The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Peter Gill - One of the best experts on this subject based on the ideXlab platform.

  • a graphical simulation model of the entire dna process associated with the analysis of Short Tandem Repeat loci
    Nucleic Acids Research, 2005
    Co-Authors: Peter Gill, James R Curran, Keith Elliot
    Abstract:

    The use of expert systems to interpret Short Tandem Repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as πextraction. ‘What-if’ scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.

  • analysis of multiplexed Short Tandem Repeat str systems using capillary array electrophoresis
    Electrophoresis, 1998
    Co-Authors: Elaine S Mansfield, Rachael R E Frazier, James M Robertson, Marina Vainer, Alice R Isenberg, Karin Ferguson, Shitse Chow, Dennis W Harris, David L Barker, Peter Gill
    Abstract:

    The profiling of polymorphic Short Tandem Repeat (STR) markers is being applied to human identification, parentage testing and genetic mapping. Reliable genotyping of these markers is facilitated by polymerase chain reaction (PCR) amplification and high-resolution electrophoretic separation. Capillary array electrophoresis (CAE) offers very rapid, high-resolution separation of the amplified DNA and potential for automated sample processing not realized employing conventional slab-gel electrophoresis. The use of CAE to type DNA samples amplified at 11 genetic loci in multiplex profiles is presented. Two sets totaling 208 samples were amplified in a multiplex fashion using AmpFlSTR-Blue or AmpFlSTR-Green I and analyzed in a blind study using CAE. With the exception of one sample, the CAE genotyping results were in complete agreement with results obtained using a single-capillary system or two slab-gel electrophoresis systems. The sample, genotype TH01 7/10, migrated similar to TH01 6.3/9.3 allele sizes, which suggested a potential band migration shift. The recommended approach to such an observation is to analyze the sample again. The sample was rerun and correct genotype verified. Allelic ladder samples were analyzed multiple times by CAE to determine sizing accuracy and precision. The sizing of over 240 allelic ladder samples yielded an average within-run precision of +/- 0.13 bp and between-run precision of +/- 0.21 bp for fragments up to 350 bp. The CAE protocols permit processing of up to 96 multiplex STR samples in under 70 min.

  • validation of highly discriminating multiplex Short Tandem Repeat amplification systems for individual identification
    Electrophoresis, 1996
    Co-Authors: C. P. Kimpton, N. Oldroyd, Andrew Urquhart, Emma S Millican, S Watson, P E Johnson, Rachael R E Frazier, Becky L Sparkes, Peter Gill
    Abstract:

    Short Tandem Repeat (STR) loci are routinely employed for individual identification. We have examined the performance and reproductibility of a highly informative co-amplification system containing the tetranucleotide STR loci: HUMVWFA31/A, HUMTH01, D20S85, D8S1179, HUMFIBRA, D21S11, and D18S51, in conjunction with the amelogenin sex test, in addition to a modified system omitting the locus D20S85. Polymerase chain reaction (PCR) products were fluorescently detected on an automated sequencer and automatically sized against an internal size standard by Genescan software. Both systems were routinely able to type 500 pg of undegraded DNA. At DNA concentrations between 50–500 pg, partial profiles were produced, but no allelic drop-out was observed. Balanced amplification of all loci occurred over a wide range of DNA concentrations from 50 pg to 10 ng. Alteration of reagent concentrations and cycling parameters from optimal resulted in variation in the efficiency of individual locus amplification relative to the other loci within the system. This was also observed at high ionic strength or extreme pH. However, at all reagent concentrations and conditions, allelic drop-out was not observed. These multiplex systems have potential in both routine forensic and intelligence database applications.

  • Highly discriminating heptaplex Short Tandem Repeat PCR system for forensic identification.
    BioTechniques, 1995
    Co-Authors: A. Urquhart, N. Oldroyd, C. P. Kimpton, Peter Gill
    Abstract:

    : We describe a highly discriminating multiplex Short Tandem Repeat PCR human identification system that gives a matching probability for Caucasians of European ancestry of 2.94 x 10(-8) or 5.66 x 10(-10) when used in combination with a previously described system. The system produces discrimination equal to or greater than four single locus probes (restriction fragment length polymorphism [RFLP] typing of variable nucleotide Tandem Repeat [VNTR] loci). The test is robust and reproducible and works with 1-10 ng of template DNA, using fluorescent detection of PCR products from either 4 or 6 Short Tandem Repeat loci and the X-Y homologous gene amelogenin, giving simultaneous sex diagnosis.

  • Short Tandem Repeat typing of bodies from a mass disaster high success rate and characteristic amplification patterns in highly degraded samples
    BioTechniques, 1995
    Co-Authors: J P Whitaker, C. P. Kimpton, Emma S Millican, T. J. Downes, T M Clayton, A J Urquhart, Peter Gill
    Abstract:

    We have used a PCR-based DNA-typing method, involving the coamplification of four tetrameric Short Tandem Repeat loci, in the analysis of a large number of severely degraded tissue samples taken from the scene of a mass disaster in which bodies were exposed to extreme thermal, physical and chemical insult. Analysis of the amplified DNA in a number of the samples revealed uniquely sized artifact PCR products resulting from the amplification of degraded genomic DNA as well as characteristic patterns in the amounts of PCR products generated from differently sized loci. This system has proved to be very reliable and robust, and we were successful in typing all of the four loci in 66% of the samples tested and at least one locus in 83% of the cases. A PCR-based sex test also proved to be very effective when applied to the degraded samples.

C. P. Kimpton - One of the best experts on this subject based on the ideXlab platform.

  • validation of highly discriminating multiplex Short Tandem Repeat amplification systems for individual identification
    Electrophoresis, 1996
    Co-Authors: C. P. Kimpton, N. Oldroyd, Andrew Urquhart, Emma S Millican, S Watson, P E Johnson, Rachael R E Frazier, Becky L Sparkes, Peter Gill
    Abstract:

    Short Tandem Repeat (STR) loci are routinely employed for individual identification. We have examined the performance and reproductibility of a highly informative co-amplification system containing the tetranucleotide STR loci: HUMVWFA31/A, HUMTH01, D20S85, D8S1179, HUMFIBRA, D21S11, and D18S51, in conjunction with the amelogenin sex test, in addition to a modified system omitting the locus D20S85. Polymerase chain reaction (PCR) products were fluorescently detected on an automated sequencer and automatically sized against an internal size standard by Genescan software. Both systems were routinely able to type 500 pg of undegraded DNA. At DNA concentrations between 50–500 pg, partial profiles were produced, but no allelic drop-out was observed. Balanced amplification of all loci occurred over a wide range of DNA concentrations from 50 pg to 10 ng. Alteration of reagent concentrations and cycling parameters from optimal resulted in variation in the efficiency of individual locus amplification relative to the other loci within the system. This was also observed at high ionic strength or extreme pH. However, at all reagent concentrations and conditions, allelic drop-out was not observed. These multiplex systems have potential in both routine forensic and intelligence database applications.

  • Highly discriminating heptaplex Short Tandem Repeat PCR system for forensic identification.
    BioTechniques, 1995
    Co-Authors: A. Urquhart, N. Oldroyd, C. P. Kimpton, Peter Gill
    Abstract:

    : We describe a highly discriminating multiplex Short Tandem Repeat PCR human identification system that gives a matching probability for Caucasians of European ancestry of 2.94 x 10(-8) or 5.66 x 10(-10) when used in combination with a previously described system. The system produces discrimination equal to or greater than four single locus probes (restriction fragment length polymorphism [RFLP] typing of variable nucleotide Tandem Repeat [VNTR] loci). The test is robust and reproducible and works with 1-10 ng of template DNA, using fluorescent detection of PCR products from either 4 or 6 Short Tandem Repeat loci and the X-Y homologous gene amelogenin, giving simultaneous sex diagnosis.

  • Short Tandem Repeat typing of bodies from a mass disaster high success rate and characteristic amplification patterns in highly degraded samples
    BioTechniques, 1995
    Co-Authors: J P Whitaker, C. P. Kimpton, Emma S Millican, T. J. Downes, T M Clayton, A J Urquhart, Peter Gill
    Abstract:

    We have used a PCR-based DNA-typing method, involving the coamplification of four tetrameric Short Tandem Repeat loci, in the analysis of a large number of severely degraded tissue samples taken from the scene of a mass disaster in which bodies were exposed to extreme thermal, physical and chemical insult. Analysis of the amplified DNA in a number of the samples revealed uniquely sized artifact PCR products resulting from the amplification of degraded genomic DNA as well as characteristic patterns in the amounts of PCR products generated from differently sized loci. This system has proved to be very reliable and robust, and we were successful in typing all of the four loci in 66% of the samples tested and at least one locus in 83% of the cases. A PCR-based sex test also proved to be very effective when applied to the degraded samples.

  • automated Short Tandem Repeat str analysis in forensic casework a strategy for the future
    Electrophoresis, 1995
    Co-Authors: Peter Gill, N. Oldroyd, C. P. Kimpton, Andrew Urquhart, Emma S Millican, S Watson, Terry J Downes
    Abstract:

    Short Tandem Repeat (STR) loci are routinely analysed for forensic purposes in the UK. Because small regions of DNa are amplified, successful results are more likely to be obtained from highly degraded material where the DNA fragment length may be < 500 bp. The method is superceeding conventional analysis with single locus probes (SLPs). Dimeric STR loci display stutter artefacts, hence STRs used in casework are restricted to tri or tetrameric loci. Some STRs are complex Repeats and have more alleles than simple Repeats – for example the locus D21S11 has 21 alleles which differ in size by 2 bp because of the presence/absence of a hexanucleotide within the block of tetrameric Repeats. These loci are of great potential interest because they combine increased discriminating power with reduced potential to stutter. Multiplexing 4 different loci with different dye labelled primers (i.e. carrying out polymerase chain reaction of 4 loci simulataneously) using the ABD 373 A automated sequencer enables a large numbers of samples to be processed. In addition data aquisition and manipulation is automated so that minimum postelectrophoresis operator input is required. It is our aim to develop a system equivalent in power to that of 4 single locus probes. To achieve this we have developed an octoplex system consisting of 7 loci and a sex test (amelogenin locus) which has a probability of chance of association of 10−9; the power of this system is equivalent to that achieved by 4 conventional SLPs.

  • a highly discriminating octoplex Short Tandem Repeat polymerase chain reaction system suitable for human individual identification
    Electrophoresis, 1995
    Co-Authors: N. Oldroyd, C. P. Kimpton, Andrew Urquhart, Emma S Millican, S Watson, Teresa Downes, Peter Gill
    Abstract:

    Through the use of fluorescence-based polymerase chain reaction systems, a highly discriminating multiplex with the potential for individual identification has been developed. The use of multiple dye technology enabling loci with overlapping size ranges to be co-amplified has enabled us to successfully amplify seven tetranucleotide Short Tandem Repeat loci within a single reaction in a discriminating power in the region of 1 × 109. Three out of the seven loci employed exhibit alleles differing in size by only 2 bp as opposed to the conventional 4 bp, which results in such loci being more powerful in terms of distinguishing between samples, particularly when co-amplified in this manner. The size ranges of the loci contained within the system are such that windows still exist for the inclusion of additional loci at a later stage, which could increase the discriminating power of the system still further. In addition, further weight and utility is lent to the system through the incorporation of a simple and reliable sex test involving the amplification of a segment of the X–Y homologous gene Amelogenin.

Richard A Mathies - One of the best experts on this subject based on the ideXlab platform.

  • integrated sample cleanup and capillary array electrophoresis microchip for forensic Short Tandem Repeat analysis
    Forensic Science International-genetics, 2011
    Co-Authors: Peng Liu, James R. Scherer, Susan A Greenspoon, Thomas N Chiesl, Richard A Mathies
    Abstract:

    Abstract A twelve-lane capillary array electrophoresis (CAE) microsystem is developed that utilizes an efficient inline capture injection process together with the classical radial microfabricated capillary array electrophoresis (μCAE) format for high-sensitivity forensic Short Tandem Repeat (STR) analysis. Biotin-labeled 9-plex STR amplicons are captured in a photopolymerized gel plug via the strong binding of streptavidin and biotin, followed by efficient washing and thermal release for CE separation. The analysis of 12 STR samples is completed in 30 min without any manual process intervention. A comparison between capture inline injection and conventional cross injection demonstrated at least 10-fold improvement in sensitivity. The limit-of-detection of the capture-CAE system was determined to be 35 haploid copies (17–18 diploid copies) of input DNA; this detection limit approaches the theoretical limits calculated using Poisson statistics and the spectral sensitivity of the instrument. To evaluate the capability of this microsystem for low-copy-number (LCN) analysis, three touch evidence samples recovered from unfired bullet cartridges in a pistol submerged in water for an hour were successfully analyzed, providing 53, 71, and 59% of the DNA profile. The high-throughput capture-CAE microsystem presented here provides a more robust and more sensitive platform for conventional as well as LCN and degraded DNA analysis.

  • integrated sample cleanup capillary electrophoresis microchip for high performance Short Tandem Repeat genetic analysis
    Analytical Chemistry, 2009
    Co-Authors: Stephanie H I Yeung, Peng Liu, Nadia Del Bueno, Susan A Greenspoon, Richard A Mathies
    Abstract:

    An integrated PCR sample cleanup and preconcentration process is developed for forensic Short Tandem Repeat (STR) analysis using a streptavidin-modified photopolymerized capture gel injector for microchip capillary electrophoresis (μCE). PCR samples generated with one biotinylated primer and one fluorescent primer provide the input to the streptavidin-based affinity capture-μCE device. Monoplex PCR samples processed by the device exhibited ∼10- to 50-fold increased fluorescence intensities, and DNA profiles generated using 9-plex STR samples displayed ∼14- to 19-fold higher signal intensities compared to those analyzed using traditional cross injection. Complete STR profiles were obtained with as few as 25 copies of DNA template using the capture-μCE device. Four DNA samples with various degrees of degradation were also tested. Samples analyzed using the capture-μCE device resulted in a significant increase of successful allele detection. The ability of our capture-μCE device and method to remove contamin...

  • integrated sample cleanup capillary electrophoresis microchip for high performance Short Tandem Repeat genetic analysis
    Analytical Chemistry, 2009
    Co-Authors: Stephanie H I Yeung, Peng Liu, Nadia Del Bueno, Susan A Greenspoon, Richard A Mathies
    Abstract:

    An integrated PCR sample cleanup and preconcentration process is developed for forensic Short Tandem Repeat (STR) analysis using a streptavidin-modified photopolymerized capture gel injector for microchip capillary electrophoresis (microCE). PCR samples generated with one biotinylated primer and one fluorescent primer provide the input to the streptavidin-based affinity capture-microCE device. Monoplex PCR samples processed by the device exhibited approximately 10- to 50-fold increased fluorescence intensities, and DNA profiles generated using 9-plex STR samples displayed approximately 14- to 19-fold higher signal intensities compared to those analyzed using traditional cross injection. Complete STR profiles were obtained with as few as 25 copies of DNA template using the capture-microCE device. Four DNA samples with various degrees of degradation were also tested. Samples analyzed using the capture-microCE device resulted in a significant increase of successful allele detection. The ability of our capture-microCE device and method to remove contaminating ions, to concentrate the sample injection plug, and to eliminate electrokinetic injection bias provides a powerful approach for integrating sample cleanup with DNA separation.

  • Integrated portable polymerase chain reaction-capillary electrophoresis microsystem for rapid forensic Short Tandem Repeat typing
    Analytical Chemistry, 2007
    Co-Authors: Peng Liu, Nathaniel Beyor, Tae-seok Seo, Kyoung Jin Shin, James R. Scherer, Richard A Mathies
    Abstract:

    A portable forensic genetic analysis system consisting of a microfluidic device for amplification and separation of Short Tandem Repeat (STR) fragments as well as an instrument for chip operation and four-color fluorescence detection has been developed. The microdevice performs polymerase chain reaction (PCR) in a 160-nL chamber and capillary electrophoresis (CE) in a 7-cm-long separation channel. The instrumental design integrates PCR thermal cycling, electrophoretic separation, pneumatic valve fluidic control, and four-color laser excited fluorescence detection. A quadruplex Y-chromosome STR typing system consisting of amelogenin and three Y STR loci (DYS390, DYS393, DYS439) was developed and used for validation studies. The multiplex amplification of these 4 loci with 35 PCR cycles followed by CE separation and 4-color fluorescence detection was completed in 1.5 h. All the amplicons can be detected with a limit of detection of 20 copies of male standard DNA in the reactor. Real-world forensic analyses of oral swab and human bone extracts from case evidence were also successfully performed. Mixture analysis demonstrated that a balanced profile can be obtained even at a male-to-female template ratio of 1:10. The successful development and operation of this portable PCR-CE system establishes the feasibility of rapid point-of-analysis DNA typing of forensic casework, of mass disaster samples or of individuals at a security checkpoint.

  • rapid and high throughput forensic Short Tandem Repeat typing using a 96 lane microfabricated capillary array electrophoresis microdevice
    Journal of Forensic Sciences, 2006
    Co-Authors: Stephanie H I Yeung, Susan A Greenspoon, M Amy S Mcguckian, Cecelia A Crouse, A Charles B S Emrich, M Jeffrey S Ban, Richard A Mathies
    Abstract:

    ABSTRACT: A 96-channel microfabricated capillary array electrophoresis (μCAE) device was evaluated for forensic Short Tandem Repeat (STR) typing using PowerPlex 16® and AmpFlSTR® Profiler Plus® multiplex PCR systems. The high-throughput μCAE system produced high-speed <30-min parallel sample separations with single-base resolution. Forty-eight previously analyzed single-source samples were accurately typed, as confirmed on an ABI Prism 310 and/or the Hitachi FMBIO II. Minor alleles in 3:1 mixture samples containing female and male DNA were reliably typed as well. The instrument produced full profiles from sample DNA down to 0.17 ng, a threshold similar to that found for the ABI 310. Seventeen nonprobative samples from various evidentiary biological stains were also correctly typed. The successful application of the μCAE device to actual forensic STR typing samples is a significant step toward the development of a completely integrated STR analysis microdevice.

Bruce Budowle - One of the best experts on this subject based on the ideXlab platform.

  • strseq a catalog of sequence diversity at human identification Short Tandem Repeat loci
    Forensic Science International-genetics, 2017
    Co-Authors: Katherine Butler Gettings, Bruce Budowle, Walther Parson, Lisa A Borsuk, David Ballard, Martin Bodner, Laurence Devesse, Jonathan L King
    Abstract:

    Abstract The STR Sequencing Project (STRSeq) was initiated to facilitate the description of sequence-based alleles at the Short Tandem Repeat (STR) loci targeted in human identification assays. This international collaborative effort, which has been endorsed by the ISFG DNA Commission, provides a framework for communication among laboratories. The initial data used to populate the project are the aggregate alleles observed in targeted sequencing studies across four laboratories: National Institute of Standards and Technology (N = 1786), Kings College London (N = 1043), University of North Texas Health Sciences Center (N = 839), and University of Santiago de Compostela (N = 944), for a total of 4612 individuals. STRSeq data are maintained as GenBank records at the U.S. National Center for Biotechnology Information (NCBI), which participates in a daily data exchange with the DNA DataBank of Japan (DDBJ) and the European Nucleotide Archive (ENA). Each GenBank record contains the observed sequence of a STR region, annotation (“bracketing”) of the Repeat region and flanking region polymorphisms, information regarding the sequencing assay and data quality, and backward compatible length-based allele designation. STRSeq GenBank records are organized within a BioProject at NCBI ( https://www.ncbi.nlm.nih.gov/bioproject/380127 ), which is sub-divided into: commonly used autosomal STRs, alternate autosomal STRs, Y-chromosomal STRs, and X-chromosomal STRs. Each of these categories is further divided into locus-specific BioProjects. The BioProject hierarchy facilitates access to the GenBank records by browsing, BLAST searching, or ftp download. Future plans include user interface tools at strseq.nist.gov, a pathway for submission of additional allele records by laboratories performing population sample sequencing and interaction with the STRidER web portal for quality control ( http://strider.online ).

  • analysis of Short Tandem Repeat and single nucleotide polymorphism loci from single source samples using a custom haloplex target enrichment system panel
    American Journal of Forensic Medicine and Pathology, 2016
    Co-Authors: Frank R Wendt, Jonathan L King, Xiangpei Zeng, Jennifer D Churchill, Bruce Budowle
    Abstract:

    Short Tandem Repeats and single nucleotide polymorphisms (SNPs) are used to individualize biological evidence samples. Short Tandem Repeat alleles are characterized by size separation during capillary electrophoresis (CE). Massively parallel sequencing (MPS) offers an alternative that can overcome limitations of the CE. With MPS, libraries are prepared for each sample, entailing target enrichment and bar coding, purification, and normalization. The HaloPlex Target Enrichment System (Agilent Technologies) uses a capture-based enrichment system with restriction enzyme digestion to generate fragments containing custom-selected markers. It offers another possible workflow for typing reference samples. Its efficacy was assessed using a panel of 275 human identity SNPs, 88 Short Tandem Repeats, and amelogenin. The data analyzed included locus typing success, depth of sequence coverage, heterozygote balance, and concordance. The results indicate that the HaloPlex Target Enrichment System provides genetic data similar to that obtained by conventional polymerase chain reaction-CE methods with the advantage of analyzing substantially more markers in 1 sequencing run. The genetic typing performance of HaloPlex is comparable to other MPS-based sample preparation systems that utilize primer-based target enrichment.

  • maximum likelihood estimates of admixture in northeastern mexico using 13 Short Tandem Repeat loci
    American Journal of Human Biology, 2002
    Co-Authors: Bruce Budowle, Li Jin, Ranajit Chakraborty, Ricardo M Cerdaflores, Sara A Barton, Ranjan Deka
    Abstract:

    Tetrameric Short Tandem Repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% ± 3.44, 39.99% ± 2.57, and 5.02% ± 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% ± 5.94, 36.99% ± 5.04, and 3.02% ± 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico. Am. J. Hum. Biol. 14:429–439, 2002. © 2002 Wiley-Liss, Inc.

  • czech population data on 10 Short Tandem Repeat loci of sgm plus str system kit using dna purified in fta cards
    Forensic Science International, 2001
    Co-Authors: Daniel Vanek, Roman Hradil, Bruce Budowle
    Abstract:

    Abstract A population study on 10 Short Tandem Repeat (STR) loci was performed on 202 unrelated Czech Caucasians. DNA, initially frozen, was thawed and placed FTA™ paper. The DNA was purified in situ. DNA was amplified by PCR using the AmpFlSTR SGM Plus amplification kit.

  • population data on the thirteen codis core Short Tandem Repeat loci in african americans u s caucasians hispanics bahamians jamaicans and trinidadians
    Journal of Forensic Sciences, 1999
    Co-Authors: Bruce Budowle, Tamyra R Moretti, Anne L Baumstark, Debra A Defenbaugh, Kathleen M Keys
    Abstract:

    Allele distributions for 13 tetrameric Short Tandem Repeat (STR) loci, CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11, were determined in African American, United States Cau- casian, Hispanic, Bahamian, Jamaican, and Trinidadian sample populations. There was little evidence for departures from Hardy- Weinberg expectations (HWE) in any of the populations. Based on the exact test, the loci that departed significantly from HWE are: D21S11 (p 5 0.010, Bahamians); CSF1PO (p 5 0.014, Trinidadi- ans); TPOX (p 5 0.011, Jamaicans and p 5 0.035, U.S. Cau- casians); and D16S539 ( p 5 0.043, Bahamians). After employing the Bonferroni correction for the number of loci analyzed (i.e., 13 loci per database), these observations are not likely to be significant. There is little evidence for association of alleles between the loci in these databases. The allelic frequency data are similar to other com- parable data within the same major population group.

John M. Butler - One of the best experts on this subject based on the ideXlab platform.

  • Recommendation of Short Tandem Repeat profiling for authenticating human cell lines, stem cells, and tissues
    In vitro cellular & developmental biology. Animal, 2010
    Co-Authors: Rita Barallon, John M. Butler, Wilhelm G. Dirks, Steven R. Bauer, Amanda Capes-davis, Elmore E, Manohar R. Furtado, Margaret C. Kline, Arihiro Kohara, Georgyi V. Los
    Abstract:

    Cell misidentification and cross-contamination have plagued biomedical research for as long as cells have been employed as research tools. Examples of misidentified cell lines continue to surface to this day. Efforts to eradicate the problem by raising awareness of the issue and by asking scientists voluntarily to take appropriate actions have not been successful. Unambiguous cell authentication is an essential step in the scientific process and should be an inherent consideration during peer review of papers submitted for publication or during review of grants submitted for funding. In order to facilitate proper identity testing, accurate, reliable, inexpensive, and standardized methods for authentication of cells and cell lines must be made available. To this end, an international team of scientists is, at this time, preparing a consensus standard on the authentication of human cells using Short Tandem Repeat (STR) profiling. This standard, which will be submitted for review and approval as an American National Standard by the American National Standards Institute, will provide investigators guidance on the use of STR profiling for authenticating human cell lines. Such guidance will include methodological detail on the preparation of the DNA sample, the appropriate numbers and types of loci to be evaluated, and the interpretation and quality control of the results. Associated with the standard itself will be the establishment and maintenance of a public STR profile database under the auspices of the National Center for Biotechnology Information. The consensus standard is anticipated to be adopted by granting agencies and scientific journals as appropriate methodology for authenticating human cell lines, stem cells, and tissues.

  • Short Tandem Repeat typing technologies used in human identity testing
    BioTechniques, 2007
    Co-Authors: John M. Butler
    Abstract:

    Short Tandem Repeat (STR) typing methods are widely used today for human identity testing applications including forensic DNA analysis. Following multiplex PCR amplification, DNA samples containing the length-variant STR alleles are typically separated by capillary electrophoresis and genotyped by comparison to an allelic ladder supplied with a commercial kit. This article offers a brief perspective on the technologies and issues involved in STR typing.

  • genetics and genomics of core Short Tandem Repeat loci used in human identity testing
    Journal of Forensic Sciences, 2006
    Co-Authors: John M. Butler
    Abstract:

    Over the past decade, the human identity testing community has settled on a set of core Short Tandem Repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

  • recent developments in y Short Tandem Repeat and y single nucleotide polymorphism analysis
    Forensic science review, 2003
    Co-Authors: John M. Butler
    Abstract:

    This article reviews new genetic markers on the Y-chromosome and methods for analyzing these Short Tandem Repeat (STR) and single nucleotide polymorphism (SNP) loci. Relative chromosomal locations for over 50 Y-chromosome STRs (Y-STRs) are described along with their Repeat motif and allele range characteristics based on published population studies. Multiplex assays for typing many of these markers in a parallel fashion are discussed, as are newly available commercial Y-STR kits. Approximately 250 SNP markers are now catalogued along the Y-chromosome (Y-SNPs) with a unified haplogroup nomenclature describing their relative relationships. Technologies for typing these Y-SNPs are reviewed including primer extension and allele-specific hybridization methods. Finally, available reference materials for standardization of allele calls, Y-STR allele nomenclature issues, and published validation and interlaboratory studies are reviewed.

  • multiplex pcr design strategy used for the simultaneous amplification of 10 y chromosome Short Tandem Repeat str loci
    Analytical and Bioanalytical Chemistry, 2003
    Co-Authors: Peter M. Vallone, Richard Schoske, Christian M Ruitberg, John M. Butler
    Abstract:

    The simultaneous amplification of multiple regions of a DNA template is routinely performed using the polymerase chain reaction (PCR) in a process termed multiplex PCR. A useful strategy involving the design, testing, and optimization of multiplex PCR primer mixtures will be presented. Other multiplex design protocols have focused on the testing and optimization of primers, or the use of chimeric primers. The design of primers, through the close examination of predicted DNA oligomer melting temperatures (T m) and primer–dimer interactions, can reduce the amount of testing and optimization required to obtain a well-balanced set of amplicons. The testing and optimization of the multiplex PCR primer mixture constructed here revolves around varying the primer concentrations rather than testing multiple primer combinations. By solely adjusting primer concentrations, a well-balanced set of amplicons should result if the primers were designed properly. As a model system to illustrate this multiplex design protocol, a 10-loci multiplex (10plex) Y chromosome Short Tandem Repeat (STR) assay is used.