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4. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing

Author

Weiler, N.E.C., Baca, K., Ballard, D., Balsa, F., Bogus, M., Børsting, C., Brisighelli, F., Červenáková, J., Chaitanya, L., Coble, M., Decroyer, V., Desmyter, S., van der Gaag, K.J., Gettings, K., Haas, C., Heinrich, J., João Porto, M., Kal, A.J., Kayser, M., Kúdelová, A., Morling, N., Mosquera-Miguel, A., Noel, F., Parson, W., Pereira, V., Phillips, C., Schneider, P.M., Syndercombe Court, D., Turanska, M., Vidaki, A., Woliński, P., Zatkalíková, L., and Sijen, T.

Published
2017
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7. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise

Author

Santos, C., Fondevila, M., Ballard, D., Banemann, R., Bento, A.M., Børsting, C., Branicki, W., Brisighelli, F., Burrington, M., Capal, T., Chaitanya, L., Daniel, R., Decroyer, V., England, R., Gettings, K.B., Gross, T.E., Haas, C., Harteveld, J., Hoff-Olsen, P., Hoffmann, A., Kayser, M., Kohler, P., Linacre, A., Mayr-Eduardoff, M., McGovern, C., Morling, N., O’Donnell, G., Parson, W., Pascali, V.L., Porto, M.J., Roseth, A., Schneider, P.M., Sijen, T., Stenzl, V., Court, D. Syndercombe, Templeton, J.E., Turanska, M., Vallone, P.M., Oorschot, R.A.H.van, Zatkalikova, L., Carracedo, Á., and Phillips, C.

Published
2015
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12. Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study

Author

Tomas, C., Axler-DiPerte, G., Budimlija, Z.M., Børsting, C., Coble, M.D., Decker, A.E., Eisenberg, A., Fang, R., Fondevila, M., Frisk Fredslund, S., Gonzalez, S., Hansen, A.J., Hoff-Olsen, P., Haas, C., Kohler, P., Kriegel, A.K., Lindblom, B., Manohar, F., Maroñas, O., Mogensen, H.S., Neureuther, K., Nilsson, H., Scheible, M.K., Schneider, P.M., Sonntag, M.L., Stangegaard, M., Syndercombe-Court, D., Thacker, C.R., Vallone, P.M., Westen, A.A., and Morling, N.

Published
2011
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20. Typing of multiple single-nucleotide polymorphisms using ribonuclease cleavage of DNA/RNA chimeric single-base extension primers and detection by MALDI-TOF mass spectrometry

Author

Mengel-Jorgensen, J., Sanchez, J.J., Borsting, C., Kirpekar, F., and Morling, N.

Subjects
Nucleotides -- Research, DNA -- Chemical properties, Mass spectrometry -- Usage, Chemistry
Abstract

A novel single-base extension (SBE) assay using cleavable and noncleavable SBE primers in the same reaction mix is described. The cleavable SBE primers consisted of deoxyribonucleotides and one ribonucleotide (hereafter denoted chimeric primers), whereas the noncleavable SBE primers consisted of only deoxyribonucleotides (hereafter denoted standard primers). Biotin-labeled dd-NTPs were used in the SBE reaction, and the SBE products were purified using the monomeric avidin triethylamine purification protocol, ensuring that only primers extended with a biotin-ddNTP in the 3'-end were isolated. A ribonuclease mix was developed to specifically cleave the chimeric primers, irrespective of the base of the ribonucleotide, whereas standard primers without a ribonucleotide were unaffected by the ribonuclease treatment. The SBE products were analyzed in linear mode using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer. The cleaved SBE products were detected in the 2000 5500 m/z range, and the noncleaved SBE products were detected in the 5500-10 000 m/z range. The method was validated by typing 17 Y chromosome single-nucleotide polymorphisms in 100 males with a 17-plex SBE package containing 9 chimeric primers and 8 standard primers.

Published
2005

21. MALDI-TOF mass spectrometric detection of multiplex single base extended primers. A study of 17 Y-chromosome single-nucleotide polymorphisms

Author

Mengel-Jorgensen, J., Sanchez, J.J., Borsting, C., Kirpekar, F., and Morling, N.

Subjects
Mass spectrometry -- Research, Nucleotides -- Research, Chemistry
Abstract

One of the most promising techniques for typing of multiple single-nucleotide polymorphism (SNP) is detection of single base extension primers (SBE) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We present a new MALDI-TOF MS protocol for typing of multiple SNPs in a single reaction. Biotin-labeled ddNTPs were used in the SBE reaction and solid phase-bound monomeric avidin was used as capturing/purification scheme allowing the exclusive release of the SBE products under gentle conditions using 5% triethylamine. We dubbed this method monomeric avidin triethylamine purification. The biotin-labeled ddNTPs contained linkers with different masses ensuring a clear separation of the alleles even for SBE primers with a mass of 10 300 Da. Furthermore, only 25-350 fmol of SBE primers were necessary in order to obtain reproducible MALDI-TOF spectra. Similar signal intensities were obtained in the 5500-10 300 m/z mass range by increasing the concentration of the longer SBE primers in the reaction. To validate the technique, 17 Y-chromosome SNPs were analyzed in 200 males. The precision and accuracy of the mass determination were analyzed by parametric statistic, and the potential use of MALDI-TOF MS for SNP typing is discussed.

Published
2004

43. A collaborative EDNAP exercise on SNaPshot (TM)-based mtDNA control region typing

Author

Weiler, N. E. C., Baca, K., Ballard, D., Balsa, F., Bogus, M., Borsting, C., Brisighelli, F., Cervenakova, J., Chaitanya, L., Coble, M., Decroyer, V., Desmyter, S., van der Gaag, K. J., Gettings, K., Haas, C., Heinrich, J., Porto, M. Joao, Kal, A. J., Kayser, M., Kudelova, A., Morling, N., Mosquera-Miguel, A., Noel, F., Parson, W., Pereira, V., Phillips, C., Schneider, P. M., Court, D. Syndercombe, Turanska, M., Vidaki, A., Wolinski, P., Zatkalikova, L., Sijen, T., Weiler, N. E. C., Baca, K., Ballard, D., Balsa, F., Bogus, M., Borsting, C., Brisighelli, F., Cervenakova, J., Chaitanya, L., Coble, M., Decroyer, V., Desmyter, S., van der Gaag, K. J., Gettings, K., Haas, C., Heinrich, J., Porto, M. Joao, Kal, A. J., Kayser, M., Kudelova, A., Morling, N., Mosquera-Miguel, A., Noel, F., Parson, W., Pereira, V., Phillips, C., Schneider, P. M., Court, D. Syndercombe, Turanska, M., Vidaki, A., Wolinski, P., Zatkalikova, L., and Sijen, T.

Abstract

A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot (TM)-based screening assay (denoted mini-mtSNaPshot) (Weiler et al., 2016) [1] that targets 18 single nucleotide polymorphism (SNP) positions in the mitochondrial (mt) DNA control region and allows for discrimination of major European mtDNA haplogroups. Besides the organising laboratory, 14 forensic genetics laboratories were involved in the analysis of 13 samples, which were centrally prepared and thoroughly tested prior to shipment. The samples had a variable complexity and comprised straightforward single-source samples, samples with dropout or altered peak sizing, a point heteroplasmy and two-component mixtures resulting in one to five bi-allelic calls. The overall success rate in obtaining useful results was high (97.6%) given that some of the participating laboratories had no previous experience with the typing technology and/or mtDNA analysis. The majority of the participants proceeded to haplotype inference to assess the feasibility of assigning a haplogroup and checking phylogenetic consistency when only 18 SNPs are typed. To mimic casework procedures, the participants compared the SNP typing data of all 13 samples to a set of eight mtDNA reference profiles that were described according to standard nomenclature (Parson et al., 2014) [2], and indicated whether these references matched each sample or not. Incorrect scorings were obtained for 2% of the comparisons and derived from a subset of the participants, indicating a need for training and guidelines regarding mini-mtSNaPshot data interpretation. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

Published
2017

46. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM (TM)

Author

Eduardoff, M., Gross, T. E., Santos, C., de la Puente, M., Ballard, D., Strobl, C., Borsting, C., Morling, N., Fusco, L., Hussing, C., Egyed, B., Souto, L., Uacyisrael, J., Court, D. Syndercombe, Carracedo, A., Lareu, M. V., Schneider, P. M., Parson, W., Phillips, C., Eduardoff, M., Gross, T. E., Santos, C., de la Puente, M., Ballard, D., Strobl, C., Borsting, C., Morling, N., Fusco, L., Hussing, C., Egyed, B., Souto, L., Uacyisrael, J., Court, D. Syndercombe, Carracedo, A., Lareu, M. V., Schneider, P. M., Parson, W., and Phillips, C.

Abstract

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq (TM) PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM (TM) system. This study assessed individual SNP genotyping precision using the Ion PGM (TM), the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM (TM) assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

Published
2016

50. Autosomal SNP typing of forensic samples with the GenPlex (TM) HID System: Results of a collaborative study

Author

Tomas, C., Axler-DiPerte, G., Budimlija, Z. M., Borsting, C., Coble, M. D., Decker, A. E., Eisenberg, A., Fang, R., Fondevila, M., Fredslund, S. Frisk, Gonzalez, S., Hansen, A. J., Hoff-Olsen, P., Haas, C., Kohler, P., Kriegel, A. K., Lindblom, B., Manohar, F., Maronas, O., Mogensen, H. S., Neureuther, K., Nilsson, H., Scheible, M. K., Schneider, P. M., Sonntag, M. L., Stangegaard, M., Syndercombe-Court, D., Thacker, C. R., Vallone, P. M., Westen, A. A., Morling, N., Tomas, C., Axler-DiPerte, G., Budimlija, Z. M., Borsting, C., Coble, M. D., Decker, A. E., Eisenberg, A., Fang, R., Fondevila, M., Fredslund, S. Frisk, Gonzalez, S., Hansen, A. J., Hoff-Olsen, P., Haas, C., Kohler, P., Kriegel, A. K., Lindblom, B., Manohar, F., Maronas, O., Mogensen, H. S., Neureuther, K., Nilsson, H., Scheible, M. K., Schneider, P. M., Sonntag, M. L., Stangegaard, M., Syndercombe-Court, D., Thacker, C. R., Vallone, P. M., Westen, A. A., and Morling, N.

Abstract

The GenPlex (TM) HID System (Applied Biosystems - AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex (TM) HID System using 250500 pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex (TM) HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex (TM) HID System with the most commonly used STR kits, 500 pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500 pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500 pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler (TM) kit (AB), GenPlex (TM) HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex (TM) HID showed a very low mean mach probability, while all STR kits except MiniFiler (TM) had very limited discriminatory power. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

Published
2011

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