98 results on '"Syndercombe Court D"'
Search Results
2. Analysis of artificially degraded DNA using STRs and SNPs—results of a collaborative European (EDNAP) exercise
- Author
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Dixon, L.A., Dobbins, A.E., Pulker, H.K., Butler, J.M., Vallone, P.M., Coble, M.D., Parson, W., Berger, B., Grubwieser, P., Mogensen, H.S., Morling, N., Nielsen, K., Sanchez, J.J., Petkovski, E., Carracedo, A., Sanchez-Diz, P., Ramos-Luis, E., Briōn, M., Irwin, J.A., Just, R.S., Loreille, O., Parsons, T.J., Syndercombe-Court, D., Schmitter, H., Stradmann-Bellinghausen, B., Bender, K., and Gill, P.
- Published
- 2006
- Full Text
- View/download PDF
3. Development and validation of the EUROFORGEN NAME (North African and Middle Eastern) ancestry panel
- Author
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Pereira, Vania, Freire-Aradas, Ana, Ballard, David, Børsting, Claus, Diez, V., Pruszkowska-Przybylska, Paulina, Ribeiro, J., Achakzai, Niaz M, Aliferi, Anastasia, Bulbul, Ozlem, Perez-Carceles, Maria D, Triki-Fendri, Soumaya, Rebai, Ahmed, Syndercombe-Court, D, Morling, Niels, Lareu, Maviky, Carracedo, Angel, The EUROFORGEN-NoE Consortium, and Phillips, Christoffer
- Subjects
0301 basic medicine ,Forensic Genetics ,Genetic Markers ,Genotyping Techniques ,MPS ,Population ,AIMs ,Black People ,Single-nucleotide polymorphism ,Ancestry-informative marker ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Pathology and Forensic Medicine ,03 medical and health sciences ,Middle East ,0302 clinical medicine ,Africa, Northern ,Gene Frequency ,Genetics ,Humans ,030216 legal & forensic medicine ,Genetic variability ,education ,Allele frequency ,education.field_of_study ,Principal Component Analysis ,Cline (biology) ,DNA Fingerprinting ,030104 developmental biology ,Geography ,Genetics, Population ,Evolutionary biology ,North african ,Middle Eastern populations ,Biogeographic ancestry ,SNPs - Abstract
Inference of biogeographic origin is an important factor in clinical, population and forensic genetics. The information provided by AIMs (Ancestry Informative Markers) can allow the differentiation of major continental population groups, and several AIM panels have been developed for this purpose. However, from these major population groups, Eurasia covers a wide area between two continents that is difficult to differentiate genetically. These populations display a gradual genetic cline from West Europe to South Asia in terms of allele frequency distribution. Although differences have been reported between Europe and South Asia, Middle East populations continue to be a target of further investigations due to the lack of genetic variability, therefore hampering their genetic differentiation from neighboring populations. In the present study, a custom-built ancestry panel was developed to analyze North African and Middle Eastern populations, designated the 'NAME' panel. The NAME panel contains 111 SNPs that have patterns of allele frequency differentiation that can distinguish individuals originating in North Africa and the Middle East when combined with a previous set of 126 Global AIM-SNPs.
- Published
- 2019
- Full Text
- View/download PDF
4. Circulating MMP9, vitamin D and variation in the TIMP-1 response with VDR genotype: mechanisms for inflammatory damage in chronic disorders?
- Author
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Timms, P.M., Mannan, N., Hitman, G.A., Noonan, K., Mills, P.G., Syndercombe-court, D., Aganna, E., Price, C.P., and Boucher, B.J.
- Published
- 2002
5. Results of a collaborative study regarding the standardization of the Y-linked STR system DYS385 by the European DNA profiling (EDNAP) group.
- Author
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Schneider, Peter M., D'Aloja, E., Dupuy, B.M., Eriksen, B., Jangblad, A., Kloosterman, A.D., Kratzer, A., Lareu, Maria-Victoria, Pfitzinger, H., Rand, S., Scheithauer, R., Schmitter, H., Skitsa, I., Syndercombe-Court, D., and Vide, M. Conceicao
- Subjects
DNA testing -- Standards - Published
- 1999
6. EFFECTS OF SYMPATHETIC AND ANGIOTENSIN CONVERTING ENZYME INHIBITION ON PLATELET ACTIVATION IN PATIENTS WITH CORONARY ARTERY DISEASE
- Author
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Sayer, JW, Syndercombe-Court, D, Gutteridge, C, Archbold, RA, and Timmis
- Published
- 1998
7. ENDOTHELIAL FUNCTION IN CORONARY ARTERY DISEASE: EFFECTS OF SYMPATHETIC AND CONVERTING ENZYME INHIBITION ON HAEMOSTATIC VARIABLES
- Author
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Sayer, J, Wilkinson, P, Syndercombe-Court, D, Gutteridge, C, and Timmis
- Published
- 1997
8. Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise
- Author
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Ingold, S., Dorum, G., Hanson, E., Berti, A., Branicki, W., Brito, P., Elsmore, P., Gettings, K. B., Giangasparo, F., Gross, T. E., Hansen, S., Hanssen, E. N., Kampmann, M. -L., Kayser, M., Laurent, F. -X., Morling, N., Mosquera-Miguel, A., Parson, W., Phillips, C., Porto, M. J., Pospiech, E., Roeder, A. D., Schneider, P. M., Johann, K. Schulze, Steffen, C. R., Syndercombe-Court, D., Trautmann, M., van den Berge, M., van der Gaag, K. J., Vannier, J., Verdoliva, V., Vidaki, A., Xavier, C., Ballantyne, J., Haas, C., Ingold, S., Dorum, G., Hanson, E., Berti, A., Branicki, W., Brito, P., Elsmore, P., Gettings, K. B., Giangasparo, F., Gross, T. E., Hansen, S., Hanssen, E. N., Kampmann, M. -L., Kayser, M., Laurent, F. -X., Morling, N., Mosquera-Miguel, A., Parson, W., Phillips, C., Porto, M. J., Pospiech, E., Roeder, A. D., Schneider, P. M., Johann, K. Schulze, Steffen, C. R., Syndercombe-Court, D., Trautmann, M., van den Berge, M., van der Gaag, K. J., Vannier, J., Verdoliva, V., Vidaki, A., Xavier, C., Ballantyne, J., and Haas, C.
- Abstract
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols. The provided primer pools for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms included 33 and 29 body fluid specific targets, respectively, to identify blood, saliva, semen, vaginal secretion, menstrual blood and skin. The results demonstrated moderate to high count values in the body fluid or tissue of interest with little to no counts in non-target body fluids. There was some inter-laboratory variability in read counts, but overall the results of the laboratories were comparable in that highly expressed markers showed high read counts and less expressed markers showed lower counts. We performed a partial least squares (PLS) analysis on the data, where blood, menstrual blood, saliva and semen markers and samples clustered well. The results of this collaborative mRNA massively parallel sequencing (MPS) exercise support targeted mRNA sequencing as a reliable body fluid identification method that could be added to the repertoire of forensic MPS panels.
- Published
- 2018
9. Body fluid identification using a targeted mRNA massively parallel sequencing approach - results of a EUROFORGEN/EDNAP collaborative exercise
- Author
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Ingold, S, Dørum, G, Hanson, E, Berti, A, Branicki, W, Brito, P, Elsmore, P, Gettings, K B, Giangasparo, F, Gross, T E, Hansen, S, Hanssen, E N, Kampmann, M-L, Kayser, M, Laurent, F-X, Morling, N, Mosquera-Miguel, A, Parson, W, Phillips, C, Porto, M J, Pośpiech, E, Roeder, A D, Schneider, P M, Schulze Johann, K, Steffen, C R, Syndercombe-Court, D, Trautmann, M, van den Berge, M, van der Gaag, K J, Vannier, J, Verdoliva, V, Vidaki, A, Xavier, C, Ballantyne, J, Haas, C, Ingold, S, Dørum, G, Hanson, E, Berti, A, Branicki, W, Brito, P, Elsmore, P, Gettings, K B, Giangasparo, F, Gross, T E, Hansen, S, Hanssen, E N, Kampmann, M-L, Kayser, M, Laurent, F-X, Morling, N, Mosquera-Miguel, A, Parson, W, Phillips, C, Porto, M J, Pośpiech, E, Roeder, A D, Schneider, P M, Schulze Johann, K, Steffen, C R, Syndercombe-Court, D, Trautmann, M, van den Berge, M, van der Gaag, K J, Vannier, J, Verdoliva, V, Vidaki, A, Xavier, C, Ballantyne, J, and Haas, C
- Abstract
In a previous study we presented an assay for targeted mRNA sequencing for the identification of human body fluids, optimised for the Illumina MiSeq/FGx MPS platform. This assay, together with an additional in-house designed assay for the Ion Torrent PGM/S5 platform, was the basis for a collaborative exercise within 17 EUROFORGEN and EDNAP laboratories, in order to test the efficacy of targeted mRNA sequencing to identify body fluids. The task was to analyse the supplied dried body fluid stains and, optionally, participants' own bona fide or mock casework samples of human origin, according to specified protocols. The provided primer pools for the Illumina MiSeq/FGx and the Ion Torrent PGM/S5 platforms included 33 and 29 body fluid specific targets, respectively, to identify blood, saliva, semen, vaginal secretion, menstrual blood and skin. The results demonstrated moderate to high count values in the body fluid or tissue of interest with little to no counts in non-target body fluids. There was some inter-laboratory variability in read counts, but overall the results of the laboratories were comparable in that highly expressed markers showed high read counts and less expressed markers showed lower counts. We performed a partial least squares (PLS) analysis on the data, where blood, menstrual blood, saliva and semen markers and samples clustered well. The results of this collaborative mRNA massively parallel sequencing (MPS) exercise support targeted mRNA sequencing as a reliable body fluid identification method that could be added to the repertoire of forensic MPS panels.
- Published
- 2018
10. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing
- Author
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Weiler, J.M., Baca, K., Ballard, D., Balsa, F., Bogus, M., Børsting, C., Brisighelli, F. (Francesca), Červenáková, J., Chaitanya, L.C. (Lakshmi), Coble, M.D. (Michael), Decroyer, V., Desmyter, S., Gaag, K. (Kristiaan) van der, Gettings, K.B., Haas, C. (Cordula), Heinrich, J., João Porto, M., Kal, A.J. (Arnoud J.), Kayser, M.H. (Manfred), Kúdelová, A., Morling, N. (Niels), Mosquera-Miguel, A., Noel, F., Parson, W. (Walther), Pereira, V., Phillips, C., Schneider, P.M. (Peter), Syndercombe-Court, D. (Denise), Turanska, M. (Martina), Vidaki, A. (Athina), Woliński, P., Zatkalíková, L. (Lívia), Sijen, T. (Titia), Weiler, J.M., Baca, K., Ballard, D., Balsa, F., Bogus, M., Børsting, C., Brisighelli, F. (Francesca), Červenáková, J., Chaitanya, L.C. (Lakshmi), Coble, M.D. (Michael), Decroyer, V., Desmyter, S., Gaag, K. (Kristiaan) van der, Gettings, K.B., Haas, C. (Cordula), Heinrich, J., João Porto, M., Kal, A.J. (Arnoud J.), Kayser, M.H. (Manfred), Kúdelová, A., Morling, N. (Niels), Mosquera-Miguel, A., Noel, F., Parson, W. (Walther), Pereira, V., Phillips, C., Schneider, P.M. (Peter), Syndercombe-Court, D. (Denise), Turanska, M. (Martina), Vidaki, A. (Athina), Woliński, P., Zatkalíková, L. (Lívia), and Sijen, T. (Titia)
- Abstract
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-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.
- Published
- 2017
- Full Text
- View/download PDF
11. DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing
- Author
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Vidaki, A. (Athina), Ballard, D. (David), Aliferi, A. (Anastasia), Miller, T.H. (Thomas H.), Barron, L.P. (Leon P.), Syndercombe-Court, D. (Denise), Vidaki, A. (Athina), Ballard, D. (David), Aliferi, A. (Anastasia), Miller, T.H. (Thomas H.), Barron, L.P. (Leon P.), and Syndercombe-Court, D. (Denise)
- Abstract
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R2 =0.92, mean absolute error (MAE)=4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R2 =0.96) with a MAE=3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE=7.1 years) and a cohort of 1011 disease state individuals (MAE=7.2 years). Furthermore, we highlighted the age markers' potential applicability in samples other than blood by predictin
- Published
- 2017
- Full Text
- View/download PDF
12. A collaborative EDNAP exercise on SNaPshot™-based mtDNA control region typing
- Author
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Weiler, NEC, Baca, K, Ballard, D, Balsa, F, Bogu, M, Børsting, Claus, Brisighelli, F, Červenáková, J, Chaitanya, L, Coble, M, Decroyer, V, Desmyter, S, van der Gaag, KJ, Gettings, K, Haas, C, Heinrich, J, Porto, MJ, Kal, AJ, Kayser, M, Kúdelová, A, Morling, Niels, Mosquera-Miguel, A, Noel, F, Parson, W, Pereira, Vania, Phillips, C, Schneider, PM, Syndercombe-Court, D, Turanska, M, Vidaki, A, Wolioski, P, Zatkalíková, L, Sijen, T, Weiler, NEC, Baca, K, Ballard, D, Balsa, F, Bogu, M, Børsting, Claus, Brisighelli, F, Červenáková, J, Chaitanya, L, Coble, M, Decroyer, V, Desmyter, S, van der Gaag, KJ, Gettings, K, Haas, C, Heinrich, J, Porto, MJ, Kal, AJ, Kayser, M, Kúdelová, A, Morling, Niels, Mosquera-Miguel, A, Noel, F, Parson, W, Pereira, Vania, Phillips, C, Schneider, PM, Syndercombe-Court, D, Turanska, M, Vidaki, A, Wolioski, P, Zatkalíková, L, and Sijen, T
- Abstract
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshot™-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.
- Published
- 2017
13. A collaborative EDNAP exercise on SNaPshotTM-based mtDNA control region typing
- Author
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Weiler, N. E. C., Baca, K., Ballard, D., Balsa, F., Bogus, M., Børsting, C., Brisighelli, Francesca, 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., Sijen, T., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Weiler, N. E. C., Baca, K., Ballard, D., Balsa, F., Bogus, M., Børsting, C., Brisighelli, Francesca, 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., Sijen, T., and Brisighelli, Francesca (ORCID:0000-0001-5469-4413)
- Abstract
A collaborative European DNA Profiling (EDNAP) Group exercise was undertaken to assess the performance of an earlier described SNaPshotTM-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.
- Published
- 2017
14. Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing
- Author
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Vidaki, A. (Athina), Giangasparo, F. (Federica), Syndercombe-Court, D. (Denise), Vidaki, A. (Athina), Giangasparo, F. (Federica), and Syndercombe-Court, D. (Denise)
- Abstract
The presence of specific body fluids at crime scenes could be linked with particular types of crime, therefore attributing a DNA profile to a specific tissue could increase the evidential significance of a match with a suspect. Current methodologies such as tissue-specific mRNA profiling are useful but drawbacks include low tissue specificity and applicability to degraded samples. In this study, the potential of 11 tissue-specific differentially methylated regions, initially identified following large-scale methylation analysis of whole blood, buccal cells and sperm, was explored in order to identify markers for blood, saliva and semen. Bisulphite pyrosequencing analysis supported previous findings, but tissue-specific differentially methylated regions for blood and buccal cells did not show enough specificity to be proposed as markers for blood and saliva, respectively. For some CpGs, a large inter-individual variation in methylation levels was also observed. Two of the semen markers (cg04382920 and cg11768416) were used for further validation on a large set of stains. These two semen-specific assays showed high sensitivity (as low as 50 pg) and stability. Future experiments will shed light on the usefulness of these markers in forensic casework.
- Published
- 2016
- Full Text
- View/download PDF
15. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™
- Author
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Eduardoff, M, Gross, T E, Santos, C, de la Puente, M, Ballard, D, Strobl, C, Børsting, C, Morling, N, Fusco, L, Hussing, C, Egyed, B, Souto, L, Uacyisrael, J, Syndercombe Court, D, Carracedo, Á, 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, Børsting, C, Morling, N, Fusco, L, Hussing, C, Egyed, B, Souto, L, Uacyisrael, J, Syndercombe Court, D, Carracedo, Á, 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™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, 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™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.
- Published
- 2016
16. Towards complete male individualization with rapidly mutating Y-chromosomal STRs
- Author
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Ballantyne, KN, Ralf, A, Aboukhalid, R, Achakzai, NM, Anjos, MJ, Ayub, Q, Balažic, J, Ballantyne, J, Ballard, DJ, Berger, B, Bobillo, C, Bouabdellah, M, Burri, H, Butler, J, Capal, T, Caratti, S, Carracedo, A, Cartault, F, Carvalho, EF, Cheng, B, Coble, MD, Comas, D, Corach, D, D'Amato, ME, Davison, S, de Carvalho, EF, de Knijff, Peter, de Ungria, M, Decorte, Ronny, Dobosz, T, Dupuy, BM, Elmrghni, S, Gliwinski, M, Gomes, SC, Grol, L, Haas, C, Hanson, E, Henke, J, Hill, CR, Holmlund, G, Honda, K, Immel, U, Inoue, S, Jobling, MA, Kaddura, M, Kim, JS, Kim, SH, Kim, W, King, TE, Klausriegler, E, Kling, D, Kovacevic, LL, Kovatsi, L, Krajewski, P, Kravchenko, S, Larmuseau, Maarten, Lee, EY, Lee, SH, Lessig, R, Livshits, LA, Marjanovic, D, Minarik, M, Mizuno, N, Moreira, H, Morling, N, Mukherjee, M, Nagaraju, J, Neuhuber, F, Nie, S, Nilasitsataporn, P, Nishi, T, Oh, HH, Olofsson, J, Onofri, V, Palo, JU, Pamjav, H, Parson, W, Payet, C, Petlach, M, Phillips, C, Ploski, R, Prasad, SPR, Primorac, D, Purnnomo, GA, Purps, J, Rangel, H, Rebala, K, Rerkamnuaychoke, B, Rey, D, Robino, C, Rodríguez, F, Roewer, L, Rosa, A, Sajantila, A, Sala, A, Salvador, J, Sanz, P, Schmitt, C, Sharma, AK, Silva, DA, Shin, KJ, Sijen, T, Sirker, M, Siváková, D, Skaro, V, Solano-Matamoros, C, Souto, L, Stenzl, V, Sudoyo, H, Syndercombe-Court, D, Tagliabracci, A, Taylor, D, Tillmar, A, Tsybovsky, IS, Tyler-Smith, C, van der Gaag, K, Vanek, D, Völgyi, A, Ward, D, Willemse, P, Winkler, C, Yap, EPH, Yong, RYY, Zupanic Pajnic, I, and Kayser, M
- Subjects
haplotypes ,paternal lineage ,RM YSTRs ,Y-STRs ,forensic ,Y-chromosome - Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database. ispartof: Human Mutation vol:35 issue:8 pages:1021-1032 status: published
- Published
- 2014
17. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- Author
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Ballantyne, K.N., Ralf, A., Aboukhalid, R., Achakzai, N.M., Anjos, M.J., Ayub, Q., Balazic, J., Ballantyne, J., Ballard, D.J., Berger, B., Bobillo, C., Bouabdellah, M., Burri, H., Capal, T., Caratti, S., Cardenas, J., Cartault, F., Carvalho, E.F., Carvalho, M., Cheng, B.W., Coble, M.D., Comas, D., Corach, D., D'Amato, M.E., Davison, S., Knijff, P. de, Ungria, M.C.A. de, Decorte, R., Dobosz, T., Dupuy, B.M., Elmrghni, S., Gliwinski, M., Gomes, S.C., Grol, L., Haas, C., Hanson, E., Henke, J., Henke, L., Herrera-Rodriguez, F., Hill, C.R., Holmlund, G., Honda, K., Immel, U.D., Inokuchi, S., Jobling, M.A., Kaddura, M., Kim, J.S., Kim, S.H., Kim, W., King, T.E., Klausriegler, E., Kling, D., Kovacevic, L., Kovatsi, L., Krajewski, P., Kravchenko, S., Larmuseau, M.H.D., Lee, E.Y., Lessig, R., Livshits, L.A., Marjanovic, D., Minarik, M., Mizuno, N., Moreira, H., Morling, N., Mukherjee, M., Munier, P., Nagaraju, J., Neuhuber, F., Nie, S.J., Nilasitsataporn, P., Nishi, T., Oh, H.H., Olofsson, J., Onofri, V., Palo, J.U., Pamjav, H., Parson, W., Petlach, M., Phillips, C., Ploski, R., Prasad, S.P.R., Primorac, D., Purnomo, G.A., Purps, J., Rangel-Villalobos, H., Rebala, K., Rerkamnuaychoke, B., Gonzalez, D.R., Robino, C., Roewer, L., Rosa, A., Sajantila, A., Sala, A., Salvador, J.M., Sanz, P., Schmitt, C., Sharma, A.K., Silva, D.A., Shin, K.J., Sijen, T., Sirker, M., Sivakova, D., Skaro, V., Solano-Matamoros, C., Souto, L., Stenzl, V., Sudoyo, H., Syndercombe-Court, D., Tagliabracci, A., Taylor, D., Tillmar, A., Tsybovsky, I.S., Tyler-Smith, C., Gaag, K.J. van der, Vanek, D., Volgyi, A., Ward, D., Willemse, P., Yap, E.P.H., Yong, R.Y.Y., Pajnic, I.Z., Kayser, M., Hjelt Institute (-2014), Forensic Medicine, PaleOmics Laboratory, and Genetic Identification
- Subjects
Male ,Rural Population ,haplotypes ,Y-chromosome ,Y-STRs ,RM Y-STRs ,paternal lineage ,forensic ,Asia ,Forensic Science ,Urban Population ,Cell- och molekylärbiologi ,education ,Paternity ,Gene Frequency ,Humans ,Alleles ,Chromosomes, Human, Y ,1184 Genetics, developmental biology, physiology ,Genetic Variation ,DNA Fingerprinting ,RM Y-STRs, Y-STRs, Y-chromosome, forensic, haplotypes, paternal lineage ,Pedigree ,Europe ,Genetics, Population ,Africa ,3111 Biomedicine ,Americas ,Cell and Molecular Biology ,Microsatellite Repeats ,Rättsmedicin - Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database. Published 2014 Wiley Periodicals, Inc.**
- Published
- 2014
18. RNA/DNA co-analysis from human skin and contact traces – results of a sixth collaborative EDNAP exercise
- Author
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Haas, C, Hanson, E, Banemann, R, Bento, A M, Berti, A, Carracedo, Á, Courts, C, De Cock, G, Drobnic, K, Fleming, R, Franchi, C, Gomes, I, Hadzic, G, Harbison, S A, Hjort, Benjamin Benn, Hollard, C, Hoff-Olsen, P, Keyser, C, Kondili, A, Maroñas, O, McCallum, N, Miniati, P, Morling, Niels, Niederstätter, H, Noël, F, Parson, W, Porto, M J, Roeder, A D, Sauer, E, Schneider, P M, Shanthan, G, Sijen, T, Syndercombe Court, D, Turanská, M, van den Berge, M, Vennemann, M, Vidaki, A, Zatkalíková, L, Ballantyne, J, Haas, C, Hanson, E, Banemann, R, Bento, A M, Berti, A, Carracedo, Á, Courts, C, De Cock, G, Drobnic, K, Fleming, R, Franchi, C, Gomes, I, Hadzic, G, Harbison, S A, Hjort, Benjamin Benn, Hollard, C, Hoff-Olsen, P, Keyser, C, Kondili, A, Maroñas, O, McCallum, N, Miniati, P, Morling, Niels, Niederstätter, H, Noël, F, Parson, W, Porto, M J, Roeder, A D, Sauer, E, Schneider, P M, Shanthan, G, Sijen, T, Syndercombe Court, D, Turanská, M, van den Berge, M, Vennemann, M, Vidaki, A, Zatkalíková, L, and Ballantyne, J
- Abstract
The European DNA profiling group (EDNAP) organized a sixth collaborative exercise on RNA/DNA co-analysis for body fluid/tissue identification and STR profiling. The task was to identify skin samples/contact traces using specific RNA biomarkers and test three housekeeping genes for their suitability as reference genes. Eight stains, a skin RNA dilution series and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 22 participating laboratories using RNA extraction or RNA/DNA co-extraction methods. Two sets of previously described skin-specific markers were used: skin1 pentaplex (LCE1C, LCE1D, LCE2D, IL1F7 and CCL27) and skin2 triplex (LOR, KRT9 and CDSN) in conjunction with a housekeeping gene, HKG, triplex (B2M, UBC and UCE). The laboratories used different chemistries and instrumentation. All laboratories were able to successfully isolate and detect mRNA in contact traces (e.g., human skin, palm-, hand- and fingerprints, clothing, car interiors, computer accessories and electronic devices). The simultaneous extraction of RNA and DNA provides an opportunity for positive identification of the tissue source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling. The skin markers LCE1C and LOR and the housekeeping gene marker B2M were detected in the majority of contact traces. Detection of the other markers was inconsistent, possibly due to the low amounts and/or poor quality of the genetic material present in shed skin cells. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid/tissue identification method that can easily be combined with current STR typing technology.
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- 2015
19. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour
- Author
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Chaitanya, L.C. (Lakshmi), Walsh, S. (Susan), Andersen, J.D. (Jeppe Dyrberg), Ansell, R. (Ricky), Ballantyne, K. (Kaye), Ballard, D.J. (David), Banemann, R. (Regine), Bauer, C.M. (Christiane Maria), Bento, A.M. (Ana Margarida), Brisighelli, F. (Francesca), Capal, T. (Tomas), Clarisse, L. (Lindy), Gross, T.E. (Theresa), Haas, C. (Cordula), Hoff-Olsen, P. (Per), Hollard, C. (Clémence), Keyser, C. (Christine), Kiesler, K.M. (Kevin), Kohler, P. (Priscila), Kupiec, T. (Tomasz), Linacre, A. (Adrian), Minawi, A. (Anglika), Morling, N. (Niels), Nilsson, H. (Helena), Norén, L. (Lina), Ottens, R. (Renée), Palo, J. (Jukka), Parson, W. (Walther), Pascali, V.L. (Vincenzo), Phillips, C. (Christopher), Porto, M.J. (Maria João), Sajantila, A. (Antti), Schneider, P.M. (Peter), Sijen, T. (Titia), Söchtig, J. (Jens), Syndercombe-Court, D. (Denise), Tillmar, A. (Andreas), Turanska, M. (Martina), Vallone, P.M. (Peter), Zatkalíková, L. (Lívia), Zidkova, A. (Anastassiya), Branicki, W. (Wojciech), Kayser, M.H. (Manfred), Chaitanya, L.C. (Lakshmi), Walsh, S. (Susan), Andersen, J.D. (Jeppe Dyrberg), Ansell, R. (Ricky), Ballantyne, K. (Kaye), Ballard, D.J. (David), Banemann, R. (Regine), Bauer, C.M. (Christiane Maria), Bento, A.M. (Ana Margarida), Brisighelli, F. (Francesca), Capal, T. (Tomas), Clarisse, L. (Lindy), Gross, T.E. (Theresa), Haas, C. (Cordula), Hoff-Olsen, P. (Per), Hollard, C. (Clémence), Keyser, C. (Christine), Kiesler, K.M. (Kevin), Kohler, P. (Priscila), Kupiec, T. (Tomasz), Linacre, A. (Adrian), Minawi, A. (Anglika), Morling, N. (Niels), Nilsson, H. (Helena), Norén, L. (Lina), Ottens, R. (Renée), Palo, J. (Jukka), Parson, W. (Walther), Pascali, V.L. (Vincenzo), Phillips, C. (Christopher), Porto, M.J. (Maria João), Sajantila, A. (Antti), Schneider, P.M. (Peter), Sijen, T. (Titia), Söchtig, J. (Jens), Syndercombe-Court, D. (Denise), Tillmar, A. (Andreas), Turanska, M. (Martina), Vallone, P.M. (Peter), Zatkalíková, L. (Lívia), Zidkova, A. (Anastassiya), Branicki, W. (Wojciech), and Kayser, M.H. (Manfred)
- Abstract
The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FT
- Published
- 2014
- Full Text
- View/download PDF
20. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
- Author
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Ballantyne, K. (Kaye), Ralf, A. (Arwin), Aboukhalid, R. (Rachid), Achakzai, N.M. (Niaz), Anjos, T. (Tania), Ayub, Q. (Qasim), Balažic, J. (Jože), Ballantyne, J. (Jack), Ballard, D.J. (David), Berger, B. (Burkhard), Bobillo, C. (Cecilia), Bouabdellah, M. (Mehdi), Burri, H. (Helen), Capal, T. (Tomas), Caratti, S. (Stefano), Cárdenas, J. (Jorge), Cartault, F. (François), Carvalho, E.F. (Elizeu), Carvalho, M. (Margarete) de, Cheng, B. (Baowen), Coble, M.D. (Michael), Comas, D. (David), Corach, D. (Daniel), D'Amato, M. (Mauro), Davison, S. (Sean), Knijff, P. (Peter) de, Ungria, M.C.A. (Maria Corazon) de, Decorte, R. (Ronny), Dobosz, T. (Tadeusz), Dupuy, B.M. (Berit), Elmrghni, S. (Samir), Gliwiński, M. (Mateusz), Gomes, S.C. (Sara), Grol, L. (Laurens), Haas, C. (Cordula), Hanson, E. (Erin), Henke, J. (Jürgen), Henke, L. (Lotte), Herrera-Rodríguez, F. (Fabiola), Hill, C.R. (Carolyn), Holmlund, G. (Gunilla), Honda, K. (Katsuya), Immel, U.-D. (Uta-Dorothee), Inokuchi, S. (Shota), Jobling, R., Kaddura, M. (Mahmoud), Kim, J.S. (Jong), Kim, S.H. (Soon), Kim, W. (Wook), King, T.E. (Turi), Klausriegler, E. (Eva), Kling, D. (Daniel), Kovačević, L. (Lejla), Kovatsi, L. (Leda), Krajewski, P. (Paweł), Kravchenko, S. (Sergey), Larmuseau, M.H.D. (Maarten), Lee, E.Y. (Eun Young), Lessig, R. (Rüdiger), Livshits, L.A. (Ludmila), Marjanović, D. (Damir), Minarik, M. (Marek), Mizuno, N. (Natsuko), Moreira, H. (Helena), Morling, N. (Niels), Mukherjee, M. (Meeta), Munier, P. (Patrick), Nagaraju, J. (Javaregowda), Neuhuber, F. (Franz), Nie, S. (Shengjie), Nilasitsataporn, P. (Premlaphat), Nishi, T. (Takeki), Oh, H.H. (Hye), Olofsson, S. (Sylvia), Onofri, V. (Valerio), Palo, J. (Jukka), Pamjav, H. (Horolma), Parson, W. (Walther), Petlach, M. (Michal), Phillips, C. (Christopher), Ploski, R. (Rafal), Prasad, S.P.R. (Samayamantri P.), Primorac, D. (Dragan), Purnomo, G.A. (Gludhug), Purps, J. (Josephine), Rangel-Villalobos, H. (Hector), Reogonekbała, K. (Krzysztof), Rerkamnuaychoke, B. (Budsaba), Gonzalez, D.R. (Danel Rey), Robino, C. (Carlo), Roewer, L. (Lutz), Rosa, A. (Anna) de, Sajantila, A. (Antti), Sala, A. (Andrea), Salvador, J.M. (Jazelyn), Sanz, P. (Paula), Schmitt, C. (Christian), Sharma, A.K. (Anisha K.), Silva, D.A. (Dayse), Shin, K.-J. (Kyoung-Jin), Sijen, T. (Titia), Sirker, M. (Miriam), Siváková, D. (Daniela), Škaro, V. (Vedrana), Solano-Matamoros, C. (Carlos), Souto, L. (L.), Stenzl, V. (Vlastimil), Sudoyo, H. (Herawati), Syndercombe-Court, D. (Denise), Tagliabracci, A. (Adriano), Taylor, D. (Duncan), Tillmar, A. (Andreas), Tsybovsky, I.S. (Iosif), Tyler-Smith, C. (Chris), Gaag, K. (Kristiaan) van der, Vanek, D. (Daniel), Völgyi, A. (Antónia), Ward, D. (Denise), Willemse, P. (Patricia), Yap, E.P.H. (Eric), Yong, Z-Y. (Ze-Yie), Pajnič, I.Z. (Irena Zupanič), Kayser, M.H. (Manfred), Ballantyne, K. (Kaye), Ralf, A. (Arwin), Aboukhalid, R. (Rachid), Achakzai, N.M. (Niaz), Anjos, T. (Tania), Ayub, Q. (Qasim), Balažic, J. (Jože), Ballantyne, J. (Jack), Ballard, D.J. (David), Berger, B. (Burkhard), Bobillo, C. (Cecilia), Bouabdellah, M. (Mehdi), Burri, H. (Helen), Capal, T. (Tomas), Caratti, S. (Stefano), Cárdenas, J. (Jorge), Cartault, F. (François), Carvalho, E.F. (Elizeu), Carvalho, M. (Margarete) de, Cheng, B. (Baowen), Coble, M.D. (Michael), Comas, D. (David), Corach, D. (Daniel), D'Amato, M. (Mauro), Davison, S. (Sean), Knijff, P. (Peter) de, Ungria, M.C.A. (Maria Corazon) de, Decorte, R. (Ronny), Dobosz, T. (Tadeusz), Dupuy, B.M. (Berit), Elmrghni, S. (Samir), Gliwiński, M. (Mateusz), Gomes, S.C. (Sara), Grol, L. (Laurens), Haas, C. (Cordula), Hanson, E. (Erin), Henke, J. (Jürgen), Henke, L. (Lotte), Herrera-Rodríguez, F. (Fabiola), Hill, C.R. (Carolyn), Holmlund, G. (Gunilla), Honda, K. (Katsuya), Immel, U.-D. (Uta-Dorothee), Inokuchi, S. (Shota), Jobling, R., Kaddura, M. (Mahmoud), Kim, J.S. (Jong), Kim, S.H. (Soon), Kim, W. (Wook), King, T.E. (Turi), Klausriegler, E. (Eva), Kling, D. (Daniel), Kovačević, L. (Lejla), Kovatsi, L. (Leda), Krajewski, P. (Paweł), Kravchenko, S. (Sergey), Larmuseau, M.H.D. (Maarten), Lee, E.Y. (Eun Young), Lessig, R. (Rüdiger), Livshits, L.A. (Ludmila), Marjanović, D. (Damir), Minarik, M. (Marek), Mizuno, N. (Natsuko), Moreira, H. (Helena), Morling, N. (Niels), Mukherjee, M. (Meeta), Munier, P. (Patrick), Nagaraju, J. (Javaregowda), Neuhuber, F. (Franz), Nie, S. (Shengjie), Nilasitsataporn, P. (Premlaphat), Nishi, T. (Takeki), Oh, H.H. (Hye), Olofsson, S. (Sylvia), Onofri, V. (Valerio), Palo, J. (Jukka), Pamjav, H. (Horolma), Parson, W. (Walther), Petlach, M. (Michal), Phillips, C. (Christopher), Ploski, R. (Rafal), Prasad, S.P.R. (Samayamantri P.), Primorac, D. (Dragan), Purnomo, G.A. (Gludhug), Purps, J. (Josephine), Rangel-Villalobos, H. (Hector), Reogonekbała, K. (Krzysztof), Rerkamnuaychoke, B. (Budsaba), Gonzalez, D.R. (Danel Rey), Robino, C. (Carlo), Roewer, L. (Lutz), Rosa, A. (Anna) de, Sajantila, A. (Antti), Sala, A. (Andrea), Salvador, J.M. (Jazelyn), Sanz, P. (Paula), Schmitt, C. (Christian), Sharma, A.K. (Anisha K.), Silva, D.A. (Dayse), Shin, K.-J. (Kyoung-Jin), Sijen, T. (Titia), Sirker, M. (Miriam), Siváková, D. (Daniela), Škaro, V. (Vedrana), Solano-Matamoros, C. (Carlos), Souto, L. (L.), Stenzl, V. (Vlastimil), Sudoyo, H. (Herawati), Syndercombe-Court, D. (Denise), Tagliabracci, A. (Adriano), Taylor, D. (Duncan), Tillmar, A. (Andreas), Tsybovsky, I.S. (Iosif), Tyler-Smith, C. (Chris), Gaag, K. (Kristiaan) van der, Vanek, D. (Daniel), Völgyi, A. (Antónia), Ward, D. (Denise), Willemse, P. (Patricia), Yap, E.P.H. (Eric), Yong, Z-Y. (Ze-Yie), Pajnič, I.Z. (Irena Zupanič), and Kayser, M.H. (Manfred)
- Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis
- Published
- 2014
- Full Text
- View/download PDF
21. Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour
- Author
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Chaitanya, L, Walsh, S, Andersen, Jd, Ansell, R, Ballantyne, K, Ballard, D, Banemann, R, Bauer, Cm, Bento, Am, Brisighelli, Francesca, Capal, T, Clarisse, L, Gross, Te, Haas, C, Hoff Olsen, P, Hollard, C, Keyser, C, Kiesler, Km, Kohler, P, Kupiec, T, Linacre, A, Minawi, A, Morling, N, Nilsson, H, Norén, L, Ottens, R, Palo, Ju, Parson, W, Pascali, Vincenzo Lorenzo, Phillips, C, Porto, Mj, Sajantila, A, Schneider, Pm, Sijen, T, Söchtig, J, Syndercombe Court, D, Tillmar, A, Turanska, M, Vallone, Pm, Zatkalíková, L, Zidkova, A, Branicki, W, Kayser, M., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224), Chaitanya, L, Walsh, S, Andersen, Jd, Ansell, R, Ballantyne, K, Ballard, D, Banemann, R, Bauer, Cm, Bento, Am, Brisighelli, Francesca, Capal, T, Clarisse, L, Gross, Te, Haas, C, Hoff Olsen, P, Hollard, C, Keyser, C, Kiesler, Km, Kohler, P, Kupiec, T, Linacre, A, Minawi, A, Morling, N, Nilsson, H, Norén, L, Ottens, R, Palo, Ju, Parson, W, Pascali, Vincenzo Lorenzo, Phillips, C, Porto, Mj, Sajantila, A, Schneider, Pm, Sijen, T, Söchtig, J, Syndercombe Court, D, Tillmar, A, Turanska, M, Vallone, Pm, Zatkalíková, L, Zidkova, A, Branicki, W, Kayser, M., Brisighelli, Francesca (ORCID:0000-0001-5469-4413), and Pascali, Vincenzo Lorenzo (ORCID:0000-0001-6520-5224)
- Abstract
The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising la
- Published
- 2014
22. Autosomal SNP typing of forensic samples with the GenPlex (TM) HID System: Results of a collaborative study
- Author
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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
23. Autosomal SNP typing of forensic samples with the GenPlex(TM) HID System: Results of a collaborative study
- Author
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Tomas, C., Axler-DiPerte, G., Budimlija, Z.M., Børsting, 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., 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., Morling, N., Tomas, C., Axler-DiPerte, G., Budimlija, Z.M., Børsting, 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., 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.
- 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 250-500 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.
- Published
- 2011
24. 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, Frisk Fredslund, S, Gonzalez, S, Hansen, A J, Hoff-Olsen, P, Haas, C, Kohler, P, Kriegel, A K, Lindblom, Bertil, 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, Frisk Fredslund, S, Gonzalez, S, Hansen, A J, Hoff-Olsen, P, Haas, C, Kohler, P, Kriegel, A K, Lindblom, Bertil, 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., Funding Agencies|Ellen and Aage Andersens Foundation
- Published
- 2011
- Full Text
- View/download PDF
25. The SNPforID Consortium. The effect of whole genome amplification on samples originating from more than one donor
- Author
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Thacker, C.R., Balogh, M.K., Børsting, Claus, Ramos, E., Sanchez, D.P., Carracedo, A., Morling, Niels, Schneider, P., Syndercombe-Court, D., Thacker, C.R., Balogh, M.K., Børsting, Claus, Ramos, E., Sanchez, D.P., Carracedo, A., Morling, Niels, Schneider, P., and Syndercombe-Court, D.
- Published
- 2006
26. Analysis of artificially degraded DNA using STRs and SNPs--results of a collaborative European (EDNAP) exercise
- Author
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Dixon, L A, Dobbins, A E, Pulker, H K, Butler, J M, Vallone, P M, Coble, M D, Parson, W, Berger, B, Grubwieser, P, Mogensen, Helle Smidt, Morling, Niels, Nielsen, Karsten, Sanchez Sanchez, Juan Jose, Petkovski, E, Carracedo, A, Sanchez-Diz, P, Ramos-Luis, E, Brion, M, Irwin, J A, Just, R S, Loreille, O, Parsons, T J, Syndercombe-Court, D, Schmitter, H, Stradmann-Bellinghausen, B, Bender, K, Gill, P, Dixon, L A, Dobbins, A E, Pulker, H K, Butler, J M, Vallone, P M, Coble, M D, Parson, W, Berger, B, Grubwieser, P, Mogensen, Helle Smidt, Morling, Niels, Nielsen, Karsten, Sanchez Sanchez, Juan Jose, Petkovski, E, Carracedo, A, Sanchez-Diz, P, Ramos-Luis, E, Brion, M, Irwin, J A, Just, R S, Loreille, O, Parsons, T J, Syndercombe-Court, D, Schmitter, H, Stradmann-Bellinghausen, B, Bender, K, and Gill, P
- Abstract
Udgivelsesdato: 2006-Dec-1, Recently, there has been much debate about what kinds of genetic markers should be implemented as new core loci that constitute national DNA databases. The choices lie between conventional STRs, ranging in size from 100 to 450 bp; mini-STRs, with amplicon sizes less than 200 bp; and single nucleotide polymorphisms (SNPs). There is general agreement by the European DNA Profiling Group (EDNAP) and the European Network of Forensic Science Institutes (ENFSI) that the reason to implement new markers is to increase the chance of amplifying highly degraded DNA rather than to increase the discriminating power of the current techniques. A collaborative study between nine European and US laboratories was organised under the auspices of EDNAP. Each laboratory was supplied with a SNP multiplex kit (Foren-SNPs) provided by the Forensic Science Service, two mini-STR kits provided by the National Institute of Standards and Technology (NIST) and a set of degraded DNA stains (blood and saliva). Laboratories tested all three multiplex kits, along with their own existing DNA profiling technique, on the same sets of degraded samples. Results were collated and analysed and, in general, mini-STR systems were shown to be the most effective. Accordingly, the EDNAP and ENFSI working groups have recommended that existing STR loci are reengineered to provide smaller amplicons, and the adoption of three new European core loci has been agreed.
- Published
- 2005
27. Selecting single nucleotide polymorphism for forensic applications
- Author
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Philips, C., Lareu, M.V., Sanchez Sanchez, Juan Jose, Brion, J., Sobrino, B., Morling, Niels, Schneider, P., Syndercombe-Court, D., Carracedo, A., Philips, C., Lareu, M.V., Sanchez Sanchez, Juan Jose, Brion, J., Sobrino, B., Morling, Niels, Schneider, P., Syndercombe-Court, D., and Carracedo, A.
- Published
- 2004
28. Population specific single nucleotide polymorphisms
- Author
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Phillips, C., Lareu, M.V., Salas, A., Fondevila, M., Lee, G.B., Carracedo, A., Morling, Niels, Schneider, P., Syndercombe-Court, D., Phillips, C., Lareu, M.V., Salas, A., Fondevila, M., Lee, G.B., Carracedo, A., Morling, Niels, Schneider, P., and Syndercombe-Court, D.
- Published
- 2004
29. Y chromosome STR haplotypes in three UK populations
- Author
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Ballard, D.J., primary, Phillips, C., additional, Thacker, C.R., additional, Robson, C., additional, Revoir, A.P., additional, and Syndercombe Court, D., additional
- Published
- 2005
- Full Text
- View/download PDF
30. Reproducibility of mtDNA analysis between laboratories: a report of the European DNA profiling group (EDNAP)
- Author
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Carracedo, A, primary, D'Aloja, E, additional, Dupuy, B, additional, Jangblad, A, additional, Karjalainen, M, additional, Lambert, C, additional, Parson, W, additional, Pfeiffer, H, additional, Pfitzinger, H, additional, Sabatier, M, additional, Syndercombe Court, D, additional, and Vide, C, additional
- Published
- 1998
- Full Text
- View/download PDF
31. Band shift analysis of three base-pair repeat alleles in the short tandem repeat locus D12S391
- Author
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Phillips, C.P, primary, Syndercombe Court, D, additional, Lareu, M.V, additional, Hasskamp, J, additional, and Carracedo, A, additional
- Published
- 1998
- Full Text
- View/download PDF
32. Administration of recombinant human granulocyte-macrophage colony- stimulating factor after chemotherapy regulates the expression and secretion of monocyte tumor necrosis factor (TNF) and TNF receptors p55 and p75
- Author
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Williams, MA, primary, Kouroumoussis, I, additional, Syndercombe-Court, D, additional, Hendry, L, additional, Newland, AC, additional, and Kelsey, SM, additional
- Published
- 1995
- Full Text
- View/download PDF
33. An investigation of the HUMVWA31A locus in British Caucasians
- Author
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Drozd, M.A., primary, Archard, L., additional, Lincoln, P.J., additional, Morling, N., additional, Nellemann, L.J., additional, Phillips, C., additional, Soteriou, B., additional, and Syndercombe Court, D., additional
- Published
- 1994
- Full Text
- View/download PDF
34. Investigation of the STR locus HUMTH01 using PCR and two electrophoresis formats: UK and Galician Caucasian population surveys and usefulness in paternity investigations
- Author
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Lareu, M.V., primary, Phillips, C.P., additional, Carracedo, A., additional, Lincoln, P.J., additional, Syndercombe Court, D., additional, and Thomson, J.A., additional
- Published
- 1994
- Full Text
- View/download PDF
35. Investigation of the between-gel and within-gel variation in fragment size determinations found when using single locus DNA probes
- Author
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Syndercombe Court, D., primary, Fedor, T., additional, Gouldstone, M., additional, Lincoln, P.J., additional, Phillips, C.P., additional, Tate, V., additional, Thomson, J.A., additional, and Watts, P.W., additional
- Published
- 1992
- Full Text
- View/download PDF
36. Increased platelet aggregate formation in patients with chronic airflow obstruction and hypoxaemia.
- Author
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Wedzicha, J A, primary, Syndercombe-Court, D, additional, and Tan, K C, additional
- Published
- 1991
- Full Text
- View/download PDF
37. Thrombolytic treatment in acute myocardial infarction: neutrophil activation, peripheral leucocyte responses, and myocardial injury.
- Author
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Ranjadayalan, K, Umachandran, V, Davies, S W, Syndercombe-Court, D, Gutteridge, C N, and Timmis, A D
- Abstract
OBJECTIVE--To examine early leucocyte responses and neutrophil activation in acute myocardial infarction treated by streptokinase and to relate the findings to coronary recanalisation and indices of myocardial damage in order to provide further information about the role of neutrophils in the evolution of injury. DESIGN--Group analysis of paired blood samples, obtained before streptokinase treatment and one hour after it, and of three indirect measures of myocardial injury: left ventricular ejection fraction, QRS score, and peak creatine kinase. SETTING--The coronary care unit of a district general hospital. PATIENTS--39 patients with acute myocardial infarction who underwent paired blood sampling (before streptokinase and one hour after streptokinase) and cardiac catheterisation 5 (3-8) days later. END POINTS--Changes in peripheral white cell and neutrophil counts and plasma elastase one hour after streptokinase infusion. Comparison of these variables in patients with and without patency of the infarct related coronary artery. Correlations between these variables and indirect measures of myocardial injury. RESULTS--Neutrophil activation, as reflected by plasma elastase, increased sharply one hour after streptokinase. Total white cell and neutrophil counts also increased. Changes tended to be more pronounced in patients with patency of the infarct related artery, though the trend was not statistically significant. Neutrophil activation before streptokinase was unrelated to indirect indices of myocardial injury but only one hour after streptokinase a weak negative correlation with left ventricular ejection fraction had developed. Peripheral neutrophil responses showed a similar relation to ejection fraction and also correlated with peak creatine kinase and QRS score. CONCLUSIONS--Thrombolytic treatment in acute myocardial infarction is associated with an abrupt reactive neutrophil response which provides an early measure of injury. It is also associated with neutrophil activation, probably in response to coronary recanalisation and myocardial reperfusion. Activated neutrophils are recognised as mediators of reperfusion injury in experimental infarction and the data in the present study provide preliminary evidence of a similar pathogenic role in the clinical setting. [ABSTRACT FROM PUBLISHER]
- Published
- 1991
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38. Statistical issues surrounding the analysis of forensic low-template DNA samples
- Author
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Steele, C. D., Balding, D. J., Syndercombe Court, D., and Greenhalgh, M.
- Subjects
614 - Abstract
Increased sensitivity of forensic DNA profiling over the last decade has led to increased stochasticity in the resulting profiles, causing difficulties for interpretation that were acknowledged by the Caddy Report [Caddy et al., 2008]. These difficulties were largely overcome with the adoption of statistical models allowing for dropout and dropin, but interpretation issues remain, several of which are tackled in this thesis. One such issue concerns the choice of allele frequency databases when the ethnic background of the true source of the crime scene DNA is unknown. I propose a heuristic for choosing a single database and adjusting the likelihood ratio calculations to allow for the possibility that a different database may be more appropriate. Another issue in general, and specifically for the database choice heuristic, is the choice of an appropriate value for the population genetics parameter FST to account for distant relatedness between the alleged contributor and an alternative source of the DNA. I present empirical estimates of FST in worldwide populations, relative to the continental-scale reference databases that are used for UK forensic DNA profiles. In the last few years many software packages for the evaluation of low-template DNA samples have emerged, including likeLTD originally developed by my supervisor Prof Balding but greatly improved and reprogrammed by myself as part of my PhD work. There remains little consensus on how to validate these software packages. I present a method of validation based on the use of multiple-replicate crime stain profiles. It relies on the intuition that sufficient replicates of even very noisy DNA profiling runs eventually generate the same information as a single high-quality replicate. I show that likeLTD performs well when assessed by this approach. Finally, I present a new statistical model that extends likeLTD to incorporate the peak height information in a crime scene profile. I show results based on simulation and laboratory trials verifying the good performance of the new model in improved discrimination between true and false hypotheses.
- Published
- 2016
39. Reply to Response to Vacuous standards - Subversion of the OSAC standards-development process.
- Author
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Morrison GS, Neumann C, Geoghegan PH, Edmond G, Grant T, Ostrum RB, Roberts P, Saks M, Syndercombe Court D, Thompson WC, and Zabell S
- Abstract
This Letter to the Editor is a reply to Mohammed et al. (2021) https://doi.org/10.1016/j.fsisyn.2021.100145, which in turn is a response to Morrison et al. (2020) "Vacuous standards - subversion of the OSAC standards-development process" https://doi.org/10.1016/j.fsisyn.2020.06.005., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Author(s).)
- Published
- 2021
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40. Brief report: isogenic induced pluripotent stem cell lines from an adult with mosaic down syndrome model accelerated neuronal ageing and neurodegeneration.
- Author
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Murray A, Letourneau A, Canzonetta C, Stathaki E, Gimelli S, Sloan-Bena F, Abrehart R, Goh P, Lim S, Baldo C, Dagna-Bricarelli F, Hannan S, Mortensen M, Ballard D, Syndercombe Court D, Fusaki N, Hasegawa M, Smart TG, Bishop C, Antonarakis SE, Groet J, and Nizetic D
- Subjects
- Animals, Cells, Cultured, Fibroblasts cytology, Humans, Mitochondria genetics, Aging physiology, Cell Differentiation physiology, Down Syndrome genetics, Induced Pluripotent Stem Cells cytology, Neurons cytology
- Abstract
Trisomy 21 (T21), Down Syndrome (DS) is the most common genetic cause of dementia and intellectual disability. Modeling DS is beginning to yield pharmaceutical therapeutic interventions for amelioration of intellectual disability, which are currently being tested in clinical trials. DS is also a unique genetic system for investigation of pathological and protective mechanisms for accelerated ageing, neurodegeneration, dementia, cancer, and other important common diseases. New drugs could be identified and disease mechanisms better understood by establishment of well-controlled cell model systems. We have developed a first nonintegration-reprogrammed isogenic human induced pluripotent stem cell (iPSC) model of DS by reprogramming the skin fibroblasts from an adult individual with constitutional mosaicism for DS and separately cloning multiple isogenic T21 and euploid (D21) iPSC lines. Our model shows a very low number of reprogramming rearrangements as assessed by a high-resolution whole genome CGH-array hybridization, and it reproduces several cellular pathologies seen in primary human DS cells, as assessed by automated high-content microscopic analysis. Early differentiation shows an imbalance of the lineage-specific stem/progenitor cell compartments: T21 causes slower proliferation of neural and faster expansion of hematopoietic lineage. T21 iPSC-derived neurons show increased production of amyloid peptide-containing material, a decrease in mitochondrial membrane potential, and an increased number and abnormal appearance of mitochondria. Finally, T21-derived neurons show significantly higher number of DNA double-strand breaks than isogenic D21 controls. Our fully isogenic system therefore opens possibilities for modeling mechanisms of developmental, accelerated ageing, and neurodegenerative pathologies caused by T21., (© 2015 AlphaMed Press.)
- Published
- 2015
- Full Text
- View/download PDF
41. Evaluation of DNA variants associated with androgenetic alopecia and their potential to predict male pattern baldness.
- Author
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Marcińska M, Pośpiech E, Abidi S, Andersen JD, van den Berge M, Carracedo Á, Eduardoff M, Marczakiewicz-Lustig A, Morling N, Sijen T, Skowron M, Söchtig J, Syndercombe-Court D, Weiler N, Schneider PM, Ballard D, Børsting C, Parson W, Phillips C, and Branicki W
- Subjects
- Age Factors, Aged, Alopecia genetics, Genetic Association Studies, Genotype, Humans, Male, Middle Aged, Phenotype, Sensitivity and Specificity, White People genetics, Alopecia diagnosis, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide
- Abstract
Androgenetic alopecia, known in men as male pattern baldness (MPB), is a very conspicuous condition that is particularly frequent among European men and thus contributes markedly to variation in physical appearance traits amongst Europeans. Recent studies have revealed multiple genes and polymorphisms to be associated with susceptibility to MPB. In this study, 50 candidate SNPs for androgenetic alopecia were analyzed in order to verify their potential to predict MPB. Significant associations were confirmed for 29 SNPs from chromosomes X, 1, 5, 7, 18 and 20. A simple 5-SNP prediction model and an extended 20-SNP model were developed based on a discovery panel of 305 males from various European populations fitting one of two distinct phenotype categories. The first category consisted of men below 50 years of age with significant baldness and the second; men aged 50 years or older lacking baldness. The simple model comprised the five best predictors: rs5919324 near AR, rs1998076 in the 20p11 region, rs929626 in EBF1, rs12565727 in TARDBP and rs756853 in HDAC9. The extended prediction model added 15 SNPs from five genomic regions that improved overall prevalence-adjusted predictive accuracy measured by area under the receiver characteristic operating curve (AUC). Both models were evaluated for predictive accuracy using a test set of 300 males reflecting the general European population. Applying a 65% probability threshold, high prediction sensitivity of 87.1% but low specificity of 42.4% was obtained in men aged <50 years. In men aged ≥50, prediction sensitivity was slightly lower at 67.7% while specificity reached 90%. Overall, the AUC=0.761 calculated for men at or above 50 years of age indicates these SNPs offer considerable potential for the application of genetic tests to predict MPB patterns, adding a highly informative predictive system to the emerging field of forensic analysis of externally visible characteristics.
- Published
- 2015
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- View/download PDF
42. The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers.
- Author
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Pereira V, Tomas C, Sanchez JJ, Syndercombe-Court D, Amorim A, Gusmão L, Prata MJ, and Morling N
- Subjects
- Genetic Markers, Greenland, Human Migration, Humans, Chromosomes, Human, X genetics, Genetic Variation, Inuit genetics
- Abstract
The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.
- Published
- 2015
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- View/download PDF
43. Increased proteasomal degradation of Bax is a common feature of poor prognosis chronic lymphocytic leukemia.
- Author
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Agrawal SG, Liu FT, Wiseman C, Shirali S, Liu H, Lillington D, Du MQ, Syndercombe-Court D, Newland AC, Gribben JG, and Jia L
- Subjects
- ADP-ribosyl Cyclase 1 metabolism, Biomarkers, Tumor metabolism, Humans, Membrane Glycoproteins metabolism, Prognosis, Survival Analysis, Thermodynamics, Time Factors, Treatment Outcome, ZAP-70 Protein-Tyrosine Kinase metabolism, Leukemia, Lymphocytic, Chronic, B-Cell diagnosis, Leukemia, Lymphocytic, Chronic, B-Cell metabolism, Proteasome Endopeptidase Complex metabolism, Protein Processing, Post-Translational, bcl-2-Associated X Protein metabolism
- Abstract
Many biologic markers are associated with poor prognosis in chronic lymphocytic leukemia (CLL), but their mechanistic role remains unclear. Bax is an essential proapoptotic protein and decreased levels in malignant cells lead to resistance to apoptosis. Using a Bax degradation activity (BDA) assay, CLL cells were found to show variable Bax instability. However, BDA did not correlate with Bax protein levels: BDA positive and negative cases had high and low baseline Bax levels. BDA positive cases showed a marked accumulation of poor prognostic markers-unmutated immunoglobulin heavy chain variable genes, ZAP-70/CD38 positivity, 11q22/17p13 deletion, and short lymphocyte doubling time. Patients with BDA positive cells had a shorter median overall survival (OS; 126 months vs not reached, P = .011) and time to first treatment (16 vs 156 months, P = .029) than BDA negative cases. Dual BDA and ZAP-70 positivity had a median OS of 84 months (P = .012). The BDA assay measures the intrinsic ubiquitin/proteasome activity of CLL cells and dynamic changes in Bax protein levels over time. Mechanistically, Bax instability may represent a final common pathway for disparate prognostic markers, as well as being itself an indicator of poor prognosis.
- Published
- 2008
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44. Development of original donor cell leukemia after successful engraftment from a second donor.
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Stevens JM, Syndercombe-Court D, Oakervee HE, McCloskey D, Jenner MJ, Gribben JG, and Cavenagh JD
- Subjects
- Adult, Humans, Male, Reoperation, Tissue Donors, Bone Marrow Transplantation adverse effects, Graft Survival, Leukemia etiology
- Published
- 2007
- Full Text
- View/download PDF
45. Reactivation of 2 genetically distinct varicella-zoster viruses in the same individual.
- Author
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Taha Y, Scott FT, Parker SP, Syndercombe Court D, Quinlivan ML, and Breuer J
- Subjects
- Adult, DNA, Viral analysis, Genetic Variation, Herpes Zoster immunology, Herpesvirus 3, Human physiology, Humans, Male, Virus Activation, Herpes Zoster virology, Herpesvirus 3, Human genetics, Immunocompetence
- Abstract
Varicella-zoster viruses recovered from 2 episodes of herpes zoster in an immunocompetent man were found to be different genotypes. The fact that the 2 isolates came from the same individual was confirmed by DNA fingerprinting. Immunity following chickenpox may not always protect against systemic reinfection. This finding raises questions about varicella-zoster virus pathogenesis and may have an impact on public health policy.
- Published
- 2006
- Full Text
- View/download PDF
46. Human peripheral blood monocytes express protease receptor-2 and respond to receptor activation by production of IL-6, IL-8, and IL-1{beta}.
- Author
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Johansson U, Lawson C, Dabare M, Syndercombe-Court D, Newland AC, Howells GL, and Macey MG
- Subjects
- Calcium immunology, Cell Differentiation immunology, Cell Line, Dendritic Cells immunology, Flow Cytometry, Humans, Interleukin-1 immunology, Interleukin-6 immunology, Interleukin-8 immunology, Macrophages immunology, Interleukin-1 biosynthesis, Interleukin-6 biosynthesis, Interleukin-8 biosynthesis, Monocytes immunology, Receptor, PAR-2 biosynthesis, Receptor, PAR-2 immunology
- Abstract
Protease-activated receptor-2 (PAR-2) belongs to a family of G-coupled receptors activated by proteolytic cleavage to reveal a tethered ligand. PAR-2 is activated by trypsin and trypsin-like serine proteases and experimentally, by receptor-activating peptides (APs), which mimic the tethered ligand. PAR-2 has recently been implicated in proinflammatory immune responses. For example, PAR-2(-/-) mice exhibit markedly diminished contact hypersensitivity reactions and are completely resistant to adjuvant-induced arthritis. The present study shows that human blood monocytes express low-level cell-surface PAR-2 ex vivo, which is up-regulated upon cell purification by the mobilization of intracellular stores of PAR-2 protein. PAR-2 expression is also present on monocyte-derived macrophages, but only a small proportion of monocyte-derived dendritic cells (DC) is PAR-2(+), and blood DC are PAR(-). Freshly isolated monocytes responded to the PAR-2 AP ASKH 95 (2-furoyl-LIGKV-OH) with the generation of a calcium flux and production of interleukin (IL)-1beta, IL-6, and IL-8. The results presented thus suggest that PAR-2 contributes to inflammatory responses by inducing the production of proinflammatory cytokines in peripheral blood monocytes.
- Published
- 2005
- Full Text
- View/download PDF
47. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives.
- Author
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Parson W, Brandstätter A, Alonso A, Brandt N, Brinkmann B, Carracedo A, Corach D, Froment O, Furac I, Grzybowski T, Hedberg K, Keyser-Tracqui C, Kupiec T, Lutz-Bonengel S, Mevag B, Ploski R, Schmitter H, Schneider P, Syndercombe-Court D, Sørensen E, Thew H, Tully G, and Scheithauer R
- Subjects
- Cooperative Behavior, DNA Primers, Humans, Polymerase Chain Reaction methods, Quality Control, Sequence Analysis, DNA standards, Clinical Laboratory Techniques standards, DNA, Mitochondrial genetics, Databases, Nucleic Acid, Forensic Medicine standards, Genetics, Population
- Abstract
This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group's mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control region or the two hypervariable regions HVI (16024-16365) and HVII (73-340) from DNA extracts, buccal swabs or bloodstains, proceeding in accordance with the protocol and strategies used in each individual laboratory. The results of the collaborative exercises were employed to identify possible sources of errors that could arise during the analysis and interpretation of mtDNA profiles. These findings were taken as a basis to tentatively make suitable arrangements for the construction of a high quality mtDNA database. One hundred fifty mtDNA profiles were submitted to the evaluating laboratory, and disaccording profiles were classified into four groups corresponding to the source of error: clerical errors, sample mix-ups, contaminations and discrepancies with respect to the mtDNA nomenclature. Overall, 14 disaccording haplotypes (16 individual errors) were observed. The errors included 10 clerical errors, 3 interpretation problems, 2 cases of sample mix-up and 1 case of point heteroplasmic mixture, where the 2 sequencing reactions brought inconsistent base calls. This corresponds to an error rate of 10.7% in a virtual mtDNA database consisting of the collaborative exercise results. However, this estimate is still conservative compared to conclusions drawn by authors of meanwhile numerous publications critically reviewing published mtDNA population databases. Our results and earlier published concerns strongly emphasize the need for appropriate safety regulations when mtDNA profiles are compiled for database purposes in order to accomplish the high standard required for mtDNA databases that are used in the forensic context.
- Published
- 2004
- Full Text
- View/download PDF
48. Haplotype combinations of calpain 10 gene polymorphisms associate with increased risk of impaired glucose tolerance and type 2 diabetes in South Indians.
- Author
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Cassell PG, Jackson AE, North BV, Evans JC, Syndercombe-Court D, Phillips C, Ramachandran A, Snehalatha C, Gelding SV, Vijayaravaghan S, Curtis D, and Hitman GA
- Subjects
- Adult, Aged, Female, Gene Frequency, Genetic Predisposition to Disease, Haplotypes, Humans, Male, Middle Aged, Quantitative Trait, Heritable, Risk Factors, Urban Population, Calpain genetics, Diabetes Mellitus, Type 2 ethnology, Diabetes Mellitus, Type 2 genetics, Indians, North American genetics, Mexican Americans genetics, Polymorphism, Genetic
- Abstract
Haplotype combination 112/121 and its intrinsic variants (UCSNP43, -19, and -63) identified within the calpain 10 gene are associated with increased risk of type 2 diabetes in Mexican-Americans. We evaluated whether this haplotype combination and its constituent haplotypes and variants contribute to increased susceptibility to impaired fasting glucose (IFG)/impaired glucose tolerance (IGT) and type 2 diabetes in a South Indian population. Two study groups were used: 95 families ascertained through a proband with type 2 diabetes and 468 subjects recruited as part of an urban survey (69.1% with normal glucose tolerance, 12.8% with IFG/IGT, and 18.2% with type 2 diabetes). The four-locus haplotype combination 1112/1121 (UCSNP44, -43, -19, and -63) in South Indians conferred both a 10.7-fold increased risk for IFG/IGT (P = 0.001) and a 5.78- to 6.52-fold increased risk for type 2 diabetes in the two study groups (families P = 0.025, urban survey P = 0.015). A combination of the 1112 haplotype with the 1221 haplotype also appeared to increase risk for both IFG/IGT and type 2 diabetes. Contrary to what might be expected, quantitative trait analysis in the families found that transmission of the disease-related 1121 and 1112 haplotypes was associated with a reduced hip size and lower waist-to-hip ratio, respectively. This study supports the paradigm that specific haplotype combinations of calpain 10 variants increase risk of both IFG/IGT and type 2 diabetes. However, the relative infrequency of the "at-risk" combinations in the South Indian population suggests that calpain 10 is not a common determinant of susceptibility to type 2 diabetes.
- Published
- 2002
- Full Text
- View/download PDF
49. An Israeli Arab patient with a de novo TNFRSF1A mutation causing tumor necrosis factor receptor-associated periodic syndrome.
- Author
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Aganna E, Zeharia A, Hitman GA, Basel-Vanagaite L, Allotey RA, Booth DR, Hawkins PN, Thacker C, Syndercombe-Court D, and McDermott MF
- Subjects
- Adolescent, Family Health, Female, Genetic Predisposition to Disease, Humans, Israel, Male, Pedigree, Receptors, Tumor Necrosis Factor, Type I, Antigens, CD genetics, Arabs genetics, Familial Mediterranean Fever genetics, Mutation, Missense, Receptors, Tumor Necrosis Factor genetics
- Abstract
Objective: To investigate genetic susceptibility to recurrent fevers, generalized severe myalgia, and migratory erythema in an Israeli Arab child with no family history of similar disease., Methods: DNA sequencing of exons 1-6 of the TNFRSF1A gene (formerly TNFR1) was performed in the patient and his parents to determine the presence of the autosomal-dominant tumor necrosis factor receptor-associated periodic syndrome (TRAPS); informative markers spanning the TNFRSF1A locus were used to genotype all available members of the patient's family. The TNFRSF1A gene was subsequently screened in 69 healthy Arab controls and 96 Caucasian controls. Formal forensic paternity testing was performed on the child., Results: We found a de novo missense mutation in exon 3 of the TNFRSF1A gene, involving a novel C-->T transition encoding a Cys70Arg (C70R) variant, in the Israeli Arab patient. Eight of the common familial Mediterranean fever (FMF) gene MEFV mutations were excluded. This mutation was not present in the parents or siblings, or among the 69 healthy Arab controls. However, another TNFRSF1A variant, Pro46Lys (P46L), was present in 1 of the Arab controls., Conclusion: We have identified a TNFRSF1A mutation associated with periodic fever in an Arab patient, and a TNFRSF1A variant, which is variably pathogenic in Caucasians, in an Arab control. This is the first report of a de novo mutation in periodic fevers in general, and also of TRAPS in the Arab population. These findings demonstrate the need to include TRAPS in the differential diagnosis of recurrent fevers in this population.
- Published
- 2002
- Full Text
- View/download PDF
50. Results of a collaborative study of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DYS19, DYS389 I and II, DYS390 and DYS393 in a PCR pentaplex format.
- Author
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Carracedo A, Beckmann A, Bengs A, Brinkmann B, Caglia A, Capelli C, Gill P, Gusmão L, Hagelberg C, Hohoff C, Hoste B, Kihlgren A, Kloosterman A, Myhre Dupuy B, Morling N, O'Donnell G, Parson W, Phillips C, Pouwels M, Scheithauer R, Schmitter H, Schneider PM, Schumm J, Skitsa I, Stradmann-Bellinghausen B, Stuart M, Syndercombe Court D, and Vide C
- Subjects
- Blood Stains, Cooperative Behavior, DNA Fingerprinting standards, Europe, Female, Haplotypes, Humans, Interinstitutional Relations, Laboratories, Male, Polymerase Chain Reaction standards, Reference Standards, DNA Fingerprinting methods, Gene Frequency genetics, Genetic Variation genetics, Minisatellite Repeats genetics, Polymerase Chain Reaction methods, Polymorphism, Genetic genetics, Y Chromosome genetics
- Abstract
A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in the frame work of the STADNAP program, i.e. standardization of DNA profiling in Europe, in order to evaluate the performance of a Y-chromosome STR pentaplex, which includes the loci DYS19, DYS389 I and II, DYS390 and DYS393 and to determine whether uniformity of results could be achieved among different European laboratories. Laboratories were asked to analyze the five Y-STRs using singleplex and multiplex conditions in three bloodstains and one mixed stain (95% female and 5% male). All the laboratories reported the same results even for the mixed stain included in the exercise. This demonstrates the reproducibility and robustness of Y-chromosome STR typing even with multiplex formats and proves the usefulness of Y-STR systems for analyzing mixed stains with a male component.A total of 930 male samples from 10 different populations from Europe were also analysed for all the loci included in the pentaplex. Eight of these ten populations also included haplotype data. As for single gene analysis, haplotype diversity was higher in Germany and Italy and lower in Western European countries and Finland. Pairwise haplotype analysis shows the Finnish departure from the rest of the populations and a relatively homogeneity in the other European populations with F(ST) estimates lower than 0.05.UPGMA analysis shows an association of Western European population (Ireland, UK, Portugal and Galicia) on the one hand and central European populations on the other.
- Published
- 2001
- Full Text
- View/download PDF
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