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PubMed2004

Short tandem repeat polymorphism and cancer risk: influence of laboratory analysis on epidemiologic findings.

Short tandem repeats (STR) are common polymorphisms in the genome. The length of STR may influence gene transcription, exhibiting diverse phenotypes. Two STRs, one trinucleotide repeats in the androgen receptor (AR) gene and one dinucleotide repeats in the insulin-like growth factor-I (IGF-I) gene, have been studied for their role in cancer, and the results are conflicting. Although there are many reasons for inconsistent findings, laboratory issues are often overlooked. DNA sizing analysis is regularly used to determine the length of STR, but its analytic validity has not been evaluated in epidemiologic studies. To examine if sizing analysis can reliably determine dinucleotide STR, we compared the method with direct DNA sequencing in analyzing CA repeats in the IGF-I gene in a small case-control study. The study enrolled 75 breast cancer cases and 75 age- and race-matched controls. DNA was extracted from buffy coats and was analyzed for CA repeats by both DNA sizing and direct sequencing. Our comparison indicated that these methods detected the same number of repeats in the short allele but not in the long allele. There was a substantial discrepancy between the methods in determining homozygous alleles. Although the two methods showed <10% of samples having an exact match on the number of repeats in both alleles, both techniques were able to detect a genotype-phenotype correlation and a racial disparity in the genotype. An association between breast cancer risk and IGF-I genotype was found in sequencing analysis but not in sizing analysis. Overall, the comparison suggests that laboratory analysis of dinucleotide STR may not be as reliable as originally thought. This unreliability in STR analysis may result in inconsistent study findings.

Adult↗
PubMed1999

The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems.

Since the first characterization of the population genetic properties of repeat polymorphisms, the number of short tandem repeat (STR) loci validated for forensic use has now grown to at least 13. Worldwide variations of allele frequencies at these loci have been studied, showing that variations of interpopulation diversity at these loci do not compromise the power of identification of individuals. However, data collected for validation of these loci for forensic use has utility beyond human identification; the origin and past migration history of modern humans can be reconstructed from worldwide variations at these loci. Furthermore, complex forensic cases previously unresolvable can now be investigated with the help of the validated STR loci. Here, we provide the absolute power of the validated set of 13 STR loci for addressing these issues using multilocus genotype data on 1,401 individuals belonging to seven populations (US European-American, US African-American, Jamaican, Italian, Swiss, Chinese and Apache Native-American). Genomic research is discovering new classes of polymorphic loci (such as the single nucleotide polymorphisms, SNPs) and lineage markers (such as the mitochondrial DNA and Y-chromosome markers); our aim, therefore, was to determine how many SNP loci are needed to match the power of this set of 13 STR loci. We conclude that the current set of STR loci is adequate for addressing most problems of human identification (including interpretations of DNA mixtures). However, if suitable number of SNPs are used that would match the power of the STR loci, they alone cannot resolve more complex cases unless they are supplemented by the validated STR loci.

Chromosome Mapping↗
PubMed2005

Y-chromosome short tandem repeat (STR) haplotypes in a Campania population sample.

Given the lack of information about Y haplotypes for Campania (southern Italy), we analyzed eight Y short tandem repeats in a sample of males from this region with the aim of establishing a Y-haplotype database that can be used for forensic purposes. The eight Y short tandem repeats were amplified by two PCR multiplex reactions: multiplex A for loci DYS19, DYS385, DYS392 and DYS393, and multiplex B for DYS389 I and II, DYS390, DYS391 and DYS385. The proportion of unique haplotypes was 100% (108 Y-chromosome haplotypes in 108 unrelated males) and the haplotype diversity discrimination index was 0.99. These data reflect the high heterogeneity of male lineage in our population and are similar to those obtained in other regions of southern Italy.

Chromosome Mapping↗
PubMed2001

Characterization of human cytomegalovirus strains by analysis of short tandem repeat polymorphisms.

Human cytomegalovirus (HCMV) strains display genetic polymorphisms, and these polymorphisms can be analyzed to study viral transmission and pathogenesis. Recently, short tandem repeat (STR) length polymorphisms have been identified in the HCMV genome. We assessed the utility of STRs in characterizing HCMV strains and found that a multiplexed PCR assay using primers based upon these STRs accurately maps HCMV strains. Using primers for 10 microsatellite regions, the STR profiles of 44 wild-type and 2 laboratory strains of HCMV were characterized. The results of STR analysis were compared with those for strain characterization using nucleotide sequencing and restriction fragment length polymorphism analysis. In each instance, STR analysis accurately and specifically identified strains that were indistinguishable or distinct by conventional molecular analysis. Analysis of short tandem repeats also detected polymorphisms that supported simultaneous excretion of two HCMV strains. These results indicate that STR analysis allows rapid, precise molecular characterization of HCMV strains.

Adult↗
PubMed1994

Genetic linkage studies in antithrombin-deficient kindreds using a highly polymorphic trinucleotide short tandem repeat (STR) within the human antithrombin gene.

PCR amplification and analysis of short tandem repeats (STR) have provided a useful tool for genetic linkage studies and for the diagnosis of genetic disorders. We have recently identified a novel trinucleotide STR, (ATT).(TAA), in the fifth intron of the human antithrombin gene (AT3) located on chromosome 1q23. PCR amplification, cloning, and sequence analysis revealed this AT3-STR to be highly polymorphic with repeat units ranging in size from (ATT)5 to (ATT)18. Ten distinct alleles were found in 81 unrelated Caucasian individuals (162 alleles) with an observed heterozygosity of 81%. Genetic linkage studies using the AT3-STR in two previously described antithrombin (AT)-deficient kindreds, AT-Hamilton (Ala 382 Thr) and AT-Amiens (Arg 47 Cys), demonstrate, in a given kindred, that a specific AT3-STR polymorphism is strongly associated with a particular AT mutation. Thus, this highly polymorphic AT3-STR should be very useful in performing linkage studies in AT-deficient kindreds as well as in investigating other chromosome 1-related genetic disorders.

Antithrombins↗
PubMed1995

Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers.

The use of short tandem repeat polymorphisms (STRPs) as marker loci for linkage analysis is becoming increasingly important due to their large numbers in the human genome and their high degree of polymorphism. Fluorescence-based detection of the STRP pattern with an automated DNA sequencer has improved the efficiency of this technique by eliminating the need for radioactivity and producing a digitized autoradiogram-like image that can be used for computer analysis. In an effort to simplify the procedure and to reduce the cost of fluorescence STRP analysis, we have developed a technique known as multiplexing STRPs with tailed primers (MSTP) using primers that have a 19-bp extension, identical to the sequence of an M13 sequencing primer, on the 5' end of the forward primer in conjunction with multiplexing several primer pairs in a single polymerase chain reaction (PCR) amplification. The banding pattern is detected with the addition of the M13 primer-dye conjugate as the sole primer conjugated to the fluorescent dye, eliminating the need for direct conjugation of the infrared fluorescent dye to the STRP primers. The use of MSTP for linkage analysis greatly reduces the number of PCR reactions. Up to five primer pairs can be multiplexed together in the same reaction. At present, a set of 148 STRP markers spaced at an average genetic distance of 28 cM throughout the autosomal genome can be analyzed in 37 sets of multiplexed amplification reactions. We have automated the analysis of these patterns for linkage using software that both detects the STRP banding pattern and determines their sizes. This information can then be exported in a user-defined format from a database manager for linkage analysis.

Chromosome Mapping↗
PubMed2003

High-density map of short tandem repeats across the human major histocompatibility complex.

The human genome contains one short tandem repeat (STR) roughly every 2,000 base pairs. They are particularly useful markers for gene mapping and disease association studies due to their high degree of polymorphism and ubiquitous frequency throughout the genome. The major histocompatibility complex (MHC) has been the focus of many disease association studies, and the recent availability of the entire sequence of the complex has logarithmically expanded the density of potential markers for fine mapping disease loci. Here we present a complete assessment of the available STRs within a 3.8-Mb genomic segment encompassing the MHC. Of 443 potential STRs identified by computer analysis and tested for variation in a single sample containing pooled DNA from 36 individuals, 249 polymorphic STRs located throughout the complex were identified. The class of repeat (di-, tri-, etc.), precise nucleotide position, position relative to known genes, PCR conditions, and D6S numbers for the 249 polymorphic STRs are provided as a resource for selecting appropriate markers to use in future studies of MHC molecular genetics and disease association.

Base Sequence↗
PubMed1994

PCR typing of DNA fragments of the short tandem repeat (STR) system HUMTH01 in Danes and Greenland Eskimos.

DNA from the short tandem repeat (STR) system HUMTH01 was amplified by the polymerase chain reaction (PCR) and analyzed by vertical electrophoresis in polyacrylamide gels followed by silver staining. DNA samples from 100 unrelated Danes, 147 unrelated Greenland Eskimos, and 89 Danish mother/child pairs were analyzed. Significant differences were observed between the distribution of fragments ('alleles'), whereby allele number 7 was considerably more frequent in Eskimos (0.687) than in Danes (0.201). The distributions of HUMTH01 phenotypes were in Hardy-Weinberg equilibrium in both the Eskimo and Danish populations. In the 89 Danish mother/child pairs, the segregation of the HUMTH01 genotypes was in accordance with the genetic model of co-dominant inheritance and no mutations were found. In a blind trial, DNA samples from 40 unrelated Danes were investigated by one of us in Copenhagen, at the FBI Forensic Science Research and Training Center (FSRTC), Quantico, and at the Institut für Rechtsmedizin, Münster, Germany. Concordant HUMTH01 types were found in 39 out of 40 individuals. The allele which led to discrepant typing results was assigned type 9.3 in two laboratories and type 10 in one laboratory.

Alleles↗
PubMed2006

Population genetic data of 15 tetrameric short tandem repeats (STRs) in Berbers from Morocco.

The allele frequency distribution of 15 short tandem repeats (STR) loci contained in the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems), was determined in two Berber populations from Asni and Bouhria, in Central and Eastern Morocco, respectively. A total of 209 individuals were typed. No deviations from the Hardy-Weinberg equilibrium were observed for Asni at the 15 STRs loci whereas for the Bouhria samples, two loci (D5S818 and TH01) showed significant departures from Hardy-Weinberg expectations (after Bonferroni's correction). All loci are highly polymorphic and population differentiation tests showed that the Moroccan samples from Asni and Bouhria have significant differences in 4 out of 15 loci (D21S11, D7S820, D16S539 and TPOX). The aim of the study was to obtain accurate allele frequencies relevant for forensic applications. Comparative analyses between our population data and other population samples gathered from the literature are also presented.

DNA Fingerprinting↗
PubMed2001

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

Databases, Factual↗
PubMed1999

Italian population data on two new short tandem repeat loci: D2S1338 and Penta E.

A population study on two new short tandem repeat (STR) loci D2S1338 (a tetranucleotide repeat) and Penta E (a pentanucleotide repeat) was performed on 208 unrelated Italian Caucasians. The DNA was amplified by polymerase chain reaction (PCR) and separation and detection of the amplified STR fragments were carried out by use of a PE/ABD PRISM 377 DNA Sequencer 377 automated system (Applied Biosystems Division/Perkin-Elmer). Both loci meet Hardy-Weinberg expectations. There is no evidence for departures from expectations between the two loci. The combined Probability of Discrimination and Probability of Exclusion for the two STR loci are 0.999155 and 0.944925, respectively. The results demonstrate that these two regions can be useful for differentiating among individuals, particularly in concert with other STR loci.

Alleles↗
PubMed2003

Polymerase chain reaction amplification of samples from Japanese monkeys using primers for human short tandem repeat loci.

We examined the species specificity of six commercially available human short tandem repeat systems (for CSF1PO, TPOX, TH01, F13A01, FESFPS and vWA) using six samples obtained from the Japanese monkey Macaca fuscata. Macaque genes were amplified with human TPOX and F13A01 primers. During electrophoresis, macaque polymerase chain reaction (PCR) products amplified with the TPOX primer migrated more slowly than human ones, and migrated close to human CSF1PO bands. Macaque PCR products amplified with the F13A01 primer also migrated more slowly than the human equivalent. The six macaque samples were classified into three types by the TPOX primer and into six types by the F13A01 primer. These results suggest that the primers for human TPOX and F13A01 loci can be used to distinguish between human and Japanese macaque samples.

Animals↗
PubMed1995

Analysis of short tandem repeat (STR) allele frequency distributions in a Balinese population.

Genotypes for 53 short tandem repeat (STR) markers distributed at an average of 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village of approximately 2200 individuals has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (P < 0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (P < 0.043). Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant allelic associations between physically unlinked loci. In addition to providing information pertinent to the issue of genetic diversity of STRs in the human population, these analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

Alleles↗
PubMed2001

Highly polymorphic short tandem repeat analyses clarify complex molecular test results.

Judicious application of highly polymorphic short tandem repeat (STR) analyses and modification of assay conditions readily distinguished nonparentage from true parentage, with occasional failure to transmit one parentally derived allele. These categories were resolved with a reliability of >99.9%, the standard applied to most DNA evidence presented in a U.S. court of law. While completing a single prenatal diagnosis submitted at 19 weeks gestation, the authors found that one polymorphic grandpaternal allele did not amplify, a duplicate control propositus' DNA sample had been switched by an outside laboratory, and recombination occurred in maternal meiosis within the mutant gene region. In two parentage cases with one available parent, a Y-linked STR or an autosomal STR was modified when transmitted to the offspring. In contrast, some apparently inconsistent results between parental DNA and offspring were resolved by purifying or diluting the original extracted DNA samples. Thus, the source of each complex molecular test result was characterized unambiguously by testing a sufficient number of highly polymorphic STR loci and by purifying or diluting troublesome DNA samples to diminish polymerase chain reaction amplification artifact.

Adult↗
PubMed2001

[Variability of short tandem repeats on the human Y chromosome].

Nine rare (biallelic) mutations and six short tandem repeats (STR) mapping to the nonrecombining portion of the Y chromosome were genotyped in 734 males from different geographical regions inhabited by the contemporary Armenian population. The analysis of molecular variance (AMOVA) showed that 48.9% of total STR genetic variation was explained by the differences between the haplogroups isolated based on biallelic polymorphism, whereas only 1.3% of genetic variation could be attributed to the differences between the geographic groups.

Armenia↗
PubMed2005

Mutations of 15 short tandem repeat loci in Chinese population.

OBJECTIVE: To explore the mutations of 15 short tandem repeat (STR) loci in PlowerPlex16 System which are world-widely used in parentage testing. METHODS: Mutations of 15 STR loci in PlowerPlex16 System were investigated in 1921 parentage testing cases from Chinese population. RESULTS: In 1921 parentage cases, seventy cases (3.644%) were found to have mutations. Among these were one case with double mutations (D21S11 and PentaD) and another case with two different mutations (D7S820 and D16S539) in two children. The total number of mutated STR loci observed was 72 over 3764 meiosis with a mutation rate of 0.128% +/- 0.1104% x 10(-3). The highest mutation rate was 0.292% at vWA and D21S11. No mutation was observed at TH01 or at TPOX. The mutated alleles coming from father were five times more than those from mother. The majority (98.611%) of mutated alleles were the results of one-step mutation. The ratio of one-step gain versus loss was 1.826:1. There was only one multiple-step mutation with a double-repeat gain observed at PentaD locus. In the PlowerPlex16 System, nine loci, namely D8S1179, Penta D, D13S317, D16S539, D7S820, D5S818, D3S1358, TH01 and TPOX, have lower mutation rates and are more suitable for parentage testing. CONCLUSION: Mutation of STR is relatively common and often makes parentage testing more complicated. Selecting stable STR locus with low mutation rate is more important in parentage testing.

Alleles↗
PubMed1995

Accurate size comparison of short tandem repeat alleles amplified by PCR.

A strategy is presented for classifying complex short tandem repeat (STR) alleles by size. Such alleles can differ in length by only 1 bp. The HUMACTBP2 locus was used as a model. Dye-labeled, PCR-amplified alleles were analyzed on an automated DNA sequencer with laser-induced fluorescence detection and fragment-sizing software. Between-gel allele sizes calculated against an in-lane allelic ladder or viral DNA size standard were too imprecise to distinguish a 1-bp difference. However, the size difference between a sample allele and its matching ladder allele provided a reliable criterion for size classification. The mean size difference +/- 3 SDs was 0.5 bp, and so an individual result within this interval signified a match. Statistically, 99.7% of the results should lie within +/- 3 SDs with virtually no chance of encountering the 9-SD difference from the mean necessary to misclassify an allele by 1 bp. The method was valid for sample alleles sized against the allelic ladder and for both sample and ladder alleles sized against the viral DNA standard. A correction for the effect of different dye labels on mobility was included in the calculations.

Alleles↗