Population genetics of nine STR loci in two populations from Brazil

The Short Tandem Repeats (STRs) D3S1358, HUMvWA31/A, HUMFIBRA/FGA, D8S 1179, D2S11, D18S51, D5S818, D13S317, and D7S820 were studied in two Brazilian populations (from Amazonia and S. Paulo) using the "AmpF1 STR Profiler Plus PCR Amplification Kit." The nine loci showed a combined discrimination power greater than 0.9999999999 and a chance of exclusion of 0.9999.     

Developmental validation of the AmpFℓSTR® Identifiler® Plus PCR Amplification Kit: an established multiplex assay with improved performance

Abstract: Analysis of length polymorphism at short tandem repeat (STR) loci utilizing multiplex polymerase chain reaction (PCR) remains the primary method for genotyping forensic samples. The AmpF?STR^® Identifiler^® Plus PCR Amplification Kit is an improved version of the AmpF?STR^® Identifiler^® PCR Amplification Kit and amplifies the core CODIS loci: D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, and vWA. Additional loci amplified in the multiplex reaction are the sex‐determinant, amelogenin, and two internationally accepted loci, D2S1338 and D19S433. While the primer sequences and dye configurations were unchanged, the AmpF?STR^® Identifiler^® Plus PCR Amplification Kit features an enhanced buffer formulation and an optimized PCR cycling protocol that increases sensitivity, provides better tolerance to PCR inhibitors, and improves performance on mixture samples. The AmpF?STR^® Identifiler^® Plus PCR Amplification Kit has been validated according to the FBI/National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The validation results support the use of the AmpF?STR^® Identifiler^® Plus PCR Amplification Kit for human identity and parentage testing.     

A time course study on STR profiles derived from human bone, muscle, and bone marrow.

The use of the polymerase chain reaction (PCR) to define deoxyribonucleic acid (DNA) types at several loci was investigated. PCR was used to amplify nine short tandem repeat (STR) loci along with the amelogenin locus on the X and Y chromosomes using the AmpF/STR Profiler Plus PCR amplification kit (Perkin Elmer). Rib bones were collected from 12 individuals. Five cm portions were buried at a depth of approximately 30 cm and 5 cm portions were left on the surface of the ground. Samples were exposed to the environment for periods of time ranging from two weeks to 17 months. Dried blood standards were prepared for use as reference standards for each rib sample. Bone, muscle, and bone marrow were collected from each sample. DNA from each tissue type was extracted. Complete profile results were obtained from the surface bone samples out to an exposure time of 17 months. None of the muscle or bone marrow samples produced complete profile results beyond eight weeks. All DNA typing results from complete or incomplete profiles were consistent with DNA typing results of the corresponding blood standard. Results suggest that using the AmpF/STR Profiler Plus PCR Amplification Kit is a valid way to establish the DNA profile of tissue types from human remains.     

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.     

13个STR基因座在亲子鉴定案例中的基因突变观察

目的 观察美国 CODIS系统的 13个 STR基因座在532例认定亲子关系的亲子鉴定案中的基因突变情况,探讨STR基因座突变率及突变类型。方法 经“Profiler Plus”及“Cofiler”试剂盒检测的587例亲子鉴定案,对其中有1～2个STR基因座不符合遗传规律者,增加HLA等血型基因和“PowerPlex16~(TM)”试剂盒检测。必要时,还增加Y-STR基因座检测和HLA等位基因测序。结果 认定亲子关系的532例,观察1052次减数分裂,发现17例亲子鉴定中的18次基因突变事件,其中16例1个STR基因座的基因发生突变,1例2个STR基因座的基因发生突变;突变的基因座包括D5S818、D3S1358、D16S539、CSFIPO、D21S11、D13S317、D7S820、vWA、D18S51和FGA,其中以FGA和D18S51基因座的突变率最高(0.29％);18次突变事件,其中来自父亲11次,来自母亲5次,无法确定2次。结论 用美国CODIS系统的STR基因座进行亲子鉴定,在有1～2个基因座不符合遗传规律时,要综合分析,并增加其它的遗传标记进行检测。     

Development and validation of the AmpFlSTR MiniFiler PCR Amplification Kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA

DNA typing of degraded DNA samples can be a challenging task when using the current commercially available multiplex short tandem repeat (STR) analysis kits. However, the ability to type degraded DNA specimens improves by redesigning current STR marker amplicons such that smaller sized polymerase chain reaction (PCR) products are generated. In an effort to increase the amount of information derived from these types of DNA samples, the AmpFlSTR MiniFiler PCR Amplification Kit has been developed. The kit contains reagents for the amplification of eight miniSTRs which are the largest sized loci in the AmpFlSTR Identifiler PCR Amplification Kit (D7S820, D13S317, D16S539, D21S11, D2S1338, D18S51, CSF1PO, and FGA). Five of these STR loci (D16S539, D21S11, D2S1338, D18S51, and FGA) also are some of the largest loci in the AmpFlSTR SGM Plus kit. This informative nine-locus multiplex, which includes the gender-identification locus Amelogenin, has been validated according to the FBI/National Standards and SWGDAM guidelines. Our results demonstrate significant performance improvements in models of DNA degradation, PCR inhibition, and nonprobative samples when compared to the AmpFlSTR Identifiler and SGM Plus kits. These data support that the MiniFiler kit will increase the likelihood of obtaining additional STR information from forensic samples in situations in which standard STR chemistries fail to produce complete profiles.     

Genetic polymorphisms of 20 STR loci in Chinese Han population in Tianjin,North China

The PowerPlex^® 21 System PCR Amplification Kit was a new PCR Amplification Kit developed for forensic laboratories, but there was a lack of data about this kit in Chinese people in Tianjin, North China. This kit contained 20 STR loci, D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA. In order to evaluate this kit and to get basic population data for its use in forensic practice in Chinese Han population, 360 unrelated Chinese Han individuals from Tianjin were typed using the Kit. Allele frequencies of the 20 STR loci and further population forensic genetic parameters were obtained. The observed genotype frequencies and expected genotype frequencies were evaluated by χ² test. No significant deviation from the Hardy–Weinberg equilibrium was observed in the population sample for the 20 STR loci. The population data in the present study can be used for routine forensic practice in Tianjin, North China.     

Population data for the AmpFl STR Identifiler PCR Amplification Kit in China Han in Jilin Province, China

Allele frequencies for the fifteen short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D19S433, THO1, D16S539, CSF1PO, TPOX, D2S1338 (AmpFl STR Identifiler PCR Amplification Kit, Applied Biosystems) were determined in a population sample of unrelated China Han in Jilin Province, China. Statistical analyses were performed using Powerstats version 1.2 and GEP-ISFGWG. The results showed that all the loci met Hardy-Weinberg expectation.     

Population data of nine STR loci,D3S1358, vWA,FGA, TH01, TPOX,CSF1PO,D5S818, D13S317 and D7S820, in Bangladeshis and Indonesians

Allele frequencies of nine short tandem repeat (STR) loci, D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, were determined for 127 unrelated Bangladeshi individuals and 105 unrelated Indonesian individuals using the AmpFLSTR Profiler Kit. The genotype frequency distributions of the nine STR loci were in the Hardy-Weinberg equilibrium for both populations.     

Flemish population data using the AmpF/STR Profiler PCR amplification kit

Population frequency data for nine short tandem repeats (STR) (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820) were determined from 280 unrelated Caucasians from the North region of Belgium (Flanders). The data were obtained using the AmpF/STR Profiler kit from Applied Biosystems.     

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。     

Analysis of STR loci in Cartagena, a Caribbean city of Colombia

Allele frequencies, together with some parameters of forensic interest were estimated for nine STRs included in the AmpF/STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) in a sample of 215 unrelated individuals from Cartagena (Colombia). For all loci, no significant deviations from Hardy-Weinberg equilibrium were observed. Comparative analysis results between our data and those from other Colombian and African population samples revealed significant differences, except with two Colombian Caribbean Coast sub-regions.     

Analysis of STR loci in Cartagena, a Caribbean city of Colombia

Allele frequencies, together with some parameters of forensic interest were estimated for nine STRs included in the AmpF/STR Profiler kit (CSF1PO, D3S1358, D5S818, D7S820, D13S317, FGA, TH01, TPOX and vWA) in a sample of 215 unrelated individuals from Cartagena (Colombia). For all loci, no significant deviations from Hardy-Weinberg equilibrium were observed. Comparative analysis results between our data and those from other Colombian and African population samples revealed significant differences, except with two Colombian Caribbean Coast sub-regions.     

广东广西地区5个群体9个STR基因座的频率调查

目的 调查广东汉族、广西汉族、广西侗族、广西壮族、广西苗族5个群体9个STR基因座多态性,探讨其在法医学检验中的应用价值。方法 应用AmpFISTR Profiler PlusTM荧光标记复合扩增系统,对广东广西5个群体4个民族的1191个无关个体的血样DNA进行9个STR基因座的复合扩增;用ABI 3100遗传分析仪对扩增产物进行分型,统计9个STR基因座的群体遗传学参数。结果 9个STR基因座在广东广西地区5个群体中的累积偶合率为1.51×10-11～8.08×10-11,累积非父排除率为0.99981—0.99990。,结论 该9个STR基因座可满足汉族、壮族、侗族、苗族群体法医学的个体识别及亲权鉴定的需要。     

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.     

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.     

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.     

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.     

Forensic and population genetic analysis of Serbian population using 21 STR loci of GlobalFiler™ PCR amplification kit

Autosomal short tandem repeats (STRs) have been widely used in forensic investigations. Prior to the application of any DNA based identification method, it is essential to estimate the allele frequencies and forensic statistical parameters of targeted STR loci in each population in order to provide a more precise reference database for forensic investigation. The GlobalFiler™ Kit is a multiplex assay that combines the 13 original CODIS loci with 7 non-overlapping loci from the expanded European Standard Set (ESS), as well as the highly discriminating SE33 locus, two Y-based loci and the sex determining maker, Amelogenin. The full complement of loci in the GlobalFiler™ Kit are: D13S317, D7S820, D5S818, CSF1PO, D1S1656, D12S391, D2S441, D10S1248, D18S51, FGA, D21S11, D8S1179, vWA, D16S539, TH01, D3S1358, AMEL, D2S1338, D19S433, DYS391, TPOX, D22S1045, SE33 and a Y-specific insertion/deletion locus (Yindel). The 6-dye GlobalFiler™ PCR Amplification kit (ThermoFisher Scientific) comprises 21 autosomal STRs have already been proven to be able to provide reliable DNA profiling results and enhance the power of discrimination between individuals. In this study, we are presenting an analysis of GlobalFiler STR loci on 209 unrelated individuals from Serbia.     

Japanese population database for nine STR loci of the AmpFlSTR Profiler kit

Allele frequencies for nine short tandem repeats (STR) loci: D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820 were determined in a Japanese population using the AmpFlSTR Profiler PCR amplification kit (Applied biosystems).