, we present an approach towards a more accurate duplicate removal by analysing flow values directly. Making use of previous findings on 454 flow data characteristics, we combine read clustering with Bayesian distance measures. Finally, we provide a benchmark with an existing algorithm. AVAILABILITY JATAC is freely available under the General Public License from http://malde.org/ketil/jatac/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Susanne Balzer
- Norwegian Marine Data Centre, Institute of Marine Research, P.O. Box 1870, N-5817 Bergen, Norway
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12
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Londin E, Yadav P, Surrey S, Kricka LJ, Fortina P. Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations. Methods Mol Biol 2013; 1015:127-46. [PMID: 23824853 DOI: 10.1007/978-1-62703-435-7_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
For the past two decades, linkage analysis and genome-wide analysis have greatly advanced our knowledge of the human genome. But despite these successes the genetic architecture of diseases remains unknown. More recently, the availability of next-generation sequencing has dramatically increased our capability for determining DNA sequences that range from large portions of one individual's genome to targeted regions of many genomes in a cohort of interest. In this review, we highlight the successes and shortcomings that have been achieved using genome-wide association studies (GWAS) to identify the variants contributing to disease. We further review the methods and use of new technologies, based on next-generation sequencing, that are becoming increasingly used to expand our knowledge of the causes of genetic disease.
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Affiliation(s)
- Eric Londin
- Computational Medicine Center, Thomas Jefferson University Jefferson Medical College, Philadelphia, PA, USA
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13
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Solonenko SA, Sullivan MB. Preparation of metagenomic libraries from naturally occurring marine viruses. Methods Enzymol 2013; 531:143-65. [PMID: 24060120 DOI: 10.1016/b978-0-12-407863-5.00008-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated by an inability to culture the vast majority of naturally occurring diversity coupled with the lack of robust, quantitative, culture-independent methods for studying this uncultured majority. However, for double-stranded DNA phages, a quantitative viral metagenomic sample-to-sequence workflow now exists. Here, we review these advances with special emphasis on the technical details of preparing DNA sequencing libraries for metagenomic sequencing from environmentally relevant low-input DNA samples. Library preparation steps broadly involve manipulating the sample DNA by fragmentation, end repair and adaptor ligation, size fractionation, and amplification. One critical area of future research and development is parallel advances for alternate nucleic acid types such as single-stranded DNA and RNA viruses that are also abundant in nature. Combinations of recent advances in fragmentation (e.g., acoustic shearing and tagmentation), ligation reactions (adaptor-to-template ratio reference table availability), size fractionation (non-gel-sizing), and amplification (linear amplification for deep sequencing and linker amplification protocols) enhance our ability to generate quantitatively representative metagenomic datasets from low-input DNA samples. Such datasets are already providing new insights into the role of viruses in marine systems and will continue to do so as new environments are explored and synergies and paradigms emerge from large-scale comparative analyses.
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Affiliation(s)
- Sergei A Solonenko
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
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14
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Loewe RP. Combinational usage of next generation sequencing and qPCR for the analysis of tumor samples. Methods 2012. [PMID: 23178393 DOI: 10.1016/j.ymeth.2012.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The combination of multiple techniques especially those adding complementary information have proven to be beneficial in terms of data consistency. The employment of quantitative PCR (qPCR) prior to next generation sequencing (NGS) methods such as RNA-Seq and mutational analysis presented here does not only enhance data in terms of CNV integration and sample choice, but also allows a faster and more efficient workflow. Correct analysis of libraries prior to sequencing has proven to be a vital step for specific assumption and to some extent for a more parallel testing. By illustrating the combination of qPCR and NGS in oncological examples, the potential of this approach is presented.
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Affiliation(s)
- Robert P Loewe
- GeneWake GmbH, Floriansbogen 2-4, 82061 Neuried bei Muenchen, Germany.
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15
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Yang X, Zhang X, Yuan D, Jin F, Zhang Y, Xu J. Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC PLANT BIOLOGY 2012; 12:110. [PMID: 22817809 PMCID: PMC3483692 DOI: 10.1186/1471-2229-12-110] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 07/20/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Somatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate and reorganize into new plants, is a notable illustration of cell totipotency. However, the precise molecular mechanisms regulating SE remain unclear. To characterize the molecular events of this unique process, transcriptome analysis, in combination with biochemical and histological approaches, were conducted in cotton, a typical plant species in SE. Genome-wide profiling of gene expression allowed the identification of novel molecular markers characteristic of this developmental process. RESULTS RNA-Seq was used to identify 5,076 differentially expressed genes during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process, associated with morphological, histological changes and endogenous indole-3-acetic acid (IAA) alteration. Bioinformatics analysis showed that the genes were enriched for basic processes such as metabolic pathways and biosynthesis of secondary metabolites. Unigenes were abundant for the functions of protein binding and hydrolase activity. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein/indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. CONCLUSION We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis.
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Affiliation(s)
- Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Fangyan Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Yunchao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
| | - Jiao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, P. R. China
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16
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Abbai NS, Govender A, Shaik R, Pillay B. Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocarbon-contaminated groundwater. Mol Biotechnol 2012; 50:39-48. [PMID: 21656086 DOI: 10.1007/s12033-011-9412-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Pyrosequence data was used to analyze the composition and metabolic potential of a metagenome from a hydrocarbon-contaminated site. Unamplified and whole genome amplified (WGA) sequence data was compared from this source. According to MG-RAST, an additional 2,742,252 bp of DNA was obtained with the WGA, indicating that WGA has the ability to generate a large amount of DNA from a small amount of starting sample. However, it was observed that WGA introduced a bias with respect to the distribution of the amplified DNA and the types of microbial populations that were accessed from the metagenome. The dominant order in the WGA metagenome was Flavobacteriales, whereas the unamplified metagenome was dominated by Actinomycetales as determined by RDPII and CARMA databases. According to the SEED database, the subsystems shown to be present for the individual metagenomes were associated with the metabolic potential that was expected to be present in the contaminated groundwater, such as the metabolism of aromatic compounds. A higher percentage (4.4) of genes associated with the metabolism of aromatic compounds was identified in the unamplified metagenome when compared to the WGA metagenome (0.66%). This could be attributed to the increased number of hydrocarbon degrading bacteria that had been accessed from this metagenome (Mycobacteria, Nocardia, Brevibacteria, Clavibacter, Rubrobacter, and Rhodoccocus). Therefore, it was possible to relate the taxonomic groups accessed to the contamination profile of the metagenome. By collating the sequencing data obtained pre- and post-amplification, this study provided insight regarding the survival strategies of microbial communities inhabiting contaminated environments.
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Affiliation(s)
- Nathlee S Abbai
- Discipline of Microbiology, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, Republic of South Africa
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17
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Zheng Z, Andersson AF, Ye W, Nyrén O, Normark S, Engstrand L. A method for metagenomics of Helicobacter pylori from archived formalin-fixed gastric biopsies permitting longitudinal studies of carcinogenic risk. PLoS One 2011; 6:e26442. [PMID: 22031833 PMCID: PMC3198776 DOI: 10.1371/journal.pone.0026442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 09/27/2011] [Indexed: 12/22/2022] Open
Abstract
The human microbiota has come into focus in the search for component causes of chronic diseases, such as gastrointestinal cancers. Presumably long induction periods and altered local environments after disease onset call for the development of methods for characterization of microorganisms colonizing the host decades before disease onset. Sequencing of microbial genomes in old formalin-fixed and paraffin-embedded (FFPE) gastrointestinal biopsies provides a means for such studies but is still challenging. Here we report a method based on laser capture micro-dissection and modified Roche 454 high-throughput pyrosequencing to obtain metagenomic profiles of Helicobacter pylori. We applied this method to two 15 year old FFPE biopsies from two patients. Frozen homogenized biopsies from the same gastroscopy sessions were also available for comparison after re-culture of H. pylori. For both patients, H. pylori DNA dissected from FFPE sections had ∼96.4% identity with culture DNA from the same patients, while only ∼92.5% identity with GenBank reference genomes, and with culture DNA from the other patient. About 82% and 60% of the predicted genes in the two genomes were captured by at least a single sequencing read. Along with sequences displaying high similarity to known H. pylori genes, novel and highly variant H. pylori sequences were identified in the FFPE sections by our physical enrichment approach, which would likely not have been detected by a sequence capture approach. The study demonstrates the feasibility of longitudinal metagenomic studies of H. pylori using decade-preserved FFPE biopsies.
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Affiliation(s)
- Zongli Zheng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anders F. Andersson
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Olof Nyrén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Swedish Institute for Communicable Disease Control, Solna, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Swedish Institute for Communicable Disease Control, Solna, Sweden
- * E-mail:
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18
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Jiang Q, Turner T, Sosa MX, Rakha A, Arnold S, Chakravarti A. Rapid and efficient human mutation detection using a bench-top next-generation DNA sequencer. Hum Mutat 2011; 33:281-9. [PMID: 21898659 DOI: 10.1002/humu.21602] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/19/2011] [Indexed: 12/20/2022]
Abstract
Next-generation sequencing (NGS) technologies can be a boon to human mutation detection given their high throughput: consequently, many genes and samples may be simultaneously studied with high coverage for accurate detection of heterozygotes. In circumstances requiring the intensive study of a few genes, particularly in clinical applications, a rapid turn around is another desirable goal. To this end, we assessed the performance of the bench-top 454 GS Junior platform as an optimized solution for mutation detection by amplicon sequencing of three type 3 semaphorin genes SEMA3A, SEMA3C, and SEMA3D implicated in Hirschsprung disease (HSCR). We performed mutation detection on 39 PCR amplicons totaling 14,014 bp in 47 samples studied in pools of 12 samples. Each 10-hr run was able to generate ∼75,000 reads and ∼28 million high-quality bases at an average read length of 371 bp. The overall sequencing error was 0.26 changes per kb at a coverage depth of ≥20 reads. Altogether, 37 sequence variants were found in this study of which 10 were unique to HSCR patients. We identified five missense mutations in these three genes that may potentially be involved in the pathogenesis of HSCR and need to be studied in larger patient samples.
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Affiliation(s)
- Qian Jiang
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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19
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Rapid flow-sorting to simultaneously resolve multiplex massively parallel sequencing products. Sci Rep 2011; 1:108. [PMID: 22355625 PMCID: PMC3216591 DOI: 10.1038/srep00108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/22/2011] [Indexed: 11/21/2022] Open
Abstract
Sample preparation for Roche/454, ABI/SOLiD and Life Technologies/Ion Torrent sequencing are based on amplification of library fragments on the surface of beads prior to sequencing. Commonly, libraries are barcoded and pooled, to maximise the sequence output of each sequence run. Here, we describe a novel approach for normalization of multiplex next generation sequencing libraries after emulsion PCR. Briefly, amplified libraries carrying unique barcodes are prepared by fluorescent tagging of complementary sequences and then resolved by high-speed flow cytometric sorting of labeled emulsion PCR beads. The protocol is simple and provides an even sequence distribution of multiplex libraries when sequencing the flow-sorted beads. Moreover, since many empty and mixed emulsion PCR beads are removed, the approach gives rise to a substantial increase in sequence quality and mean read length, as compared to that obtained by standard enrichment protocols.
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20
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Abstract
We describe a protocol for construction and quantification of libraries for emulsion PCR (emPCR)-based sequencing platforms such as Roche 454 or Ion Torrent PGM. The protocol involves library construction using customized Y adapters, quantification using TaqMan-MGB (minor groove binder) probe-based quantitative PCR (qPCR) and calculation of an optimal template-to-bead ratio based on Poisson statistics, thereby avoiding the need for a laborious titration assay. Unlike other qPCR methods, the TaqMan-MGB probe specifically quantifies effective libraries in molar concentration and does not require specialized equipment. A single quality control step prior to emulsion PCR ensures that libraries contain no adapter dimers and have an optimal length distribution. The presented protocol takes ∼7 h to prepare eight barcoded libraries from genomic DNA into libraries that are ready to use for full-scale emPCR. It will be useful, for example, to allow analyses of precious clinical samples and amplification-free metatranscriptomics.
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Huang J, Zheng Z, Andersson AF, Engstrand L, Ye W. Rapid screening of complex DNA samples by single-molecule amplification and sequencing. PLoS One 2011; 6:e19723. [PMID: 21625543 PMCID: PMC3098247 DOI: 10.1371/journal.pone.0019723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/08/2011] [Indexed: 11/19/2022] Open
Abstract
Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
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Affiliation(s)
- Jiaqi Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Zongli Zheng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Anders F. Andersson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Swedish Institute for Communicable Infectious Disease Control, Solna, Sweden
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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22
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Lin YS, Liu FGR, Wang TY, Pan CT, Chang WT, Li WH. A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples. Nucleic Acids Res 2010; 39:e28. [PMID: 21131285 PMCID: PMC3061071 DOI: 10.1093/nar/gkq1249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A practical way to reduce the cost of surveying single-nucleotide polymorphism (SNP) in a large number of individuals is to measure the allele frequencies in pooled DNA samples. PyrosequencingTM has been frequently used for this application because signals generated by this approach are proportional to the amount of DNA templates. The PyrosequencingTM pyrogram is determined by the dispensing order of dNTPs, which is usually designed based on the known SNPs to avoid asynchronistic extensions of heterozygous sequences. Therefore, utilizing the pyrogram signals to identify de novo SNPs in DNA pools has never been undertook. Here, in this study we developed an algorithm to address this issue. With the sequence and pyrogram of the wild-type allele known in advance, we could use the pyrogram obtained from the pooled DNA sample to predict the sequence of the unknown mutant allele (de novo SNP) and estimate its allele frequency. Both computational simulation and experimental PyrosequencingTM test results suggested that our method performs well. The web interface of our method is available at http://life.nctu.edu.tw/∼yslin/PSM/.
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Affiliation(s)
- Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
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