Genetic analysis of 15 STR loci in Chinese Han population from West China

Microsatellite Instability Analysis (MSA) for Bladder Cancer: Past History and Future Directions

Microsatellite instability (MSI), the spontaneous loss or gain of nucleotides from repetitive DNA tracts, is a diagnostic phenotype for gastrointestinal, endometrial, colorectal, and bladder cancers; yet a landscape of instability events across a wider variety of cancer types is beginning to be discovered. The epigenetic inactivation of the MLH1 gene is often associated with sporadic MSI cancers. Recent next-generation sequencing (NGS)-based analyses have comprehensively characterized MSI-positive (MSI+) cancers, and several approaches to the detection of the MSI phenotype of tumors using NGS have been developed. Bladder cancer (here we refer to transitional carcinoma of the bladder) is a major cause of morbidity and mortality in the Western world. Cystoscopy, a gold standard for the detection of bladder cancer, is invasive and sometimes carries unwanted complications, while its cost is relatively high. Urine cytology is of limited value due to its low sensitivity, particularly to low-grade tumors. Therefore, over the last two decades, several new "molecular assays" for the diagnosis of urothelial cancer have been developed. Here, we provide an update on the development of a microsatellite instability assay (MSA) and the development of MSA associated with bladder cancers, focusing on findings obtained from urine analysis from bladder cancer patients as compared with individuals without bladder cancer. In our review, based on over 18 publications with approximately 900 sample cohorts, we provide the sensitivity (87% to 90%) and specificity (94% to 98%) of MSA. We also provide a comparative analysis between MSA and other assays, as well as discussing the details of four different FDA-approved assays. We conclude that MSA is a potentially powerful test for bladder cancer detection and may improve the quality of life of bladder cancer patients.

Genetic analysis of two STR loci (VWA and TPOX) in the Iranian province of Khuzestan

OBJECTIVES

Short tandem repeat (STR) loci are the most informative DNA genetic markers for attempting to individualize biological material for application in paternity and forensic cases.

MATERIALS AND METHODS

Blood samples were collected and the total genomic DNA was extracted. The DNA samples were used for genotyping VWA and TPOX STR loci using PCR and polyacrylamide gel electrophoresis.

RESULTS

This report presents allele frequency data and parameters of biological or legal interest, such as heterozygosity value, polymorphic information content (PIC), genetic diversity index (GD) and population parameter (θ) in Arab and non-Arab population of Khuzestan province (Iran) for the loci VWA and TPOX. Blood samples (N= 392 for VWA and N=308 for TPOX) were collected from individuals unrelated throughout Khuzestan province. The loci were genotyped using the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE) and silver staining. Chi-square test showed that neither STR loci were in agreement with the Hardy-Weinberg equilibrium.

CONCLUSION

The examined STR loci in this study have proven a relatively high genetic variation in the Iranian population. The data could be used for construction of a forensic genetic database for the Iranian population.

Genetic analysis of 15 STR loci from a Xibe population in Liaoning, Northeast of China

BACKGROUND

In view of their high level of variability, autosomal short tandem repeats (STRs) are very useful as markers in the disciplines of forensic and population genetics studies.

AIM

To investigate the diversity distributions of allelic frequencies of 15 loci from a sample from the Chinese Xibe ethnic group in Liaoning.

SUBJECTS AND METHODS

Fifteen STR loci for 150 unrelated Xibe individuals from Liaoning, China were amplified simultaneously in a fluorescence-based reaction using a 2720 Thermal cycler (ABI). Separation and detection of the amplified product were conducted with the Li-COR 4300 DNA Analyzer.

RESULTS

In total, 117 alleles were observed, with the corresponding allele frequencies ranging from 0.001 to 0.507. D18S51 had the highest polymorphism (PIC = 0.840) among all 15 STR loci, whereas TPOX had the lowest (PIC = 0.590). The power of discrimination ranged from 0.801 for TH01 locus to 0.957 for D18S51 locus, whereas the power of exclusion ranged from a minimum 0.316 for TPOX locus to a maximum 0.720 for D21S11 locus. The phylogenetic tree established among worldwide populations showed that the Xibe population is far from other populations.

CONCLUSION

Databases for the 15 STR loci will be useful for personal identification and paternity tests in the Xibe population and for the establishment of phylogenetic relationships between populations.

Genetic polymorphism of 15 STR loci in Chinese Han population from Shanghai municipality in East China

The aim of this study was to estimate the allelic frequencies of the fifteen STRs included in AmpFlSTR(®) Identifiler(®) PCR Amplification Kit (Applied Biosystems, USA) in a sample of 186 unrelated individuals resident in Shanghai. Allelic frequencies and forensic parameters were calculated. All loci showed no departure from Hardy-Weinberg equilibrium. The obtained frequencies were compared with other previously reported population data.

Evaluation of the allele-sharing approach, known as the IBS method, in kinship analysis

To infer relatedness from genetic data based on short tandem repeats, the exact method, in which shared allele frequencies are applied to relevant equations, has been conventionally used. An alternative approach is the IBS method that is based on the number of shared alleles between individuals. In the present study, the performance of the IBS method in pairwise kinship analysis was compared with the exact method using simulated data of 10,000 genotype pairs for 15 loci in the ABI Identifiler system. The likelihood ratio in allele-sharing of zero, one and two was calculated from joint probabilities based on allele frequencies of the Japanese population. Whereas the IBS method generally produced lower values of combined indices, smaller deviations of the distributions were evident. The threshold for identification of full siblings relative to non-relatives was comparable with that of the exact method, indicating that both inference powers were almost identical. The likelihood ratio in the IBS method depends on the heterozygosity at a locus, and heterozygosities of the 15 loci were consistent across various population groups, particularly in East Asians. The convenience of fixed LR values in the IBS method is beneficial for cases with uncertain allele frequencies and rare alleles.

Short-tandem repeat analysis in seven Chinese regional populations

In the present study, we investigated the application of 13 short tandem repeat (STR) loci (D13S317, D7S820, TH01, D16S539, CSFIPO, VWA, D8S1179, TPOX, FGA, D3S1358, D21S11, D18S51 and D5S818) routinely used in forensic analysis, for delineating population relationships among seven human populations representing the two major geographic groups, namely the southern and northern Chinese. The resulting single topology revealed pronounced geographic and population partitioning, consistent with the differences in geographic location, languages and eating habits. These findings suggest that forensic STR loci might be particularly powerful tools in providing the necessary fine resolution for reconstructing recent human evolutionary history.