Genetic Polymorphisms of 19 STR Loci in Populations of Three Culture Region in Shandong / 法医学杂志

OBJECTIVES@#To analyse the genetic polymorphisms of 19 autosomal STR loci in Han population of east, middle-northwest and southwest-south Shandong and to explore its genetic relationships among the population of these three regions.@*METHODS@#STR loci of 1 044 unrelated Han individuals in three Shandong regions were typed with a Goldeneye® DNA ID System 20A kit. The allele frequency and population genetics parameters of 19 autosomal STR loci were statistically analysed by Modified-Powerstates software. The genetic distances among the population in three regions were calculated by Arlequin v3.5 software. The phylogenetic tree was conducted using MEGA v4.0 software.@*RESULTS@#Fifteen of 19 autosomal STR loci were detected with the H values greater than 0.7, PIC values greater than 0.7, and DP values greater than 0.9 in the populations of all three Shandong regions. Among the populations in these three regions, the genetic distance between the populations in middle-northwest and southwest-south Shandong was closest （Fst=0.000 16）, followed by east and southwest-south Shandong （Fst=0.0003 6）. The genetic distance between the populations in east and middle-northwest Shandong was the farthest （Fst=0.000 66, P<0.05）.@*CONCLUSIONS@#The 19 autosomal STR loci show good genetic polymorphisms in Han population of three Shandong regions, and 15 of them are high. There are genetic differences between the populations in east and middle-northwest Shandong.

Application of Multiple Genetic Markers in a Case of Determination of Half Sibling / 法医学杂志

OBJECTIVE@#A case of half sibling was determined with multiple genetic markers, which could be potentially applied for determination of half sibling relationship from same father.@*METHODS@#Half sibling relationship was detected by 39 autosomal STR genetic markers, 23 Y-chromosomal STR genetic markers and 12 X -chromosomal STR genetic markers among ZHAO -1, ZHAO -2, ZHAO -3, ZHAO -4, and ZHAO-5.@*RESULTS@#According to autosomal STR, Y-STR and X-STR genotyping results, it was determined that ZHAO-4 (alleged half sibling) was unrelated with ZHAO-1 and ZHAO-2; however, ZHAO-3 (alleged half sibling), ZHAO-5 (alleged half sibling) shared same genetic profile with ZHAO-1, and ZHAO-2 from same father.@*CONCLUSION@#It is reliable to use multiple genetic markers and family gene reconstruction to determine half sibling relationship from same father, but it is difficult to determination by calculating half sibling index with ITO and discriminant functions.

Analysis of monotherapy prostate brachytherapy in patients with prostate cancer. Initial PSA and Gleason are important for recurrence?

Purpose To evaluate the clinical outcome of a cohort of localized prostate cancer patients treate with 125-I permanent brachytherapy at the São José Hospital – CHLC, Lisbon. Materials and Methods A retrospective analysis was carried out on 429 patients with low and intermediate-risk of prostate adenocarcinoma, according to the recommendations of the EORTC, who underwent 125I brachytherapies in intraoperative dosimetry “real-time” system between September 2003 and September 2013. Results The mean follow-up was 71.98 months. Biochemical relapse of disease by rising PSA (Phoenix criterion) was observed in 18 patients (4.2%). Through the application of Kaplan-Meier survival curves in this sample, the rate of survival at 6 years without biochemical relapse was higher than 95%. By Iog rank test comparing biochemical relapse with initial PSA (15-10 and <10) and Gleason values (7 and <7), there was no statistical difference (P=0.830) of the initial PSA in the probability of developing biochemical relapse. In relation to Gleason score, it was noted a statistical difference (P<0.05), demonstrating that patients with Gleason 7 are more likely to develop biochemical relapse. Conclusions Brachytherapy as monotherapy is at present an effective choice in the treatment of localized prostate adenocarcinoma. Biochemical relapses are minimal. The initial PSA showed no statistically difference in the rate of relapses, unlike the value Gleason, where it was demonstrated that patients with Gleason 7 have a higher probability of biochemical relapse. Cases with PSA bounce should be controlled before starting a salvage treatment. .

Forensic Investigation of Goldeneye™ DNA ID 22NC Kit / 法医学杂志

OBJECTIVE@#To investigate the genetic data of 21 autosomal STR included in Goldeneye™ DNA ID 22NC Kit in Chinese Han nationality and to evaluate the forensic application.@*METHODS@#By detected 500 unrelated healthy individuals in Chinese Han nationality of East China with Goldeneye™ DNA ID 22NC Kit, allele frequencies, population genetics parameters and linkage disequilibrium information of the 21 autosomal STR were statistically analyzed.@*RESULTS@#In the 21 autosomal STR, no deviations from Hardy-Weinberg equilibrium were detected and all loci were independent form each other. DP values of 21 autosomal STR were all above 0.85, and the combined discrimination power was 1-3.616 5 x 10(-26). Combined mean exclusion chance of this system in duo cases was 1-2.786 81 x10(-6), in trio cases was 1-8.545 82 x 10(-1).@*CONCLUSION@#Twenty-one autosomal STR included in Goldeneye™ DNA ID 22NC Kit are highly polymorphic in the Han nationality. Combined with Goldeneye™ DNA ID 20A Kit, the kit can satisfy the needs for full-sibling testing and facilitate the solution of this kind of case tools.

Validation of GlobalFiler® PCR Amplification Kit and the STR Polymorphism / 法医学杂志

OBJECTIVE@#To test the technical parameters of GlobalFiler® PCR Amplification Kit for its application to forensic application value and to investigate the genetic polymorphisms.@*METHODS@#The validation was conducted in sensitivity, mixed samples, species specificity, adaptability, survivability, consistency, peak height balance and stability. The amplification and detection of the genomic DNA from 373 unrelated individuals from Beijing Han nationality were extracted by automation workstation.@*RESULTS@#Global-Filer® PCR Amplification Kit was adaptive to some mixed, degraded and inhibited samples. The power of sensitivity and adaptability and peak height balance showed well. The distributions of genotype frequencies for 21 STR loci in the population were all in accordance with Hardy-Weinberg equilibrium (P > 0.05). The PIC value of the 21 STR loci was among 0.536 to 0.940; the H value was among 0.558 to 0.933; the DP value was among 0.783 to 0.992; the PE value was among 0.243 to 0.874.@*CONCLUSION@#GlobalFiler® PCR Amplification Kit is suitable for criminal cases and DNA database in forensic practice. And 21 STR loci in Beijing Han nationality have high polymorphism, which have application value in forensic practice and population genetics.

Identificação de loci microssatélites com potencial de amplificação na espécie de Peixe-Rei (Odontesthes humensis) / Identification of microsatellite loci with amplification potential in "pejerrey" (Odontesthes humensis)

In this work, 25,806 potentially amplifiable microsatellite loci (PAL) were identified in pejerrey, (Odontesthes humensis), with 21% of dinucleotide, 22% trinucleotide, 37% tetranucleotide, 13% pentanucleotide and 7% hexanucleotide. Of the total loci, 167 were classified as "Best PAL", more likely to be variables in populations. The results show that with a small coverage of the genome it was possible to identify a large number of microsatellite loci...

Genetic diversity of 15 autosomal short tandem repeats loci using the AmpFLSTR ® Identifiler™ kit in a Bhil Tribe Population from Gujarat state, India.

MATERIALS AND METHODS: The genetic diversity and forensic parameters based on 15 autosomal short tandem repeats (STR) loci; D8S1179,D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317,D16S539, D2S1338, D19S433, vWA, TPOX, D18S51,D5S818, and FGA in AmpFLSTR® Identifiler™ kit from Applied Biosystems, Foster City, CA, USA were evaluated in saliva samples of 297 unrelated individuals from the Bhil Tribe population of Gujarat state, India to study genetic diversities and relatedness of this population with other national and international populations. RESUITS: Statistical analysis of the data revealed all loci were within Hardy-Weinberg Equilibrium expectations with the exception of the locus vWA (0.019) and locus D18S51 (0.016). The neighbour joining phylogeny tree and Principal Co-ordinate Analysis plot constructed based on Fst distances from autosomal STRs allele frequencies of the present study and other national as well as international populations show clustering of all the South Asian populations in one branch of the tree, while Middle Eastern and African populations cluster in a separate branch. CONCLUSION: Our findings reveal strong genetic affinities seen between the Indo-European (IE) speaking Bhil Tribe of Gujarat and Dravidian groups of South India.

Linkage disequilibrium and mutation rate analysis of sixteen X-STR loci / 法医学杂志

OBJECTIVE@#To assess the patterns of linkage disequilibrium (LD) of 16 STR loci on X chromo- some and investigate the genetic stability.@*METHODS@#Genomic DNA samples extracted from blood stains from 500 unrelated individuals and 885 lineage members from Eastern Chinese Han population were genotyped through multiplex amplification using IDtyperX-16 kit by our independent research followed by capillary electrophoresis. LD was assessed by PowerMarker v3.25 software and mutation rate of every locus was analyzed.@*RESULTS@#LD were not found at the 16 X-STR loci. Allele mutations were observed at 10 loci. Among them, mutation rates of DXS6809 and DXS7132 were both up to 0.0048.@*CONCLUSION@#When the 16 X-STR loci included in IDtyperX-16 kit were used for parentage testing, product princi- ples can be applied to calculate the likelihood, but mutation should be taken into consideration in the case that the genotypes do not meet the genetic law (especially at DXS6809 and DXS7132).

Characterisation of pks15/1 in clinical isolates of Mycobacterium tuberculosis from Mexico

Tuberculosis (TB) is an infectocontagious respiratory disease caused by members of the Mycobacterium tuberculosis complex. A 7 base pair (bp) deletion in the locus polyketide synthase (pks)15/1 is described as polymorphic among members of the M. tuberculosis complex, enabling the identification of Euro-American, Indo-Oceanic and Asian lineages. The aim of this study was to characterise this locus in TB isolates from Mexico. One hundred twenty clinical isolates were recovered from the states of Veracruz and Estado de Mexico. We determined the nucleotide sequence of a ± 400 bp fragment of the locus pks15/1, while genotypic characterisation was performed by spoligotyping. One hundred and fifty isolates contained the 7 bp deletion, while five had the wild type locus. Lineages X (22%), LAM (18%) and T (17%) were the most frequent; only three (2%) of the isolates were identified as Beijing and two (1%) EAI-Manila. The wild type pks15/1 locus was observed in all Asian lineage isolates tested. Our results confirm the utility of locus pks15/1 as a molecular marker for identifying Asian lineages of the M. tuberculosis complex. This marker could be of great value in the epidemiological surveillance of TB, especially in countries like Mexico, where the prevalence of such lineages is unknown.

Genetic polymorphisms of 19 STR loci in Shandong Han population / 法医学杂志

OBJECTIVE@#To investigate the genetic polymorphisms of 19 STR Loci in Shandong Han population in order to provide the genetic data for paternity testing.@*METHODS@#The genotypes of 205 unrelated individuals in Shandong Han population were typed by Goldeneye 20A kit to get the allele frequencies and population genetic parameters of 19 STR loci. Four kits, Identifiler kit, SinoFiler kit, PowerPlex 16 kit, and Goldeneye 20A kit, were compared with each other and used in the analysis of a special paternity test case.@*RESULTS@#The population genetic parameters of 19 STR loci in Shandong Han Population were obtained. The cumulative discrimination power (CDP) and cumulative probability of exclusion (CPE) ranked from high to low were Goldeneye 20A kit, SinoFiler kit, PowerPlex 16 kit and Identifiler kit, respectively. As duo case, the result of the real case showed that Identifiler kit had no excluding loci, and none of the SinoFiler kit, PowerPlex 16 kit or Goldeneye 20A kit could exclude fatherhood.@*CONCLUSION@#Compared with Identifiler kit, SinoFiler kit, and PowerPlex 16 kit, Goldeneye 20A kit shows the higher efficiency than the others, but is not completely satisfied for duo cases.

Genetic polymorphisms of 16 STR loci in Tibetan Mastiff / 法医学杂志

OBJECTIVE@#To explore the genetic polymorphisms of 16 STR loci from 449 Tibetan Mastiffs in order to set up gene polymorphism database of Tibetan Mastiff.@*METHODS@#The PCR amplification was performed using the 16 STR loci fluorescent multiple amplification kit for dog. The amplified products were detected and statistically analyzed.@*RESULTS@#In the 16 STR loci from 449 Tibetan Mastiffs, CDP was 0.999 999 999 999 999 and CEP was 0.999 997 795. Except FH2010 (10 alleles), PEZ21 (12 alleles), and PEZ05 (13 alleles), the other STR loci had more than 15 alleles. In the 16 STR loci, H was > 0.5 and PIC was > 0.7.@*CONCLUSION@#The 16 STR loci have high polymorphism to be suitable for individual identification and paternity testing of Tibetan Mastiff. The data obtained through this study can be used to establish DNA polymorphism database of Tibetan Mastiff.

Genomic instability at the 13q31 locus and somatic mtDNA mutation in the D-loop site correlate with tumor aggressiveness in sporadic Brazilian breast cancer cases

OBJECTIVE: Genomic instability is a hallmark of malignant tissues. In this work, we aimed to characterize nuclear and mitochondrial instabilities by determining short tandem repeats and somatic mitochondrial mutations, respectively, in a cohort of Brazilian sporadic breast cancer cases. Furthermore, we performed an association analysis of the molecular findings and the clinical pathological data. METHODS: We analyzed 64 matched pairs of breast cancer and adjacent non-cancerous breast samples by genotyping 13 nuclear short tandem repeat loci (namely, D2S123, TPOX, D3S1358, D3S1611, FGA, D7S820, TH01, D13S317, D13S790, D16S539, D17S796, intron 12 BRCA1 and intron 1 TP53) that were amplified with the fluorescent AmpFlSTR Identifiler Genotyping system (Applied Biosystems, USA) and by silver nitrate staining following 6% denaturing polyacrylamide gel electrophoresis. Somatic mtDNA mutations in the D-loop site were assessed with direct sequencing of the hypervariable HVI and HVII mitochondrial regions. RESULTS: Half of the cancer tissues presented some nuclear instability. Interestingly, the D13S790 locus was the most frequently affected (36%), while the D2S123 locus presented no alterations. Forty-two percent of the cases showed somatic mitochondrial mutations, the majority at region 303-315 poly-C. We identified associations between Elston grade III, instabilities at 13q31 region (p = 0.0264) and mtDNA mutations (p = 0.0041). Furthermore, instabilities at 13q31 region were also associated with TP53 mutations in the invasive ductal carcinoma cases (p= 0.0207). CONCLUSION: Instabilities at 13q31 region and the presence of somatic mtDNA mutations in a D-loop site correlated with tumor aggressiveness.

Forensic application of expressmarker 22 STR loci direct PCR amplification kit / 法医学杂志

OBJECTIVE@#To explore the application value of Expressmarker 22 STR loci direct PCR amplification kit.@*METHODS@#One thousand nine hundred and forty-eight samples (including samples spotted on FTA cards, filter papers and case samples) were tested using Expressmarker 22 STR loci direct PCR amplification kit. At the same time, all were tested using Sinofiler kit, Identifiler kit and PowerPlex 16 kit respectively for comparison. The genotypes were compared at the same STR loci among these four kits to test the sensitivity and accuracy of Expressmarker 22 STR loci direct PCR amplification kit.@*RESULTS@#97.79% samples were successfully typed using Expressmarker 22 STR loci direct PCR amplification kit. The genotype profiles of the same samples using Expressmarker 22 STR loci direct PCR amplification kit were consistent with Sinofiler kit, Identifiler kit and PowerPlex 16 kit at the same STR loci.@*CONCLUSION@#Expressmarker 22 STR loci direct PCR amplification kit can provide huge information and accurate results

Genetic polymorphism of 16 Y-STR loci in Miao, Yao and Dong nationalities of Guangxi population / 法医学杂志

OBJECTIVE@#To investigate the genetic polymorphisms of 16 Y-STR loci and to evaluate the forensic application in Miao, Yao and Dong nationalities of Guangxi population.@*METHODS@#Genotypes of Y-STR loci were tested in a total of 253 healthy unrelated individuals (67 Miao people, 99 Yao people, 87 Dong people) using AmpFlSTR Yfiler PCR amplification kit. Allele frequencies and population genetics parameters of the 16 Y-STR loci were statistically analyzed. The allele frequencies were compared among the three nationalities.@*RESULTS@#Most alleles were detected at locus DYS385 while fewest alleles were detected at locus DYS437 among the three nationalities. GD values were ranged from 0.2619 (DYS438) to 0.9417 (DYS385) for Miao nationality, 0.3170 (DYS391) to 0.955 9 (DYS385) for Yao nationality and 0.305 3 (DYS391) to 0.943 3 (DYS385) for Dong nationality, respectively. There were no statistically significant differences detected (P>0.05) at loci of DYS391 and DYS438 among the three nationalities.@*CONCLUSION@#The 16 Y-STR loci can be applied to practices and basic research of forensic genetics in the three main nationalities of Guangxi population.

Forensic application of investigator HDplex kit in Han nationality of Eastern China / 法医学杂志

OBJECTIVE@#To investigate the genetic data of 12 autosomal STR loci included in Investigator HDplex kit and to evaluate its forensic application in Han nationality of Eastern China.@*METHODS@#A total of 484 unrelated healthy individuals in Han nationality of Eastern China were investigated with Investigator HDplex kit. Allele frequencies, population genetics parameters and linkage disequilibrium information of the 12 autosomal STR loci were statistically analyzed.@*RESULTS@#No deviations from Hardy-Weinberg equilibrium were detected and all loci were independent form each other within the studied 484 unrelated healthy individuals. DP values of the 12 autosomal STR loci were all above 0.8, and CDP was 0.999 999 999 92. The cumulative probability of paternity exclusion in duo and in trio were 0.999 82 and 0.999 998 6, respectively.@*CONCLUSION@#Investigator HDplex kit with 12 highly polymorphic STR loci in Han nationality of Eastern China could be used effectively for forensic DNA genotyping.

Identification of sibling brothers using STR and Y-biallelic markers / 法医学杂志

OBJECTIVE@#To explore the methods for identification of sibling brothers with Y-STR locus mutation by detection of genetic markers on autosome and Y-biallelic.@*METHODS@#Goldeneye 20A and 18NC kit were used to genotyped the 35 STRs on autosome from two men. PowerPlex Y kit and Yfiler kit were used to genotyped the 16 STRs on Y chromosome full sibling index was calculated by ITO method. Twenty Y-biallelic markers were genotyped by fragment length discrepant allele specific PCR or general PCR.@*RESULTS@#Relationship of sibling brothers was found to have mutation of 2 loci on 16 Y-STR and the identical genetype of 20 Y-biallelic markers as well as a cumulative full sibling index of 4.3149 x 10(6) from 35 STRs on autosome.@*CONCLUSION@#In identification of paternal linage of Y-STR mutation, more genetic information can be acquired by detection of Y-biallelic markers including SNP and InDel.

Mycobacterial Interspersed Repetitive Unit typing in Mycobacterium tuberculosis isolates from Sichuan Province in China.

Background & objectives: Emergence and spread of drug resistant Mycobacterium tuberculosis is a serious threat to tuberculosis (TB) control programme. Therefore, the objective of this study was to genotype drug-resistant M. tuberculosis strains isolated from patients in Sichuan, China, using Mycobacterial Interspersed Repetitive Units (MIRU) for epidemiological analysis. Methods: Drug-resistance testing of M. tuberculosis isolates from pulmonary TB patients was confirmed by proportion method. Twelve MIRU loci were analyzed on 80 drug-resistant and 9 susceptible isolates by polymerase chain reaction and agarose gel electrophoresis. Hunter-Gaston discriminatory index (HGI) values were determined for each 12 MIRU loci for the evaluation of their discrimination power. Results: Among 12 MIRU loci examined, polymorphic bands could be generated on 11 loci. Sixty five isolates had distinct MIRU patterns, while other 24 belonged to 8 clusters and resistant to at least one anti-TB drug tested. The association between the MIRU patterns and the mutation patterns of drug-resistance relevant target genes was not significant among the drug-resistant isolates. Interpretation & conclusions: The results showed that with a satisfactory discrimination power exhibited, the 12 loci based MIRU typing could be a valuable tool for epidemiological studies in M. tuberculosis isolates from Sichuan.

Genetic polymorphisms of 21 non-CODIS STR loci / 法医学杂志

OBJECTIVE@#To investigate genetic polymorphisms of 21 non-CODIS STR loci in Han population from the east of China and to explore their forensic application value.@*METHODS@#Twenty-one non-CODIS STR loci, were amplified with AGCU 21+1 STR kit and DNA samples were obtained from 225 unrelated individuals of the Han population from the east of China. The PCR products were analyzed with 3130 Genetic Analyzer and genotyped with GeneMapper ID v3.2 software. The genetic data were statistically analyzed with PowerStats v12.xls and Cervus 2.0 software.@*RESULTS@#The distributions of 21 non-CODIS STR loci satisfied the Hardy-Weinberg equilibration. The heterozygosity (H) distributions were 0.596-0.804, the discrimination power (DP) were 0.764-0.948, the probability of exclusion of duo-testing (PEduo) were 0.176-0.492, the probability of exclusion of trios-testing (PEtrio) were 0.334-0.663, and the polymorphic information content (PIC) were 0.522-0.807. The cumulative probability of exclusion (CPE) of duo-testing was 0.999707, the CPE of trios-testing was 0.9999994, and the cumulated discrimination power (CDP) was 0.99999999999999999994.@*CONCLUSION@#Twenty-one non-CODIS STR loci are highly polymorphic. They can be effectively used in personal identification and paternity testing in trios cases. They can also be used as supplement in the difficult cases of diad paternity testing.

Effect of urinary trypsin inhibitor on DNA genotyping in urine samples / 法医学杂志

OBJECTIVE@#To study the effect of urinary trypsin inhibitor (UTI) on STR genotyping with urinary samples.@*METHODS@#Midstream urine samples of 5 male and 5 female volunteers were collected respectively, sub-packaged, added with different concentration of UTI and stored at -80 degrees C. Genomic DNA was extracted from those urinary samples, of which STR profiles were genotyped with IdentifilerTM kit at 8 different time points. Results of genotyping in urinary samples were compared with those of the homogenous blood control samples and the successful rate of genotyping in different group of urinary samples treated with UTI was determined.@*RESULTS@#Fifteen STR loci included in Identifiler system were all detected in control blood samples and urinary samples stored for 1 day. STR locus loss was observed and all 15 STR loci disappeared in female urinary samples untreated with UTI while those storage periods prolonged to 3 and 9 days, respectively. However, all 15 STR loci could be detected in female urinary samples treated with UTI and stored for as long as 9 days. No STR loci could be detected in male urinary samples preserved without UTI for 7 days while 9 STR loci detected preserved with UTI for 9 days. There was no significant difference among the average detection ratios of STR loci in female urinary samples treated with UTI at concentrations of 0.2, 0.4 or 0.6 microg/mL and stored for 30 days, mean of which was as high as 0.8400 +/- 0.0423, statistically higher than that in male urinary samples (0.1600 +/- 0.0423).@*CONCLUSION@#Detection rate of STR loci in urinary samples preserved with UTI was increased significantly, which results in prolonging the storage periods of urinary samples for personal identification.

Development and application of X-chromosomal STR multiplex amplification system / 法医学杂志

OBJECTIVE@#To explore the application of X-chromosomal STR(X-STR) for forensic identification and paternity testing.@*METHODS@#Six X-STR loci DXS6801, DXS9902, DXS6809, DXS6803, DXS6804 and DXS6799 were amplified in a single PCR reaction. PCR products were analyzed using capillary electrophoresis and 3100 Genetic Analyzer and GeneMapper ID v3.1 Analysis Software.@*RESULTS@#The alleles of all six X-STR loci were successfully obtained with unambiguous genotyping, high sensitivity and reproducibility.@*CONCLUSION@#The multiplex PCR of six X-STR loci is useful in forensic identification, particularly for sisters cases.