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PubMed1999

Genetic diversity of two African and sixteen South American populations determined on the basis of six hypervariable loci.

A total of 582 individuals (1,164 chromosomes) from two African, eight African-derived South American, five South American Amerindian, and three Brazilian urban populations were studied at four variable number of tandem repeat (VNTR) and two short tandem repeat (STR) hypervariable loci. These two sets of loci did not show distinct allele profiles, which might be expected if different processes promoted their molecular differentiation. The two African groups showed little difference between them, and their intrapopulational variation was similar to those obtained in the African-derived South American communities. The latter showed different degrees of interpopulation variability, despite the fact that they presented almost identical average degrees of non-African admixture. The F(ST) single locus estimates differed in the five sets of populations, probably due to genetic drift, indicating the need to consider population structure in the evaluation of their total variability. A high interpopulational diversity was found among Amerindian populations in relation to Brazilian African-derived isolated communities. This is probably a consequence of the differences in the patterns of gene flow and genetic drift that each of these semi-isolated groups experienced.

Alleles↗
PubMed1998

Highly sensitive DNA typing for detecting tumors transmitted by transplantation.

DNA typing of a variable number of tandem repeats (VNTRs) and of short tandem repeats (STRs) is a modern forensic method for the identification of biological material. In many cases, amplification by the polymerase chain reaction (PCR), especially of STRs, allows DNA typing of minute amounts of or degraded DNA. Here we describe the successful use of forensic DNA typing to clarify the origin of a malignant tumor. We report two cases of metastatic malignant melanoma of unknown origin that developed a few months after transplantation in two recipients of kidneys from the same donor. Fresh metastatic tissue and blood from the first recipient, reference DNA of the donor, and only paraffin-embedded tissue from the second recipient were available for analysis. To investigate whether the melanoma originated in the donor, DNA analysis of nine polymorphic loci was performed. The results of the analysis showed that, in both cases, the tumors were genetically different from the recipient DNA but matched the donor DNA. One incident of allele loss was attributed to a mutation event. We conclude that the metastatic melanoma in both recipients originated in the donor and was transmitted by renal transplantation.

Adult↗
PubMed1999

Phenylketonuria mutations in Germany.

We report the spectrum of mutations and associated modified haplotypes in patients with phenylketonuria living in Germany. A total of 546 independent alleles was investigated, including 411 of German and 65 of Turkish descent. Mutations were identified for 535 PKU alleles (98%) and there were 91 different mutations. The most common mutation was R408W on 22% of alleles. Two mutations, IVS12+1G-->A and IVS10-11G-->A accounted for just under 10% of alleles, whereas the remaining mutations were found at relative frequencies of 6% or less; 43 mutations were observed once only. IVS10-11G-->A was the most common mutation (38% of alleles) in the subgroup of patients of Turkish descent. Modified haplotypes were determined from the analysis of four silent mutations, three diallelic restriction fragment length polymorphisms, a variable number of tandem repeats minisatellite and a short tandem repeat microsatellite in the phenylalanine hydroxylase gene, showing that a considerable proportion of mutations must have recurred in independent founders; other mutations may have changed chromosomal haplotype backgrounds by gene conversion. The spectrum of PKU mutations in Germany reflects the history of a heterogenous Central European population living at the crossroads of migration throughout the centuries.

Exons↗
PubMed1999

Efficient DNA fingerprinting method for the identification of cross-culture contamination of cell lines.

In order to identify cross-culture contamination of cell lines, we applied DNA fingerprinting using variable number of tandem repeat (VNTR) loci and short tandem repeat (STR) loci amplified by polymerase chain reaction (PCR) instead of a radioisotope labeled multilocus probe. Eleven cell lines were used for the Apo B and D1S80 loci detection, and twelve cell lines were examined in the Y-chromosome analysis. The data obtained from the sister cell lines NALM-6 and B85, two MOLM-1 cultures from two cryopreserved tubes, and four subclones of BALM-9 and its sister cell line BALM-10, displayed clear and distinct bands of each PCR product for both Apo B and D1S80. Detection of a Y-chromosome DNA sequence is another very informative marker for the identification of cell lines, if the Y-chromosome is present. We examined eight cell lines for the expression of four STR loci; the data thus generated were compared with the results previously reported from other laboratories. The resulting electrophoretic banding patterns showed that our "home-made" STR detection system is a useful and efficient tool for the authentication of cell lines. PCR detection of VNTR and STR loci represents a simple, rapid and powerful DNA fingerprinting technique to authenticate human cell lines and to detect cross-culture contamination. This PCR technique may be used in lieu of the more time-consuming, labor-intensive and radioactive Southern blot multilocus method.

Base Sequence↗
PubMed2004

Characteristics and a comparison of three classes of microsatellite-based markers and their application in plants.

Microsatellites (SSR--simple sequence repeats, STR--short tandem repeats, SSLP--simple sequence length polymorphism, VNTR--variable number of tandem repeats) are the class of repetitive DNA sequences present in all living organisms. Particular characteristics of microsatellites, such as their presence in the genomes of all living organisms, high level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping and positional cloning of genes. The three most popular types of markers containing microsatellite sequences that are presently used are: (1) SSR (simple sequence repeats), generated by amplifying in a PCR reaction with the use of primers complementary to flanking regions; (2) ISSR (inter-simple sequence repeats), based on the amplification of regions between inversely oriented closely spaced microsatellites; and (3) SAMPL (selective amplification of microsatellite polymorphic loci), which utilises AFLP (amplified fragment-length polymorphism) methodology, with one exception--for the second amplification, one of the starters is complementary to the microsatellite sequence. The usefulness of the three above-mentioned markers for numerous purposes has been well documented for plants.

Databases, Nucleic Acid↗
PubMed2005

[Analysis on genetic polymorphism of 5 STR loci selected from X chromosome].

OBJECTIVE: To select short tandem repeats(STR) from X chromosome. METHODS: STR is a universal genetic marker that has changeable polymorphism and stable heredity in human genome. It is a specific DNA segment composed of 2-6 base pairs as its core sequence. It is an ideal DNA marker used in linkage analysis and gene mapping. In this study, 8 short tandem repeats were selected from two genomic clones on X chromosome by using BCM Search Launcher. Primers amplifying the STR loci were designed by using Primer 3.0 according to the unique sequence flanking the STRs. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. RESULTS: Five of these STRs were polymorphic. Chi-square test indicated that the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P>0.05). CONCLUSION: Five polymorphic short tandem repeats have been identified on chromosome X and will be useful for linkage analysis and gene mapping.

Chromosomes, Human, X↗
PubMed2002

[Linkage analysis of X-linked nuclear protein gene in Smith-Fineman-Myers syndrome].

OBJECTIVE: To determine the linkage between Smith-Fineman-Myers syndrome (SFMS) and X-linked nuclear protein(XNP) locus. METHODS: Polymerase chain reaction and denaturing polyacrylamide gel electrophoresis were used to genotype two polymorphic short tandem repeats within XNP gene. RESULTS: One of the two short tandem repeats was informative in SFMS family from Shandong, China. Recombination between SFMS locus and XNP gene was observed in the SFMS family. CONCLUSION: XNP gene is not associated with the disease in the SFMS family from Shandong, China. SFMS exhibits locus heterogeneity at molecular level.

Abnormalities, Multiple↗
PubMed1995

Investigation of species specificity using nine PCR-based human STR systems.

Several eukaryotic genomes contain polymorphic markers consisting of trimeric and tetrameric short tandem repeats (STR). Recent reports have demonstrated the variability of short tandem repeat (STR) polymorphisms at a variety of loci among several human population groups. Currently, there are nine commercially available STR PCR systems from Promega Corporation that may be utilized for human identification. We report here the analysis of 23 different species DNA's using these nine STR primer systems to assess their specificity for human euchromatin. The STR systems tested include, CSF1PO, TPOX, THO1, HPRTB, FESFPS, vWF and F13A01 as single systems and as triplex systems (CSF1PO/TPOX/THO1 and HPRTB/FESFPS/vWF). There were no STR PCR products observed for seventeen of the twenty-three species regardless of the STR system. Amplified STR fragments were detected in rhesus DNA for CSF1PO, TPOX and HPRTB systems. STR PCR products were detected for human, gorilla, chimpanzee, and orangutan DNAs using eight of the nine systems. FESFPS primers did not amplify DNA fragments from any of the species tested. Most of the STR PCR products detected from primate DNAs electrophoretically migrated outside of the human allelic ladder fragments and as a result, allele designations were not possible.

Animals↗
PubMed2004

[Genetic polymorphism of cytomegalovirus strains responsible of congenital infections].

OBJECTIVES: Congenital Cytomegalovirus (CMV) infection is the main cause of neurological handicap in young children. The objective for studying genetic polymorphism of strains responsible for congenital infection is to identify CMV strains or groups of strains which would be more frequent in this context and/or which would be responsible for more severe congenital infection. METHODS: In this paper, we report and analyze the literature concerning the genetic polymorphism of CMV strains responsible of congenital infection, in the genes coding for the envelop protein B and the non structural UL144 protein and in the CMV short tandem repeats. RESULTS AND CONCLUSION: All UL144 and gB genotypes can be vertically transmitted from mothers to fetuses, none of these studies has shown any link between the genotypes and the severity of congenital disease. Moreover, no link between short tandem repeats polymorphism and severity of congenital disease has been demonstrated. However, short tandem repeats analysis may be a powerful tool to study the epidemiology of CMV congenital infections.

Cytomegalovirus↗
PubMed2004

Testing for parentage and kinship.

PURPOSE OF REVIEW: Parentage analyses are of interest to workers in health care, law enforcement, immigration and other fields. This review describes recent applications, technical advances, and quality improvements. RECENT FINDINGS: Mutations at short tandem repeat sequence loci confound interpretations of genetic data used to assess all blood relationships. Rates of the usual mutation type (change in repeat number) are probably related to specific alleles at each locus as well as to allele length, locus, and gender. Short tandem repeat sequences have relatively limited information content per locus. Intermediate tandem repeat sequence loci may be better. In immigration proceedings, probabilities can be calculated for excluding parentage in blood relatives who might impersonate the biologic parent. Unrelated immigrants from a subpopulation may appear to be related, but it is now possible to statistically determine the effect of population substructure on kinship determinations. In forensic analyses, sex chromosomal (X and Y) short tandem repeat sequences and mitochondrial DNA sequence variations have helped identify the parental lineages of human remains. Recent laboratory quality improvements include a way to estimate the frequency of common mother-child specimen mislabeling in routine paternity cases. In prenatal testing there are now methods for avoiding erroneous assignment of contaminant maternal alleles to the fetus. False paternity exclusions can be avoided by adhering to a standard of the American Association of Blood Banks requiring duplicate DNA isolation and retesting of excluded men. SUMMARY: Laboratory technology and quality have advanced, but genetic tests with greater information content are needed. Better communication is highly desirable between persons requesting tests and parentage laboratories.

DNA Fingerprinting↗
PubMed2004

[Genetic polymorphism of 3 STR loci on chromosome X and its forensic application in Chinese population].

To investigate the genetic polymorphisms of three short tandem repeats loci of chromosome X in Chinese Han population in Chengdu area and its use in forensic science. Three X-chromosome linked short tandem repeat loci were analyzed by PCR followed by polyacrylamide gel electrophoresis. Hardy-Weinberg equilibrium was tested and forensic interested value was calculated . The power of exclution of DXS6804, DXS9896 and GATA144D04 is 0.5990, 0.6220, 0.4280, respectively. The result showed that all the three STR loci were polymorphic among 100 unrelated females and 120 unrelated males from Chinese Han population. Chi(2) tests demonstrated that genotype frequencies in females did not depart from Hardy-Weinberg equilibrium. Three X-chromosome linked short tandem repeat loci have high polymorphism, they can be applied to forensic medicine and population genetics.

Alleles↗
PubMed1996

STR typing in a deficiency case of disputed paternity.

In a case of disputed paternity where the alleged father was dead and the children and their mothers were available for testing, we analyzed 23 conventional hemogenetic markers and six short tandem repeat loci. We deduced the possible types of the alleged father and calculated the probability of paternity. Conventional phenotypings did not provide conclusive proof of paternity. In contrast, typing of the short tandem repeat loci gave a combined probability of paternity of 0.9986, establishing paternity. The present study demonstrates the power of short tandem repeat typing as a tool for solving such a deficiency case.

Alleles↗
PubMed2001

Extensive allelic variation among Francisella tularensis strains in a short-sequence tandem repeat region.

Members of the genus Francisella and the species F. tularensis appear to be genetically very similar despite pronounced differences in virulence and geographic localization, and currently used typing methods do not allow discrimination of individual strains. Here we show that a number of short-sequence tandem repeat (SSTR) loci are present in F. tularensis genomes and that two of these loci, SSTR9 and SSTR16, are together highly discriminatory. Labeled PCR amplification products from the loci were identified by an automated DNA sequencer for size determination, and each allelic variant was sequenced. Simpson's index of diversity was 0.97 based on an analysis of 39 nonrelated F. tularensis isolates. The locus showing the highest discrimination, SSTR9, gave an index of diversity of 0.95. Thirty-two strains isolated from humans during five outbreaks of tularemia showed much less variation. For example, 11 of 12 strains isolated in the Ljusdal area, Sweden in 1995 and 1998 had identical allelic variants. Phenotypic variants of strains and extensively cultured replicates within strains did not differ, and, for example, the same allelic combination was present in 55 isolates of the live-vaccine strain of F. tularensis and another one was present in all 13 isolates of a strain passaged in animals. The analysis of short-sequence repeats of F. tularensis strains appears to be a powerful tool for discrimination of individual strains and may be useful for a detailed analysis of the epidemiology of this potent pathogen.

Alleles↗
PubMed1995

A collection of ordered tetranucleotide-repeat markers from the human genome. The Utah Marker Development Group.

A collection of 1,069 human PCR-based genetic markers has been developed, and their distribution over the 22 autosomes and the X chromosome has been determined. Each marker was developed around a short-tandem-repeat DNA sequence. The majority (85%) of the markers described here were selected to contain tetranucleotide repeats, because these repeats show better stability during PCR than do dinucleotide repeats. Linkage maps constructed from genotypes collected with these markers in four CEPH pedigrees (1331, 1332, 1362, and 884) covered 3,417 cM of the human genome. More than 600 of the loci revealed heterozygosities > .70. Overall, 444 loci were ordered, with odds > 100:1 against inversion of adjacent loci. The average distance between markers was 7.4 cM on the autosomes and 24.8 cM on the X chromosome. Likely locations (100:1 odds intervals) were assigned for the remaining 621 short-tandem-repeat polymorphisms, as well as for 160 other markers that are present on the framework maps published by the Cooperative Human Linkage Center. Four markers specific to the Y chromosome are also reported here. From our maps, 347 markers were chosen to define "index" maps for each of the 22 autosomes. The index markers detect loci with an average heterozygosity of .85 and cover 3,169 cM of the autosomes, with an average distance between markers of 9.2 cM. These polymorphic short tandem repeats will be highly useful as reagents for the ongoing genetic and physical mapping of the human genome and for characterization of genetic changes in cancer.

Base Sequence↗
PubMed2005

Genetic variation and willingness to participate in epidemiologic research: data from three studies.

The differences in common genetic polymorphism frequencies by willingness to participate in epidemiologic studies are unexplored, but the same threats to internal validity operate as for studies with nongenetic information. We analyzed single nucleotide polymorphism genotypes, haplotypes, and short tandem repeats among control groups from three studies with different recruitment designs that included early, late, and never questionnaire responders, one or more participation incentives, and blood or buccal DNA collection. Among 2,955 individuals, we compared 108 genotypes, 8 haplotypes, and 9 to 15 short tandem repeats by respondent type. Among our main comparisons, single nucleotide polymorphism genotype frequencies differed significantly (P < 0.05) between respondent groups in six instances, with 13 expected by chance alone. When comparing the odds of carrying a variant among the various response groups, 19 odds ratios were </=0.70 or >/=1.40, levels that might be notably different. Among the various respondent group comparisons, haplotype and short tandem repeat frequencies were not significantly different by willingness to participate. We observed little evidence to suggest that genotype differences underlie response characteristics in molecular epidemiologic studies, but a greater variety of genes should be examined, including those related to behavioral traits potentially associated with willingness to participate. To the extent possible, investigators should evaluate their own genetic data for bias in response categories.

Community Participation↗
PubMed1995

Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics.

In a substructured population the overall heterozygote deficiency can be predicted from the number of subpopulations (s), their time of divergence (t), and the nature of the mutations. At present the true mutational mechanisms at the hypervariable DNA loci are not known. However, the two existing mutation models (the infinite allele model (IAM) and the stepwise mutation model (SMM)) provide some guides to predictions from which the possible effect of population substructuring may be evaluated, assuming that the subpopulations do not exchange any genes among them during evolution. The theory predicts that the loci with larger mutation rate, and consequently showing greater heterozygosity within subpopulations, should exhibit a smaller proportional heterozygote deficiency (GST) and, hence, the effects of population substructuring should be minimal at the hypervariable DNA loci (an order of magnitude smaller than that at the blood group and protein loci). Applications of this theory to data on six Variable Number of Tandem Repeat (VNTR) loci and five short tandem repeat (STR) loci in the major cosmopolitan populations of the USA show that while the VNTR loci often exhibit a large significant heterozygote deficiency, the STR loci do not show a similar tendency. This discordant finding may be ascribed to the limitations, coalescence and nondetectability of alleles associated with the restriction fragment length polymorphism (RFLP) analysis through which the VNTR loci are scored. Such limitations do not apply to the polymerase chain reaction (PCR) method, through which the STR loci are scored. The implications of these results are discussed in the context of the forensic use of DNA typing data.

DNA↗
PubMed2005

The specific power of parentage exclusion in a child's blood relatives.

BACKGROUND: The impersonation of parent and child by two other blood relatives is an important problem in parentage analysis involving potential immigrants. STUDY DESIGN AND METHODS: A statistic (AR) is proposed, based on the specific power of exclusion of paternity, which describes the ability of a child's test results to demonstrate evidence of nonparentage under the hypothesis that an ostensible parent is actually an older sibling. A case illustrates the value of A(R): a woman and her two alleged children were typed at 3 variable number of tandem repeat (VNTR) loci after 18 short tandem repeat (STR) loci initially showed strong evidence of the woman's maternity of one child and her exclusion from parentage of the second. AR and 1 - AR were calculated from the STR types of the first child. RESULTS: The woman was excluded from maternity of both children with the additional VNTR tests. Given the 18 STR test findings of the first child, the probability was 12 percent that there would be no inconsistencies with parentage in a sibling pretending to be a parent. CONCLUSION: The value 1 - AR, siblings not excluded from parentage, explains how a seemingly large number of examined loci can fail to reveal even one genetic inconsistency if two siblings have posed as parent and child. Approximately 25 STR loci appear necessary to achieve 95 percent confidence of detecting at least one genetic inconsistency indicative of nonparentage.

Adult↗
PubMed1998

Preimplantation diagnosis of thalassemias.

PURPOSE: Preimplantation genetic diagnosis (PGD) is an important option for couples at risk of having children with beta-globin mutations to avoid selective abortions of affected fetuses following prenatal diagnosis. METHODS: We performed PGD for thalassemia in 12 clinical cycles (IVS1-110, and IVS-745 mutations) using biopsy of the first and second polar bodies (PBs) extruded from oocytes during maturation and fertilization, coupled with nested polymerase chain reaction analysis and restriction digestion. RESULTS: A total of 118 oocytes was obtained, of which 78 had results for both the first and the second PBs. This resulted in the selection and transfer of 30 unaffected embryos (2.5 embryos per cycle). To avoid a possible misdiagnosis due to allele dropout (ADO), we have also introduced simultaneous detection of two highly polymorphic linked markers, a short tandem repeat immediately at the 5' end of the globin gene and HUMTH01 which is a syntenic short tandem repeat. The application of multiplex polymerase chain reaction of the beta-globin gene and linked polymorphic markers enabled detection of ADO in five first PBs, thus avoiding the transfer of potentially affected embryos resulting from their corresponding oocytes. CONCLUSIONS: Confirmation studies of the embryos resulting from the oocytes predicted to contain an affected gene confirmed the diagnosis in 98% of the cases, thus demonstrating the accuracy and reliability of PB PGD of thalassemia mutations. The application of PB analysis in six patients resulted in two ongoing pregnancies with a thalassemia-free fetus already confirmed in both of them by prenatal diagnosis.

Alleles↗