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3. Diagnostic application of Padlock Probes - Multiplex Detection of Plant Pathogens using universal microarray

Author

Szemes, M., Bonants, P.J.M., de Weerdt, M., Baner, J., Landegren, U., Schoen, C.D., Szemes, M., Bonants, P.J.M., de Weerdt, M., Baner, J., Landegren, U., and Schoen, C.D.

Abstract

Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target sequences. Upon hybridization to the target, the two ends are brought into contact, allowing PLP circularization by ligation. PLPs provide extremely specific target recognition, which is followed by universal amplification and microarray detection. Since target recognition is separated from downstream processing, PLPs enable the development of flexible and extendable diagnostic systems, targeting diverse organisms. To adapt padlock technology for diagnostic purposes, we optimized PLP design to ensure high specificity and eliminating ligation on non-target sequences under real-world assay conditions. We designed and tested 11 PLPs to target various plant pathogens at the genus, species and subspecies levels, and developed a prototype PLP-based plant health chip. Excellent specificity was demonstrated toward the target organisms. Assay background was determined for each hybridization using a no-target reference sample, which provided reliable and sensitive identification of positive samples. A sensitivity of 5 pg genomic DNA and a dynamic range of detection of 100 were observed. The developed multiplex diagnostic system was validated using genomic DNAs of characterized isolates and artificial mixtures thereof. The demonstrated system is adaptable to a wide variety of applications ranging from pest management to environmental microbiology

Published
2005

5. REPRODUCTIVE (EPI) GENETICS

Author

Sertyel, S., primary, Kolankaya, A., additional, Yigit, A., additional, Cengiz, F., additional, Kunacaf, G., additional, Akman, M. A., additional, Gurgan, T., additional, Yu, B., additional, DeCherney, A., additional, Segars, J., additional, Russanova, V., additional, Howard, B., additional, Serafini, P., additional, Kimati, C., additional, Hassun, P., additional, Cuzzi, J., additional, Peres, M., additional, Riboldi, M., additional, Gomes, C., additional, Fettback, P., additional, Alegretti, J., additional, motta, E., additional, Lappa, C., additional, Ottolini, C. S., additional, Summers, M. C., additional, Sage, K., additional, Rogers, S., additional, Griffin, D. K., additional, Handyside, A. H., additional, Thornhill, A. R., additional, Ubaldi, F., additional, Capalbo, A., additional, Wright, G., additional, Elliott, T., additional, Maggiulli, R., additional, Rienzi, L., additional, Nagy, Z. P., additional, Cinar Yapan, C., additional, Beyazyurek, C., additional, Ekmekci, C. G., additional, Altin, G., additional, Yesil, M., additional, Yelke, H., additional, Kahraman, S., additional, Khalil, M., additional, Rittenberg, V., additional, Khalaf, Y., additional, El-toukhy, T., additional, Alvaro Mercadal, B., additional, Imbert, R., additional, Demeestere, I., additional, De Leener, A., additional, Englert, Y., additional, Costagliola, S., additional, Delbaere, A., additional, Zimmermann, B., additional, Ryan, A., additional, Baner, J., additional, Gemelos, G., additional, Dodd, M., additional, Rabinowitz, M., additional, Hill, M., additional, Sandalinas, M., additional, Garcia-Guixe, E., additional, Jimenez-Macedo, A., additional, Gimenez, C., additional, Wemmer, N., additional, Potter, D., additional, Keller, J., additional, Cater, E., additional, Lynch, C., additional, Jenner, L., additional, Berrisford, K., additional, Campbell, A., additional, Keown, N., additional, Rouse, H., additional, Craig, A., additional, Fishel, S., additional, Palomares, A. R., additional, Lendinez Ramirez, A. M., additional, Martinez, F., additional, Ruiz Galdon, M., additional, Reyes Engel, A., additional, Mamas, T., additional, Xanthopoulou, L., additional, Heath, C., additional, Doshi, A., additional, Serhal, P., additional, SenGupta, S. B., additional, Plaza, S., additional, Templin, C., additional, Saguet, F., additional, Claustres, M., additional, Girardet, A., additional, Biricik, A., additional, Colamaria, S., additional, Bono, S., additional, Spizzichino, L., additional, Fiorentino, F., additional, Alegretti, J. R., additional, Barros, B., additional, Motta, E. L. A., additional, Tulay, P., additional, Naja, R. P., additional, Cascales-Roman, O., additional, Cawood, S., additional, Montjean, D., additional, Ravel, C., additional, Belloc, S., additional, Cohen-Bacrie, P., additional, Bashamboo, A., additional, McElreavey, K., additional, Benkhalifa, M., additional, Filippini, G., additional, Radovanovic, J., additional, Spalvieri, S., additional, Marabella, D., additional, Timperi, P., additional, Suter, T., additional, Jemec, M., additional, Traversa, M., additional, Marshall, J., additional, Leigh, D., additional, McArthur, S., additional, Zhang, L., additional, Yilmaz, A., additional, Zhang, X. Y., additional, Son, W. Y., additional, Holzer, H., additional, Ao, A., additional, Horcajadas, J. A., additional, Munne, S., additional, Fisher, J., additional, Ketterson, K., additional, Wells, D., additional, Bisignano, A., additional, Rubio, C., additional, Mateu, E., additional, Milan, M., additional, Mercader, A., additional, Bosch, E., additional, Labarta, E., additional, Crespo, J., additional, Remohi, J., additional, Simon, C., additional, Pellicer, A., additional, Garrido, N., additional, Buendia, P., additional, Delgado, A., additional, Escrich, L., additional, Poo, M. E., additional, Held, K., additional, Baukloh, V., additional, Arps, S., additional, Wittmann, S. T., additional, Petrussa, L., additional, Van de Velde, H., additional, De Rycke, M., additional, Ajredin, N., additional, Tac, H. A., additional, Yelke, H. K., additional, Basile, N., additional, Bronet, F., additional, Nogales, M. C., additional, Ariza, M., additional, Martinez, E., additional, Linan, A., additional, Gaytan, A., additional, Meseguer, M., additional, Christopikou, D., additional, Tsorva, E., additional, Economou, K., additional, Davies, S., additional, Mastrominas, M., additional, Avo Santos, M., additional, M. Lens, S., additional, C. Fauser, B., additional, S. E. Laven, J., additional, B. Baart, E., additional, Nakano, T., additional, Akamatsu, Y., additional, Sato, M., additional, Hashimoto, S., additional, Maezawa, T., additional, Himeno, T., additional, Ohnishi, Y., additional, Inoue, T., additional, Ito, K., additional, Nakaoka, Y., additional, Morimoto, Y., additional, Al Sharif, J., additional, Alhalabi, M., additional, Abou Alchamat, G., additional, Madania, A., additional, Khatib, A., additional, Kinj, M., additional, Monem, F., additional, Mahayri, Z., additional, Ajlouni, A., additional, Othman, A., additional, Chung, J. T., additional, Tan, S. L., additional, Burnik Papler, T., additional, Fon Tacer, K., additional, Devjak, R., additional, Juvan, P., additional, Virant-Klun, I., additional, Vrtacnik Bokal, E., additional, Zheng, H. Y., additional, Chen, S. L., additional, Chen, X., additional, Tang, Y., additional, Li, L., additional, Ye, D. S., additional, Yang, X. H., additional, Eichenlaub-Ritter, U., additional, Trapphoff, T., additional, Hastreiter, S., additional, Haaf, T., additional, Asada, H., additional, Maekawa, R., additional, Tamura, I., additional, Tamura, H., additional, Sugino, N., additional, Zakharova, E., additional, Zaletova, V., additional, Krivokharchenko, I., additional, Ata, B., additional, Kaplan, B., additional, Danzer, H., additional, Glassner, M., additional, and Opsahl, M., additional

Published
2012
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6. SESSION 70: GENETICS: WHAT GENOMES GONE WRONG CAN TELL US

Author

ElInati, E., primary, Kuentz, P., additional, Redin, C., additional, Vanden Meerschaut, F., additional, Nasr-Esfahani, M., additional, Gurgan, T., additional, Louanjli, N., additional, Iqbal, N., additional, Carre Pigeon, F., additional, Gourabi, H., additional, Brugnon, F., additional, Gitlin, S., additional, De Sutter, P., additional, Muller, J., additional, Viville, S., additional, Dul, E. C., additional, van Echten-Arends, J., additional, Groen, H., additional, Kastrop, P. M. M., additional, Amory-van Wissen, L. C. P., additional, Engelen, J. J. M., additional, Land, J. A., additional, Coonen, E., additional, van de Werken, C., additional, van der Heijden, G. W., additional, van Veen-Buurman, C. J. H., additional, Laven, J. S. E., additional, Peters, A. H. F. M., additional, Baart, E. B., additional, Rabinowitz, M., additional, Gemelos, G., additional, Banjevic, M., additional, Zimmermann, B., additional, Baner, J., additional, Levy, B., additional, Hill, M., additional, Mertzanidou, A., additional, Spits, C., additional, Van de Velde, H., additional, Sermon, K., additional, Wells, D., additional, Alfarawati, S., additional, Konstantinidis, M., additional, Jaroudi, S., additional, Fragouli, E., additional, Minasi, M. G., additional, Ruberti, A., additional, Rubino, P., additional, Iammarrone, E., additional, Biricick, A., additional, Zavaglia, D., additional, Nuccitelli, A., additional, Colasante, A., additional, Fiorentino, F., additional, and Greco, E., additional

Published
2012
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11. Titius Continuatus Et Illustratus, Das ist: Loci Theologici, Historici Et Patrici, Oder Theologisches Exempel-Buch : In welchem Nach dem Methodo des seligen Herrn Titii nebenst vielen schönen merckwürdigen Reden und Geschichten/ ... fast bey jeder Abtheilung deren Locorum, allerhand herrliche Dicta SS. Patrum zu befinden. Aus alten und neuen Scribenten/ ... zusammengetragen/ Und/ nebenst einem vollständigen Indice Mit einer Anweisung/ wie solches und des Titii Exempel-Buch ... nützlichen zu gebrauchen/ samt einer Vorrede des ... Herrn D. Martini Geieri. [et]c.

Author

Geier, Martin, Maukisch, Johannes, Starch, Sebastianus Gottfried, Schertzer, Joh. Ad., Baner, J. A., Lehmann, Georgius, Furmannus, Godofredus, Ittig, Thomas, Bose, Gottfried Christianus, Rappold, Frid., Mayer, Johannes Ulricus, Laurentius, Johannes, Knauth, Gottfried, Schneider, Johannes Daniel, Birnbaum, A., Schneider, Daniel, Geier, Martin, Maukisch, Johannes, Starch, Sebastianus Gottfried, Schertzer, Joh. Ad., Baner, J. A., Lehmann, Georgius, Furmannus, Godofredus, Ittig, Thomas, Bose, Gottfried Christianus, Rappold, Frid., Mayer, Johannes Ulricus, Laurentius, Johannes, Knauth, Gottfried, Schneider, Johannes Daniel, Birnbaum, A., and Schneider, Daniel

Abstract

Durch M. Daniele Schneidern/ ..., Schlüsselseiten aus dem Exemplar der ULB Halle: AB 44 1/k, 6

12. Titius Continuatus Et Illustratus, Das ist: Loci Theologici, Historici Et Patrici, Oder Theologisches Exempel-Buch : In welchem Nach dem Methodo des seligen Herrn Titii nebenst vielen schönen merckwürdigen Reden und Geschichten/ ... fast bey jeder Abtheilung deren Locorum, allerhand herrliche Dicta SS. Patrum zu befinden. Aus alten und neuen Scribenten/ ... zusammengetragen/ Und/ nebenst einem vollständigen Indice Mit einer Anweisung/ wie solches und des Titii Exempel-Buch ... nützlichen zu gebrauchen/ samt einer Vorrede des ... Herrn D. Martini Geieri. [et]c.

Author

Geier, Martin, Maukisch, Johannes, Starch, Sebastianus Gottfried, Schertzer, Joh. Ad., Baner, J. A., Lehmann, Georgius, Furmannus, Godofredus, Ittig, Thomas, Bose, Gottfried Christianus, Rappold, Frid., Mayer, Johannes Ulricus, Laurentius, Johannes, Knauth, Gottfried, Schneider, Johannes Daniel, Birnbaum, A., Schneider, Daniel, Geier, Martin, Maukisch, Johannes, Starch, Sebastianus Gottfried, Schertzer, Joh. Ad., Baner, J. A., Lehmann, Georgius, Furmannus, Godofredus, Ittig, Thomas, Bose, Gottfried Christianus, Rappold, Frid., Mayer, Johannes Ulricus, Laurentius, Johannes, Knauth, Gottfried, Schneider, Johannes Daniel, Birnbaum, A., and Schneider, Daniel

Abstract

Durch M. Daniele Schneidern/ ..., Schlüsselseiten aus dem Exemplar der ULB Halle: AB 44 1/k, 6

14. Informatics-based, highly accurate, noninvasive prenatal paternity testing.

Author

Ryan A, Baner J, Demko Z, Hill M, Sigurjonsson S, Baird ML, and Rabinowitz M

Subjects
Adult, Cell-Free System, DNA blood, Female, Genetic Testing, Gestational Age, Humans, Male, Polymorphism, Single Nucleotide, Pregnancy, Computational Biology methods, Paternity, Prenatal Diagnosis methods
Abstract

Purpose: The aim of the study was to evaluate the diagnostic accuracy of an informatics-based, noninvasive, prenatal paternity test using array-based single-nucleotide polymorphism measurements of cell-free DNA isolated from maternal plasma., Methods: Blood samples were taken from 21 adult pregnant women (with gestational ages between 6 and 21 weeks), and a genetic sample was taken from the corresponding biological fathers. Paternity was confirmed by genetic testing of the infant, products of conception, control of fertilization, and/or preimplantation genetic diagnosis during in vitro fertilization. Parental DNA samples and maternal plasma cell-free DNA were amplified and analyzed using a HumanCytoSNP-12 array. An informatics-based method measured single-nucleotide polymorphism data, confirming or rejecting paternity. Each plasma sample with a sufficient fetal cell-free DNA fraction was independently tested against the confirmed father and 1,820 random, unrelated males., Results: One of the 21 samples had insufficient fetal cell-free DNA. The test correctly confirmed paternity for the remaining 20 samples (100%) when tested against the biological father, with P values of <10(-4). For the 36,400 tests using an unrelated male as the alleged father, 99.95% (36,382) correctly excluded paternity and 0.05% (18) were indeterminate. There were no miscalls., Conclusion: A noninvasive paternity test using informatics-based analysis of single-nucleotide polymorphism array measurements accurately determined paternity early in pregnancy.

Published
2013
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15. Noninvasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci.

Author

Zimmermann B, Hill M, Gemelos G, Demko Z, Banjevic M, Baner J, Ryan A, Sigurjonsson S, Chopra N, Dodd M, Levy B, and Rabinowitz M

Subjects
Female, Humans, Karyotype, Male, Pregnancy, Sex Chromosome Aberrations, Chromosomes, Human, Maternal Serum Screening Tests, Sex Chromosome Disorders diagnosis, Trisomy diagnosis
Abstract

Objective: This study aims to develop a noninvasive prenatal test on the basis of the analysis of cell-free DNA in maternal blood to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y., Methods: A total of 166 samples from pregnant women, including 11 trisomy 21, three trisomy 18, two trisomy 13, two 45,X, and two 47,XXY samples, were analyzed using an informatics-based method. Cell-free DNA from maternal blood was isolated, amplified using a multiplex polymerase chain reaction (PCR) assay targeting 11,000 single nucleotide polymorphisms on chromosomes 13, 18, 21, X, and Y in a single reaction, and sequenced. A Bayesian-based maximum likelihood statistical method was applied to determine the chromosomal count of the five chromosomes interrogated in each sample, along with a sample-specific calculated accuracy for each test result., Results: The algorithm correctly reported the chromosome copy number at all five chromosomes in 145 samples that passed a DNA quality test, for a total of 725/725 correct calls. The average calculated accuracy for these samples was 99.92%. Twenty-one samples did not pass the DNA quality test., Conclusions: This informatics-based method noninvasively detected fetuses with trisomy 13, 18, and 21, 45,X, and 47,XXY with high sample-specific calculated accuracies for each individual chromosome and across all five chromosomes., (© 2012 John Wiley & Sons, Ltd.)

Published
2012
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16. Diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays.

Author

Szemes M, Bonants P, de Weerdt M, Baner J, Landegren U, and Schoen CD

Subjects
Animals, Fungi genetics, Fungi isolation & purification, Nematoda genetics, Nematoda isolation & purification, Oomycetes genetics, Oomycetes isolation & purification, Plant Diseases parasitology, Molecular Diagnostic Techniques, Oligonucleotide Array Sequence Analysis methods, Oligonucleotide Probes chemistry, Plant Diseases microbiology
Abstract

Padlock probes (PLPs) are long oligonucleotides, whose ends are complementary to adjacent target sequences. Upon hybridization to the target, the two ends are brought into contact, allowing PLP circularization by ligation. PLPs provide extremely specific target recognition, which is followed by universal amplification and microarray detection. Since target recognition is separated from downstream processing, PLPs enable the development of flexible and extendable diagnostic systems, targeting diverse organisms. To adapt padlock technology for diagnostic purposes, we optimized PLP design to ensure high specificity and eliminating ligation on non-target sequences under real-world assay conditions. We designed and tested 11 PLPs to target various plant pathogens at the genus, species and subspecies levels, and developed a prototype PLP-based plant health chip. Excellent specificity was demonstrated toward the target organisms. Assay background was determined for each hybridization using a no-target reference sample, which provided reliable and sensitive identification of positive samples. A sensitivity of 5 pg genomic DNA and a dynamic range of detection of 100 were observed. The developed multiplex diagnostic system was validated using genomic DNAs of characterized isolates and artificial mixtures thereof. The demonstrated system is adaptable to a wide variety of applications ranging from pest management to environmental microbiology.

Published
2005
Full Text
View/download PDF

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