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Phillips C, Gelabert-Besada M, Fernandez-Formoso L, García-Magariños M, Santos C, Fondevila M, Ballard D, Syndercombe Court D, Carracedo Á, Victoria Lareu M. “New turns from old STaRs”: Enhancing the capabilities of forensic short tandem repeat analysis. Electrophoresis 2014; 35:3173-87. [DOI: 10.1002/elps.201400095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/25/2014] [Accepted: 05/15/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Christopher Phillips
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Miguel Gelabert-Besada
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Luis Fernandez-Formoso
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | | | - Carla Santos
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - Manuel Fondevila
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
| | - David Ballard
- Department of Forensic and Analytical Science; King's College London; London UK
| | | | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
- Center of Excellence in Genomic Medicine Research; King Abdulaziz University; Jeddah Saudi Arabia
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Legal Medicine; University of Santiago de Compostela; Santiago de Compostela Spain
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Wu JF, Xia L, Liu YX, Zhang X, Li C, Li ML. The high incidence of STR D21S1446 homozygosity in Han and She populations living in South Eastern China. J Assist Reprod Genet 2011; 29:337-41. [PMID: 22193752 DOI: 10.1007/s10815-011-9699-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022] Open
Abstract
PURPOSE This study investigated the allelic frequency of 4 short terminal repeats (STRs) in Han and She populations from eastern China. METHODS DNA samples from Han (N = 110) and She (N = 110) healthy subjects were amplified using PCR and primers specific for the STRs. D21S11 and D21S1446 (chromosome 21) and D18S865 and D18S535 (chromosome 18). The frequency and homozygocity of different STRs were evaluated. RESULTS For both populations, D21S11 and D18S535 were more polymorphic than D21S1446 and D18S865, and the D21S1446 1 allele was very common (48.6% and 55.0% for the Han and She groups, respectively).The Han and She groups significantly differed from one another in respect to the distribution of D21S11, D18S865, and D18S535 allelic frequency (all P -values ≤ 0.48) but had a similar allelic distribution for D21S1446 (P = 0.106). D21S1446 was found to be homozygous about 50% of the time which was significantly greater compared to the other STRs analyzed. CONCLUSION This study found that the Han and She differ genetically at 3 autosomal STRs located on chromosome 18 and 21. The STR D21S1146 was often homozygous within these groups, indicating it would be poor marker for analyzing trisomy within these populations.
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Affiliation(s)
- Jin-Fang Wu
- Department of Obstetrics and Gynecology, Xi'an Jiaotong University Medical School Second Affiliated Hospital, Xi Wu Road 157, Xi'an City, Xi'an, 710004, China.
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Tobe SS, Linacre A. DNA typing in wildlife crime: recent developments in species identification. Forensic Sci Med Pathol 2010; 6:195-206. [PMID: 20526699 DOI: 10.1007/s12024-010-9168-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, Strathclyde University, WestCHEM, Glasgow, UK
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Tamura A, Iwata M, Fukunishi S, Nishio H, Suzuki K. Identification of newly polymorphic intron 40 markers of the von Willebrand factor gene in a Japanese population. Leg Med (Tokyo) 2009; 11:129-31. [PMID: 19144556 DOI: 10.1016/j.legalmed.2008.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 10/03/2008] [Accepted: 11/12/2008] [Indexed: 11/29/2022]
Abstract
We investigated a region of repetitive DNA located in intron 40 of the von Willebrand factor (vWF) gene (nucleotides [nt] 1639-2404; i.e., F8VWF). We identified 13 alleles and 33 genotypes in 49 unrelated Japanese individuals. The heterozygosity of the region was 0.897. Direct sequence analyses revealed five single-base substitutions, one tetranucleotide (TTAT) insertion, and seven short tandem repeats (STRs) in the intron; four of the STRs and one single-base substitution had been reported previously. The four new base substitutions we identified were 1849T>A, 2122C>T, 2180C>T, and 2192C>T. The novel TTAT tetranucleotide was inserted between nt 2057 and 2058. The three newly identified STRs were 1978(TATC)(1-2), 2193(ATCT)(5-13), and 2234(TGTA)(5-7). The five single-base substitutions and the TTAT insertion were identified only with 3' downstream of vWA allele 14.
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Affiliation(s)
- Akiyoshi Tamura
- Department of Legal Medicine, Osaka Medical College, 2-7 Takatsuki, Osaka 569-8686, Japan.
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Hering S, Augustin C, Edelmann J, Heidel M, Chamaon K, Dressler J, Szibor R. Complex variability of intron 40 of the von Willebrand factor (vWF) gene. Int J Legal Med 2007; 122:67-71. [PMID: 17273877 DOI: 10.1007/s00414-006-0149-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Accepted: 12/13/2006] [Indexed: 10/23/2022]
Abstract
Intron 40 of the von Willebrand factor (vWF) gene exhibits a highly variable region of about 0.65 kb, which contains 5 juxtaposed STRs. We sequenced 0.65 kb amplicons from 68 chromosomes and found 2 frequent indel polymorphisms and 5 SNPs. The 68 chromosomes investigated here presented a total of 47 different haplotypes. Regarding the SNP allele distribution in our sample, we arranged our results of the vWF intron 40 into a system of 3 haplotypes, i.e. haplotypes a, b and c. Our review may be valuable in further optimising vWF typing in forensic applications and in avoiding pitfalls. Further attempts to develop sophisticated techniques may soon enable haplotyping using autosomale STR clusters.
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Affiliation(s)
- Sandra Hering
- Institut für Rechtsmedizin, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
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Ago K, Orihara Y, Ago M, Nakagawa S, Ogata M. Evaluation of the species specificity for six human short tandem repeat loci CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA, in the Japanese macaque. Leg Med (Tokyo) 2004; 6:102-8. [PMID: 15039053 DOI: 10.1016/j.legalmed.2003.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2003] [Revised: 10/17/2003] [Accepted: 12/17/2003] [Indexed: 11/29/2022]
Abstract
We examined six human short tandem repeat (STR) loci (c-fms proto-oncogene for CSF-1 receptor, CSF1PO; thyroid peroxidase, TPOX; tyrosine hydroxylase, TH01; coagulation factor XIII a subunit, F13A01; c-fes/fps proto-oncogene, FESFPS and von Willebrand factor, vWA) in the Japanese macaque, Macaca fuscata, using commercially available human STR kits. No products were amplified by polymerase chain reaction (PCR) using the human CSF1PO, TH01, FESFPS and vWA primers. Macaque DNAs were amplified with human TPOX and F13A01 primers. Macaque PCR products amplified with the TPOX and F13A01 primers migrated more slowly than human ones during electrophoresis. Sequencing results showed that the nucleotide sequences of the counterpart of the TPOX and F13A01 STR loci in the Japanese macaque were closely similar to those of the human genes except for tandem repeat regions. The macaque products amplified with human TPOX and F13A01 primers were highly polymorphic, with four variants of the former and 15 variants of the latter in the nine samples. These results indicate that the commercially available kits can be used to discriminate the Japanese macaque samples from human samples.
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Affiliation(s)
- Kazutoshi Ago
- Department of Legal Medicine, Graduate School of Medicine and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Japan.
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Walsh SJ, Robinson SL, Turbett GR, Davies NP, Wilton AN. Characterisation of variant alleles at the HumD21S11 locus implies unique Australasian genotypes and re-classification of nomenclature guidelines. Forensic Sci Int 2003; 135:35-41. [PMID: 12893133 DOI: 10.1016/s0379-0738(03)00170-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several variant alleles of the HumD21S11 locus have only been reported in Australasian population samples. Fifteen such alleles were observed in Caucasian and Australian Aborigine sub-population databases compiled from residents of the state of Western Australia. Each variant was sequenced to authenticate the allelic designation and determine the structural conformation. Nine novel structural variants are described. The structure of the repeat region of these rare alleles combined with the STR designation brings aspects of the HumD21S11 nomenclature guidelines into question, in particular the designation of common incomplete repeats (or "0.2's"). The conformation of the sequences provides evidence in support of a genetic relationship between the Australian Aborigine and the Papuan people.
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Affiliation(s)
- Simon J Walsh
- Science and Justice Consulting, P.O. Box 83, Surry Hills, NSW 2010, Australia.
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Ago K, Ago M, Orihara Y, Nakagawa S, Ogata M. Polymerase chain reaction amplification of samples from Japanese monkeys using primers for human short tandem repeat loci. Leg Med (Tokyo) 2003; 5 Suppl 1:S204-6. [PMID: 12935590 DOI: 10.1016/s1344-6223(02)00112-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examined the species specificity of six commercially available human short tandem repeat systems (for CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA) using six samples obtained from the Japanese monkey Macaca fuscata. Macaque genes were amplified with human TPOX and F13A01 primers. During electrophoresis, macaque polymerase chain reaction (PCR) products amplified with the TPOX primer migrated more slowly than human ones, and migrated close to human CSF1PO bands. Macaque PCR products amplified with the F13A01 primer also migrated more slowly than the human equivalent. The six macaque samples were classified into three types by the TPOX primer and into six types by the F13A01 primer. These results suggest that the primers for human TPOX and F13A01 loci can be used to distinguish between human and Japanese macaque samples.
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Affiliation(s)
- Kazutoshi Ago
- Department of Legal Medicine, Faculty of Medicine, Kagoshima University, Sakuragaoka 8-35-1, Kagoshima 890-8520, Japan.
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Medintz IL, Paegel BM, Blazej RG, Emrich CA, Berti L, Scherer JR, Mathies RA. High-performance genetic analysis using microfabricated capillary array electrophoresis microplates. Electrophoresis 2001; 22:3845-56. [PMID: 11700713 DOI: 10.1002/1522-2683(200110)22:18<3845::aid-elps3845>3.0.co;2-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.
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Affiliation(s)
- I L Medintz
- Department of Chemistry, University of California, Berkeley 94720, USA
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Medintz IL, Berti L, Emrich CA, Tom J, Scherer JR, Mathies RA. Genotyping Energy-Transfer-Cassette-labeled Short-Tandem-Repeat Amplicons with Capillary Array Electrophoresis Microchannel Plates. Clin Chem 2001. [DOI: 10.1093/clinchem/47.9.1614] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Background: Genetic analysis of microsatellite DNA is a powerful tool used in linkage analysis, gene mapping, and clinical diagnosis. To address the expanding needs of studies of short tandem repeats (STRs), we demonstrated high-performance STR analysis on a high-throughput microchannel plate-based platform.
Methods: Energy-transfer-cassette-labeled STR amplicons were separated and typed on a microfabricated 96-channel radial capillary array electrophoresis (CAE) microchannel plate system. Four-color detection was accomplished with a laser-excited confocal fluorescence rotary scanner.
Results: Multiplex STR analysis with single base-pair resolution was demonstrated on denaturing polyacrylamide gel media. The high-throughput multiplex capabilities of this genetic analysis platform were demonstrated by the simultaneous separation of STR amplicons representing 122 samples in ninety-six 5.5-cm-long channels in <8 min. Sizing values obtained for these amplicons on the CAE microchannel plate were comparable to those measured on a conventional commercial CAE instrument and exhibit <1% sizing variance.
Conclusions: Energy-transfer-cassette labeling and microfabricated CAE microchannel plates allow high-performance multiplex STR analyses.
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Affiliation(s)
- Igor L Medintz
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Lorenzo Berti
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Charles A Emrich
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Jennifer Tom
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - James R Scherer
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Richard A Mathies
- Department of Chemistry, University of California, Berkeley, CA 94720
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Abstract
We report the use of DNA profiles from six STR loci for inferring the ethnic origin of a crime stain and discuss how such inference may be used as intelligence information to reduce the expected number of interviews to resolve a case. To enable this work, databases have been created for five British ethnic groups (Caucasians, Afro-Caribbeans, Indian sub-continentals, Southeast Asians and Middle Easterners) that together comprise 99.7% of the UK population.
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Affiliation(s)
- A L Lowe
- Forensic Science Service, 2960 Trident Court, Birmingham Business Park, Solihull, B37 7YN, West Midlands, UK.
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Lazaruk K, Wallin J, Holt C, Nguyen T, Walsh PS. Sequence variation in humans and other primates at six short tandem repeat loci used in forensic identity testing. Forensic Sci Int 2001; 119:1-10. [PMID: 11348787 DOI: 10.1016/s0379-0738(00)00388-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A large number of alleles from the six different short tandem repeat (STR) loci FGA, D3S1358, vWA, CSF1PO, TPOX and TH01, used in human identity testing were sequenced to provide support for the robustness of fluorescent STR DNA typing by allele size. Sequence information for some of these loci (FGA, vWA, TH01) is an extension of published work, whereas no extensive sequence information is available with respect to the D3S1358, CSF1PO, and TPOX loci. Sequencing of alleles at each locus has provided quantitative data with respect to the true nucleotide length of common alleles, and of alleles that vary in length from the common alleles. All alleles that were identified as "off-ladder" alleles through fluorescent typing at these STR loci have proven to be true length variant alleles. Sequencing at the D3S1358 and CSF1PO loci allowed for the establishment of a common nomenclature for these loci. A correlation between percent stutter and the length of the core tandem repeat is demonstrated at the FGA locus. Alleles in which the core tandem repeat is interrupted by a repeat unit of different sequence have a reduced percent stutter. DNA samples from three non-human primates (chimpanzee, orangutan, and gorilla) were compared to the human sequences, and shown to differ markedly across loci with respect to their homology. The effects of primer binding site mutations on the amplification efficiency at a particular locus, and methods used to interpret amplification imbalance of heterozygous alleles at a locus is also addressed.
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Affiliation(s)
- K Lazaruk
- Applied Biosystems, 850 Lincoln Centre Drive, M/S 404/1, Foster City, CA 94404, USA.
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