Genetic polymorphisms of 19 STR loci in han popu-lation from Hainan and its application in paternity testing / 中国法医学杂志

Objective To construct a database for the genetic polymorphism of 19 STR loci in Han population from Hainan province. To investigate the application of 19 STR loci in the paternity testing. Methods The genotypes of 462 unrelated individuals in Hainan were detected with GoldeneyeTM 20A PCR Amplification Kit. 19-STR database was acquired, analyzed and evaluated in 283 paternity testing cases. Results No deviations of allele frequency from Hardy-Weinberg equilibrium expectations were found for Chi-square test (P>0.05). Observed heterozygosity (Hobs) varied between 0.603 and 0.914, total discrimination power (TDP) of 19 STR loci was more than 0.999999999999999, cumulative probability of exclusion (CPE) for triplet cases was 0.999999994. In all 283 paternity testing cases, triplets and duos were 170 and 113 respectively; there were 36 (12.7%) excluded cases comparing to 247 confirmed cases (87.3%). 14 mutation events were observed, and all were one-step mutation. Conclusion 14 out of 19 loci showed highly polymorphic in Han population from Hainan, and 19 STR system has high cumulative probability of exclusion and can meet the needs of paternity test of the local region. But mutation should be paid special attention to.

Isolation and chatracterization of microsatellite markers in Tupaia belangeri chinensis / 中国比较医学杂志

Objective To screen out specific microsatellite markers for use in Tupaia belangeri chinensis genetic testing. Methods Firstly to screen about 700 microsatellite loci from whole genome.Secondly to choose about 100 better loci without defect factors.Lastly 46 primers were designed by 33 tree shrew’ s microsatellite loci obtained from whole genome and other references.Agarose gel electrophoresis and polyacrylamide gel electrophoresis were used for PCR products, and better loci based on electrophoresis results were chosen.Then STR scan was used to select the microsatellite loci combination for genetic testing.Results Twenty-two microsatellite loci were selected with a significant Stutter peak on STR scanning.Comparing the alternative loci and ultimately selected loci, there were two loci available in the five alternative loci of T.glis.The coincidence rate between T.glis and T.b.chinensis was 40%.There were two loci available in the five alternative loci of T.minor, and the coincidence rate between T.minor and T.b.chinensis was 40%.There were two loci available in the three alternative loci of T.belangeri, and the coincidence rate between T.belangeri and T.b. chinensis was about 70%.Conclusions The 22 microsatellite loci screened in this study are well applied for genetic testing of Tupaia belangeri chinensis, therefore, provide a scientific basis for the genetic quality monitoring of tree shrews.

Genetic polymorphisms of HPRTB, DXS6803 and DXS6809 STR loci in Tianjin Han female population / 天津医药

Objective To investigate genetic polymorphisms of HPRTB, DXS6803 and DXS6809 STR loci in Tianjin Han female population, and to provide experimental data in the prenatal diagnosis of aneuploidies accurately and rapidly. Methods A total of 150 blood samples were collected in Tianjin Han population. QF-PCR and capillary electrophoresis were used in this study. The relevant data were analyzed by ABI Prism GeneMapper v3.0 software. Two homozygotes were se?lected from each locus for sequencing. The frequencies of the genotypes were checked using Chi-square test to verify Hardy-Weinberg Equilibrium. Data of genetic polymorphisms were calculated by PowerStatsV12 software. Results A total of 150 samples were successfully amplified in 24 hours. The 10, 6 and 10 alleles and 22, 12 and 29 genotypes were found respec?tively in HPRTB, DXS6803 and DXS6809 loci. The most common alleles were 14, 13 and 14. The higher frequencies of gen?otypes were 14-14, 12-13 and 13-14. No significant deviations from the Hardy-Weinberg equilibrium were observed in these three STR loci (χ2=10.554, 5.783 and 15.355, respectively, P>0.05). Values of He were 0.748, 0.649 and 0.806 for these three STR loci respectively. Values of Ho were 0.607, 0.700 and 0.713 respectively. Values of PIC were 0.706, 0.599 and 0.775 respectively. Values of PD were 0.894, 0.814 and 0.931 respectively. And values of PE were 0.299, 0.428 and 0.449 respectively. Conclusion HPRTB, DXS6803 and DXS6809 STR loci were highly polymorphic, which are favorable genetic markers on chromosome X and can be used in rapid prenatal genetic diagnosis.

Genetic relationship among twenty-six populations using Y-STR polymorphism information / 解剖学报

Objective To study the genetic relationship of the Y chromosomal short tandem repeat gene loci in Lanzhou Han population and other 25 populations .Methods The frequency of alleles of Y-STRloci was obtained from a sample of 500 unrelated individuals living in Lanzhou City , and other 25 populations in different areas collected from the published data were used to calculate the genetic similarity coefficient and genetic distance .Phylogenetic trees based on the genetic distance were established .Results Populations of Lanzhou , Beijing, Shanxi and Inner Mongolia were in an identical cluster .Compared with minorities , the genetic distance between Lanzhou Han population and Inner Mongolia Mongolian population was dramatically smaller from other subpopulations .The populations in Malays and Indians were far from the other groups .Conclusion The Y-STR gene frequency distribution in 26 populations has identified differentiation in race, clime and evolution, and it is basically identical with the classification of human races which is similar to or according with other molecular anthropology research conclusions .

Study of polymorphisms in autosomal microsatellite loci among mongolian population / Монголын Анагаах Ухаан

IndroductionThe short tandem repeats (STR) are rich source of highly polymorphic markers in the human genome. In this study, we used a commercially available multiplex STR typing kit to study 15 STR systems (D3S1358, THO1, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA,) in the Mongolians population, and estimated the allele and genotype frequencies. These 15 STR loci include 2 new pentanucleotide repeat STR loci, Penta E and Penta D, so are not studied in Mongolians.GoalTo determine allele frequency of STR loci D3S1358, THO1,D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, FGA Penta E, Penta D in Mongolian population.Materials and MethodsThe liquid blood, blood stain and saliva samples were taken from 165 unrelated individuals from Mongolian. Extraction DNA: Genomic DNA was extracted from whole blood samples by the standard method of phenol-chloroform-isoamyl alcohol and Wizard Genomic DNA Purification kit, Promega Corporation [21], from blood stain and saliva samples QIAamp DNA micro kit, Qiagen [25], AccuPrep Genomic DNA Extration kit, Bioneer, Koreans extraction method respectively.PCR: PCR amplification was performed using 10-15 ng genomic DNA template according to manufacturer’s protocol (PowerPlex® 16 and PowerPlex® 16HS kit, Promega Corporation, USA). Typing: DNA typing was performed on the ABI Prism 310 Genetic Analyzer (Applied Biosystems) using the recommended protocol. The results were analyzed by Data Collection (Version 1.1), GeneScan (Version 3.1), and Genotyper (Version 3.1) softwares (AppliedBiosystems).ResultsWe assessed forensic and population genetic studies using 15 STR loci included in s sample of 165 unrelated individuals from Mongolian. Allele frequency were listed in Table 2. Totally 20 alleles /5, 7-25/ were found from microsatellite Penta E locus and allele 11 has most frequent (0.1128). 6-16 alleles were found from Penta D locus and allele 9 has most frequent (0.3262). This result is interesting because allele 6 of Penta D locus was found rarely among other populations. But relatively higher frequency of allele 6 (0.0183) was found in Mongolian population. A population comparison based in genetic distance and genetic diversity calculated from allele frequencies of the 15 STR loci from obtained five different populations is shown the Table 3. Conclusions:1. Penta E locus was highly polymorphic, and 20 alleles were found in this Mongolians population and allele 11 was most frequent.2. Penta D locus was 20 alleles were found in this Mongolians population and allele 9 was most frequent.

Frequency of Alleles D16S539, D7S820, D13S317 in a population sample in National Capital District, Papua New Guinea

The allele and genotype frequency values of the three tetranucleotide short tandem repeat (STR) loci, D7S820, D13S317 and D16S359, were analysed in blood samples of 25 unrelated randomly selected individuals in the National Capital District, Papua New Guinea. Gene-Print Silver-STR III Multiplex kit (Promega Corp., Medison, WI, USA) was used for the PCR amplification in GeneAmp®PCR System 9700 thermal cycler (Applied iosystems). Data analysis was carried out using the PowerStatsV12.xl workbook template obtained from Promega Corporation. The three STR loci were in Hardy-Weinberg equilibrium. Five alleles (9 – 13) were identified for D16S539, five alleles (8 – 12) for D7S820 and six alleles (8, 9, 11 – 14) for D13S317. No new or microvariant alleles were observed. The most frequent genotypes for D16S539 were 11-11 and 11-12; for D7S820 were 10-11 and 12-12; for D13S317 was 8-12. Observed Heterozygosity was highest in D13S317 (0.880). The combined power of discrimination was 0.99733 and the combined power of exclusion was 0.9363. The data suggests that the three loci are useful for identity testing, forensics and for solving paternity cases among the population in National Capital District, Papua New Guinea.

A Korean population study for the COfiler STR loci (D3S1358, D16S539, TH01, TPOX, CSF1PO, D7S820) / 대한법의학회지

In the United States, the Federal Bureau of Investigation (FBI) officially launched its national DNA database. This database, named the combined DNA Index System (CODIS), included one gender-determining amelogenin and 13 polymorphic short tandem repeats (STR) loci. To introduce a new STR system, a population database for the relevant population must be established for the statistical analysis of forensic cases. AmpFlSTR Profiler Plus PCR Amplification Kit (Profiler Plus Kit) and AmpFlSTR COfiler PCR Amplification Kit (COfiler Kit) are required to obtain information from all the 13 CODIS core STR loci. Study on 9 STR loci using Profiler Plus kit was already performed in a Korean population, but not yet on 6 STR loci using COfiler Kit. This study intends to evaluate usefulness of 6 COfiler STR loci (D3S1358, D16S539, TH01, TPOX, CSF1PO, D7S820) in forensic identification. Buccal swab samples obtained from 300 randomly selected unrelated Koreans. DNA was extracted from the buccal swab samples and multiplex polymerase chain reaction (PCR) was performed using the COfiler Kit to amplify it. And using automated DNA sequencer and computer program, the allele and genotype frequency distribution is investigated and statistical analysis was performed for the PCR products. The following results were obtained: 1. The observed heterozygosity at each STR locus ranged from 0.650 to 0.800 and the expected heterozygosity at each STR locus ranged from 0.642 to 0.787. 2. The polymorphism information content (PIC) at each STR locus ranged from 0.583 to 0.752 and is higher than 0.5 for all loci to have relatively high information content. 3. The power of discrimination (PD) at each STR locus ranged from 0.811 to 0.921 and the combined power of discrimination is calculated to be 0.999996. 4. The mean exclusion chance (MEC) at each STR locus ranged from 0.386 to 0.576 and the combined mean exclusion chance is calculated to be 0.98088. Based on the results of this study, 6 COfiler STR loci may be useful in forensic identification including finding an individual in relation to criminal case and paternity testing.

A genetic study of 9 STR loci in 5 populations living in Guangdong and Guangxi provinces / 中国法医学杂志

Objective To investigate the genetic polymorphisms of 9 STR loci in Guangdong Han population, Guangxi Han population, Dong population, Zhuang population, and Miao population. Method DNA samples from 328 unrelated individuals in Guangdong Han population and Guangxi Han Population, 199 Zhuang popultion, 162 Dong population, 194 Miao population were screened by using AmpFISTR Profiler PlusTM PCR Amplification Kit and 3100 Genetic Analyzer. Results The genotype frequencies of these 9 STR loci meet the Hardy - Weinberg expectations.The matching probabilities of these 9 STR loci were between 1.51 x 10-11- 8.08 x 10-11 .The cumulative exclusion chances of paternity were 0.99981 - 0.99990. Conclusion Our results showed that the The Profiler Plus?PCR Amplification systems of 9 STR loci are useful in forensic case work in Guangdong Han population, Guangxi Han population, Dong population,Zhuang population and Miao population.

Genetic polymorphic studies on 15 loci of 3 populations in Guangxi province / 中国法医学杂志

Objective To study the genetic polymorphism of 15 STR loci of 3 populations in Guangxi province. Methords DNA samples of unrelated individuals from 314 Gelao population,332 Mulao population,238 Yao population were analyzed using AmpFlSTR IdentifilerTM PCR Amplification Kit and 3100 Genetic Analyzer. Results The matching probability of the 15 STR loci was 1.839 ?10-16 ~ 5.073 ? 10 -17 and combined paternity of exclusion was 0.9999983 ~ 0.9999991 in the 3 populations. Conclusion The results showed that the 15 STR loci in Identifiler?PCR Amplification systems were useful for forensic case works in Gelao population, Mulao population and Yao population .

The practical use of fluorescence-based STR typing technique for decomposed tissues / 中国法医学杂志

To detect STR genotypes of degraded DNA from decomposed tissues. The PCR apmlified products of 40 degraded DNA samples, which were purified from decomposed muscles after death for 1～6 weeks, were separated by denaturing polyacrylamide. The genotypes were analyzed by 377 DNA sequencer and 2 fluorescence-based multiplex amplification systems which contain 12 STR loci and lsex locus. The specific PCR products of 12 STR loci and 1 sex locus of the 40 samples were typed precisely and rapidly. The method described here is very useful in forensic case works, especially for the seriously degraded DNA samples.

Mutations observed at 13 CODIS STR loci in cases of paternity testing / 中国法医学杂志

Objective Mutations of 13 CODIS (Combined DNA Index System) STR core loci in 532 cases of paternity testing were observed in confirming paternity, the mutation rate and the mutation type were studied. Methods 587 cases of paternity testing were routinely carried out using AmpFe STR Profiler Plus and Cofiler PCR Amplification Kits. When one or two STR exclusions were found, then HLA system and other blood groups were tested by molecular typing, and sixteen STR loci were genotyped by using PowerPlexl6 PCR Amplification Kit. If necessary, the genotyping of Y chromosome specific STR and HLA allelic sequencing were added. Results 1052 meiosis were observed among the 532 cases in confirmed paternity, 18 mutation events were found in 17 paternity cases. Single-locus mutation was observed in 16 cases, and mutation at two STR loci was observed in one case. The observed mutational loci include: D5S818, D3S1358, D16S539, CSFIPO, D21S11, D13S317, D7S820, vWA, D18S51 and FGA. The mutation rates for D18S51 and FGA loci were both 0.29% , which were the highest among the ten mutational loci. 11 events of paternal source mutations, 5 events of maternal source mutations and two events of indistinguishable mutations were observed in 18 STR mutational events. Conclusion When one or two STR exclusions were found in paternity testing, other more genetic markers must be detected as complement before making final conclusions.

A study on the gene alterations in 9 STR loci and Amelogenin locus in cancerous tissues / 中国法医学杂志

Objective To study genetic alterations in 9 STR loci and the Amelogenin locus in various tumor tissues. Methods twenty cancer tissues taken from 20 different unrelated individuals and their blood specimens were examined with Chelex-100 extraction of DNA, Profiler Plus PCR amplification and 310 Genetic Analyzer. Results All of the 10 STR loci exist genetic alterations. The genetic alterations occurred in 6out of 20 cases. The rate of genetic alteration was 30%. Six genetic alterations were found in one tumor tissue. Conclusion The forensic community has to take be cautious not to use the tumor tissue for personnel identification.