Genetic polymorphism of 14 non-CODIS STR loci for forensic use in southeast China population

We investigated 14 polymorphic STR loci (D1S2142, D2S1360, D3S1545, D7S1517, D10S2325, D12S391, D13S1492, D14S306, D15S659, D16S3253, D18S1270, D19S253, D20S470, D21S1437) which are not included in the standard sets of forensic loci (CODIS) in a sample of 216 unrelated healthy southeast Chinese individuals. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. The accumulated powers of discrimination and power of exclusion for the 14 loci were 99.9999999999 and 99.999998%, respectively. No linkage was observed between the 14 loci and the traditional set of STR markers included in commercially available kits (the AmpFLSTR IdentifilerTM 15 System loci). We thus considered the studied 14 STRs are informative and when necessary, can be used as the candidate genetic markers in the study and application in genetics and forensic practice.     

Identifiler^TM系统在亲子鉴定中的突变观察和分析

目的观察和分析IdentifilerTM系统15个短串联重复序列(STR)位点在亲子鉴定中的突变现象。方法用IdentifilerTM试剂盒检测2712例亲子鉴定案例。结果在2362例认定亲子关系的案例中,观察到51例中有1个STR位点发生突变。突变的位点包括D8S1179、D21S11、D7S820、CSF1PO、D3S1358、D13S317、D16S539、D2S1338、D19S433、vWA、D18S51、D5S818和FGA。其中以D21S11位点突变率最高(0.369%);突变的等位基因来自父亲36次,来自母亲7次,无法确定9次。结论STR位点突变是较为常见的现象,采用IdentifilerTM系统进行亲子鉴定,遇到1～2个STR位点不符合遗传规律时,有必要增加突变率低、稳定性好的STR位点进行复核。     

Mutations of short tandem repeat loci in Identifiler system

OBJECTIVE: To explore and analyze the mutations of 15 Short Tandem Repeat (STR) loci using Identifiler system in paternity identification. METHODS: 2712 cases of paternity testing were carried out using Identifiler PCR Amplification Kit. RESULTS: Of the 2362 paternity testing cases, mutations of single locus were observed in 51 cases. The mutation loci included D8S1179, D21S11, D7S820, CSF1PO, D3S1358, D13S317, D16S539, D2S1338, D19S433, vWA, D18S51, D5S818 and FGA, with the D21S11 locus having a highest mutation rate (0.369%). Thirty-six of the STR mutations were from paternal source, 7 from maternal source, and the rest (9) were undeterminable. The mutation rates at D21S11 were highest (0.369%). CONCLUSION: Mutations of STR loci are relatively common in human genome. Therefore, retesting of additional relatively stable STR loci with lower mutation rates is necessary when one or two loci exclusions are encountered in paternity testing.     

复合扩增D16S539、D7S820、D13S317基因座的DNA分型及法医学应用

通过对3个位于不同染色体上的STR基因座（D165539,D7S820,D13S317）所组成的复合扩增体系的DNA分型研究,以期在实际法医物证检验中增加检验基因座,以提高总的个体识别率。笔者运用复合扩增技术,经4％变性聚丙烯酸胺凝胶电泳分离扩增产物和银染检测,首次对108个无关中国人个体的D16S539,D7S820,D13S317基因座进行研究,检测出中国人群中3个基因座的等位基因数均为7个;偶合率P（m）分别为0．0847、0．0740、0．0741;个体识别率DP值分别为0．9153、0．9260、0．9259;杂合度分别为77．7％、79.1％、79．3％;各基因座亲子关系指数PItypical分别为2．24、2．39、2．42。3个STR基因座总的个体识别率很高,达0．9995;总的亲子关系指数PItypical达12．96;所有基因座经卡方检验符合Hardy－Weinberg平衡。通过以上数据可以看出,D165539,D7S820,D13S317基因座所组成的复合扩增体系在中国人群中等位基因分布较好,个体识别率很高,适合用于法医个体识别及亲子鉴定。     

DNATyper^TM15基因座的研究与选择

目的为研发复合扩增荧光检测试剂盒,对现有的STR基因座进行分析研究并优选新的高鉴别力基因座。方法收集汉族、锡泊族、畲族、壮族、藏族等5个民族群体血样共1200份,提取DNA,应用复合扩增方法检测1200名5个民族群体无关个体的24个基因座的等位基因分布。结果TPOX和TH01基因座的等位基因在5个民族群体中分布不平衡;D2S1338、D6S1043和Penta E等3个STR基因座在5个民族群体中均具有高度遗传多态性,等位基因频率分布均匀,在各群体间无显著差异,而且等位基因传递遵循孟德尔遗传规律。结论确定出DNATyperTM15试剂盒中的14个适合中国人群体遗传学特征和法医学应用的STR基因座。     

Allelic distribution of nine short tandem repeat (STR), HLA-DQA1, and polymarker loci in an Omani sample population

Allele frequency distributions of nine short tandem repeat (STR) loci, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D7S820, and D13S317, HLA-DQA1 and polymarker (PM) loci were studied in a sample population from Sultanate of Oman, Middle East. Blood samples were collected from 162 unrelated individuals. For all STR, HLA-DQA1 and PM loci, no deviations from Hardy-Weinberg equilibrium, based on the exact test, were observed. The most discriminating loci were D18S51 (PD=0.966) and FGA (PD=0.964), while the least informative locus is GYPA (PD=0.585). The allele frequency data may be useful in forensic case work.     

Allele frequencies for 15 STR loci in Van-Ağri districts of the Eastern Anatolia region of Turkey

Allele frequencies of 13 tetrameric short tandem repeat (STR) loci (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA) and 2 pentameric short tandem repeat loci (Penta E and Penta D) included in the PowerPlex 16 kit were obtained from a sample of 116 unrelated individuals in Van-A?ri districts of the Eastern Anatolia region of Turkey. The expected performance of these loci for personal identification and paternity testing in this population was estimated.     

Genetic polymorphisms of 15 AmpFlSTR identifiler loci in Romani population from Northwestern Croatia

The 15 AmpFlSTR identifiler PCR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were analyzed in the sample of 100 unrelated Romani individuals from Northwestern Croatia. The agreement with HWE was confirmed for all loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 15 studied loci were 0.9999999999999996243580692 and 0.999990752, respectively. According to the presented data, D2S1338 proved to be the most informative marker. Population comparisons revealed significantly different F(ST) values for all analyzed population pairs.     

Distribution of alleles of 15 STR loci of the Powerplex 16 Multiplex system in four predominant population groups of South India

Allele distribution of the 15 STR loci of Powerplex 16 Multiplex System were studied in four predominant population groups of South India for evaluating their significance in human identification and population study: Iyengar Brahmin (65), Gowda (59), Lingayat (98) and Muslim (45) from the state of Karnataka. The loci analyzed are--D3S1358, THOI, D2ISI I, D18S51, D5S818, Penta E, D13S317, D7S820, D16S539, CSFIPO, Penta D, vWA, D8S179, TPOX and FGA. Out of 15 STR loci Penta D and D18S51 were found highly polymorphic in the studied populations.     

青岛地区汉族人群13个STR基因座的频率分布及法医学应用

目的　调查青岛地区汉族人群无关个体的 13个STR基因座 (D3S135 8、VWA、FGA、D8S1179、D2 1S11、D18S5 1、D5S818、D13S317、D7S82 0、D16S5 39、TH0 1、TPOX、CSFIPO)的基因频率分布 ,研究其遗传多态性及其在法医学个体识别及亲子鉴定中的应用价值。　方法　用美国ABI - 310型遗传分析仪对ProfilerPlus和Cofiler两个系统的 13个STR基因座的复合扩增产物进行毛细管电泳及四色荧光自动分析检测 ,基因分型软件为GeneScanv3.1和Genotyperv2 .5 .2。　 结果　获得 13个STR基因座在青岛地区汉族人群的基因频率分布数据 ,13个STR基因座的PIC >0 .5 ,DP >0 .71,CCE =0 .999999,TDP值接近 1,TPm =1.2× 10 -14 ,家系调查符合孟德尔遗传规律。　结论　ProfilerPlus和Cofiler两个系统的 13个STR基因座在法医学个体识别及亲子鉴定中具有较高的应用价值。     

MiniSTR multiplex systems based on non-CODIS loci for analysis of degraded DNA samples

We describe two short amplicon autosomal short tandem repeat (miniSTR) quadruplex systems for eight loci D1S1171, D2S1242, D3S1545, D4S2366, D12S391, D16S3253, D20S161, and D21S1437, unlinked from the combined DNA index system (non-CODIS) loci, using newly designed primer sets. The results of an assay of 411 Japanese individuals showed that polymerase chain reaction (PCR) products within the eight loci were less than 150bp in size, without the seven additional bases for adenylation. The frequency distributions in the loci showed no deviations from Hardy-Weinberg equilibrium expectations. The accumulated power of discrimination and power of exclusion for the eight loci were 0.9999999991 and 0.998, respectively. For assay of highly degraded DNA, including artificially degraded samples and the degraded forensic casework samples assessed with the present miniSTR quadruplex systems, the systems proved quite effective in analyzing degraded DNA.     

Allele frequencies and genetic data of 16 highly polymorphic loci in Koreans

Allele and genotype frequencies for the 15 STR loci (FGA, vWA, MBP-L, MBP-H, HumTh01, D3S1358, D3S2406, D5S818, D7S820, D8S1179, D13S317, D18S51, D19S253, and D21S11) and two VNTR loci (D1S80 and D17S5) in a sample of unrelated Koreans were determined.     

Maine Caucasian population DNA database using twelve short tandem repeat loci

A population study of Caucasians residing in Maine was conducted using the AmpF1STR Profiler PCR Amplification Kit and the AmpF1STR Profiler Plus PCR Amplification Kit (Applied Biosystems Division (ABD) of Perkin Elmer, Foster City, CA). The kits contain the reagents necessary to amplify 12 different STR loci and the gender marker Amelogenin using two multiplex PCR, each containing nine STR loci. Thus, there is an overlap of six STR loci. The 12 STR loci are TH01, TPOX, CSF1PO, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820. These loci represent 12 of the 13 core loci selected by the CODIS STR standardization project. Dye-labeled amplification products were separated and detected using the capillary electrophoresis instrument ABI Prism 310 Genetic Analyzer. Allele frequencies were determined for the 12 STR loci. Statistical analysis of the data included Hardy-Weinburg equilibrium (HWE) analysis, pairwise independence testing, power of discrimination (PD), and probability of exclusion (PE).     

16 STR data of a Greek population

Allele frequencies for 16 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, and SE33) were calculated for a sample of 300 unrelated individuals from Greece. No deviations from Hardy–Weinberg equilibrium were observed for all loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 16 tested STR loci were 0.999999999 and 0.999999816, respectively. Population comparisons were carried out and low genetic distances were found between our data and those previously published for other neighbouring European populations.     

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.     

Validation of nine non-CODIS STR loci for forensic use in a population from Central Poland

The D7S1517, D3S1744, D12S391, D2S1360, D6S474, D8S1132, D5S2500, D10S2325 and D4S236613 are STR loci potentially useful for forensic purposes whose analysis has recently become facilitated by availability of a commercial kit. The purpose of the study was to evaluate the usefulness of these loci for forensic identification in a population of Central Poland. The distribution of alleles of the nine STRs was determined in sample of 353 unrelated individuals born in Central Poland and indices of forensic informativeness were calculated. The studied loci were highly informative and did not show departures from Hardy-Weinberg equilibrium. For the loci located on the same chromosomes (D2S1360, D3S1744 D4S2366, D5S2500, D7S1517, D8S1132, D12S391) as other loci commonly used for identification purposes (TPOX, D2S1338, D3S1358, FGA, D5S818, D7S820, D8S1179 and D12S391) appropriate pairwise analysis of linkage disequilibrium was performed. In all cases no statistically significant deviation from independence was found. We conclude that the studied STRs are informative and, when necessary, can be used to extend the results obtained with other STRs commonly analyzed for identification purposes, in particular the CODIS set.     

Population genetic studies on the tetrameric short tandem repeat loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 in Egypt.

The short tandem repeat loci (STRs) D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 and a locus allowing for sex-discrimination (amelogenin) can be co-amplified by the polymerase chain reaction using a commercially available kit (AmpFlSTR Profiler plus, Perkin-Elmer Biosystems, San Jose, CA) and subsequently typed using capillary electrophoresis (ABI Prism 310 Genetic analyzer, Perkin Elmer Applied Biosystems, San Jose CA). To establish databases for these loci for an Arab population sample from Egypt, 140 unrelated persons were typed. Analysis of these data revealed that all loci except for VWA were in Hardy-Weinberg equilibrium, that the combined mean paternity exclusion chance (MEC) was 0.999875 and that the combined discriminating power (DP) was 2.635 x 10(-11). The allelic distributions found in the Egyptian sample were significantly different at four loci from those found for an Austrian Caucasian population, at all nine loci from an African-American sample and at six of six loci from a Chinese sample. No evidence of linkage equilibrium between any of the co-amplified loci was found. Our results support that the combination of multiplex PCR and capillary electrophoresis can both save time and yield excellent results for paternity testing and stain analysis.     

6个miniSTR基因座荧光标记复合扩增的遗传多态性

目的评价6个miniSTR基因座在DNA高度降解检材中的法医学应用价值,并调查广东汉族人群6个miniSTR基因座的遗传多态性。方法采用两个复合扩增PCR体系、四色荧光标记及毛细管电泳技术,对D1S1677,D2S441,D4S2364,D10S1248,D14S1434,D22S1045基因座进行基因型检测。结果6个miniSTR基因座均获得了清晰的基因型分型结果,扩增片段均小于120bp,分别检出7、7、5、8、8、7个等位基因和14、11、11、19、12、14种基因型,基因型分布均符合Hardy-Weinberg平衡。6个miniSTR基因座在广东汉族群体的个人识别率和非父排除率分别依次为0.863、0.895、0.792、0.894、0.814、0.904和0.392、0.360、0.353、0.568、0.378、0.513。10例IdentifilerTM试剂盒未能正确分型的高度降解DNA样本,采用6个miniSTR基因座复合扩增体系检测均提高了分型成功率结论6个miniSTR基因座荧光标记复合扩增体系在DNA高度降解检材的检测中具有较高的应用价值,并且在广东地区汉族群体中具有较好的遗传多态性。     

Genetic variation of 15 STR autosomal loci in the Maracaibo population from Venezuela

Allele frequencies for 15 short tandem repeats (STRs) autosomal loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, included in the AmpFLSTR Identifiler, Applied Biosystems) were studied in the city of Maracaibo, Venezuela and were compared with other published Latin-American populations for the same loci. Population and forensic parameters were estimated.     

New alleles and mutational events at 14 STR loci from different German populations

The molecular origin of DNA mutations and the mutation rates were analyzed at 14 short tandem repeat (STR) loci with samples from trio cases derived from 10 different German population samples. STR loci comprised of D2S1360, D3S1744, D4S2366, D5S2500, D6S474, D7S1517, D8S1132, D10S2325, D12S391, D18S51, D19S246, D20S480, D21S226, and D22S689. In a total of 488 meioses, 16 isolated genetic inconsistencies in 8 different STRs were observed, whereas no mutations were found at the other loci. The data of five mutations suggested the presence of silent or null alleles due to sequence variation in primer binding site. This could be confirmed for four suspected cases by the use of alternative primer sets and by DNA sequence analyses. Furthermore, this study revealed nine new allelic variants at five different loci.