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PubMed1997

Typing of the short tandem repeat D8S347 locus with different fluorescence markers.

The short tandem repeat (STR) locus D8S347 was analyzed by capillary electrophoresis. Sequencing data and a population study of 203 individuals from a southwestern German population are presented. We detected 12 different alleles, 340-388 bp in length, and found 40 different genotypes. The heterozygosity index was 85.7%. Futhermore, we investigated the consequences of different fluorescent dyes, namely 6-FAM, HEX, and ROX, on the ABI-calculated fragment sizes of defined (i.e., sequenced) alleles (348-376 bp in length). 6-FAM-labeled fragments appear to be smaller than the corresponding HEX- or ROX-labeled fragments. On average, 6-FAM-labeled fragments differ by 3.52 bp from the sequencing data, HEX-labeled ones by 2.04 bp, and ROX-labeled ones by 1.42 bp. Generally, small alleles differ less from the expected sequencing data than larger ones.

Chromosome Mapping↗
PubMed1997

A new allele at the short tandem repeat locus HumF13A01.

We investigated the (AAAG)n short tandem repeat (STR) polymorphism HumF13A01 an Austrian Caucasoid population sample (n = 674). PCR amplified fragments were detected on an automatic A.L.F. DNA sequencer using laser-induced fluorescence. A total of 14 alleles could be identified including a new 179 bp allele which was designated allele 3. Sequence determination of allele 3 confirmed the typing results by revealing three continuous copies of the core repeat, whereas in sequencing of 54 additional alleles no further variants or microheterogeneities could be observed. The population data showed no significant deviation from Hardy-Weinberg equilibrium.

Austria↗
PubMed2002

Diverse eukaryotic transcripts suggest short tandem repeats have cellular functions.

Previously thought "junk" DNA, short tandem repeats consisting of (GATA)n, or its compliment, were found in varied metazoan eukaryotic genomes but were rare in yeast and bacterial genomes. The (GATA)n sequence was found in cDNAs encoding mRNAs with known functions. At least 16 of 18 such transcripts encode membrane-associated proteins including: plasma membranes, synapses, mitochondrial membranes, nuclear envelopes, and brush border membranes. Flanking sequences were diverse but (GATA)n sequences clustered around 500 bases from stop codons. The (GATA)n sequences occurred in both orientations and showed constrained polymorphism. In sets of splice variants with and without (GAUA)n, the STR containing transcripts were the most abundant. These observations suggest that (GATA)n sequences probably function. In many cases, the function may be to encode post-transcriptional signals for mRNAs encoding membrane-associated proteins.

Animals↗
PubMed2003

Transcribed short tandem repeats occur in couples with strongly preferred registers.

Short tandem repeats (STRs) have been widely observed, but most STRs have no recognized organization or function. Here we show that for diverse mRNAs, 84% of (GC)(n) repeats were found unexpectedly coupled with another STR, (GU)(n). These STR couples exhibited preferred polarity and register. In 3(') untranslated mRNA sequences (UTRs) 100% of (GC)(n>6) repeats were tightly coupled with (GU)(n). For (GC)(n), stem folding energy correlated with the length and number of neighboring, non-folding (GU)(n) partners (p=0.014). Approximately 20% of (AU)(n>/=14) repeats were coupled with (GU)(n). The STR couple (AC)(n)(AG)(n) also exhibited polarity and register preferences. The sequence arrangement at STR-couple joints was conserved rigorously, suggesting that these sequences were under selection pressure. Some STR couples may function as mRNA processing landmarks, based on alternative transcript comparisons. These observations suggest that some transcribed STRs may be functional UTR signals with predictable organization and usage patterns.

3' Untranslated Regions↗
PubMed1999

Sex-specific migration patterns in Central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA.

Eight Y-linked short-tandem-repeat polymorphisms (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in four populations of Central Asia, comprising two lowland samples-Uighurs and lowland Kirghiz-and two highland samples-namely, the Kazakhs (altitude 2,500 m above sea level) and highland Kirghiz (altitude 3,200 m above sea level). The results were compared with mtDNA sequence data on the same individuals, to study possible differences in male versus female genetic-variation patterns in these Central Asian populations. Analysis of molecular variance (AMOVA) showed a very high degree of genetic differentiation among the populations tested, in discordance with the results obtained with mtDNA sequences, which showed high homogeneity. Moreover, a dramatic reduction of the haplotype genetic diversity was observed in the villages at high altitude, especially in the highland Kirghiz, when compared with the villages at low altitude, which suggests a male founder effect in the settlement of high-altitude lands. Nonetheless, mtDNA genetic diversity in these highland populations is equivalent to that in the lowland populations. The present results suggest a very different migration pattern in males versus females, in an extended historical frame, with a higher migration rate for females.

Alleles↗
PubMed1997

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80.

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.

Black People↗
PubMed1998

Sequencing using capillary electrophoresis of short tandem repeat alleles separated and purified by high performance liquid chromatography.

Polymerase chain reaction (PCR) amplified alleles need to be isolated and purified before carrying out additional analysis to confirm sequence, number of repeats and microvariants within a short tandem repeat (STR) locus. Also, PCR amplification of tetranucleotide repeat loci, used in DNA typing assays, often result in heteroduplex formation, adding to the complexity of analysis. Sequencing reactions require single specific target DNA for reliable sequencing analysis. Alkylated poly(styrene-divinylbenzene) columns at elevated temperature and gradient elution conditions increase the efficiency of separation to allow for the purification of PCR products. Using the separation technique of ion-pairing reverse-phase (IPRP) high performance liquid chromatography (HPLC), molecular biologists can separate and purify DNA fragments without alteration to the double-stranded DNA sequencing properties. In this study, the IP-RP chromatography technique has been demonstrated by separation of alleles of the short tandem repeat loci of TH01, vWA31, F13A01 and FES/ FPS. Alleles differing in size range of 12 to 4 base pairs were separated by IPRP/HPLC and individual alleles were peak-captured, then cycle-sequenced. These HPLC fractions required no additional steps prior to cycle sequencing. Capillary electrophoresis (CE) was used to sequence the alleles. Furthermore, CE offers advantages over traditional slab methods via automation and higher applied voltages. Interestingly, unlike traditional gel electrophoresis, samples were introduced into the sieving matrix by electrokinetic injection, which allows for multiple injections from a single sample, a key feature for method development. Applied voltage was 320 V per centimeter using a nonderivatized fused silica capillary with an interior diameter of 50 microm and a total length of 47 centimeters. The total analysis time including capillary filling and pre-electrophoresis was less than 30 min for a 220-bp fragment. A sequencing rate of 530 bp/h was achieved using these conditions. By combining the techniques of HPLC separation and CE sequencing, the results confirmed the sequence and number of nucleotide repeats for each STR loci. An average sequencing efficiency of 97% was achieved. Additionally, this method defined the absence of a 9.3 microvariant for a TH01 heterozygous individual previously typed as a 9, 9.3/10 using slab gel electrophoresis. The techniques described can be applied to other DNA purification and isolation problems.

Alleles↗
PubMed2026

Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.

BACKGROUND: Short tandem repeats (STRs) are repetitive DNA sequences with 1–6 nucleotide repeat units, exhibiting high polymorphism due to varying repeat counts. STRs are more variable than SNPs and can cause genetic disorders. With population-scale cattle whole-genome sequencing data available, whole-genome STR identification has attracted new interest, but challenges remain due to the lack of standardized methods, sequencing data limitations, and the diversity of STR-calling tools. This study compared six STR-calling tools: HipSTR, GangSTR, and ExpansionHunter for short-read data, and Straglr, RepeatHMM, and LongTR for Oxford Nanopore (ONT) long-read data—using sequences from five Holstein cattle (two parent–offspring trios with a shared sire). This is the first cattle study to evaluate short- and long-read STR callers using both data types from the same animals. RESULTS: In short-read data, ExpansionHunter identified the highest number of polymorphic STRs (pSTRs) (327,690), followed by HipSTR (205,900) and GangSTR (110,680), with 93,023 loci detected by all three tools. In long-read data, LongTR detected 470,250 pSTRs, RepeatHMM 224,185, and Straglr 90,275, with only 33,253 loci shared among them. Mendelian consistency of STR genotypes in the trio offspring was high (> 0.8) for all short-read tools, with HipSTR and GangSTR highest at 0.98. LongTR was the only long-read tool with high consistency (0.88). Short-read tools also showed higher concordance in STR genotypes among themselves than was observed among long-read tools. However, long-read tools had a clear advantage in detecting large STRs. Relative to computational efficiency, HipSTR and GangSTR (short-reads), and LongTR (long-reads) required less memory and shorter runtimes than the other tools. CONCLUSIONS: Tool selection is critical for accurate whole-genome STR identification in cattle. For short-read data, HipSTR showed relatively high Mendelian consistency and concordance compared to the other tools, while ExpansionHunter was able to detect longer STRs but with lower Mendelian consistency. For long-read data, LongTR demonstrated higher consistency and computational efficiency relative to the other tools. Based on these results, HipSTR and LongTR are suggested as preferred options for short-read and ONT long-read datasets, respectively, in cattle STR analysis. These recommendations are based on the metrics observed in this study, and confirmatory analyses across additional breeds, larger sample sizes, and validated truth sets are encouraged.

Animals↗
PubMed1999

Simultaneous genetic typing from multiple short tandem repeat loci using a 96-capillary array electrophoresis system.

Short tandem repeat (STR) markers are highly polymorphic and widely used in human identification and genetic mapping. We demonstrate fast and reliable genotyping based on the four STR loci vWF, THO1, TPOX, CSF1PO by multiple-capillary array electrophoresis. Extracted human genomic DNA was amplified by polymerase chain reaction (PCR). The PCR products were mixed with pooled allelic ladder as an absolute standard and coinjected from a 96-vial tray. Separations were performed in polyvinylpyrrolidone (PVP) sieving matrix with a one-hour turnaround time, with no degradation over 27 runs. Simultaneous one-color laser-induced fluorescence detection was achieved by using a charge-coupled device (CCD) camera. The allele peaks for the unknown sample were identified by comparing the normalized peak intensities of the mixtures to those of the pooled ladder by using a straightforward algorithm. An extremely high level of confidence in matching the bands was indicated with negligible crosstalk (< 0.89%) between adjacent capillaries. This scheme is applicable for STR genotyping with high resolution, high speed and high throughput.

Algorithms↗
PubMed1995

Population genetics of short tandem repeat (STR) loci.

To investigate the population genetics of short tandem repeat (STR) polymorphisms in human populations, we have studied the allele frequency distributions of four STR loci (HUMTH01, HUMVWA31, HUMF13A1 and HUMFES) in 16 different population surveys which can be categorised within three broadly defined ethnic groups: Caucasian, Asian (Indian subcontinent), and African (Afro-Caribbean and US black). We have observed that allele frequency distributions of populations within ethnic groups are similar; consequently, genetic distances are an order of magnitude lower than between ethnic groups. Inbreeding coefficients (F-statistics) and calculations of the number of mean heterozygous loci per individual, along with estimates of variance, did not suggest that the populations were substructured. This included a study of an immigrant Asian population known to comprise at least three different sub-groups. Finally, an indication of the discriminating power is given by calculation of likelihood ratios (LR) of each individual tested across all four loci. Approximately 70% of Caucasians give an LR of greater than 10,000; the test is even more discriminating in Afro-Caribbeans--approximately 90% of tests are greater than 10,000.

Alleles↗
PubMed1995

Spanish population data on 7 tetrameric short tandem repeat loci.

Allele and genotype frequencies for 7 tetrameric short tandem repeat loci were determined in a Spanish population sample (N = 186-244) using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver staining. The loci were HUMFES/FPS, HUMVWA, HUMTHO1, HUMF13B, HUMCSF1PO, HUMF13A1 and HUMTPOX and all loci met Hardy-Weinberg expectations. In addition, little evidence was found for association of alleles among the 7 loci. Thus the allele frequency data can be used in identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Spanish population.

Gene Frequency↗
PubMed2000

Sequence variation of two hypervariable short tandem repeats at the D22S683 and D6S477 loci.

For two short tandem repeats at the D22S683 and D6S477 loci, 30 and 22 selected alleles, respectively were sequenced. A total of 20 different alleles were found for the D22S683 locus and 12 alleles for the D6S477 locus. In both systems the alleles were designated according to the total number of repeats. D22S683 is a hypervariable STR consisting of blocks of (TATC) repeats with a basic sequence structure (TATATC)n (TATC)n (ATC)0-1 (TATC)n. The D6S477 locus consists of blocks of (TCTA) repeats with a basic sequence structure (TCTA)n (TA)1 (TCTA)0-2 (TA)0-1 (TCTA)n. Population data showed a heterozygosity of 0.89 for D22S683 and 0.75 for D6S477. These STRs are promising markers for forensic genetics as they are robust and can be easily included in multiplexes.

Alleles↗
PubMed2005

Phylogenetic relationship of the populations within and around Japan using 105 short tandem repeat polymorphic loci.

We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at K> or =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.

Asia, Southeastern↗
PubMed2001

A model for the involvement of Okazaki fragments maturation in the expansion of short tandem repeats.

We propose a model for the expansion of short tandem repeats (ESTR), a phenomenon which has been found to occur in human DNA and is associated with a dozen of neuromuscular diseases. The model is based mainly on theoretical considerations and recovers experimental data from the literature; it also finds support in preliminary results obtained by us in multiprimed polymerase chain reactions designed to assess the effects of a downstream primer on the fidelity of the elongation of an upstream one. The model links the occurrence of the ESTR to a defective maturation of the Okazaki fragments (OF), and in particular to an improper processing of their 3' termini. This may occur when the last OF approaches the 5' terminus of the previous one in a susceptible region of the template. It is postulated here that when a growing OF has progressed past the priming region and its main portion has been synthesized, upon approaching its conclusion, the final elongation may take place in a region of the template where certain triplets are repeated: in that case a series of aberrations on the elongation mechanism may occur. These aberrations could involve (a) the displacement of the 5' terminus of the penultimate, properly matured OF, enacted by the incoming 3' terminus of the last OF, (b) the switch of the latter to the displaced strand of the former as template, (c) the fold-back on itself of the growing 3' terminus of the last OF, (d) its assumption of an unusual structure because of the repetition, and (e) some impairment of its removal by structure-specific exo-endonuclease(s). Derangements of this last part of the process may trigger the ESTR.

Base Sequence↗
PubMed1998

Short tandem repeat polymorphism evolution in humans.

Forty-five dinucleotide short tandem repeat polymorphisms were typed in ten large samples of a globally distributed set of populations. Although these markers had been selected for high heterozygosity in European populations, we found them to be sufficiently informative for linkage analysis in non-Europeans. Heterozygosity, mean number of alleles, and mean number of private alleles followed a common trend: they were highest in the African samples, were somewhat lower in Europeans and East Asians, and were lowest in Amerindians. Genetic distances also reflected this pattern, and distances modelled after the stepwise mutation model yielded trees that were less in agreement with other genetic and archaeological evidence than distances based on differentiation by drift (FST). Genetic variation in non-Africans seems to be a subset of that in Africans, supporting the replacement hypothesis for the origin of modern humans.

Alleles↗
PubMed2005

A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci.

The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as pi(extraction). 'What-if' scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.

Computer Graphics↗
PubMed2002

Population study of six short tandem repeat loci in Antalya, Turkey.

Population studies of six short tandem repeat loci were carried out in a sample of unrelated Turkish individuals living in Antalya province, southwest Turkey. After electrophoresis in polyacrylamide gels, 8 alleles could be identified for THO1, 6 for TPOX and CSF1PO, 9 for VWA, 7 for FES, and 14 for F13A01. There was a significant deviation from the Hardy-Weinberg equilibrium between observed and expected values for FES and TPOX loci.

Alleles↗
PubMed2000

Loss of heterozygosity detected in a short tandem repeat (STR) locus commonly used for human DNA identification.

Short tandem repeat (STR) markers are commonly used in basic genetic research and in human identification testing. Clinically, STRs can be used to study genetic alterations in tumors. A genetic deletion common to many types of cancer is referred to as the loss of heterozygosity (LOH). Numerous examples of LOH in cancer have been described and some have been mapped to areas located in close proximity to markers employed in human identity testing. Despite this fact, LOH has rarely been observed for STR loci commonly employed in forensic testing. Recently, for medico-legal purposes, we were asked to determine whether a tissue biopsy originated from a particular individual. For a reference source we assessed two specimens, one from normal tissue and one from cancerous tissue. When both reference specimens were used to generate DNA profiles, we observed LOH at one STR locus, D13S317. As demonstrated in other cancers only the cancerous biopsy demonstrated LOH. The forensic community should be cognizant of these unusual circumstances because, as identification of human DNA continues to be used more extensively, certain instances will arise in which reference material will not be readily available. In these situations, archived specimens may be employed as a reference source. Clinical specimens such as tissue biopsies should be used with caution if they have not been confirmed to contain normal tissue.

DNA Fingerprinting↗