Short Tandem Repeat Loci CSF1PO Research Articles

Inferring Human Phylogenies Using Three CODIS STR Markers (CSF1PO, TPOX and TH01)

Over the past several decades polymorphic genetic loci have been discussed for their utility in human phylogenetic inferences. Short Tandem Repeat (STR) loci have shown promising results for this purpose. Unfortunately, allele frequency data of polymorphic loci are largely confined to few populations. Therefore, the number of shared loci declines as the number of population increases. We hypothesize that even a smaller number of STR loci can be used efficiently for phylogenetic purposes if an appropriate theoretical and statistical strategy is employed. This strategy provides a feasible and cost effective method to choose appropriate STR loci for phylogenetic studies. For this purpose, an empirical study was conducted using allele frequency data of three STR loci CSF1PO, TPOX, and TH01 across 98 human populations from the literature (references are available at http://dnaa.bravehost.com/ index.html and http://www.cstl.nist.gov/strbase/population/Omnipop). The choice of markers was based on locus polymorphism, high heterozygosity, low mutation rate, less artifacts and independence between the loci. Three methods were used to measure genetic distances between the populations; Cavalli Sforza’s chord distance (DC), Nei’s genetic (DA) and Nei’s standard genetic distances (DST). Coefficient of variation (CV) was calculated across hundred (100) datasets obtained by re-sampling of the original dataset for each of the genetic distance methods. CV was in order of DST >DA >DC. Therefore, a consensus tree based on DC was constructed using Neighbour Joining (NJ), Unweighted Pair Group Method with Arithmatic mean (UPGMA) and Maximum Likelihood (ML) methods. NJ and UPGMA methods got more statistical support that is higher bootstrap values than ML (NJ> UPGMA> ML). Validation study was performed using (A) Principal Component Analysis (B) Comparison with trees reported for other molecular markers (C) STR genotyping of five Pakistani subpopulations. Results strongly supported our hypothesis that the three STR markers CSF1PO, TPOX, and TH01 are successful in delineating ethnic, geographic and linguistic differentiation between the populations.

STR polymorphisms in Sri Lanka: evaluation of forensic utility in identification of individuals and parentage testing

This preliminary study was carried out to determine the allele frequencies and forensic efficiency parameters for the short tandem repeat loci CSF1PO, TPOX, THO1, D16S539, D7S820, D13S317, vWA, FESFPS and F13B in a test sample population of Sri Lankans. Test samples were obtained from 305 non-related individuals originating from all 9 provinces of Sri Lanka. DNA was extracted from whole blood using chelex-100 and amplified by PCR using the GenePrint STR kit and silver stained. Final DNA profiles were analysed for forensic efficiency parameters and paternity indices using PowerStats version 12. Possible divergence from Hardy-Weinberg Equilibrium was tested using the chi-square test and exact test. All common alleles in the allelic ladders were found in the test sample studied. PIC values >0.5 for all 9 STR loci indicate this STR system to be informative and useful for identification purposes. The D13S317, vWA and D7S820 loci were found to be the most polymorphic markers of the system studied. No deviations from Hardy-Weinberg Equilibrium were found for any of the loci examined. The results indicate that the 9 STR loci system described here is suitable for estimating DNA profile frequencies in human identification and forensic and parentage testing for legal purposes among Sri Lankans.

Genetic Profile of Three Short Tandem Repeat Loci CSF1PO, TPOX, and TH01 in a Chinese Korean Population

POPULATION: Chinese Korean.

Evaluation of the species specificity for six human short tandem repeat loci CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA, in the Japanese macaque

We examined six human short tandem repeat (STR) loci (c-fms proto-oncogene for CSF-1 receptor, CSF1PO; thyroid peroxidase, TPOX; tyrosine hydroxylase, TH01; coagulation factor XIII a subunit, F13A01; c-fes/fps proto-oncogene, FESFPS and von Willebrand factor, vWA) in the Japanese macaque, Macaca fuscata, using commercially available human STR kits. No products were amplified by polymerase chain reaction (PCR) using the human CSF1PO, TH01, FESFPS and vWA primers. Macaque DNAs were amplified with human TPOX and F13A01 primers. Macaque PCR products amplified with the TPOX and F13A01 primers migrated more slowly than human ones during electrophoresis. Sequencing results showed that the nucleotide sequences of the counterpart of the TPOX and F13A01 STR loci in the Japanese macaque were closely similar to those of the human genes except for tandem repeat regions. The macaque products amplified with human TPOX and F13A01 primers were highly polymorphic, with four variants of the former and 15 variants of the latter in the nine samples. These results indicate that the commercially available kits can be used to discriminate the Japanese macaque samples from human samples.

Population genetic study of eight short tandem repeat loci CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, F13B and LPL in the Western Romanian population

Allele frequencies for eight tetranucleotide short tandem repeat (STR) loci—CSF1PO, TPOX, TH01, F13A01, FESFPS, vWA, F13B, LPL—were obtained from a population sample of 105–122 unrelated individuals born in Transylvania and Banat (Romania).

Analysis and Interpretation of Short Tandem Repeat Microvariants and Three-Banded Allele Patterns Using Multiple Allele Detection Systems

The Palm Beach County Sheriffs Office (PBSO) Crime Laboratory and the Alabama Department of Forensic Sciences (ADFS) have validated and implemented analysis of short tandem repeat (STR) sequences on casework using silver staining kit and SYBR Green I detection systems and are presently validating fluorescently tagged STR alleles using the Hitachi FMBIO 100 instrument. Concurrently, the Broward County Sheriff's Office (BSO) Crime Laboratory is validating the ABI Prism310 Genetic Analyzer capillary electrophoresis STR detection system (ABI CE310) from Perkin Elmer Applied BioSystems. During the course of analyzing over 10,000 individuals for the STR loci CSF1PO, TPOX and THO1 (CTT) using silver staining for allele detection, 42 samples demonstrated alleles that were "off ladder," contained three-banded patterns at a single locus, or exhibited an apparent THO1 "9.3,10" allele pattern. PBSO, ADFS and BSO Crime Laboratories have collaborated on the verification of the allele patterns observed in these 42 samples using the following allele detection systems: (1) manual silver staining, (2) SYBR Green I staining, and/or (3) fluorescently tagged amplified products separated by polyacrylamide gel electrophoresis or capillary electrophoresis followed by laser detection. Regardless of the CTT allele detection system utilized, concordant results were obtained for 41 of the 42 samples. The only exception was a sample in which a wide band within the THO1 locus was identified as a THO1 "9.3, 10" genotype by silver staining kit and SYBR Green I staining but was verified to be a THO1 "9.3" homozygote by all other allele detection systems. Manual allele detection could readily identify microvariants, as a visual assessment of stained gels clearly shows that alleles do not migrate coincident with well-characterized allele size standards. As would be predicted, however, the manual detection systems did not provide adequate resolution to approximate the basepair size for off-ladder variants. All fluorescent software program systems were consistent in designating alleles "not in range" or "off ladder," thereby indicating true microvariants. All single-locus three-banded patterns were detected using all of the STR multiplex systems. In addition, individual locus-specific primers verified multiplexed amplified products were specific for the locus in question.

Development and Population Study of an Eight-Locus Short Tandem Repeat (STR) Multiplex System

Amplification of short tandem repeat (STR) loci has become a useful tool for human identification applications. To improve throughput and efficiency for such uses, the polymorphic STR loci CSF1PO, TPOX, TH01, vWA, D16S539, D7S820, D13S317, D5S818, F13A01, FESFPS, F13B, and LPL have been evaluated, developed, and configured into fluorescently labeled multiplex systems. Eight of these STR loci were combined to generate the PowerPlex System, a two-color multiplex system that supports rapid, accurate, reliable analysis and designation of alleles. The remaining four loci comprise the FFFL System, a one-color multiplex system. The PowerPlex System may be evaluated alternatively as two one-color, four-locus multiplex systems, CTTv Multiplex and GammaSTR Multiplex. The products of multiplex amplification may be analyzed with a variety of fluorescence detection instruments. Determination of genotypes of over 200 individuals from each of three different population/ethnic groups revealed independence of inheritance of the loci and allowed calculation of matching probability, typical paternity index, and power of exclusion for each multiplex.

Italian Population Data on the Polymarker System and on the Five Short Tandem Repeat Loci CSF1PO, TPOX, TH01, F13B, and vWA

A population study on five short tandem repeat (STR) loci and five sequence specific polymorphism loci was performed on unrelated Italian Caucasians. Separation and detection of the amplified STR fragments were carried out by high resolution vertical denaturing polyacrylamide gel electrophoresis (PAGE) and silver staining, respectively. The sequence specific loci were analyzed using the AmpliType PM Typing Kit (Perkin Elmer, Foster City, CA). All loci, except Gc (p = 0.031), meet Hardy-Wienberg expectations. In addition, there is no evidence for association of alleles between pairs of loci. The combined power of discrimination for the five STR loci is 0.9999862 and for the PM loci is 0.99503. The results suggest that these loci may be useful for human identification cases in Italy.