STR primer concordance study.

Over 1500 population database samples comprising African Americans, Caucasians, Hispanics, Native Americans, Chamorros and Filipinos were typed using the PowerPlex 16 and the Profiler Plus/COfiler kits. Except for the D8S1179 locus in Chamorros and Filipinos from Guam, there were eight examples in which a typing difference due to allele dropout was observed. At the D8S1179 locus in the population samples from Guam, there were 13 examples of allele dropout observed when using the Profiler Plus kit. The data support that the primers used in the PowerPlex 16, Profiler Plus, and COfiler kits are reliable for typing reference samples that are for use in CODIS. In addition, allele frequency databases have been established for the STR loci Penta D and Penta E. Both loci are highly polymorphic.     

D8S1179基因座等位基因丢失现象的研究

目的 探讨在进行STR分型时发生的等位基因“丢失”情况的原因。方法 分别采用Profiler Plus试剂盒和GenBank数据库设计的引物,对D8S1179基因座进行基因分型,并对丢失的等位基因进行测序分析。结果D8S1179基因座丢失的等位基因在第147位碱基出现G-A转换。在中国人群中,该位置出现碱基转换的频率是0.50×10-2(在2013个无关个体中观察到10例无关变异事件)。结论 第147位碱基转换正好位于Prfiler Plus试剂盒中D8S1179基因座的引物结合区域,导致扩增时等位基因丢失。     

Population data for 11 STR loci in northeast China Han

Allele frequencies for the nine tetrameric short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820 (AmpFlSTR Profiler Plus PCR amplification kit, PE Applied Biosystems) and two pentameric STR loci Penta D and Penta E (PowerPlex 16 system, Promega Corporation) were determined in a population sample of unrelated China Han.     

Swiss Caucasian population data for the STR loci D2S1338 and D19S433 using the AmpFISTR SGM plus PCR amplification kit

Allele and genotype frequencies for the ten STR loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, FGA were determined in a Swiss Caucasian population sample (n=206) using the AmpFISTR SGM Plus Amplification kit. Electrophoresis was carried out on an ABI PRISM CE 310 Genetic Analyzer instrument. Previously, allele frequencies were published for the 13 STR loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, TPOX, CSF1PO and D16S539 for the same samples (n=206) amplified with the AmpFISTR Profiler Plus and Cofiler PCR Amplification kits. Since the results for the eight loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, THO1, D16S539 shared between the AmpFISTR SGM Plus, Profiler Plus and Cofiler PCR Amplification kits already are published, only the allele frequencies for the two STR loci D2S1338 and D19S433 are reported in this paper. The two loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 15 loci (amplified with the Profiler, Cofiler, and SGM Plus amplification kits). The allelic frequency data can be used in forensic analyses to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.     

3种常用PCR扩增试剂盒检验血样DNA的结果比较

目的探讨常用的ProfilerPlusTM、IdentifilerTM与Powerplex(16试剂盒检验血样DNA的差异。方法510名无关中国汉族个体血样,分别用ProfilerPlusTM与Powerplex(16试剂盒进行DNA检验,然后对有不同检验结果的同一样本,再用ProfilerPlusTM、IdentifilerTM与Powerplex(16等三种试剂盒进行检验,并比较其结果。结果在510名个体血样的DNA检测结果中,发现同一样本有不同结果的有7例,其差异率为1.3725%;ProfilerPlusTM、IdentifilerTM与Powerplex(16各有1例在D13S317或FGA基因座上出现等位基因缺失现象,缺失率为0.1961%;ProfilerPlusTM有5例在D8S1179基因座上出现扩增严重不平衡现象,相应的IdentifilerTM与Powerplex(16试剂盒的检验结果为正常杂合子。结论ProfilerPlusTM、IdentifilerTM与Powerplex(16试剂盒检验血样DNA均会出现扩增不平衡和/或基因丢失现象,其发生几率IdentifilerTM与Powerplex(16试剂盒较ProfilerPlusTM少。     

Population data of nine STRs of Mexican-Mestizos from Mexico City

One hundred and thirteen individuals were PCR-typed for nine STR loci with the AmpFlSTR Profiler Plus PCR amplification kit, including the following autosomal STRs: D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820. Allele frequencies for each STR were estimated, and they were compared to other populations. Genotype distribution by locus and by two-loci combination was in agreement with Hardy-Weinberg expectations for all nine STRs. For this region of Mexico, the combined probability of exclusion (PE) and power of discrimination (PD) were estimated: PE=99.964% and PD>99.999%.     

Portuguese population and paternity investigation studies with a multiplex PCR--the AmpFlSTR Profiler Plus

A Portuguese Caucasian population of 146 unrelated individuals was studied. DNA samples were amplified by multiplex PCR for D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 using the AmpFlSTR Profiler Plus PCR Amplification Kit (Perkin-Elmer). All loci met Hardy-Weinberg expectations. Forensic statistical parameters were according to those obtained by other authors. Statistical differences were observed concerning three loci when comparing the Portuguese Caucasian population and an Italian Caucasian population, although these differences mainly concern the less frequent alleles. Eighty-three paternity investigation cases were analysed. Exclusions in between three and nine loci were observed in all the 23 exclusion cases obtained. Most of the non-exclusion cases had probability of paternity > 99.9%. Two cases with an isolated genetic incompatibility between the alleged father and the child were detected, which may indicate probable mutation cases. These results demonstrate that the AmpFlSTR Profiler Plus is a suitable multiplex for paternity investigation in the Portuguese population.     

Allele frequencies for nine STR loci in a Korean ethnic group from northeast China

Allele frequencies for the nine tetrameric short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 (AmpFlSTR) Profiler Plus PCR Amplification kit, PE Applied Biosystems) were determined in 109 unrelated Korean ethnic group individuals from northeast China.     

A single mutation in the FGA locus responsible for false homozygosities and discrepancies between commercial kits in an unusual paternity test case

We report an unusual paternity test case showing multiple peculiarities. Using AmpFlSTR Profiler Plus and AmpFlSTR Identifiler PCR Amplification kits, the alleged father and the two children were apparently homozygous at the FGA locus, but using the PowerPlex 16 kit the three individuals were found to be heterozygous. Drop-out was caused by a single mutation event in the presumptive binding site of the reverse primer. In addition, three inconsistencies were detected between the daughter and the alleged father among 18 STR markers. The occurrence of the rare null allele at the FGA locus and case history suggested that the true father was the brother of the alleged father. Furthermore, a single-step repeat maternal mutation was also detected at D16S539. This puzzling case was solved by using multiple analytical approaches, including the use of different primer pairs, the use of a high number of STR markers, and the characterization of the mutation causing the "null allele."     

Profiler Plus系统在法医学DNA检验中的问题探讨

以Profiler Plus系统生产厂商提供的检验条件,在实际工作中对大规模样品进行了检验分析.结果显示该系统尚存在等位基因丢失、额外等位基因、同一荧光标记不同基因座等位基因重叠公布、罕见等位基因与亚型等非技术操作性问题.对有关样品应用Power Plex1.2,Power Plex16系统进行了检验验证.     

False homozygosities at various loci revealed by discrepancies between commercial kits: implications for genetic databases

Routine control of 2055 consecutive genotypes revealed discrepancies between the profiles established with the SGM plus and/or Profiler plus kits on one hand, and the profiles established with the Powerplex16 kit on the other hand. Furthermore, five discrepancies for vWA, three for D8S1179, two for FGA and three for D18S51 loci were found. In 10 cases (loci vWA, FGA, D18S51, D8S1179), the SGM plus and/or Profiler plus profiles showed homozygosity and the Powerplex16 genotype revealed heterozygosities which were confirmed to be true, both by typing with individual primer pairs and DNA sequencing. In four cases (two discrepancies at locus FGA, one at D18S51 and an abnormal paternity pattern for D5S818), the Powerplex16 kit showed apparent homozygosity and the SGM plus and/or Profiler plus kits showed heterozygosity. Mutation analysis could be performed for some of these individuals and evidenced variants, presumably leading to an annealing failure of one primer; the identified mutations are reported. It is suggested that databases should include information about the kits used to determine the profiles while ensuring that the primer sequences are made available.     

STR data for the AmpFlSTR Profiler Plus loci from Greece

Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 143 unrelated individuals living in different regions of Greece.     

STR data (AmpFlSTR profiler plus) from north Portugal

Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 365-427 unrelated individuals born in north Portugal.     

STR data (AmpFlSTR Profiler Plus and GenePrint CTTv) from Mozambique

Allele frequencies for twelve STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and GenePrint CTTv kit (VWA, TH01, TPO and CSF1PO) were estimated from a sample of 110 unrelated individuals from Mozambique.     

STRs data for the loci D3S1385, vWA,FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 from Córdoba (Argentina)

Allele and genotype frequencies for nine STRs loci included in the AmpFlSTR Profiler Plus kit (D3S1385, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820), were determined from urban and countryside population of Córdoba (Argentina). All loci meet the Hardy-Weinberg expectation, and there is little evidence for alleles association between these nine loci. The results demonstrate that these loci can be useful for databasing purposes in human identification and parentage testing in the population of Córdoba (Argentina).     

STR data for the AmpFlSTR SGM Plus and Profiler loci from Taiwan

Allele frequencies for the 15 STRs included in the AmpFlSTR SGM Plus and Profiler kit (D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, THO1, FGA, TPOX, CSF1PO, D5S818, D13S317 and D7S820) were obtained from a sample of 597 unrelated individuals living in Taiwan. All loci, except for D8S1179 and D5S818, are in Hardy-Weinberg equilibrium.     

Genetic data of 9 STR loci from Henan Province (central China)

Allele frequencies of the nine short tandem repeats (STR) loci D8S1179, D21S11, D18S51, D5S818, D3S1358, D7S820, vWA, FGA (AmpFlSTR Profiler Plus) were determined in a population sample of unrelated individuals living in central China.     

Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples

The amplification and typing conditions for the 13 core CODIS loci and their forensic applicability were evaluated. These loci are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Results were obtained using the multiplex STR systems AmpFlSTR Profiler Plus and AmpFlSTR COfiler (Applied Biosystems, Foster City, CA), GenePrint PowerPlex (Promega Corporation, Madison, WI), and subsets of these kits. For detection of fluorescently labeled amplified products, the ABI Prism 310 Genetic Analyzer, the ABI Prism 377 DNA Sequencer, the FMBIO II Fluorescent Imaging Device, and the Fluorlmager were utilized. The following studies were conducted: (a) evaluation of PCR parameter ranges required for adequate performance in multiplex amplification of STR loci, (b) determination of the sensitivity of detection of the systems, (c) characterization of non-allelic PCR products, (d) evaluation of heterozygous peak intensities, (e) determination of the relative level of stutter per locus, (f) determination of stochastic PCR thresholds, (g) analysis of previously typed case samples, environmentally insulted samples, and body fluid samples deposited on various substrates, and (h) detection of components of mixed DNA samples. The data demonstrate that the commercially available multiplex kits can be used to amplify and type STR loci successfully from DNA derived from human biological specimens. There was no evidence of false positive or false negative results and no substantial evidence of preferential amplification within a locus. Although at times general balance among loci labeled with the same fluorophore was not observed, the results obtained were still valid and robust. Suggested criteria are provided for determining whether a sample is derived from a single source or from more than one contributor. These criteria entail the following: (a) the number of peaks at a locus, (b) the relative height of stutter products, and (c) peak height ratios. Stochastic threshold levels and the efficiency of non-templated nucleotide addition should be considered when evaluating the presence of mixtures or low quantity DNA samples. Guidelines, not standards, for interpretation should be developed to interpret STR profiles in cases, because there will be instances in which the standards may not apply. These instances include (a) a primer binding site variant for one allele at a given locus, (b) unusually high stutter product, (c) gene duplication, and (d) translocation.     

Population genetics of 10 STR loci in a population of Central Poland

Allele frequencies for the 10 short tandem repeats (STRs) included in AmpFlSTR SGM Plus amplification kit (D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, FGA) were estimated from a sample of 500 unrelated individuals born in Central Poland.     

Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit

Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.