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Chia WC, Khoo TS, Abdul Wahid SFS, Razak NFA, Alauddin H, Raja Sabudin RZA, Othman A, Hassan R, Hussin NH. Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT). Ann Hematol 2019; 98:1279-1291. [PMID: 30783731 DOI: 10.1007/s00277-019-03626-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 01/28/2019] [Indexed: 11/26/2022]
Abstract
Short tandem repeat (STR) analysis is used in chimerism monitoring after allogeneic hematopoietic stem cell transplantation (HSCT) for patients with various hematologic malignancies. Commercial forensic STR kits often contain loci with huge differences in power of discrimination (PD) across populations, causing some loci to be less informative for chimerism analysis in certain populations. This study aimed to construct a new STR multiplex panel with highly informative loci for efficient chimerism analysis. Thirteen STR markers which exhibit high PD (> 0.9) in at least 80% of 50 populations globally were selected to form a new panel and used in STR analysis of 253 Malaysian subjects. Cumulative power of discrimination (CPD) and combined power of exclusion (CPE) were determined from 253 Malaysian individuals. Loci informativity was assessed and compared to the commercial AmpFLSTR Identifiler PCR Amplification kit in 14 donor-recipient pairs. The new panel had detected 202 unique alleles including five novel alleles from the 253 individuals with high CPD and CPE (> 0.99999999999999999 and > 0.999999997 respectively). All loci from the new panel in the donor-recipient pair analysis showed higher than 50% informativity, while five loci from the commercial kit demonstrated lower than 50% informativity. Four loci from the new panel ranked the highest informativity. A sequenced allelic ladder which consists of 202 unique alleles from the 253 subjects was also developed to ensure accurate allele designation. The new 13-loci STR panel, thus, could serve as an additional powerful, accurate, and highly informative panel for chimerism analysis for HSCT patients.
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Affiliation(s)
- Wui Chuen Chia
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Tze Sean Khoo
- UKM Medical Molecular Biology Institute, National University of Malaysia, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia
| | - S Fadilah S Abdul Wahid
- Cell Therapy Center, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Noor Farisah Abdul Razak
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Hafiza Alauddin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Raja Zahratul Azma Raja Sabudin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia
| | - Ainoon Othman
- Department of Medical Science II, Faculty of Medicine and Health Science, Islamic Science University of Malaysia, Kuala Lumpur, Malaysia
| | - Roshida Hassan
- National Blood Centre, Jalan Tun Razak, Titiwangsa, 50400, Kuala Lumpur, Malaysia
| | - Noor Hamidah Hussin
- Hematology Unit, Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, Cheras, 56000, Kuala Lumpur, Malaysia.
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2
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Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 2016; 25:214-226. [DOI: 10.1016/j.fsigen.2016.09.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 11/22/2022]
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3
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Mutation rates of 15 X chromosomal short tandem repeat markers. Int J Legal Med 2014; 128:579-87. [DOI: 10.1007/s00414-014-1016-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/30/2014] [Indexed: 11/25/2022]
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4
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Diegoli TM, Coble MD. Development and characterization of two mini-X chromosomal short tandem repeat multiplexes. Forensic Sci Int Genet 2010; 5:415-21. [PMID: 20943451 DOI: 10.1016/j.fsigen.2010.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 10/19/2022]
Abstract
This study presents the development and characterization of two X chromosomal short tandem repeat (STR) multiplexes utilizing reduced-size amplicons (less than 200 base pairs) for identity and kinship testing with degraded DNA. Approximately 1360 samples across 4 U.S. population groups were typed for 15 X chromosomal STR markers: DXS6789, DXS7130, DXS9902, GATA31E08, DXS7424, GATA165B12, DXS101, DXS6795, GATA172D05, DXS10147, DXS8378, DXS7132, DXS6803, HPRTB, and DXS7423. A high degree of polymorphism was observed for each marker and both multiplexes were sensitive down to 200pg of pristine DNA. The two proposed multiplexes are suitable for forensic use, and show potential for improved analysis of compromised bone samples.
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Affiliation(s)
- Toni M Diegoli
- Armed Forces DNA Identification Laboratory, Research Section, 1413 Research Blvd., Suite 101, Rockville, MD 20850, USA.
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5
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Gomes I, Pereira R, Mayr WR, Amorim A, Carracedo A, Gusmão L. Evaluation of DXS9902, DXS7132, DXS6809, DXS7133, and DXS7423 in humans and chimpanzees: sequence variation, repeat structure, and nomenclature. Int J Legal Med 2009; 123:403-12. [DOI: 10.1007/s00414-009-0357-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
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Tillmar AO, Mostad P, Egeland T, Lindblom B, Holmlund G, Montelius K. Analysis of linkage and linkage disequilibrium for eight X-STR markers. Forensic Sci Int Genet 2008; 3:37-41. [DOI: 10.1016/j.fsigen.2008.09.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 08/21/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
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Edelmann J, Hering S, Augustin C, Szibor R. Haplotypes and haplotype stability within a 126.6kb region at Xq28. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Builes J, Martinez R, Espinal C, Aguirre D, Bravo M, Gusmão L. Allele distribution of three X-chromosome STR loci in an antioquian population sample. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2008. [DOI: 10.1016/j.fsigss.2007.10.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Edelmann J, Hering S, Augustin C, Szibor R. Characterisation of the STR markers DXS10146, DXS10134 and DXS10147 located within a 79.1 kb region at Xq28. Forensic Sci Int Genet 2007; 2:41-6. [PMID: 19083788 DOI: 10.1016/j.fsigen.2007.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Revised: 06/26/2007] [Accepted: 08/06/2007] [Indexed: 11/19/2022]
Abstract
Three polymorphic X-chromosomal STR markers within a 79 kb region at Xq28 were studied and registered in the GDB as DXS10146, DXS10134 and DXS10147. These markers were molecular characterised and evaluated for their forensic usage. As a result DXS10134 was recently integrated in the commercial available test kit Mentype Argus X-8. At locus DXS10146 we found 23 alleles with PIC and HET values of 0.878 and 0.887. Locus DXS10134 showed 17 alleles with PIC and HET values of 0.844 and 0.858. At locus DXS10147 only 5 alleles with some lower PIC and HET values of 0.636 and 0.692 were found. Additionally, the already known and closely linked STR DXS7423 was included into the haplotyping and recombination studies. Testing this cluster a German population of 404 males revealed the presence of 311 haplotypes. Recombination analysis was performed in 109 father-daughter-grandson trios in which two crossing over events were observed located in the 65.8 kb region between DXS10146 and DXS10134. By using this STR complex for haplotyping in kinship testing further genetic analyses are required to establish an exact recombination rate.
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Affiliation(s)
- Jeanett Edelmann
- Institute of Legal Medicine, University Leipzig, Leipzig, Germany.
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Zarrabeitia MT, Mijares V, Riancho JA. Forensic efficiency of microsatellites and single nucleotide polymorphisms on the X chromosome. Int J Legal Med 2007; 121:433-7. [PMID: 17436009 DOI: 10.1007/s00414-007-0169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 03/20/2007] [Indexed: 10/23/2022]
Abstract
Polymorphisms located on the X chromosome are being increasingly used in forensic studies. However, they have not been studied as extensively as the autosomal and Y-linked polymorphisms. Therefore, we planned to study the population genetics of two sets of X-linked markers, including short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), and particularly analyze the differences at the microgeographical level. Six X-linked STRs (DXS 9895, DXS 7132, DXS 9898, DXS 6789, GATA 172D05, and DXS 7130) and ten SNPs (rs1229078, rs1544545, rs4442270, rs1874111, rs5968332, rs1166756, rs12849634, rs5932595, rs203648, and rs611711) were studied in two population samples from Cantabria, northern Spain, a mixed coastal population and a relatively isolated small population in the Pas valley. There were statistically significant differences in allelic frequencies of the six STRs studied between both populations. On the other hand, only one out of ten SNPs studied showed between-population differences. Overall Fst values were 0.4-2.9% and 1.8-2.2% for the STRs and the SNPs, respectively. The overall power of discrimination for female samples was higher than 99.99% for both groups of markers. Therefore, these sets of X-linked STRs and SNPs seem to be potentially useful in forensic genetics, but care should be taken when interpreting results from cases that originate from small and relatively isolated populations.
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Affiliation(s)
- María T Zarrabeitia
- Unit of Legal Medicine, University of Cantabria, Av. Herrera Oria sn, 39011, Santander, Spain.
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Turrina S, Atzei R, Filippini G, De Leo D. Development and forensic validation of a new multiplex PCR assay with 12 X-chromosomal short tandem repeats. Forensic Sci Int Genet 2007; 1:201-4. [PMID: 19083757 DOI: 10.1016/j.fsigen.2007.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Accepted: 01/27/2007] [Indexed: 11/17/2022]
Abstract
One multiplex system for the co-amplification of 12 X-chromosomal short tandem repeats (STRs) DXS7132, DXS8378, DXS6809, DXS7133, DXS6789, DXS7424, GATA172D05, HPRTB, DXS7423, GATA31E08, DXS101, DXS6807 and amelogenin was analysed in a sample of 200 (100 males and 100 females) unrelated healthy individuals living in Northern Italy. The chi2-test for genotype distribution of the X-chromosomal STRs showed no significant deviation from the Hardy-Weinberg equilibrium (HWE). Allele frequencies between female and male samples were not significantly different in all examined markers. In the kinship cases involving 40 family trios with daughter and 10 father/daughter duos, no mutation was detected. The combined power of discrimination (PDc) of the 12 X-STRs for both females and males was PDc > 0.999999.
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Affiliation(s)
- Stefania Turrina
- Department of Medicine and Public Health, Institute of Legal Medicine, Forensic Genetic Laboratory, University of Verona, Policlinico G.B. Rossi, 37134 Verona, Italy
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12
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Liu Q, Li S. Patterns of genetic polymorphism at the 10 X-chromosome STR loci in Mongol population. Forensic Sci Int 2006; 158:76-9. [PMID: 16280221 DOI: 10.1016/j.forsciint.2005.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Revised: 04/01/2005] [Accepted: 04/13/2005] [Indexed: 10/25/2022]
Abstract
Genetic diversity at 10 X-chromosome STR loci has been approved and widely used for forensic science field. In this paper, we have studied this genetic diversity in various Mongol ethnic group with geographic backgrounds. Allele frequencies of 10 X-chromosome STR loci, including DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789 and DXS101, were obtained from healthy unrelated individuals (53 females and 47 males) of Mongol ethnic group lived in north China. Gene diversity analysis showed that the average heterozygosity was uniformly high (0.687) in the studied population. The coefficient of PIC was 0.99998.
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Affiliation(s)
- Qingbo Liu
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an Shaanxi 710061, China
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Bini C, Ceccardi S, Ferri G, Pelotti S, Alù M, Roncaglia E, Beduschi G, Caenazzo L, Ponzano E, Tasinato P, Turchi C, Buscemi L, Mazzanti M, Tagliabracci A, Toni C, Spinetti I, Domenici R, Presciuttini S. Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples. A collaborative study. Forensic Sci Int 2005; 153:231-6. [PMID: 15982841 DOI: 10.1016/j.forsciint.2005.05.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 04/20/2005] [Accepted: 05/10/2005] [Indexed: 11/28/2022]
Abstract
Many X-chromosome short tandem repeats (X-STRs) have been validated for forensic use even if further studies are needed on allele frequencies and mutation rates to evaluate the extent of polymorphism in different populations and to establish reference databases useful for forensic applications and for anthropological studies. A single multiplex reaction of seven X-STRs, which includes the DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807, DXS101 loci, is presented and their allele frequency distribution in a large population sample including 556 subjects (268 females and 288 males) analysed by five forensic laboratories of Central and Northern Italy is shown. Our results demonstrate the feasibility of a single amplification/detection reaction involving seven markers of the X chromosome, which can be fruitfully used in complex kinship analysis.
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Affiliation(s)
- Carla Bini
- Department of Medicine and Public Health, Section of Legal Medicine, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy.
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Zarrabeitia MT, Alonso A, Martin J, Gonzalez-Gay MA, Martin-Escudero JC, de Pancorbo MM, Sanz P, Ruiz-Cabello F, Riancho JA. Study of six X-linked tetranucleotide microsatellites: population data from five Spanish regions. Int J Legal Med 2005; 120:147-50. [PMID: 16328422 DOI: 10.1007/s00414-005-0057-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 10/10/2005] [Indexed: 11/28/2022]
Abstract
We studied six X-linked microsatellites in a large group of Spanish individuals (n=614) from five different regions located in northern, central and southern Spain. All the markers had tetranucleotide repeat units (DXS9895, DXS9898, DXS7130, DXS7132, GATA172D05 and DXS6789). They were amplified in two triplex PCR reactions. There were no significant sex- or region-related differences in allelic frequencies, suggesting that general national databases can be adequate as a reference for X-linked markers. The analysis of those six short tandem repeats combined in 316 males revealed 300 different "temporary haplotypes", 283 of which were found only once. There was no evidence for statistically significant linkage disequilibrium among the loci studied. Therefore these markers are quite polymorphic and useful for forensic purposes.
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Affiliation(s)
- Maria T Zarrabeitia
- Unit of Legal Medicine, Faculty of Medicine, University of Cantabria, Santander, Spain.
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Gu S, Li S. X-chromosome STRs analysis of Ewenke ethnic population. Forensic Sci Int 2005; 158:72-5. [PMID: 16280222 DOI: 10.1016/j.forsciint.2005.04.026] [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: 09/27/2004] [Revised: 04/11/2005] [Accepted: 04/13/2005] [Indexed: 10/25/2022]
Abstract
X-chromosome STR, known as microsatellite, is a kind of the most information genetic markers for specific biological materials. Because the size of X-chromosome STR alleles is small, generally including 100-350 nucleotides, it is relatively easy to be amplified and detected with high sensitivity. We have investigated 10 X-chromosome STR loci in an Ewenke ethnic population who live in Neimengu of northeast China. Allele frequencies of 10 X-chromosome STR loci, including DXS7133, DXS6799, DXS8378, DXS7423, DXS6804, HPRTB, DXS7424, DXS7132, DXS6789 and DXS101, were obtained from healthy unrelated individuals (45 females and 53 males) of Ewenke ethnic group.
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Affiliation(s)
- Shanzhi Gu
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an Shaanxi 710061, China
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Zalán A, Völgyi A, Jung M, Peterman O, Pamjav H. Hungarian population data of four X-linked markers: DXS8378, DXS7132, HPRTB, and DXS7423. Int J Legal Med 2005; 121:74-7. [PMID: 16237560 DOI: 10.1007/s00414-005-0051-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Accepted: 09/01/2005] [Indexed: 10/25/2022]
Abstract
DXS8378, DXS7132, HPRTB, and DXS7423 microsatellite markers located in four different X-chromosomal linkage groups were studied in the Hungarian population. After genotyping unrelated men (219) and women (165), forensic efficiency parameters showing that the four X-linked short tandem repeats are informative for forensic applications were calculated. With fragment and sequence analysis, one microvariant allele (11.2) was identified in the HPRTB locus. A deviation from the Hardy-Weinberg equilibrium could not be detected. Investigations of 96 father-child meioses revealed one mutation in the DXS7132 locus. For comparison of 22 different populations, G-tests were carried out.
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Affiliation(s)
- Andrea Zalán
- Institute of Forensic Medicine, Ministry of Justice, PO Box 31, 1363, Budapest, Hungary
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Vauhkonen H, Vauhkonen M, Sipponen P, Sajantila A. Correlation between the allelic distribution of STRs in a Finnish population and phenotypically different gastrointestinal tumours: a study using four X-chromosomal markers (DXS7423, DXS8377, ARA, DXS101). Ann Hum Genet 2005; 68:555-62. [PMID: 15598214 DOI: 10.1046/j.1529-8817.2004.00134.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Microsatellite instability in tumours has been suggested as a model to study the process of short tandem repeat (STR) mutations. In the present study we have determined the allelic variation of four X-STRs (DXS7423, DXS8377, DXS101 and ARA) in a Finnish population of 103 individuals, and assessed whether a comparable allelic distribution could be found in a series of gastrointestinal cancers differing by the level of microsatellite instability. Fifty-seven gastric and colorectal cancers were stratified by autosomal STRs, and the mononucleotide marker BAT-26 into stable, low-level unstable and high-level unstable microsatellite (MSI-H) cancers, of which the last produced the majority of X-STR alleles. For the four markers analysed, a significant correlation of allele distribution between our Finnish population sample and MSI-H tumours was noted. Together, the eight MSI-H tumours found represented 80%, 66-80% and 100% of the DXS101 alleles in the Finnish, and in previously described Caucasian and Korean population samples, respectively. Of the ARA, DXS7423 and DXS8377 alleles in the Finnish population, 42%, 75% and 79% were found in the MSI-H cancers, respectively. The results suggest that analysis of STR variation in a relatively small number of MSI-H cancers may aid in pre-evaluation of their allelic distribution in a population.
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Affiliation(s)
- H Vauhkonen
- Laboratory of Forensic Biology, Department of Forensic Medicine, University of Helsinki, Kytösuontie 11, P.O. Box 40, 00014 Helsinki, Finland.
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Hering S, Brundirs N, Kuhlisch E, Edelmann J, Plate I, Benecke M, Van PH, Michael M, Szibor R. DXS10011: studies on structure, allele distribution in three populations and genetic linkage to further q-telomeric chromosome X markers. Int J Legal Med 2004; 118:313-9. [PMID: 15248074 DOI: 10.1007/s00414-004-0467-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Accepted: 04/16/2004] [Indexed: 11/29/2022]
Abstract
The hypervariable tetranucleotide STR polymorphism DXS10011 is a powerful marker for forensic purposes. Investigation of this STR led to an allele nomenclature which is in consensus with the ISFG recommendations. DXS10011 is located at Xq28 and genetically closely linked to DXS7423 and DXS8377 but is unlinked to HPRTB and more distant X-chromosomal STRs. DXS10011 is a very complex marker exhibiting some structural variants within alleles of identical length. Two types of repeat structure (regular and inter-alleles) are known and described as types A and B. Two SNPs which are in strong linkage disequilibrium to the different sequence types were found in the repeat flanking region. The type A sequence consists of a long stretch of uninterrupted homogenous repeats which is highly susceptible to slippage mutation during male meiosis.
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Affiliation(s)
- Sandra Hering
- Institut für Rechtsmedizin, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
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Edelmann J, Lessig R, Hering S, Brundirs N, Kuhlisch E, Szibor R. Allele frequencies for X-chromosomal microsatellites in different populations. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0531-5131(03)01837-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Szibor R, Edelmann J, Hering S, Plate I, Wittig H, Roewer L, Wiegand P, Calì F, Romano V, Michael M. Cell line DNA typing in forensic genetics--the necessity of reliable standards. Forensic Sci Int 2004; 138:37-43. [PMID: 14642717 DOI: 10.1016/j.forsciint.2003.09.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The incorporation of reference DNA is crucial to the validation of any DNA typing protocol. This paper aims to provide a panel of reference DNAs for actual forensic profiling strategies, i.e. autosomal and gonosomal STR typing as well as mtDNA sequencing. We have characterised three human lymphoid cell lines, GM9947, GM9948 and GM3657, and considered 58 autosomal and gonosomal microsatellites as well as the mitochondrial control region sequence. Well-established markers and STRs recently developed for forensic use were involved. K562 DNA samples which we purchased from two different suppliers were also analysed. They revealed conflicting results with regard to the ChrX STR marker genotype. Hence, we suggest that K562 is no longer used for the calibration of profiling techniques. Our investigation establishes a panel of one female and two male DNA samples as an STR allelic ladder calibration tool and offers information on six alleles of each autosome (AS) marker, three alleles of each X chromosome (ChrX) marker and two alleles of each ChrY marker. In addition, sequences of the mitochondrial control region of the three DNAs are communicated in order to provide sequencing quality control.
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Affiliation(s)
- Reinhard Szibor
- Institut für Rechtsmedizin, Otto-von-Guericke-Universität Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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Szibor R, Edelmann J, Zarrabeitia MT, Riancho JA. Sequence structure and population data of the X-linked markers DXS7423 and DXS8377--clarification of conflicting statements published by two working groups. Forensic Sci Int 2003; 134:72-3. [PMID: 12842361 DOI: 10.1016/s0379-0738(03)00079-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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