Menu
doi: 10.3325/cmj.2011.52.368
The ABI PRISM® 310 Genetic Analyzer is an automated system for sequencing, sizing, and quantitating nucleic acids. The system achieves unparalleled ease of use through the integration of ABI PRISM. ABI PRISM® 310 Genetic Analyzer User’s Manual. Choice of Sequencing Analysis.
310 Genetic Analyzer User Guide
- ABI PRISM 373 DNA sequencer with XL upgrade: User’s manual. ABI Prism 310 Genetic analyzer: User’s manual. ABI PRISM 377 DNA Sequencer For Sequencing and GeneScan Analysis Software Applications: User’s manual. ABI PRISM 3100 Genetic Analyzer: User’s Manual.
- Abi prism® 310 genetic analyzer test ccd 4-color and seq fill capillary run modules before performing any troubleshooting work on your abi prism® 310 genetic analyzer, please read the instrument user’s manual for safety and warranty information and further details on use of the system.
- PowerPlex® 5C Matrix Standards, 310 50. Refer to the ABI PRISM® 310 Genetic Analyzer User’s Manual for instructions on cleaning the pump block, installing the capillary, calibrating the autosampler and adding polymer to the syringe.
- Precision from Run-to-Run on ABI 310 Size deviation of 70 samples and two allelic ladders from one injection of allelic ladder on a single ABI PRISM 310 Genetic Analyzer run From Identifiler User’s Manual Data to be Reviewed from Electropherograms Identifiler kit ladder and sample data Final Answer Desired.
PMID: 21674833
This article has been cited by other articles in PMC.
Abstract
Aim
To investigate allele distribution and genetic parameters of a population-based sample from Maghreb region.
Methods
Allele frequencies for 5 new autosomal short tandem repeat (STR) markers (D10S1248, D22S1045, D2S441, D1S1656, and D12S391) and several forensic parameters were determined for 95 unrelated individuals.
Results
The combined power of discrimination and power of exclusion for the 5 loci were high (0.9999991 and 0.9954757, respectively). Allele frequencies were compared with previously published population data. Significant differences were found between Maghreb population and all other populations at the locus D2S441. Also, significant differences were found between the Maghreb and the African American population at the D22S1045, D1S1656, and D12S391 loci, between Maghreb and Caucasian population at the D1S1656 locus, and between Maghreb and Hispanic population at the D22S1045 locus.
Conclusions
Typing of the 5 new STR loci may provide a useful addition to the previously established sets of autosomal STRs.
Short tandem repeats (STR) are widely used for forensic testing. Ordinary paternity cases are solved by commercially available multiplexes kits, however, for more difficult cases, such as complex kinship analysis, additional STRs are needed to obtain better results. Besides, as many national DNA databases are growing and a large number of comparisons are being made within and between databases, concern for possible false-positive results may arise. This increases the need to introduce additional loci. The first European Standard Set (ESS) of loci included only 7 STRs loci, but the European Network of Forensic Science Institutes and the European DNA Profiling recommended to extend the ESS loci by adopting additional 3 miniSTRs loci (D10S1248, D22S1045, D2S441) and 2 additional polymorphic loci in 2006 (D1S1656, D12S391) (,).
D-link 5222l setup. These new 5 loci improve the discriminatory power of forensic analysis and, by amplifying fragments well below current average amplicon sizes, can enhance genotyping success when analyzing highly degraded DNA (,).
In order to verify and allow their use in forensics, the usefulness of ESS STR loci, it is necessary to obtain sufficient data from different populations.
Methods
Saliva samples were obtained in 2010 from 95 unrelated, healthy immigrants from Maghreb region, whose both parents were born in Maghreb region (Morocco, Egypt, and Tunisia).
Lg tromm wm2277hs manual. Genomic DNA was extracted from buccal swabs using Chelex® 100 method (Biorad, Richmond, CA, USA) ().
PCR amplifications were performed in a GeneAmp® PCR System 9700 Gold Plate (Applied Biosystems, Foster City, CA, USA) using the commercial kit AmpFiSTR® NGM (Applied Biosystems), according to manufacturer’s recommendations (6). Typing was performed by capillary electrophoresis using an ABI Prism® 310 Genetic Analyzer (Applied Biosystems) and allele calling was performed with the software GeneMapperID V3.2 (Applied Biosystems), using manufacturer’s allelic ladders, bins, and panels.
For quality control, the laboratory regularly participates in the quality control proficiency testing programs provided by the GEDNAP group (German DNA Profiling, http://www.gednap.org).
Allele frequencies at each locus were calculated by direct counting. Statistical parameters of forensic interest were estimated: observed and expected heterozygosity (Hobs, Hexp) and standard error (7), polymorphism information content (), power of discrimination (9), and power of exclusion (). ARLEQUIN software, version 3.11 (11) was used to asses deviations from Hardy-Weinberg equilibrium. Allele frequencies were compared with previously published population data using an exact test through the ARLEQUIN software, version 3.11 (11).
Results and discussion
A total of 95 samples were analyzed (Table 1). Deviation from Hardy-Weinberg equilibrium was detected for D22S1045 (P = 0.0037), D2S441 (P = 0.0006), and D12S391 (P = 0.0002) loci, even after a Bonferroni correction () for multiple testing (P < 0.0100). These deviations could be explained by an excess of homozygotes due to population substructure (Wahlund effect within the communities) or by a high inbreeding rate due to widespread endogamy (,). A larger sample size could help in understanding which of the two hypotheses is correct.
Table 1
Allele frequencies and statistical parameters for D10S1248, D22S1045, D2S441, D1S1656, and D12S391 short tandem repeat loci in a population sample from Maghreb region (n = 95)*
D10S1248 | D22S1045 | D2S441 | D1S1656 | D12S391 | Allele |
---|---|---|---|---|---|
0.0105 | 6 | ||||
0.0053 | 8 | ||||
0.0053 | 0.0053 | 9 | |||
0.0894 | 0.0263 | 10 | |||
0.0105 | 0.1263 | 0.3632 | 0.0579 | 11 | |
0.0842 | 11.3 | ||||
0.0632 | 0.0053 | 0.0632 | 0.1526 | 12 | |
0.0211 | 12.3 | ||||
0.2526 | 0.0211 | 0.0053 | 0.1105 | 13 | |
0.0526 | 13.3 | ||||
0.3263 | 0.1052 | 0.2789 | 0.0894 | 14 | |
0.0053 | 14.3 | ||||
0.2367 | 0.3316 | 0.0263 | 0.1632 | 0.0263 | 15 |
0.0474 | 15.3 | ||||
0.0737 | 0.3368 | 0.0105 | 0.1421 | 0.0105 | 16 |
0.0632 | 16.3 | ||||
0.0211 | 0.0474 | 0.0421 | 0.1000 | 17 | |
0.0526 | 0.0158 | 17.3 | |||
0.0158 | 0.0053 | 0.1947 | 18 | ||
0.0316 | 0.0263 | 18.3 | |||
0.0053 | 0.1632 | 19 | |||
0.0105 | 0.0263 | 19.3 | |||
0.1368 | 20 | ||||
0.0053 | 20.3 | ||||
0.0789 | 21 | ||||
0.0737 | 22 | ||||
0.0684 | 23 | ||||
0.0474 | 24 | ||||
0.0211 | 25 | ||||
0.0053 | 26 | ||||
0.7263 | 0.6000 | 0.6421 | 0.8737 | 0.7895 | Hobs |
0.7636 | 0.7465 | 0.7672 | 0.8937 | 0.8852 | Hexp |
4.3589 × 10−2 | 4.4631 × 10−2 | 4.3362 × 10−2 | 3.1624 × 10−2 | 3.27 × 10−2 | SE |
0.7365 | 0.0037 | 0.0006 | 0.0625 | 0.0002 | HWE |
0.7264 | 0.7076 | 0.7365 | 0.8843 | 0.8747 | PIC |
0.9084 | 0.8981 | 0.9029 | 0.9702 | 0.9660 | PD |
0.5470 | 0.5273 | 0.5702 | 0.7858 | 0.7705 | PE |
*Abbreviations: Hobs – observed heterozygosity; Hexp – expected heterozygosity; SE – standard error; HWE – P values from exact test for Hardy-Weinberg equilibrium; PIC – polymorphism information content; PD – power of discrimination; PE – power of exclusion.
The combined power of discrimination and power of exclusion for the 5 new ESS STR loci were 0.9999991 and 0.9954757, respectively. Based on heterozygosity, D1S1656 may be considered the most informative locus (Hobs = 0.8737) and therefore especially useful in forensic investigations.
Allele frequencies for the 5 new ESS STR were compared with previously published population data (-) using an exact test and the ARLEQUIN software (11) (Table 2). No significant differences were found from the already published data for the locus D10S1248; significant differences were found between Maghreb population data and all other populations at the locus D2S441. Also, significant differences were detected between Maghreb and the African American population at the D22S1045, D1S1656, and D12S391 loci, as well as between Maghreb and Caucasian population at the D1S1656 locus, and between Maghreb and Hispanic population at the D22S1045 locus.
Table 2
Comparison of the allele frequencies for D10S1248, D22S1045, D2S441, D1S1656, and D12S391 loci between the Maghreb population and other populations*
Compared population | Exact test (P ± standard error) | ||||
---|---|---|---|---|---|
D10S1248 | D22S1045 | D2S441 | D1S1656 | D12S391 | |
Italians (Northern Italy) (15) | 0.16620 ± 0.0278 | 0.09550 ± 0.0205 | 0.00330 ± 0.0012 | 0.71785 ± 0.0216 | 0.12015 ± 0.0242 |
Italians (Southern Italy) (16) | 0.07545 ± 0.0198 | 0.31770 ± 0.0270 | 0.01630 ± 0.0077 | 0.93385 ± 0.0199 | 0.95185 ± 0.0107 |
Polish (17) | 0.19565 ± 0.0392 | 0.51925 ± 0.0280 | 0.01200 ± 0.0044 | 0.22390 ± 0.0295 | 0.88705 ± 0.0164 |
African Americans (18) | 0.06760 ± 0.0221 | <0.00001 | <0.00001 | 0.02960 ± 0.0079 | 0.00020 ± 0.0002 |
Caucasians (18) | 0.11240 ± 0.0256 | 0.06825 ± 0.0147 | 0.00025 ± 0.0003 | 0.01295 ± 0.0055 | 0.35415 ± 0.0428 |
Hispanics (18) | 0.17650 ± 0.0164 | 0.02290 ± 0.0168 | <0.00001 | 0.16995 ± 0.0343 | 0.26690 ± 0.0342 |
*P – value of the exact test of population differentiation with 10 000 steps in the Markov chain length and 1000 steps of dememorization). In bold – significant differences (P < 0.05).
The obtained data demonstrate that these 5 new ESS STR loci are very useful for forensic purposes; the Maghreb population database could be helpful when testing individuals from this region.
Acknowledgments
Funding None.
Ethical approval Not required.
Declaration of authorship VC was in charge of technical organization aspects of the study. NC was in charge of organization aspects of the study. AV was in charge of organization aspects of the study.
Competing interests All authors have completed the Unified Competing Interest form at www.icmje.org/coi_disclosure.pdf (available on request from the corresponding author) and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous 3 years; no other relationships or activities that could appear to have influenced the submitted work.
References
1. Gill P, Fereday L, Morling N, Schneider PM. The evolution of DNA databases – recommendations for new European STR loci. Forensic Sci Int. 2006;156:242–4. doi: 10.1016/j.forsciint.2005.05.036. [PubMed] [CrossRef] [Google Scholar]
2. Gill P, Fereday L, Morling N, Schneider PM. New multiplexes for Europe-amendments and clarification of strategic development. Forensic Sci Int. 2006;163:155–7. doi: 10.1016/j.forsciint.2005.11.025. [PubMed] [CrossRef] [Google Scholar]
3. Coble MD, Butler JM. Characterization of new miniSTR loci to aid analysis of degraded DNA. J Forensic Sci. 2005;50:43–53. doi: 10.1520/JFS2004216. [PubMed] [CrossRef] [Google Scholar]
4. Phillips C, Fernandez-Formoso L, Garcia-Magarińos M, Porras L, Tvedebrink T, Amigo J, et al. Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel. Forensic Sci Int Genet. 2011;5:155–69. doi: 10.1016/j.fsigen.2010.02.003. [PubMed] [CrossRef] [Google Scholar]
5. Walsh PS, Metzger DA, Higuchi R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques. 1991;10:506–13. [PubMed] [Google Scholar]
6. Applied Biosystem. AmpFlSTR® NGM™ PCR Amplification Kit User’s Manual. Foster City (CA): Applied Biosystem; 2009. [Google Scholar]
7. Nei M. Molecular evolutionary genetics. New York (NY): Columbia University Press; 1987. [Google Scholar]
8. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32:314–31.[PMC free article] [PubMed] [Google Scholar]
9. Huston KA. Statistical analysis of STR data. Profiles DNA. 1998;1:14–5.[Google Scholar]
10. Ohno Y, Sebetan IM, Akaishi S. A simple method for calculating the probability of excluding paternity with any number of codominant alleles. Forensic Sci Int. 1982;19:93–8. doi: 10.1016/0379-0738(82)90155-4. [PubMed] [CrossRef] [Google Scholar]
11. Excoffier L, Laval G, Schneider S. Arlequin, version 3.1: an integrated software package for population genetics data analysis. Bern (Switzerland): University of Bern; 2006. [Google Scholar]
12. Bland JM, Altman DG. Multiple significance tests: the Bonferroni method. BMJ. 1995;310:170.[PMC free article] [PubMed] [Google Scholar]
13. Yang RC. Zygotic associations and multilocus statistics in a nonequilibrium diploid population. Genetics. 2000;155:1449–58.[PMC free article] [PubMed] [Google Scholar]
14. Overall AD, Nichols RA. A method for distinguishing consanguinity and population substructure using multilocus genotype data. Mol Biol Evol. 2001;18:2048–56. [PubMed] [Google Scholar]
15. Cortellini V, Cerri N, Verzeletti A. Population data on 5 non-CODIS STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in a population sample from Brescia county (Northern Italy). Forensic Sci Int Genet. 2011;5:e97–8. doi: 10.1016/j.fsigen.2010.12.008. [PubMed] [CrossRef] [Google Scholar]
16. Barbaro A, Cormaci P, Votano S, Agostino A. Allele frequencies of the new European Standard Set (ESS) loci in a population of Southern Italy (Calabria) Forensic Sci Int Genet 2011. Mar 11. [Epub ahead of print]10.1016/j.fsigen.2011.02.002 [PubMed] [CrossRef] [Google Scholar]
17. Parys-Proszek A, Kupiec T, Wolanska-Nowak P, Branicki W. Genetic variation of 15 autosomal STR loci in a population sample from Poland. Leg Med(Tokyo) 2010;12:246–8. doi: 10.1016/j.legalmed.2010.05.002. [PubMed] [CrossRef] [Google Scholar]
Abi 310 Genetic Analyzer
18. Budowle B, Ge J, Chakraborty R, Eisenberg AJ, Green R, Mulero J, et al. Population genetic analyses of the NGM STR loci. Int J Legal Med. 2011;125:101–9. doi: 10.1007/s00414-010-0516-7. [PubMed] [CrossRef] [Google Scholar]
3500 Genetic Analyzer User Guide
Articles from Croatian Medical Journal are provided here courtesy of Medicinska Naklada