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PubMed2001

Short tandem repeat-based identification of individuals and parents.

Estimation of short tandem repeat (STR) multilocus genotype frequencies for the identification of individuals and estimation of allele frequencies for parentage assignment both depend on (a) testing a lot of loci, (b) high levels of polymorphism at each locus tested, and (c) independence among alleles. Independence is critical, because the estimation of multilocus genotype and gamete frequencies is based on multiplying individual allele frequencies to produce a composite frequency estimate. Independence among alleles at a locus is known as Hardy-Weinberg equilibrium, whereas allelic independence between loci is known as linkage equilibrium. The frequency at which individual identification may be declared is a matter of opinion, as there is no scientific way to specify certainty based on frequency estimates. Similarly absolute assignment of parentage is impossible in theory; in practice it is more difficult than individual identification, because only half as much information is available (gamete vs genotype frequency) and because mutation may confound parentage analysis.

DNA Fingerprinting↗
PubMed1998

Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences.

The presence of repeated DNA (short tandemly repeated repetitive [STRR] and long tandemly repeated repetitive [LTRR]) sequences in the genome of cyanobacteria was used to generate a fingerprint method for symbiotic and free-living isolates. Primers corresponding to the STRR and LTRR sequences were used in the PCR, resulting in a method which generate specific fingerprints for individual isolates. The method was useful both with purified DNA and with intact cyanobacterial filaments or cells as templates for the PCR. Twenty-three Nostoc isolates from a total of 35 were symbiotic isolates from the angiosperm Gunnera species, including isolates from the same Gunnera species as well as from different species. The results show a genetic similarity among isolates from different Gunnera species as well as a genetic heterogeneity among isolates from the same Gunnera species. Isolates which have been postulated to be closely related or identical revealed similar results by the PCR method, indicating that the technique is useful for clustering of even closely related strains. The method was applied to nonheterocystus cyanobacteria from which a fingerprint pattern was obtained.

Journal Article↗
PubMed1998

Genetic differentiation of complete hydatidiform moles coexisting with normal fetuses by short tandem repeat-derived deoxyribonucleic acid polymorphism analysis.

OBJECTIVE: We applied deoxyribonucleic acid polymorphism analysis on the basis of differences in the number of short tandem repeat sequences to genetically differentiate dizygotic twins with complete hydatidiform moles and normal fetuses from partial moles presenting a similar appearance. STUDY DESIGN: Six pregnant women exhibiting apparent moles and coexisting fetuses were the subjects of this study. Eight polymorphic loci including short tandem repeat sequences were amplified by polymerase chain reaction from deoxyribonucleic acid of peripheral leukocytes of parents, umbilical cord, grossly normal placenta-villi, and molar tissue. The segregation of alleles among samples were determined by comparing band patterns on polyacrylamide gels. RESULTS: In all 6 cases amplifications of polymorphic loci provided sufficient information to determine the parental origin. At informative loci the alleles of cord and placenta-villi were transmitted from both patients and husbands whereas molar tissue had only paternal alleles. These allele segregations indicated 2 different genetic origins, namely, normal parental for a fetus and androgenetic for molar tissue, and thus the diagnosis of dizygotic twins with a complete hydatidiform mole and a normal fetus was made. Additionally, the molar component was defined as a heterozygous mole in 2 cases. CONCLUSION: Short tandem repeat-derived deoxyribonucleic acid polymorphism analysis was demonstrated to be a useful and precise procedure for the differential diagnosis of a complete hydatidiform coexisting with a normal fetus and the determination of its zygosity as well.

Adult↗
PubMed2000

A short tandem repeat-based phylogeny for the human Y chromosome.

Human Y-chromosomal short tandem repeat (STR) data provide a potential model system for the understanding of autosomal STR mutations in humans and other species. Yet, the reconstruction of STR evolution is rarely attempted, because of the absence of an appropriate methodology. We here develop and validate a phylogenetic-network approach. We have typed 256 Y chromosomes of indigenous descent from Africa, Asia, Europe, Australia, and highland Papua New Guinea, for the STR loci DYS19, DXYS156Y, DYS389, DYS390, DYS392, and DYS393, as well as for five ancient biallelic mutation events: two poly (A) length variants associated with the YAP insertion, two independent SRY-1532 mutations, and the 92R7 mutation. We have used our previously published pedigree data from 11,000 paternity-tested autosomal STR-allele transfers to produce a two-class weighting system for the Y-STR loci that is based on locus lengths and motif lengths. Reduced-median-network analysis yields a phylogeny that is independently supported by the five biallelic mutations, with an error of 6%. We find the earliest branch in our African San (Bushmen) sample. Assuming an age of 20,000 years for the Native American DYS199 T mutation, we estimate a mutation rate of 2.6x10-4 mutations/20 years for slowly mutating Y STRs, approximately 10-fold slower than the published average pedigree rate.

Africa↗
PubMed1993

Genetic variation in the Italian population at five tandem repeat loci amplified in vitro: use in paternity testing.

A multilocus genotype survey of 190 to 352 chromosomes was performed in Italians. Genomic DNA of five tandem repeat loci was amplified in vitro with the polymerase chain reaction. Variable number of tandem repeat (VNTR) or short tandem repeat loci investigated were: D1S80; AP0B, located in the 3' flanking region of the apolipoprotein B gene; D17S5; F8VWF, located in intron 40 of the von Willebrand factor gene; and D6S89. The repeat motif was from 2 to 70 bp. The polymerase chain reaction product size was from 100 to 1070 bp. Relative allele frequencies exhibited bimodal or complex distributions. The number of alleles detected in the sample varied from 10 for F8VWF to 20 for D1S80. The observed heterozygote frequencies of the loci ranged from 0.75 for D17S5 and F8VWF to 0.83 for D1S80, and were in accord with expected frequencies. No mutations were detected in a total of 566 meioses for the five loci studied. The most frequent genotype for all five loci combined has a frequency of 4.1 x 10(-6). In 90 parental determination cases, D1S80, AP0B, D17S5 and F8VWF gave conclusive information in 39/45 exclusions and in 21/45 attributions.

Adult↗
PubMed1993

Improved separation of PCR amplified VNTR alleles by a vertical polyacrylamide gel electrophoresis.

The effect of a stacking gel, the pH and crosslinking agent concentration on the resolution and sharpness of PCR amplified VNTR alleles in a vertical discontinuous polyacrylamide gel electrophoresis system was investigated. The experiments show that the use of a low crosslinking agent concentration, a stacking gel and a wide pH difference between the gel buffer and the electrophoresis buffer at the beginning of the electrophoresis resulted in reduced band width and increasing resolution in silver-stained polyacrylamide gels. The importance of sharp DNA fragments is especially emphasized when analyzing multi-allelic DNA loci, that exhibit alleles differing from only few bp to few dozen bp in length, such as variable number of tandem repeat (VNTR) or short tandem repeat (STR) loci.

Alleles↗
PubMed2002

Acute myeloid leukaemia of donor cell origin developing 5 years after allogeneic bone marrow transplantation for chronic myeloid leukaemia.

We report the case of a male patient with Ph-positive CML who developed AML 5 years after allogeneic BMT. Clinically, the AML seemed to develop on the basis of a myelodysplasia. The myeloid origin of blasts has been proven by immunophenotyping. The variable number of tandem repeats (VNTRs) and short tandem repeat (STR) showed donor-type haemopoiesis. The interphase FISH showed the XX genotype directly in the morphologically identifiable blasts and in the CD34-positive sorted bone marrow cells. This proved the new leukaemia to be of donor origin. The necessity of using multiple techniques and the advantage of combined immunophenotyping and FISH methods in this case is emphasized.

Acute Disease↗
PubMed1995

DNA profile match probabilities in a subdivided population: when can subdivision be ignored?

Li and Chakravarti [Li, C.C. & Chakravarti, A. (1994) Hum. Hered. 44, 100-109] compared the probability (MO) of a random match between the two DNA profiles of a pair of individuals drawn from a random-mating population to the probability (MF) of the match between a pair of random individuals drawn from a subdivided population. The level of heterogeneity in this subdivided population is measured by the parameter F, where there is no subdivision when F = 0 and increasing values of F indicate increasing subdivisions. Li and Chakravarti concluded that it is conservative to use the match probability MO, which is derived under the assumption that the two individuals are drawn from a homogeneous random-mating population without subdivision. However, MO may not be always greater than MF, even for biologically reasonable values of F. We explore here those mathematical conditions under which MO is less than MF, and we find that MO is not conservative mainly when there is an allele with a much higher frequency than all the other alleles. When empirical data for both variable number of tandem repeat (VNTR) and short tandem repeat (STR) systems are evaluated, we find that in the majority of cases MO represents a conservative probability of a match, and so the subdivision of human populations may usually be ignored for a random match, although not, of course, for relatives. Loci for which MO is not conservative should be avoided for forensic inference.

Alleles↗
PubMedDate not supplied

Geographic contiguity and genetic affinity among five ethnic populations of Manipur, India: further molecular studies based on VNTR and STR loci.

BACKGROUND: Apart from traditional markers studied among a few numerically small, geographically defined surveys among Mongoloid populations in northeastern parts of India, very little is known about their genomic diversity at the molecular level. PRIMARY OBJECTIVE: This study seeks to investigate how best the variable number tandem repeat (VNTR) and short tandem repeat (STR) loci together can detect the patterns of the genetic affinity among five geographically contiguous, linguistically and socio-culturally diverse Mongoloid-affiliated populations of Manipur in northeastern regions of India. SUBJECT AND METHODS: Blood samples were collected from unrelated and randomly selected volunteers of five ethnic populations (Meitei, Kuki, Naga, Hmar and Manipuri Muslim) from different parts of the state. Allelic variation in four minisatellite loci (D1S7, D4S139, D5S110 and D17S79) and three STR loci (vWA, FESFPS and F13AO1) was studied. RESULTS: Average heterozygosity values among the five groups for the minisatellite range from 68% to 94%, while the hypervariable three STR loci were between 60% and 88%. In the populations, all the studied loci were highly polymorphic, with almost no departure from Hardy-Weinberg equilibrium. The gene differentiation for the VNTR loci was lower and moderate (G(st) = 0.030) in comparison with microsatellites (G(st) = 0.043). The neighbour-joining method of clustering based on both type of molecular markers reveals a close cluster for the tribal groups of Kuki, Naga and Hmar, while Manipur Muslim stand distinct in both the trees. The clustering pattern obtained from the combined DNA marker loci matches more closely the pattern from STR loci than that obtained from VNTR loci. CONCLUSIONS: The results reinforce that using both VNTR and STR loci in detecting regional genetic affinity among the populations is more effective than using VNTR or STR independently, and also confirm the results obtained from the serological and electrophoretic data. However, the clustering pattern obtained from combined DNA markers is more in conformity with the pattern obtained by STR loci rather than with VNTR loci. Despite linguistic, geographical and cultural barriers, the populations show genetic affinity among the four populations except in the case of the migrant Manipur Muslim group.

Asian People↗
PubMed2001

Association between minihaplotypes and mutations at the PAH locus in Polish hyperphenylalaninemic patients.

Hereditary hyperphenylalaninemia (HPA) is a disorder of amino acid metabolism and results from an insufficiency of hepatic phenylalanine hydroxylase (PAH). HPA phenotypes form a spectrum ranging from classical phenylketonuria (PKU) to mild hyperphenylalaninemia (MHP). The phenotypic diversity reflects heterogeneity at the molecular level, and more than 320 different mutations in the PAH gene are known to date. The association of 3 mutations (R408W, IVS10 and A403V) common in different European populations with a variable number tandem repeat (VNTR) and short tandem repeat sites (minihaplotype) in the PAH gene was examined in a group of Polish PKU and MHP patients. Additionally, minihaplotypes were established for another 16 mutations. The presented data support the hypothesis that the R408W/VNTR3/STR238 allele originated among pre-Indo-Europeans on the territory in present-day Lithuania and Belarus. Mutation IVS10nt-11g-->a (IVS10) is strongly associated with VNTR7/STR250 minihaplotype and is possibly of Mediterranean origin.

Haplotypes↗
PubMedDate not supplied

Phenylketonuria mutations and linked haplotypes in the Lithuanian population: origin of the most common R408W mutation.

A genealogical study was performed in Lithuanian phenylketonuria (PKU) families with the aim of tracing the origins of the R408W/haplotype 2/VNTR3 allele. The relative frequency of six phenylalanine hydroxylase (PAH) mutations (R408W, R158Q, R261Q, G272X, IVS10nt-11g --> a, and IVS12nt1g --> a) common in Eastern European populations and their association with variable number of tandem repeat (VNTR) and short tandem repeat (STR) sites in the PAH gene were examined in 130 PKU Lithuanian chromosomes, including 95 of Baltic, 28 of Slavonic and 7 of unknown origin. R408W was found to be the most frequent (70%) mutation in both Balts or Slavonians with a uniform frequency distribution. No statistically significant differences in the frequency distribution of the other mutations analysed were found. In Balts and Slavonians, the R408W mutation is strongly associated with the three-copy VNTR and the 240-bp STR allele. The frequency of this association is 68% in both ethnic groups. The genealogical data provided in this paper indicate that the most common R408W/VNTR3/STR240 allele arose in ancient times possibly among pre-Indo-Europeans and suggest that the high frequency of the R408W mutation and associated minihaplotype in Balts of Lithuania is due to a founder effect.

Evolution, Molecular↗
PubMed2000

Molecular determination of RhD phenotype by DNA typing: clinical applications.

Rhesus D (RhD) typing is performed by agglutination methods; however, in clinical situations where these techniques cannot be performed, RhD DNA typing is an alternative approach. The Rh antigens are encoded by the RHD and RHCE genes. In RhD-negative individuals the RHD gene is absent or grossly deleted, but variations in the arrangement of the RH locus in different populations are emerging. The aim of this study was to analyse the gross organization of the RH genes in our population using a previously described multiplex polymerase chain reaction (PCR) method with some modifications. We studied 253 DNA samples from Argentinian blood donors, 15 samples with a reduced expression of the D antigen and 1 Dc- phenotype. We evaluated the clinical utility of this method to ascertain the RhD antigen in 10 patients with warm-type autoimmune haemolytic anaemia (AIHA) and 14 samples of amniotic fluids. All Rh phenotypes were properly characterized and no discrepancies with serological typing were found. Analyses performed in the Dc- phenotype suggest the presence of a hybrid RHCE-RHD gene. DNA typing confirmed the RhD-negative type of one AIHA sample in which serological tests were inconclusive. Foetal DNA typing correctly indicated the RhD in every foetus. VNTR (variable number of tandem repeats) and STR (short tandem repeats) analysis detected maternal contamination in two amniocentesis samples and confirmed the foetal origin of 12. This multiplex PCR strategy is suitable for RhD determination in clinical situations in which serological typing cannot be accomplished with its usual ease.

Alleles↗
PubMed2000

Laboratory and field evaluation of polymerase chain reaction-based forensic DNA profiling for use in identification of human blood meal sources of Aedes aegypti (Diptera: Culicidae).

We modified polymerase chain reaction (PCR)-based forensic DNA profiling for field studies on the feeding behavior of Aedes aegypti, the principal mosquito vector of dengue virus. Human DNA was extracted from oral swabs of human subjects and from blood-engorged mosquitoes, DNA was quantified by slot blot, and alleles at variable number tandem repeats and three short tandem repeats loci were amplified by PCR. Alleles were separated electrophoretically and then visualized by silver staining. A custom software program was written to match DNA fingerprints of potential human hosts to allelic profiles detected in engorged mosquitoes, and to calculate error rates for identification of human hosts of single and multiple-host blood meals. At 29 degrees C in the laboratory, human DNA recovered from mosquito blood meals declined an average of 67% 8 h after feeding and 90% after 24 h. We obtained complete allelic profiles from seven of 10 mosquitoes collected after 24 h. In a field trial, complete DNA profiles were obtained successfully for 43 people living in a rural village in south central Thailand and for 20 of 100 Ae. aegypti that contained blood and were collected in those peoples' homes. Blood imbibed from more than one person was detected in 45% (9 of 20) of the meals. Sixty-five percent of the meals contained blood from nonresidents of the house in which the mosquito was collected or from people who were not profiled; data consistent with the hypothesis that human movement is important for the spread of dengue virus within and among communities. When using alleles at four loci, all of the Thais and nine members spanning three generations of a Chinese-American family had unique allelic profiles. Error rates from classifying possible multiple-host meals as single-host meals were low (1-8%), with the highest error associated with closely related people. Results from our laboratory and field studies indicated that DNA profiling can be used to study the details and epidemiological implications of Ae. aegypti blood-feeding behavior.

Aedes↗
PubMed1995

Quantitative determination of bone marrow transplant engraftment using fluorescent polymerase chain reaction primers for human identity markers.

We have developed a quantitative, nonisotopic method using variable number tandem repeat (VNTR) and short tandem repeat (STR) markers for monitoring donor cell engraftment in marrow transplant recipients. Posttransplant DNA from the recipient is amplified with fluorescent polymerase chain reaction (PCR) primers for polymorphic markers that distinguish donor alleles from recipient alleles. The fluorescent PCR products are then separated on agarose or acrylamide gels on the Applied Biosystems 373A Sequencer (Foster City, CA). Using GeneScan 672 software (Applied Biosystems) to analyze the separated alleles, we can correlate allele peak areas to the percentage of donor or recipient DNA. We quantitate engraftment in a mixed chimeric sample by mixing pretransplant recipient and donor DNAs in a range of percentages and amplifying the mixtures to produce a standard curve. By amplifying and analyzing the posttransplant sample DNA(s), we can determine the extent of engraftment by interpolating the percent peak area of the informative allele(s) from this standard curve. This approach provides a precision of measurement ranging, depending on the marker, from 3.5% to 8.0% (percent coefficient of variation) and an accuracy of engraftment determination ranging from 97% to 99%, with a sensitivity of detection of 1% donor or recipient DNA. We retrospectively analyzed a panel of 32 patients and found seven to be informative for some degree of mixed chimerism, indicative of either residual normal host cells or leukemic relapse. An analysis of different cell lineages obtained posttransplant showed different degrees of engraftment in myeloid and T-cell populations. In summary, this method can provide an accurate, quantitative assessment of mixed chimerism in patients posttransplant. Such information may be useful in the future in guiding early implementation of additional treatment designed to circumvent graft failure or suppress relapse.

Base Sequence↗
PubMed1993

Evidence for human meiotic recombination interference obtained through construction of a short tandem repeat-polymorphism linkage map of chromosome 19.

An improved linkage map for human chromosome 19 containing 35 short tandem repeat polymorphisms (STRPs) and one VNTR (D19S20) was constructed. The map included 12 new (GATA)n tetranucleotide STRPs. Although total lengths of the male (114 cM) and female (128 cM) maps were similar, at both ends of the chromosome male recombination exceeded female recombination, while in the interior portion of the map female recombination was in excess. Cosmid clones containing the STRP sequences were identified and were positioned along the chromosome by fluorescent in situ hybridization. Four rounds of careful checking and removal of genotyping errors allowed biologically relevant conclusions to be made concerning the numbers and distributions of recombination events on chromosome 19. The average numbers of recombinations per chromosome matched closely the lengths of the genetic maps computed by using the program CRIMAP. Significant numbers of chromosomes with zero, one, two, or three recombinations were detected as products of both female and male meioses. On the basis of the total number of observed pairs of recombination events in which only a single informative marker was situated between the two recombinations, a maximal estimate for the rate of meiotic STRP "gene" conversion without recombination was calculated as 3 x 10(-4)/meiosis. For distances up to 30 cM between recombinations, many fewer chromosomes which had undergone exactly two recombinations were observed than were expected on the basis of the assumption of independent recombination locations. This strong new evidence for human meiotic interference will help to improve the accuracy of interpretation of clinical DNA test results involving polymorphisms flanking a genetic abnormality.

Base Sequence↗
PubMed2000

Short tandem-repeat polymorphism/alu haplotype variation at the PLAT locus: implications for modern human origins.

Two dinucleotide short tandem-repeat polymorphisms (STRPs) and a polymorphic Alu element spanning a 22-kb region of the PLAT locus on chromosome 8p12-q11.2 were typed in 1,287-1,420 individuals originating from 30 geographically diverse human populations, as well as in 29 great apes. These data were analyzed as haplotypes consisting of each of the dinucleotide repeats and the flanking Alu insertion/deletion polymorphism. The global pattern of STRP/Alu haplotype variation and linkage disequilibrium (LD) is informative for the reconstruction of human evolutionary history. Sub-Saharan African populations have high levels of haplotype diversity within and between populations, relative to non-Africans, and have highly divergent patterns of LD. Non-African populations have both a subset of the haplotype diversity present in Africa and a distinct pattern of LD. The pattern of haplotype variation and LD observed at the PLAT locus suggests a recent common ancestry of non-African populations, from a small population originating in eastern Africa. These data indicate that, throughout much of modern human history, sub-Saharan Africa has maintained both a large effective population size and a high level of population substructure. Additionally, Papua New Guinean and Micronesian populations have rare haplotypes observed otherwise only in African populations, suggesting ancient gene flow from Africa into Papua New Guinea, as well as gene flow between Melanesian and Micronesian populations.

Africa South of the Sahara↗
PubMed2005

Measurement of chimerism in cynomolgus monkeys using human-specific short tandem repeat-based assay.

Preclinical testing of a mixed chimerism mediated organ transplant tolerance strategy, in a cynomolgus macaque model, would be facilitated by the establishment of a reliable technique for quantitative assessment of chimerism. Among various techniques used for measurement of chimerism in humans, microsatellite DNA profiling has been considered the most versatile one that can discriminate between two individuals. We adopted a commercially available short tandem repeat profiling methodology to cynomolgus monkeys using two human specific alleles, TPOX and CSF1PO. Polymerase chain reaction (PCR) was used to amplify these alleles, and the analysis of the PCR products was performed by capillary electrophoresis. Of 54 cynomolgus macaques investigated, only one pair with the same ABO blood type demonstrated identity at both alleles. This implies that this technique should interfere minimally with the assignment of donor-recipient pairs based upon molecular tissue typing or mixed lymphocyte cultures.

Animals↗
PubMed1993

VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

Alleles↗