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Liu Y, Bhagwate A, Winham SJ, Stephens MT, Harker BW, McDonough SJ, Stallings-Mann ML, Heinzen EP, Vierkant RA, Hoskin TL, Frost MH, Carter JM, Pfrender ME, Littlepage L, Radisky DC, Cunningham JM, Degnim AC, Wang C. Quality control recommendations for RNASeq using FFPE samples based on pre-sequencing lab metrics and post-sequencing bioinformatics metrics. BMC Med Genomics 2022; 15:195. [PMID: 36114500 PMCID: PMC9479231 DOI: 10.1186/s12920-022-01355-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background Formalin-fixed, paraffin-embedded (FFPE) tissues have many advantages for identification of risk biomarkers, including wide availability and potential for extended follow-up endpoints. However, RNA derived from archival FFPE samples has limited quality. Here we identified parameters that determine which FFPE samples have the potential for successful RNA extraction, library preparation, and generation of usable RNAseq data. Methods We optimized library preparation protocols designed for use with FFPE samples using seven FFPE and Fresh Frozen replicate pairs, and tested optimized protocols using a study set of 130 FFPE biopsies from women with benign breast disease. Metrics from RNA extraction and preparation procedures were collected and compared with bioinformatics sequencing summary statistics. Finally, a decision tree model was built to learn the relationship between pre-sequencing lab metrics and qc pass/fail status as determined by bioinformatics metrics. Results Samples that failed bioinformatics qc tended to have low median sample-wise correlation within the cohort (Spearman correlation < 0.75), low number of reads mapped to gene regions (< 25 million), or low number of detectable genes (11,400 # of detected genes with TPM > 4). The median RNA concentration and pre-capture library Qubit values for qc failed samples were 18.9 ng/ul and 2.08 ng/ul respectively, which were significantly lower than those of qc pass samples (40.8 ng/ul and 5.82 ng/ul). We built a decision tree model based on input RNA concentration, input library qubit values, and achieved an F score of 0.848 in predicting QC status (pass/fail) of FFPE samples. Conclusions We provide a bioinformatics quality control recommendation for FFPE samples from breast tissue by evaluating bioinformatic and sample metrics. Our results suggest a minimum concentration of 25 ng/ul FFPE-extracted RNA for library preparation and 1.7 ng/ul pre-capture library output to achieve adequate RNA-seq data for downstream bioinformatics analysis.
Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01355-0.
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Lukindu M, Love RR, Guelbeogo MW, Small ST, Stephens MT, Campbell NR, Sagnon N, Costantini C, Besansky NJ. High-Throughput Genotyping of Common Chromosomal Inversions in the Afrotropical Malaria Mosquito Anopheles Funestus. Insects 2020; 11:E693. [PMID: 33065978 PMCID: PMC7650614 DOI: 10.3390/insects11100693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 11/16/2022]
Abstract
Polymorphic chromosomal inversions have been implicated in local adaptation. In anopheline mosquitoes, inversions also contribute to epidemiologically relevant phenotypes such as resting behavior. Progress in understanding these phenotypes and their mechanistic basis has been hindered because the only available method for inversion genotyping relies on traditional cytogenetic karyotyping, a rate-limiting and technically difficult approach that is possible only for the fraction of the adult female population at the correct gonotrophic stage. Here, we focus on an understudied malaria vector of major importance in sub-Saharan Africa, Anopheles funestus. We ascertain and validate tag single nucleotide polymorphisms (SNPs) using high throughput molecular assays that allow rapid inversion genotyping of the three most common An. funestus inversions at scale, overcoming the cytogenetic karyotyping barrier. These same inversions are the only available markers for distinguishing two An. funestus ecotypes that differ in indoor resting behavior, Folonzo and Kiribina. Our new inversion genotyping tools will facilitate studies of ecotypic differentiation in An. funestus and provide a means to improve our understanding of the roles of Folonzo and Kiribina in malaria transmission.
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Affiliation(s)
- Martin Lukindu
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - R. Rebecca Love
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Moussa W. Guelbeogo
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Scott T. Small
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | - Melissa T. Stephens
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
| | | | - N’Fale Sagnon
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
| | - Carlo Costantini
- Centre National de Recherche et Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso; (M.W.G.); (N.S.); (C.C.)
- 5 MIVEGEC, University of Montpellier, CNRS 5290, IRD 224, F-34394 Montpellier, France
| | - Nora J. Besansky
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA; (M.L.); (R.R.L.); (S.T.S.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA;
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Buechler SA, Stephens MT, Hummon AB, Ludwig K, Cannon E, Carter TC, Resnick J, Gökmen-Polar Y, Badve SS. ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing. Sci Rep 2020; 10:12123. [PMID: 32694712 PMCID: PMC7374173 DOI: 10.1038/s41598-020-69083-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/03/2020] [Indexed: 01/02/2023] Open
Abstract
Colorectal cancer (CRC) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for CMS subtyping. In this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1-4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, ColoType was also implemented with targeted RNA-sequencing (Illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNA-sequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, ColoType by targeted RNA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology.
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Affiliation(s)
- Steven A Buechler
- Department of Applied and Computational Mathematics and Statistics, Harper Cancer Research Institute, University of Notre Dame, 102B Crowley Hall, Notre Dame, IN, 46556, USA.
| | - Melissa T Stephens
- Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Katelyn Ludwig
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emily Cannon
- Department of Applied and Computational Mathematics and Statistics, Harper Cancer Research Institute, University of Notre Dame, 102B Crowley Hall, Notre Dame, IN, 46556, USA
| | - Tonia C Carter
- Center for Precision Medicine Research, Marshfield Clinic, Marshfield, WI, USA
| | - Jeffrey Resnick
- Department of Pathology, Marshfield Clinic, Marshfield, WI, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA
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Dodean RA, Kancharla P, Li Y, Melendez V, Read L, Bane CE, Vesely B, Kreishman-Deitrick M, Black C, Li Q, Sciotti RJ, Olmeda R, Luong TL, Gaona H, Potter B, Sousa J, Marcsisin S, Caridha D, Xie L, Vuong C, Zeng Q, Zhang J, Zhang P, Lin H, Butler K, Roncal N, Gaynor-Ohnstad L, Leed SE, Nolan C, Huezo SJ, Rasmussen SA, Stephens MT, Tan JC, Cooper RA, Smilkstein MJ, Pou S, Winter RW, Riscoe MK, Kelly JX. Discovery and Structural Optimization of Acridones as Broad-Spectrum Antimalarials. J Med Chem 2019; 62:3475-3502. [PMID: 30852885 DOI: 10.1021/acs.jmedchem.8b01961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Malaria remains one of the deadliest diseases in the world today. Novel chemoprophylactic and chemotherapeutic antimalarials are needed to support the renewed eradication agenda. We have discovered a novel antimalarial acridone chemotype with dual-stage activity against both liver-stage and blood-stage malaria. Several lead compounds generated from structural optimization of a large library of novel acridones exhibit efficacy in the following systems: (1) picomolar inhibition of in vitro Plasmodium falciparum blood-stage growth against multidrug-resistant parasites; (2) curative efficacy after oral administration in an erythrocytic Plasmodium yoelii murine malaria model; (3) prevention of in vitro Plasmodium berghei sporozoite-induced development in human hepatocytes; and (4) protection of in vivo P. berghei sporozoite-induced infection in mice. This study offers the first account of liver-stage antimalarial activity in an acridone chemotype. Details of the design, chemistry, structure-activity relationships, safety, metabolic/pharmacokinetic studies, and mechanistic investigation are presented herein.
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Affiliation(s)
- Rozalia A Dodean
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Papireddy Kancharla
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States
| | - Yuexin Li
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Victor Melendez
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lisa Read
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Charles E Bane
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Brian Vesely
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Mara Kreishman-Deitrick
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Chad Black
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Qigui Li
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Richard J Sciotti
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Raul Olmeda
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Thu-Lan Luong
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Heather Gaona
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Brittney Potter
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Jason Sousa
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Sean Marcsisin
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Diana Caridha
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lisa Xie
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Chau Vuong
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Qiang Zeng
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Jing Zhang
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Ping Zhang
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Hsiuling Lin
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Kirk Butler
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Norma Roncal
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Lacy Gaynor-Ohnstad
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Susan E Leed
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Christina Nolan
- Division of Experimental Therapeutics , Walter Reed Army Institute of Research , Silver Spring , Maryland 20910 , United States
| | - Stephanie J Huezo
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | - Stephanie A Rasmussen
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | | | | | - Roland A Cooper
- Department of Natural Sciences and Mathematics , Dominican University of California , San Rafael , California 94901 , United States
| | - Martin J Smilkstein
- Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Sovitj Pou
- Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Rolf W Winter
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Michael K Riscoe
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
| | - Jane X Kelly
- Department of Chemistry , Portland State University , Portland , Oregon 97201 , United States.,Department of Veterans Affairs Medical Center , Portland , Oregon 97239 , United States
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Konar A, Choudhury O, Bullis R, Fiedler L, Kruser JM, Stephens MT, Gailing O, Schlarbaum S, Coggeshall MV, Staton ME, Carlson JE, Emrich S, Romero-Severson J. High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra. BMC Genomics 2017; 18:417. [PMID: 28558688 PMCID: PMC5450186 DOI: 10.1186/s12864-017-3765-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 05/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The statistical inference of linear order must be as accurate as possible for the correct ordering of sequence scaffolds and contigs to chromosomal locations. Accurate maps also facilitate the discovery of chromosome segments containing allelic variants conferring resistance to the biotic and abiotic stresses that threaten forest trees worldwide. We used ddRADseq for genetic mapping in the tree Quercus rubra, with an approach optimized to produce a high-quality map. Our study design also enabled us to model the results we would have obtained with less depth of coverage. Results Our sequencing design produced a high sequencing depth in the parents (248×) and a moderate sequencing depth (15×) in the progeny. The digital normalization method of generating a de novo reference and the SAMtools SNP variant caller yielded the most SNP calls (78,725). The major drivers of map inflation were multiple SNPs located within the same sequence (77% of SNPs called). The highest quality map was generated with a low level of missing data (5%) and a genome-wide threshold of 0.025 for deviation from Mendelian expectation. The final map included 849 SNP markers (1.8% of the 78,725 SNPs called). Downsampling the individual FASTQ files to model lower depth of coverage revealed that sequencing the progeny using 96 samples per lane would have yielded too few SNP markers to generate a map, even if we had sequenced the parents at depth 248×. Conclusions The ddRADseq technology produced enough high-quality SNP markers to make a moderately dense, high-quality map. The success of this project was due to high depth of coverage of the parents, moderate depth of coverage of the progeny, a good framework map, an optimized bioinformatics pipeline, and rigorous premapping filters. The ddRADseq approach is useful for the construction of high-quality genetic maps in organisms lacking a reference genome if the parents and progeny are sequenced at sufficient depth. Technical improvements in reduced representation sequencing (RRS) approaches are needed to reduce the amount of missing data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3765-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arpita Konar
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Olivia Choudhury
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Rebecca Bullis
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Lauren Fiedler
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | | | - Melissa T Stephens
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Oliver Gailing
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Scott Schlarbaum
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, 37996, USA
| | - Mark V Coggeshall
- School of Natural Resources, University of Missouri-Columbia, Columbia, MO, 65211, USA.,Hardwood Tree Improvement and Regeneration Center, USDA Forest Service Northern Research Station, West Lafayette, IN, 47907, USA
| | - Margaret E Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - John E Carlson
- Department of Ecosystem Science and Management, Penn State, University Park, State College, PA, 16802, USA
| | - Scott Emrich
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jeanne Romero-Severson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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6
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Rund SSC, Yoo B, Alam C, Green T, Stephens MT, Zeng E, George GF, Sheppard AD, Duffield GE, Milenković T, Pfrender ME. Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation. BMC Genomics 2016; 17:653. [PMID: 27538446 PMCID: PMC4991082 DOI: 10.1186/s12864-016-2998-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/05/2016] [Indexed: 11/16/2022] Open
Abstract
Background Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia. Results Here we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods. Conclusions This research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel functional annotation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2998-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel S C Rund
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.,Centre for Immunity, Infection and Evolution, Institute of Evolution, University of Edinburgh, Edinburgh, EH9 3FL, UK.,Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Boyoung Yoo
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.,Present Address: Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Camille Alam
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Taryn Green
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Melissa T Stephens
- Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Erliang Zeng
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.,Notre Dame Genomics and Bioinformatics Core Facility, University of Notre Dame, Notre Dame, IN, 46556, USA.,Present Address: Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA.,Present Address: Department of Computer Science, University of South Dakota, Vermillion, SD, 57069, USA
| | - Gary F George
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Aaron D Sheppard
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Giles E Duffield
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Tijana Milenković
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.,Interdisciplinary Center for Network Science and Applications (iCeNSA), University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael E Pfrender
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA. .,Notre Dame Environmental Change Initiative, University of Notre Dame, Notre Dame, IN, 46556, USA.
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7
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Nair SC, Pattaradilokrat S, Zilversmit MM, Dommer J, Nagarajan V, Stephens MT, Xiao W, Tan JC, Su XZ. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii. Mol Biochem Parasitol 2014; 194:9-15. [PMID: 24685548 DOI: 10.1016/j.molbiopara.2014.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 11/18/2022]
Abstract
The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes.
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Affiliation(s)
- Sethu C Nair
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sittiporn Pattaradilokrat
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Martine M Zilversmit
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melissa T Stephens
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Wenming Xiao
- Metabolism Branch, National Cancer Institutes, National Institutes of Health, Bethesda, MD 20892, USA
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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