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Ivanov V, Lee KM, Mutanen M. ddRAD Sequencing and DNA Barcoding. Methods Mol Biol 2024; 2744:213-221. [PMID: 38683321 DOI: 10.1007/978-1-0716-3581-0_13] [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: 05/01/2024]
Abstract
Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.
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Affiliation(s)
- Vladislav Ivanov
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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2
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Ahn J, Jeong H, Seo BG, Park KS, Hwangbo C, Kim HG, Koh JS, Kim J. Genome-wide association study for vascular aging highlights pathways shared with cardiovascular traits in Koreans. Front Cardiovasc Med 2022; 9:1058308. [PMID: 36620623 PMCID: PMC9813851 DOI: 10.3389/fcvm.2022.1058308] [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: 09/30/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Vascular aging plays a pivotal role in the morbidity and mortality of older people. Reactive hyperemia index (RHI) detected by pulse amplitude tonometry (PAT) is a non-invasive measure of vascular endothelial function and aging-induced pathogenesis of both microvascular and macrovascular diseases. We conducted a genome-wide association study (GWAS) to comprehensively identify germline genetic variants associated with vascular aging in a Korean population, which revealed 60 suggestive genes underlying angiogenesis, inflammatory response in blood vessels, and cardiovascular diseases. Subsequently, we show that putative protective alleles were significantly enriched in an independent population with decelerated vascular aging phenotypes. Finally, we show the differential mRNA expression levels of putative causal genes in aging human primary endothelial cells via quantitative real-time polymerase chain reaction (PCR). These results highlight the potential contribution of genetic variants in the etiology of vascular aging and may suggest the link between vascular aging and cardiovascular traits.
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Affiliation(s)
- JaeKyoung Ahn
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Hankyeol Jeong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Bo-Gyeong Seo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Division of Life Science, College of National Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki-Soo Park
- Department of Preventive Medicine, College of Medicine and Institute of Health Science, Gyeongsang National University, Jinju, Republic of Korea,Center for Farmer’s Safety and Health, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Cheol Hwangbo
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Division of Life Science, College of National Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Han-Gyul Kim
- Department of Internal Medicine, Gyeongsang National University School of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jin-Sin Koh
- Department of Internal Medicine, Gyeongsang National University School of Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea,*Correspondence: Jin-Sin Koh,
| | - Jaemin Kim
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea,Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea,Jaemin Kim,
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3
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Urtiaga GO, Domingues WB, Komninou ER, Martins AWS, Blödorn EB, Dellagostin EN, Woloski RDS, Pinto LS, Brum CB, Tovo-Rodrigues L, Campos VF. DNA microarray for forensic intelligence purposes: High-density SNP profiles obtained directly from casework-like samples with and without a DNA purification step. Forensic Sci Int 2022; 332:111181. [PMID: 35042181 DOI: 10.1016/j.forsciint.2022.111181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
SNP analyses from a forensic intelligence perspective have proven to be an important tool to restrict the number of suspected offenders and find missing persons. DNA microarray assays have been demonstrated as a potential feature in forensic analysis, like such as forensic genetic genealogy. The objective of this study was to describe the results from DNA microarray assay from saliva samples deposited on a glass surface collected from by a double swab technique, commonly applied in crime scenes. Eighteen samples from the same person were subjected to Infinium® Global Screening Array-24 v1.0 (~642.824 SNP markers) in two different protocols - with or without the DNA purification procedure. The measured genotype was compared with a Consensus Genotype, obtained from standard control samples, and the parameters such as Call Rate and GenCall Scores were evaluated. Results showed that the Call Rate parameter is enough to estimate the probability of obtaining a correct genotype in the SNP assay. Reliable genotypes with a confidence level of more than 90% (at least 90.15%) were observed in Call Rates above 69.41%, regardless of the experimental condition. Our data demonstrate that DNA Microarray from samples collected under conditions such as those found at crime scenes can generate high-density SNP genetic profiles with a confidence level greater than 90%. Enzymatic adjustments and protocol changes may enable DNA microarray assays for crime analysis and investigation purposes eliminating the purification step in the future. Our data suggest that DNA microarray can support criminal investigation teams from a forensic intelligence perspective.
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Affiliation(s)
- Gabriel O Urtiaga
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Núcleo de Identificação, Superintendência da Polícia Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rafael Dos S Woloski
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano S Pinto
- Laboratório de Bioinformática e Proteômica, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Clarice B Brum
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciana Tovo-Rodrigues
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius F Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
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Van der Heyden H, Dutilleul P, Duceppe M, Bilodeau GJ, Charron J, Carisse O. Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada. MOLECULAR PLANT PATHOLOGY 2022; 23:339-354. [PMID: 34921486 PMCID: PMC8828460 DOI: 10.1111/mpp.13158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/19/2023]
Abstract
Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec-Les Jardins de Napierville-to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.
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Affiliation(s)
- Hervé Van der Heyden
- Cie de Recherche PhytodataSherringtonQuébecCanada
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | - Pierre Dutilleul
- Department of Plant ScienceMcGill UniversityMontrealQuébecCanada
| | | | | | | | - Odile Carisse
- Agriculture and Agri‐Food CanadaSt‐Jean‐sur‐RichelieuQuébecCanada
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Ivanov V, Marusik Y, Pétillon J, Mutanen M. Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae). Sci Rep 2021; 11:2177. [PMID: 33500478 PMCID: PMC7838170 DOI: 10.1038/s41598-021-81788-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Although species delimitation is often controversial, emerging DNA-based and classical morphology-based methods are rarely compared using large-scale samplings, even less in the case of widely distributed species that have distant, allopatric populations. In the current study, we examined species boundaries within two wolf spider species of the genus Pardosa (Araneae, Lycosidae), P. riparia and P. palustris. Wolf spiders constitute an excellent model for testing the relevance of traditional vs. modern methods in species and population delimitation because several closely related species are distributed over cross-continental geographic ranges. Allopatric populations of the two Pardosa species were sampled across Europe to Far East Russia (latitudinal range > 150°) and several dozen individuals were studied using morphological characters (morphometry of three measures for both sexes, plus five in males only and two in females only), DNA barcoding (COI sequencing) and double-digest restriction site associated DNA sequencing (ddRADseq). The results obtained allow for changing the taxonomic status of two Far East Russian populations to subspecies and ddRADseq proved to be a powerful tool for taxonomic research despite scarce sampling and inherent subjectivity of species delimitation in allopatry. Overall, this study pleads for both multi-criteria and more population-based studies in taxonomy.
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Affiliation(s)
- Vladislav Ivanov
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Yuri Marusik
- grid.493323.c0000 0004 0399 5314Institute for Biological Problems of the North, RAS, Magadan, Russia ,grid.412219.d0000 0001 2284 638XDepartment of Zoology and Entomology, University of the Free State, Bloemfontein, 9300 South Africa
| | - Julien Pétillon
- grid.410368.80000 0001 2191 9284UMR CNRS ECOBIO, Université de Rennes 1, Rennes, France
| | - Marko Mutanen
- grid.10858.340000 0001 0941 4873Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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6
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Qiao Y, Liu W, Lu N, Xu Z, Tu J, Lu Z. Rapid droplet multiple displacement amplification based on the droplet regeneration strategy. Anal Chim Acta 2021; 1141:173-179. [DOI: 10.1016/j.aca.2020.10.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022]
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7
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Casso M, Turon X, Pascual M. Single zooids, multiple loci: independent colonisations revealed by population genomics of a global invader. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02069-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers. Curr Biol 2018; 28:2436-2444.e14. [PMID: 30017483 DOI: 10.1016/j.cub.2018.05.070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 05/23/2018] [Indexed: 11/22/2022]
Abstract
A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest in males [3-9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10-12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13-17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers." Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitochondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species.
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9
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Parras-Moltó M, Rodríguez-Galet A, Suárez-Rodríguez P, López-Bueno A. Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses. MICROBIOME 2018; 6:119. [PMID: 29954453 PMCID: PMC6022446 DOI: 10.1186/s40168-018-0507-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/19/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND Viruses are key players regulating microbial ecosystems. Exploration of viral assemblages is now possible thanks to the development of metagenomics, the most powerful tool available for studying viral ecology and discovering new viruses. Unfortunately, several sources of bias lead to the misrepresentation of certain viruses within metagenomics workflows, hindering the shift from merely descriptive studies towards quantitative comparisons of communities. Therefore, benchmark studies on virus enrichment and random amplification protocols are required to better understand the sources of bias. RESULTS We assessed the bias introduced by viral enrichment on mock assemblages composed of seven DNA viruses, and the bias from random amplification methods on human saliva DNA viromes, using qPCR and deep sequencing, respectively. While iodixanol cushions and 0.45 μm filtration preserved the original composition of nuclease-protected viral genomes, low-force centrifugation and 0.22 μm filtration removed large viruses. Comparison of unamplified and randomly amplified saliva viromes revealed that multiple displacement amplification (MDA) induced stochastic bias from picograms of DNA template. However, the type of bias shifted to systematic using 1 ng, with only a marginal influence by amplification time. Systematic bias consisted of over-amplification of small circular genomes, and under-amplification of those with extreme GC content, a negative bias that was shared with the PCR-based sequence-independent, single-primer amplification (SISPA) method. MDA based on random priming provided by a DNA primase activity slightly outperformed those based on random hexamers and SISPA, which may reflect differences in ability to handle sequences with extreme GC content. SISPA viromes showed uneven coverage profiles, with high coverage peaks in regions with low linguistic sequence complexity. Despite misrepresentation of certain viruses after random amplification, ordination plots based on dissimilarities among contig profiles showed perfect overlapping of related amplified and unamplified saliva viromes and strong separation from unrelated saliva viromes. This result suggests that random amplification bias has a minor impact on beta diversity studies. CONCLUSIONS Benchmark analyses of mock and natural communities of viruses improve understanding and mitigate bias in metagenomics surveys. Bias induced by random amplification methods has only a minor impact on beta diversity studies of human saliva viromes.
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Affiliation(s)
- Marcos Parras-Moltó
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Ana Rodríguez-Galet
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Patricia Suárez-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Alberto López-Bueno
- Centro de Biología Molecular Severo Ochoa (Universidad Autónoma de Madrid/Consejo Superior de Investigaciones Científicas), Madrid, Spain.
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Ivanov V, Lee KM, Mutanen M. Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression. Mol Ecol 2018; 27:1681-1695. [PMID: 29575366 DOI: 10.1111/mec.14564] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 02/23/2018] [Accepted: 03/01/2018] [Indexed: 12/31/2022]
Abstract
Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.
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Affiliation(s)
- Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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11
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Lee KM, Kivelä SM, Ivanov V, Hausmann A, Kaila L, Wahlberg N, Mutanen M. Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus. Syst Biol 2018; 67:925-939. [DOI: 10.1093/sysbio/syy029] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 04/10/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kyung Min Lee
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
| | - Sami M Kivelä
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, EE-51014 Tartu, Estonia
| | - Vladislav Ivanov
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
| | - Axel Hausmann
- SNSB – Bavarian State Collection of Zoology, Münchhausenstr. 21, D-81247 Munich, Germany
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, FI-00014 University of Helsinki, P. Rautatiekatu 13, P.O. Box 17, Helsinki, Finland
| | - Niklas Wahlberg
- Department of Biology, Sölvegatan 37, Lund University, SE-223 62 Lund, Sweden
| | - Marko Mutanen
- Department of Ecology and Genetics, University of Oulu, Pentti Kaiteran katu 1, FI-90014, Oulu, Finland
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Dagnall CL, Morton LM, Hicks BD, Li S, Zhou W, Karlins E, Teshome K, Chowdhury S, Lashley KS, Sampson JN, Robison LL, Armstrong GT, Bhatia S, Radloff GA, Davies SM, Tucker MA, Yeager M, Chanock SJ. Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays. BMC Genomics 2018; 19:182. [PMID: 29510662 PMCID: PMC5838969 DOI: 10.1186/s12864-018-4572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/01/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. RESULTS Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input. CONCLUSIONS Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.
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Affiliation(s)
- Casey L Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA. .,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Belynda D Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shengchao Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedest Teshome
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Salma Chowdhury
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kerrie S Lashley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Department of Population Sciences, City of Hope, Duarte, CA, USA.,Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gretchen A Radloff
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stella M Davies
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, USA
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Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. Whole metagenome profiles of particulates collected from the International Space Station. MICROBIOME 2017; 5:81. [PMID: 28716113 PMCID: PMC5514531 DOI: 10.1186/s40168-017-0292-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/27/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized. METHODS This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. RESULTS Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples. CONCLUSION Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.
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Affiliation(s)
- Nicholas A Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Aram Avila-Herrera
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jonathan E Allen
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Aleksandra Checinska Sielaff
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
- Present Address: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Bækvad-Hansen M, Bybjerg-Grauholm J, Poulsen JB, Hansen CS, Hougaard DM, Hollegaard MV. Evaluation of whole genome amplified DNA to decrease material expenditure and increase quality. Mol Genet Metab Rep 2017; 11:36-45. [PMID: 28487825 PMCID: PMC5408502 DOI: 10.1016/j.ymgmr.2017.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 02/04/2023] Open
Abstract
Aim The overall aim of this study is to evaluate whole genome amplification of DNA extracted from dried blood spot samples. We wish to explore ways of optimizing the amplification process, while decreasing the amount of input material and inherently the cost. Our primary focus of optimization is on the amount of input material, the amplification reaction volume, the number of replicates and amplification time and temperature. Increasing the quality of the amplified DNA and the subsequent results of array genotyping is a secondary aim of this project. Methods This study is based on DNA extracted from dried blood spot samples. The extracted DNA was subsequently whole genome amplified using the REPLIg kit and genotyped on the PsychArray BeadChip (assessing > 570,000 SNPs genome wide). We used Genome Studio to evaluate the quality of the genotype data by call rates and log R ratios. Results The whole genome amplification process is robust and does not vary between replicates. Altering amplification time, temperature or number of replicates did not affect our results. We found that spot size i.e. amount of input material could be reduced without compromising the quality of the array genotyping data. We also showed that whole genome amplification reaction volumes can be reduced by a factor of 4, without compromising the DNA quality. Discussion Whole genome amplified DNA samples from dried blood spots is well suited for array genotyping and produces robust and reliable genotype data. However, the amplification process introduces additional noise to the data, making detection of structural variants such as copy number variants difficult. With this study, we explore ways of optimizing the amplification protocol in order to reduce noise and increase data quality. We found, that the amplification process was very robust, and that changes in amplification time or temperature did not alter the genotyping calls or quality of the array data. Adding additional replicates of each sample also lead to insignificant changes in the array data. Thus, the amount of noise introduced by the amplification process was consistent regardless of changes made to the amplification protocol. We also explored ways of decreasing material expenditure by reducing the spot size or the amplification reaction volume. The reduction did not affect the quality of the genotyping data.
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Affiliation(s)
- Marie Bækvad-Hansen
- Corresponding author at: Danish Center for Neonatal Screening, Department of Congenital Diseases, Statens Serum Institut, Artillerivej 5, DK-2300, Copenhagen S, Denmark.Danish Center for Neonatal ScreeningDepartment of Congenital DiseasesStatens Serum InstitutArtillerivej 5Copenhagen SDK-2300Denmark
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15
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Bing Z, Tian J, Zhang J, Li X, Wang X, Yang K. An Integrative Model of miRNA and mRNA Expression Signature for Patients of Breast Invasive Carcinoma with Radiotherapy Prognosis. Cancer Biother Radiopharm 2017; 31:253-60. [PMID: 27610468 DOI: 10.1089/cbr.2016.2059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Radiotherapy is widely used in breast cancer treatment. The radiotherapy for breast invasive carcinoma (BRCA) presents challenges with the complex clinical factors, and too many genes have been found to be associated with BRCA radiotherapy prognosis. The aim of this study was to construct an integrative model to combine the clinical data and RNA expression data (including microRNA and mRNA) to predict the survival durations of BRCA patients with radiotherapy. Also, the authors try to find the key regulation pairs between mRNA and miRNA from prediction. They collected mRNA and microRNA expression profiles and gathered the corresponding clinical data of 73 BRCA patients with radiotherapy from The Cancer Genome Atlas (TCGA). According to an integrative model from univariate Cox regression between RNA expression and patient survival, they classified the patients with radiotherapy into low-risk and high-risk groups. The results showed that nine mRNAs were considered as protective genes and five miRNAs and eight mRNAs were considered as high-risk genes. Moreover, the high-risk group has a significantly shorter survival time in comparison with the low-risk group by the log-rank test (p = 0.0039). The reliability of the gene signature was validated by an independent data set from the Gene Expression Omnibus (GEO). Furthermore, three pairs of miRNA-mRNA, closely associated to survival, were identified. These findings and method may prove valuable for improving the clinical management of BRCA patients with radiotherapy.
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Affiliation(s)
- Zhitong Bing
- 1 Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University , Lanzhou, China .,2 Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province , Lanzhou, China .,3 Institute of Modern Physics of Chinese Academy of Sciences , Lanzhou, China
| | - Jinhui Tian
- 1 Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University , Lanzhou, China .,2 Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province , Lanzhou, China
| | - Jingyun Zhang
- 1 Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University , Lanzhou, China .,2 Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province , Lanzhou, China
| | - Xiuxia Li
- 1 Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University , Lanzhou, China .,2 Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province , Lanzhou, China
| | - Xiaohu Wang
- 4 Gansu Provincial Cancer Hospital , Lanzhou, China
| | - Kehu Yang
- 1 Evidence Based Medicine Center, School of Basic Medical Science of Lanzhou University , Lanzhou, China .,2 Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province , Lanzhou, China
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16
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Bianchi-Frias D, Basom R, Delrow JJ, Coleman IM, Dakhova O, Qu X, Fang M, Franco OE, Ericson NG, Bielas JH, Hayward SW, True L, Morrissey C, Brown L, Bhowmick NA, Rowley D, Ittmann M, Nelson PS. Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations. Mol Cancer Res 2016; 14:374-84. [PMID: 26753621 DOI: 10.1158/1541-7786.mcr-15-0330] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED Prostate cancer-associated stroma (CAS) plays an active role in malignant transformation, tumor progression, and metastasis. Molecular analyses of CAS have demonstrated significant changes in gene expression; however, conflicting evidence exists on whether genomic alterations in benign cells comprising the tumor microenvironment (TME) underlie gene expression changes and oncogenic phenotypes. This study evaluates the nuclear and mitochondrial DNA integrity of prostate carcinoma cells, CAS, matched benign epithelium and benign epithelium-associated stroma by whole-genome copy-number analyses, targeted sequencing of TP53, and FISH. Array comparative genomic hybridization (aCGH) of CAS revealed a copy-neutral diploid genome with only rare and small somatic copy-number aberrations (SCNA). In contrast, several expected recurrent SCNAs were evident in the adjacent prostate carcinoma cells, including gains at 3q, 7p, and 8q, and losses at 8p and 10q. No somatic TP53 mutations were observed in CAS. Mitochondrial DNA (mtDNA) extracted from carcinoma cells and stroma identified 23 somatic mtDNA mutations in neoplastic epithelial cells, but only one mutation in stroma. Finally, genomic analyses identified no SCNAs, LOH, or copy-neutral LOH in cultured cancer-associated fibroblasts, which are known to promote prostate cancer progression in vivo IMPLICATIONS The gene expression changes observed in prostate cancer-adjacent stroma and the attendant contribution of the stroma to the development and progression of prostate cancer are not due to frequent or recurrent genomic alterations in the TME.
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Affiliation(s)
- Daniella Bianchi-Frias
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ilsa M Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olga Dakhova
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Xiaoyu Qu
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Min Fang
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Omar E Franco
- Departments of Urologic Surgery and Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Nolan G Ericson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jason H Bielas
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Simon W Hayward
- Departments of Urologic Surgery and Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Lawrence True
- Department of Pathology, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, Washington
| | - Neil A Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Rowley
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Pathology, University of Washington, Seattle, Washington. Department of Urology, University of Washington, Seattle, Washington. Department of Medicine, University of Washington, Seattle, Washington.
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Bodelon C, Vinokurova S, Sampson JN, den Boon JA, Walker JL, Horswill MA, Korthauer K, Schiffman M, Sherman ME, Zuna RE, Mitchell J, Zhang X, Boland JF, Chaturvedi AK, Dunn ST, Newton MA, Ahlquist P, Wang SS, Wentzensen N. Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer. Carcinogenesis 2015; 37:188-196. [PMID: 26660085 DOI: 10.1093/carcin/bgv171] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 11/07/2015] [Indexed: 11/14/2022] Open
Affiliation(s)
- Clara Bodelon
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Svetlana Vinokurova
- Institute of Carcinogenesis , NN Blokhin Cancer Research Center , Moscow , Russia
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Johan A den Boon
- Morgridge Institute for Research.,McArdle Laboratory for Cancer Research and.,Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Joan L Walker
- University of Oklahoma Health Sciences Center , Oklahoma City, OK,USA
| | - Mark A Horswill
- Morgridge Institute for Research.,Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA
| | - Keegan Korthauer
- Departments of Statistics and of Biostatistics and Medical Informatics , University of Wisconsin-Madison , Madison, WI,USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Mark E Sherman
- Division of Cancer Prevention, Breast and Gynecologic Cancer Research Group, National Cancer Institute, NIH , Bethesda, MD , USA
| | - Rosemary E Zuna
- University of Oklahoma Health Sciences Center , Oklahoma City, OK,USA
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Xijun Zhang
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - Anil K Chaturvedi
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
| | - S Terence Dunn
- University of Oklahoma Health Sciences Center , Oklahoma City, OK,USA
| | - Michael A Newton
- Departments of Statistics and of Biostatistics and Medical Informatics , University of Wisconsin-Madison , Madison, WI,USA
| | - Paul Ahlquist
- Morgridge Institute for Research.,McArdle Laboratory for Cancer Research and.,Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, USA.,Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI, USA, and
| | - Sophia S Wang
- Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute , City of Hope, Duarte, CA,USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics , National Cancer Institute , NIH , Bethesda, MD,USA
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18
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McKinney DM, Fu Z, Le L, Greenbaum JA, Peters B, Sette A. Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing. Hum Immunol 2015; 76:917-22. [PMID: 26027778 PMCID: PMC4662932 DOI: 10.1016/j.humimm.2015.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 04/17/2015] [Accepted: 04/30/2015] [Indexed: 02/05/2023]
Abstract
We report the development of a general methodology to genotype HLA class I and class II loci. A Whole Genome Amplification (WGA) step was used as a sample sparing methodology. HLA typing data could be obtained with as few as 300 cells, underlining the usefulness of the methodology for studies for which limited cells are available. The next generation sequencing platform was validated using a panel of cell lines from the International Histocompatibility Working Group (IHWG) for HLA-A, -B, and -C. Concordance with the known, previously determined HLA types was 99%. We next developed a panel of primers to allow HLA typing of alpha and beta chains of the HLA DQ and DP loci and the beta chain of the DRB1 locus. For the beta chain genes, we employed a novel strategy using primers in the intron regions surrounding exon 2, and the introns surrounding exons 3 through 4 (DRB1) or 5 (DQB1 and DPB1). Concordance with previously determined HLA Class II types was also 99%. To increase throughput and decrease cost, we developed strategies combining multiple loci from each donor. Multiplexing of 96 samples per run resulted in increases in throughput of approximately 8-fold. The pipeline developed for this analysis (HLATyphon) is available for download at https://github.com/LJI-Bioinformatics/HLATyphon.
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Affiliation(s)
- Denise M McKinney
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Zheng Fu
- Bioinformatics Core Facility, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Lucas Le
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Jason A Greenbaum
- Bioinformatics Core Facility, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA
| | - Alessandro Sette
- Department of Vaccine Development, La Jolla Institute for Allergy and Immunology, 9820 Athena Circle, La Jolla, CA 92037, USA.
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Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science 2015; 350:94-98. [PMID: 26430121 DOI: 10.1126/science.aab1785] [Citation(s) in RCA: 385] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurons live for decades in a postmitotic state, their genomes susceptible to DNA damage. Here we survey the landscape of somatic single-nucleotide variants (SNVs) in the human brain. We identified thousands of somatic SNVs by single-cell sequencing of 36 neurons from the cerebral cortex of three normal individuals. Unlike germline and cancer SNVs, which are often caused by errors in DNA replication, neuronal mutations appear to reflect damage during active transcription. Somatic mutations create nested lineage trees, allowing them to be dated relative to developmental landmarks and revealing a polyclonal architecture of the human cerebral cortex. Thus, somatic mutations in the brain represent a durable and ongoing record of neuronal life history, from development through postmitotic function.
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Affiliation(s)
- Michael A Lodato
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Semin Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Gilad D Evrony
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bhaven K Mehta
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amir Karger
- Research Computing, Harvard Medical School, Boston, MA, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Thomas W Chittenden
- Research Computing, Harvard Medical School, Boston, MA, USA.,Complex Biological Systems Alliance, North Andover, MA, USA
| | - Alissa M D'Gama
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xuyu Cai
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA; and Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Tu J, Guo J, Li J, Gao S, Yao B, Lu Z. Systematic Characteristic Exploration of the Chimeras Generated in Multiple Displacement Amplification through Next Generation Sequencing Data Reanalysis. PLoS One 2015; 10:e0139857. [PMID: 26440104 PMCID: PMC4595205 DOI: 10.1371/journal.pone.0139857] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/16/2015] [Indexed: 11/18/2022] Open
Abstract
Background The chimeric sequences produced by phi29 DNA polymerase, which are named as chimeras, influence the performance of the multiple displacement amplification (MDA) and also increase the difficulty of sequence data process. Despite several articles have reported the existence of chimeric sequence, there was only one research focusing on the structure and generation mechanism of chimeras, and it was merely based on hundreds of chimeras found in the sequence data of E. coli genome. Method We finished data mining towards a series of Next Generation Sequencing (NGS) reads which were used for whole genome haplotype assembling in a primary study. We established a bioinformatics pipeline based on subsection alignment strategy to discover all the chimeras inside and achieve their structural visualization. Then, we artificially defined two statistical indexes (the chimeric distance and the overlap length), and their regular abundance distribution helped illustrate of the structural characteristics of the chimeras. Finally we analyzed the relationship between the chimera type and the average insertion size, so that illustrate a method to decrease the proportion of wasted data in the procedure of DNA library construction. Results/Conclusion 131.4 Gb pair-end (PE) sequence data was reanalyzed for the chimeras. Totally, 40,259,438 read pairs (6.19%) with chimerism were discovered among 650,430,811 read pairs. The chimeric sequences are consisted of two or more parts which locate inconsecutively but adjacently on the chromosome. The chimeric distance between the locations of adjacent parts on the chromosome followed an approximate bimodal distribution ranging from 0 to over 5,000 nt, whose peak was at about 250 to 300 nt. The overlap length of adjacent parts followed an approximate Poisson distribution and revealed a peak at 6 nt. Moreover, unmapped chimeras, which were classified as the wasted data, could be reduced by properly increasing the length of the insertion segment size through a linear correlation analysis. Significance This study exhibited the profile of the phi29MDA chimeras by tens of millions of chimeric sequences, and helped understand the amplification mechanism of the phi29 DNA polymerase. Our work also illustrated the importance of NGS data reanalysis, not only for the improvement of data utilization efficiency, but also for more potential genomic information.
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Affiliation(s)
- Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Jing Guo
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Junji Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Shen Gao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Bei Yao
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
- * E-mail:
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21
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Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Metagenomic analysis of the airborne environment in urban spaces. MICROBIAL ECOLOGY 2015; 69:346-55. [PMID: 25351142 PMCID: PMC4312561 DOI: 10.1007/s00248-014-0517-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 10/09/2014] [Indexed: 05/04/2023]
Abstract
The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.
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Affiliation(s)
- Nicholas A. Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - James B. Thissen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | | | - Jonathan E. Allen
- Computation/Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Mark Rojas
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - George Golovko
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | - Yuriy Fofanov
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX USA
| | | | - Crystal J. Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
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Abstract
The increasing interest towards cellular heterogeneity within cell populations has pushed the development of new protocols to isolate and analyze single cells. PCR-based amplification techniques are widely used in this field. However, setting up an experiment and analyzing the results can sometimes be challenging. The aim of this chapter is to provide a general overview on single-cell PCR analysis focusing on the potential pitfalls and on the possible solutions to successfully perform the analysis.
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Shojaei Saadi HA, Vigneault C, Sargolzaei M, Gagné D, Fournier É, de Montera B, Chesnais J, Blondin P, Robert C. Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates. BMC Genomics 2014; 15:889. [PMID: 25305778 PMCID: PMC4201692 DOI: 10.1186/1471-2164-15-889] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 10/03/2014] [Indexed: 01/21/2023] Open
Abstract
Background Genome-wide profiling of single-nucleotide polymorphisms is receiving increasing attention as a method of pre-implantation genetic diagnosis in humans and of commercial genotyping of pre-transfer embryos in cattle. However, the very small quantity of genomic DNA in biopsy material from early embryos poses daunting technical challenges. A reliable whole-genome amplification (WGA) procedure would greatly facilitate the procedure. Results Several PCR-based and non-PCR based WGA technologies, namely multiple displacement amplification, quasi-random primed library synthesis followed by PCR, ligation-mediated PCR, and single-primer isothermal amplification were tested in combination with different DNA extractions protocols for various quantities of genomic DNA inputs. The efficiency of each method was evaluated by comparing the genotypes obtained from 15 cultured cells (representative of an embryonic biopsy) to unamplified reference gDNA. The gDNA input, gDNA extraction method and amplification technology were all found to be critical for successful genome-wide genotyping. The selected WGA platform was then tested on embryo biopsies (n = 226), comparing their results to that of biopsies collected after birth. Although WGA inevitably leads to a random loss of information and to the introduction of erroneous genotypes, following genomic imputation the resulting genetic index of both sources of DNA were highly correlated (r = 0.99, P<0.001). Conclusion It is possible to generate high-quality DNA in sufficient quantities for successful genome-wide genotyping starting from an early embryo biopsy. However, imputation from parental and population genotypes is a requirement for completing and correcting genotypic data. Judicious selection of the WGA platform, careful handling of the samples and genomic imputation together, make it possible to perform extremely reliable genomic evaluations for pre-transfer embryos. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-889) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Institut des nutraceutiques et des aliments fonctionnels, Faculté des sciences de l'agriculture et de l'alimentation, Pavillon des services, Université Laval, Québec G1V 0A6, Canada.
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24
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Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, Drury E, Mead D, Gu Y, Miles A, MacInnis B, Newbold C, Berriman M, Kwiatkowski DP. Optimized whole-genome amplification strategy for extremely AT-biased template. DNA Res 2014; 21:661-71. [PMID: 25240466 PMCID: PMC4263299 DOI: 10.1093/dnares/dsu028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.
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Affiliation(s)
| | | | | | | | | | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Yong Gu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Newbold
- Wellcome Trust Sanger Institute, Hinxton, UK Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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25
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Kvist T, Sondt-Marcussen L, Mikkelsen MJ. Partition enrichment of nucleotide sequences (PINS)--a generally applicable, sequence based method for enrichment of complex DNA samples. PLoS One 2014; 9:e106817. [PMID: 25203653 PMCID: PMC4159240 DOI: 10.1371/journal.pone.0106817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/11/2014] [Indexed: 12/20/2022] Open
Abstract
The dwindling cost of DNA sequencing is driving transformative changes in various biological disciplines including medicine, thus resulting in an increased need for routine sequencing. Preparation of samples suitable for sequencing is the starting point of any practical application, but enrichment of the target sequence over background DNA is often laborious and of limited sensitivity thereby limiting the usefulness of sequencing. The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. A 275,000 fold enrichment of a target DNA sample containing integrated human papilloma virus is demonstrated. Specifically, a sample containing 0.0028 copies of target sequence per ng of total DNA was enriched to 786 copies per ng. The starting concentration of 0.0028 target copies per ng corresponds to one copy of target in a background of 100,000 complete human genomes. The enriched sample was subsequently amplified using rapid genome walking and the resulting DNA sequence revealed not only the sequence of a the truncated virus, but also 1026 base pairs 5' and 50 base pairs 3' to the integration site in chromosome 8. The demonstrated enrichment method is extremely sensitive and selective and requires only minimal knowledge of the sequence to be enriched and will therefore enable sequencing where the target concentration relative to background is too low to allow the use of other sample preparation methods or where significant parts of the target sequence is unknown.
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26
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Rheindt FE, Fujita MK, Wilton PR, Edwards SV. Introgression and Phenotypic Assimilation in Zimmerius Flycatchers (Tyrannidae): Population Genetic and Phylogenetic Inferences from Genome-Wide SNPs. Syst Biol 2013; 63:134-52. [DOI: 10.1093/sysbio/syt070] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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27
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Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ. Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing. PLoS One 2013; 8:e73455. [PMID: 24039948 PMCID: PMC3767809 DOI: 10.1371/journal.pone.0073455] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 07/03/2013] [Indexed: 11/19/2022] Open
Abstract
Bacillus anthracis is the potentially lethal etiologic agent of anthrax disease, and is a significant concern in the realm of biodefense. One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis. We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background. We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples. We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid. Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database. Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis. We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing. Our results, in combination with the capacity of sequencing for providing insights into the genomic characteristics of complex and novel organisms, suggest that these platforms should be considered important components of a biosurveillance strategy.
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Affiliation(s)
- Nicholas A. Be
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - James B. Thissen
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Shea N. Gardner
- Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Kevin S. McLoughlin
- Global Security Directorates, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | | | | | - Sally R. Ellingson
- Department of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Thomas S. Brettin
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Paul J. Jackson
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Crystal J. Jaing
- Physical and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail:
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28
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Vydelingum NA, Sorbara L, Wagner P, Srivastava S. Standards in molecular diagnostics for the discovery and validation of clinically useful cancer biomarkers. Expert Rev Mol Diagn 2013; 13:421-3. [PMID: 23782249 DOI: 10.1586/erm.13.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent discoveries in cancer biology have greatly increased the understanding of cancer at the molecular level, but translating this knowledge into clinically useful diagnostic tests has proved challenging. More efficient transfer of new molecular tests into patient care requires better standardization of laboratory practices, measurement methods and data management. The workshop assembled experts from National Cancer Institute, US FDA, National Institute of Standards and Technology, academia and industry, to address the most efficient approaches to biomarker standardization and validation. The workshop participants described the current state of research in molecular diagnostics standardization and addressed three questions: what has worked? What has not?And what needs improving?
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Affiliation(s)
- Nadarajen A Vydelingum
- Division of Cancer Prevention, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA.
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Vanhomwegen J, Berthet N, Mazuet C, Guigon G, Vallaeys T, Stamboliyska R, Dubois P, Kennedy GC, Cole ST, Caro V, Manuguerra JC, Popoff MR. Application of high-density DNA resequencing microarray for detection and characterization of botulinum neurotoxin-producing clostridia. PLoS One 2013; 8:e67510. [PMID: 23818983 PMCID: PMC3688605 DOI: 10.1371/journal.pone.0067510] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 05/22/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Clostridium botulinum and related clostridia express extremely potent toxins known as botulinum neurotoxins (BoNTs) that cause severe, potentially lethal intoxications in humans. These BoNT-producing bacteria are categorized in seven major toxinotypes (A through G) and several subtypes. The high diversity in nucleotide sequence and genetic organization of the gene cluster encoding the BoNT components poses a great challenge for the screening and characterization of BoNT-producing strains. METHODOLOGY/PRINCIPAL FINDINGS In the present study, we designed and evaluated the performances of a resequencing microarray (RMA), the PathogenId v2.0, combined with an automated data approach for the simultaneous detection and characterization of BoNT-producing clostridia. The unique design of the PathogenID v2.0 array allows the simultaneous detection and characterization of 48 sequences targeting the BoNT gene cluster components. This approach allowed successful identification and typing of representative strains of the different toxinotypes and subtypes, as well as the neurotoxin-producing C. botulinum strain in a naturally contaminated food sample. Moreover, the method allowed fine characterization of the different neurotoxin gene cluster components of all studied strains, including genomic regions exhibiting up to 24.65% divergence with the sequences tiled on the arrays. CONCLUSIONS/SIGNIFICANCE The severity of the disease demands rapid and accurate means for performing risk assessments of BoNT-producing clostridia and for tracing potentials sources of contamination in outbreak situations. The RMA approach constitutes an essential higher echelon component in a diagnostics and surveillance pipeline. In addition, it is an important asset to characterise potential outbreak related strains, but also environment isolates, in order to obtain a better picture of the molecular epidemiology of BoNT-producing clostridia.
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Affiliation(s)
- Jessica Vanhomwegen
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Nicolas Berthet
- Institut Pasteur, Epidemiology and Pathophysiology of Oncogenic Viruses, Paris, France
- CNRS, UMR3569, Paris, France
| | | | - Ghislaine Guigon
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
| | - Tatiana Vallaeys
- CNRS – CC093 Université Montpellier II, UMR5119 Ecosystèmes lagunaires, Montpellier, France
| | - Rayna Stamboliyska
- Department of Biology II, University of Munich (LMU), Planegg-Martinsried, Germany
| | - Philippe Dubois
- Institut Pasteur, Laboratory for Urgent Responses to Biological Threats, Paris, France
| | - Giulia C. Kennedy
- Department of Research and Development, Veracyte, Inc., South San Francisco, California, United States of America
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France
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