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PubMed2001

The development of preimplantation genetic diagnosis for myotonic dystrophy using multiplex fluorescent polymerase chain reaction and its clinical application.

Preimplantation genetic diagnoses (PGD) for single gene defects require considerable time and resources for the standardization of polymerase chain reactions that are rapid, sensitive and reliable. Developing tests for the trinucleotide repeat diseases, where the expansion of unstable repeats produces the phenotypes, are particularly complex. One of these disorders is myotonic dystrophy where, at present, diagnosis at the single cell level relies on the detection of the normal alleles from both the affected and unaffected parent. The incorporation of short tandem repeat polymorphisms in the assay can give additional information to improve the accuracy of diagnosis. We have developed a multiplex fluorescent reaction for myotonic dystrophy and one of two closely mapped, highly heterozygous, short tandem repeats (D19S219 and D19S559) on chromosome 19 to reduce the possibility of misdiagnosis due to contamination, act as a control for allelic drop-out and maximize the number of embryos genotyped. This protocol was designed as a general diagnosis for myotonic dystrophy, using the most informative of the two polymorphisms for each couple. Subsequently this approach was used in a PGD treatment cycle.

Adult↗
PubMed2006

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis.

We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

Asian People↗
PubMed2000

46,XY monozygotic twins with discordant sex phenotype.

OBJECTIVE: To analyze male and female sex differentiation in monozygotic twins. DESIGN: Retrospective study. SETTING: Multiple academic centers. PATIENT(S): A pair of monozygotic twins. INTERVENTION(S): Skin and blood samples were obtained for DNA analysis and karyotyping. MAIN OUTCOME MEASURE(S): Mutation within the SRY gene was analyzed by the polymerase chain reaction-single-stranded conformation polymorphism test. Monozygosity was ascertained by short tandem repeat analysis. Karyotypes were studied in blood and skin fibroblasts. RESULT(S): SRY was present in both twins, but no mutations were detected in the SRY conserved motif. Monozygosity was confirmed by the use of short tandem repeat analysis in four loci: c-fms, thyroid peroxidase, von Willebrand factor, and tyrosine hydroxylase. The karyotype was 46,XY uniformly in both twins. CONCLUSION(S): Monozygotic twins can develop discordant male and female phenotypes despite the presence of a common karyotype and despite the presence of intact testis-determining genes. In the present case, this could be due to mutation or to mosaicism involving occult 45,X cell lines in the dysgenetic gonads.

DNA-Binding Proteins↗
PubMed2000

Extensive amplification and transposition of a novel repetitive element, xstir, together with its terminal inverted repeat in the evolution of Xenopus.

A DNA fragment containing short tandem repeat sequences (approximately 86-bp repeat) was isolated from a Xenopus laevis cDNA library. Southern blot and in situ hybridization analyses revealed that the repeat was highly dispersed in the genome and was present at approximately 1 million copies per haploid genome. We named this element Xstir (Xenopus short tandemly and invertedly repeating element) after its arrangement in the genome. The majority of the genomic Xstir sequences were digested to monomer and dimer sizes with several restriction enzymes. Their sequences were found to be highly homogeneous and organized into tandem arrays in the genome. Alignment analyses of several known sequences showed that some of the Xstir-like sequences were also organized into interspersed inverted repeats. The inverted repeats consisted of an inverted pair of two differently modified Xstirs separated by a short insert. In addition, these were framed by another novel inverted repeat (Xstir-TIR). The Xstir-TIR sequence was also found at the ends of tandem Xstir arrays. Furthermore, we found that Xstir-TIR was linked to a motif characterizing the T2 family which belonged to a vertebrate MITE (miniature inverted-repeat transposable element) family, suggesting the importance of Xstir-TIR for their amplification and transposition. The present study of 11 anuran and 2 urodele species revealed that Xstir or Xstir-like sequences were extensively amplified in the three Xenopus species. Genomic Xstir populations of X. borealis and X. laevis were mutually indistinguishable but significantly different from that of X. tropicalis.

Animals↗
PubMed1996

The 1591C mutation in triosephosphate isomerase (TPI) deficiency. Tightly linked polymorphisms and a common haplotype in all known families.

In order to investigate the basis of the repeated occurrence of the 1591C mutation (TPI 1591C, 105 Glu-Asp) in multiple unrelated families throughout the world, we studied five microsatellite and short tandem repeat markers that lie within a 1.77 megabase region which includes the TPI gene. We also studied an intragenic polymorphic marker that lies within intron 5 of the TPI gene. This polymorphism, recently described by others, is characterized by either an A or a G at position 2262 (the A in the initiation ATG is designated as +1 for both genomic and cDNA nucleotides). With very minor exceptions, all of the known families in the world with the 1591C mutation were available for study. These included five families from the U.S., three from France, one from Greece, one (of Turkish origin) from Germany, and two from Australia. Although we did not have the opportunity to directly study five families from the U.K., key data concerning the 2262 intragenic polymorphism in these subjects were made available to us. Four of the microsatellite and short tandem repeat markers were linked, but in apparent equilibrium. In contrast, a polymorphic repeat pentamer in the CD4 gene, thought to lie telomeric to TPI, was in apparent complete linkage disequilibrium with the TPI 1591C mutation. The intragenic polymorphism was also in apparent complete linkage disequilibrium with the mutation. In unrelated persons of known phase (1591C homozygotes or normal controls), the comparative allele frequencies for the CD4 pentameric repeat were 1.0 (14/14 alleles) in homozygous TPI 1591C subjects and 0.412 (28/68 alleles) in normal subjects (p < 0.0001). Again, in persons of known phase, the comparative allele frequencies for the A form of the intragenic 2262 A or G polymorphism were 1.0 (14/14 alleles) in 1591C homozygotes and 0.130 (7/54 alleles) in normals (p < 0.0001). Haplotypes were discernible in all of the 1591C homozygotes and in several of the heterozygotes and normals. The CD4 162, TPI 2262A haplotype was found on only two of thirty-eight normal chromosomes, but was universally associated with 1591C. The data indicate that all TPI 1591C subjects are descendants of a common ancestor who probably lived in what is now England or France. The original mutation probably occurred well in excess of 1000 years ago.

Australia↗
PubMed2003

Sequence variation in the promoter region of the cholinergic receptor muscarinic 3 gene and asthma and atopy.

BACKGROUND: Muscarinic acetylcholine receptors are members of the superfamily of G protein-coupled, 7 transmembrane- spanning proteins. They are important in the development of airway hyperresponsiveness. In the lung the M3 receptor, encoded by the cholinergic receptor muscarinic 3 gene, is present in airway smooth muscle and mediates smooth muscle contraction. OBJECTIVE: We considered the cholinergic receptor muscarinic 3 gene as a possible candidate gene for bronchial asthma and initiated studies to identify polymorphisms in the promoter region. METHOD: We identified 4 single-nucleotide polymorphisms (-708A/G, -627G/C, -513C/A, and -492C/T) and 2 short tandem repeat polymorphisms, a tetranucleotide (CTTT)12-20 and a dinucleotide (GT)6-19 repeat. RESULTS: None of the identified single nucleotide polymorphisms were significantly more frequent in asthmatic patients (n = 76) compared with in healthy control subjects (n = 81). Furthermore, there was no evidence for nonrandom transmission of short tandem repeat polymorphism haplotypes to individuals with asthma or bronchial hyperresponsiveness (P >.50) in a large Hutterite pedigree. However, there was significant nonrandom transmission of haplotypes to individuals with skin test reactivity to cockroach allergens (global transmission disequilibrium test: chi2 = 38.55, P =.013). CONCLUSIONS: These results suggest a possible role for this gene in atopic disorders.

Allergens↗
PubMed2005

Effects of electron-beam irradiation on whole genome amplification.

Electron-beam (E-beam) irradiation, currently being used to sterilize mail addressed to selected ZIP codes in the United States, has significant negative effects on the genomic integrity of DNA extracted from buccal-cell washes. We investigated the yield, composition, and genotyping performance of whole genome amplified DNA (wgaDNA) derived from 24 matched samples of E-beam-irradiated and nonirradiated genomic DNA (gDNA) as a model for the effects of degraded gDNA on the performance of whole genome amplification. gDNA was amplified using the Multiple Displacement Amplification method. Three methods of DNA quantification analysis were used to estimate the yield and composition of wgaDNA, and 65 short tandem repeat and single nucleotide polymorphism genotyping assays were used to evaluate the genotyping performance of irradiated and nonirradiated gDNA and wgaDNA. Compared with wgaDNA derived from nonirradiated gDNA, wgaDNA derived from irradiated gDNA exhibited a significantly reduced yield of wgaDNA and significantly reduced short tandem repeat and single nucleotide polymorphism genotyping completion and concordance rates (P < 0.0001). Increasing the amount of irradiated gDNA input into whole genome amplification improved genotyping performance of wgaDNA but not to the level of wgaDNA derived from nonirradiated gDNA. Multiple Displacement Amplification wgaDNA derived from E-beam-irradiated gDNA is not suitable for genotyping analysis.

DNA↗
PubMed2005

Concordance of genotypes in pre- and post-lung transplantation DNA samples.

Genetic epidemiology studies of end-stage lung disease are potentially hindered by low numbers of participants due to early death of patients from the underlying disease, or due to exclusion from studies after patients have had lung transplants, because of concern about bias of genotype data due to chimerism. The number of participants enrolled in genetic studies of end-stage lung disease could be increased by including those individuals who have undergone lung transplant. We hypothesized that individuals who have had lung transplants can be included in genetic epidemiology studies that use single nucleotide polymorphism and short tandem repeat marker data, without confounding due to chimerism. Ten probands with severe, early-onset chronic obstructive pulmonary disease were included in this analysis. Pre- and post-lung transplant DNA samples were used in the investigation of concordance of genotype results for 12 short tandem repeat markers and 23 single nucleotide polymorphisms. Concordance was observed for all genotypes before and after lung transplant. We conclude that the risk of biasing genetic epidemiology studies due to donor lung-related DNA microchimerism is low, and that the inclusion of post-lung transplantation participants will allow for larger genetic epidemiology studies of individuals with end-stage lung disease.

DNA-Binding Proteins↗
PubMedDate not supplied

[Quantification of human DNA from forensic samples via real time PCR by the help of a telomerase assay].

Quantitative data concerning the content of human DNA and the effect of PCR inhibitors in a sample would provide very important information within a forensic DNA analysis. With the help of real-time PCR it is possible to test DNA samples for these influencing factors. However, the amplified DNA segments detected by means of usual TaqMan DNA probes are longer than most of the short tandem repeats to be investigated. Because of possible DNA degradation, a DNA probe located in the human telomerase transcriptase gene was successfully tested on forensic samples in the present study. Its amplified DNA segment is only 94 bases in length and, thus, shorter than the short tandem repeats. Therefore, it seems perfectly suited for the examination of degraded DNA. With the telomerase probe it was possible to obtain accurate results of the influence factors mentioned above. Based on the findings of this examination and on a case example, in which the poorly preserved remains of a baby were subjected to paternity testing, the possible uses of the telomerase assay are discussed.

Adult↗
PubMed1992

Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups.

Trimeric and tetrameric short tandem repeats (STRs) represent a rich source of highly polymorphic markers in the human genome that may be studied with the polymerase chain reaction (PCR). We report the analysis of a multilocus genotype survey of 97-380 chromosomes in U.S. Black, White, Mexican-American, and Asian populations at five STR loci located on chromosomes 1, 4, 11, and X. The heterozygote frequencies of the loci ranged from 0.36 to 0.91 and the number of alleles from 6 to 20 for the 20 population and locus combinations. Relative allele frequencies exhibited differences between populations and unimodal, bimodal, and complex distributions. Although deviations were noted at some locus-population test combinations, genotype data from the loci were consistent overall with Hardy-Weinberg equilibrium by three tests. Population subheterogeneity within each ethnic group was not detected by two additional tests. No mutations were detected in a total of 860 meioses for two loci studied in the CEPH kindreds and five loci studied in other families. An indirect estimate of the mutation rates gave values from 2.3 x 10(-5) to 15.9 x 10(-5) for the five loci. Higher mutation rates appear to be associated with greater numbers of tandem repeats in the core motif. The most frequent genotype for all five loci combined appears to have a frequency of 7.59 x 10(-4). Together, these results suggest that trimeric and tetrameric STR loci are useful markers for the study of new mutations and genetic linkage analysis and for application to personal identification in the medical and forensic sciences.

Alleles↗
PubMed1998

Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat.

In 10,844 parent/child allelic transfers at nine short-tandem-repeat (STR) loci, 23 isolated STR mismatches were observed. The parenthood in each of these cases was highly validated (probability >99.97%). The event was always repeat related, owing to either a single-step mutation (n=22) or a double-step mutation (n=1). The mutation rate was between 0 and 7 x 10(-3) per locus per gamete per generation. No mutations were observed in three of the nine loci. Mutation events in the male germ line were five to six times more frequent than in the female germ line. A positive exponential correlation between the geometric mean of the number of uninterrupted repeats and the mutation rate was observed. Our data demonstrate that mutation rates of different loci can differ by several orders of magnitude and that different alleles at one locus exhibit different mutation rates.

Adult↗
PubMed2002

[A method for rapid and early diagnosis of trisomy 21 using molecular techniques].

OBJECTIVE: Using molecular techniques, we typed 2 short tandem repeat (STR) loci on 21 chromosome to establish the method for rapid and accurate diagnosis of trisomy 21. METHODS: Genomic DNA samples from 50 individuals diagnosed previously by karyotype as trisomy 21 and 40 children with severe mental retardation (IQ < 50) suspected of trisomy 21 were analyzed for 2 short tandem repeat loci on 21 chromosome, D21S1435 and D21S2055. Typing was carried out after polymerase chain reaction (PCR) and silver staining. The trisomy was identified by the number of alleles: 3 alleles bands whose density is same, two alleles bands with one obvious higher density compared to the other and one allele band whose density is three times than the normal control. RESULTS: All of the complete trisomy 21 were detected by this method; the parental source was easily determined. CONCLUSION: This method for diagnosing trisomy 21 is rapid and accurate.

Chromosomes, Human, Pair 21↗
PubMed2001

[Linkage analysis and mutation detection of GRIA3 in Smith--Fineman--Myers syndrome].

To determine the role of GRIA3 in the etiology of Smith--Fineman--Myers syndrome (SFMS), polymorphic short tandem repeats within GRIA3 gene were genotyped by PCR and denaturing polyacrylamide gel electrophoresis to test linkage between GRIA3 and the gene responsible for SFMS. The open reading frame of GRIA3 was detected for mutation by PCR amplification and direct sequencing in affected and normal males from SFMS family. One of the two short tandem repeats was informative in SFMS family. Tight linkage between SFMS locus and GRIA3 gene was established by STR3 within GRIA3 gene. No disease--causing mutation was found within the open reading frame of GRIA3 gene. The disease in SFMS family from Shandong (China) is not caused by the mutation within open reading frame of GRIA3 gene.

Abnormalities, Multiple↗
PubMed1993

Telomeric repeat [TTAGGG]n sequences of human chromosomes are conserved in chimpanzee (Pan troglodytes).

Using a series of genetic parameters, attempts have been made for more than two decades to establish the close kinship of human (Homo sapiens) with chimpanzee (Pan troglodytes). Molecular and cytogenetic data presently suggest that the two species are closely related. The recent isolation of a human telomeric probe (P5097-B.5) has prompted us to cross hybridize it to chimpanzee chromosomes in order to explore convergence and/or divergence of the telomeric repeat sequences (TTAGGG)n. On hybridization, the human probe bound to both ends (telomeres) of chimpanzee chromosomes, suggesting a concerted evolution of tandemly repeated short simple sequences (TTAGGG)n. Even the terminal heterochromatin of chimpanzee chromosomes was found to be endowed with telomeric repeats, suggesting that evolution of heterochromatin and capping with tandemly repeated short sequences are highly complex phenomena.

Animals↗
PubMed2003

Genetic diversity within the R408W phenylketonuria mutation lineages in Europe.

The R408W phenylketonuria mutation in Europe has arisen by recurrent mutation in the human phenylalanine hydroxylase (PAH) locus and is associated with two major PAH haplotypes. R408W-2.3 exhibits a west-to-east cline of relative frequency reaching its maximum in the Balto-Slavic region, while R408W-1.8 exhibits an east-to-west cline peaking in Connacht, the most westerly province of Ireland. Spatial autocorrelation analysis has demonstrated that the R408W-2.3 cline, like that of R408W-1.8, is consistent with a pattern likely to have been established by human dispersal. Genetic diversity within wild-type and R408W chromosomes in Europe was assessed through variable number tandem repeat (VNTR) nucleotide sequence variation and tetranucleotide short tandem repeat (STR) allelic associations. Wild-type VNTR-8 chromosomes exhibited two major cassette sequence organizations: (a1)5-b3-b2-c1 and (a1)5-b5-b2-c1. R408W-1.8 was predominantly associated with (a1)5-B5-B2-C1. Both wild-type vntr-3 and r408w-2.3 chromosomes exhibited a single invariant cassette sequence organization, a2-b2-c1. STR allele distributions associated with the cassette variants were consistent with greater diversity in the wild-type VNTR-8 lineage and were suggestive of different levels of diversity between R408W-1.8 and R408W-2.3. The finding of greater genetic diversity within the wild-type VNTR-8 lineage compared to VNTR-3 suggests that VNTR-8 may be older within the European population. However, in the absence of a more extensive STR data-set, no such conclusions are possible for the respective R408W mutant lineages.

Amino Acid Substitution↗
PubMedDate not supplied

Genetic relationships among Japanese, northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian populations based on allelic frequencies at four VNTR (D1S80, D4S43, COL2A1, D17S5) and one STR (ACTBP2) loci.

The genetic polymorphism at four variable number of tandem repeats (D1S80, D4S43, COL2A1, D17S5) and one short tandem repeat (ACTBP2) loci was assessed by polymerase chain reaction analysis of genomic DNA obtained from blood samples of eight human populations (Japanese, Northern Han, Hui, Uygur, Kazakh, Saudi Arabian, Greek, Italian). Allele frequencies at all loci were in the Hardy-Weinberg equilibrium for each population. With the exception of ACTBP2, the allelic distribution patterns for these loci revealed a marked genetic divergence among the eight populations. A dendrogram constructed by the neighbor-joining method based on the allele frequencies of the five loci suggested that the five Asian populations (Japanese, Northern Han, Hui, Uygur, and Kazakh) formed one cluster, whereas the two European populations and one West Asian population (Italian, Greek, and Saudi Arabian) formed another. The genetic relationship among these populations may have been greatly influenced by admixture as a result of the migration of individuals along the Silk Road throughout history.

Alleles↗
PubMedDate not supplied

Genomic analysis of ABO chimeras and mosaics using hematopoietic colony-derived DNA.

BACKGROUND: While there are many case reports dealing with ABO mosaicism and chimerism, there have been few attempts to determine the patient's genotype. STUDY DESIGN AND METHODS: Peripheral blood and buccal mucosa were obtained from three persons with ABO mosaicism or chimerism. DNA extracted from hematopoietic progenitor cell-derived colonies and from peripheral blood and buccal mucosa were analyzed by polymerase chain reaction-restriction fragment length polymorphism methods. In addition, analyses of short tandem repeat markers were carried out. RESULTS: Hematopoietic progenitor cell-derived DNA analysis revealed that, in two of the three persons there were 2 apparently distinct progenitor cell lineages whose percentages were close to those in the peripheral blood of the patients, as analyzed by flow cytometry; the exception was Subject 3, who had myelodysplastic syndrome (MDS). Short tandem repeat analysis showed that the former two subjects had two pairs of ABO alleles and the latter subject, with MDS, had loss of heterozygosity in some colony-derived DNA as well as blood DNA. CONCLUSION: The subjects without MDS had two distinct hematopoietic cell lineages that led to their ABO chimeric status. The subject with MDS was assumed to have an ABO mosaicism caused by the somatic deletion of the ABO gene in the hematopoietic progenitor cells.

ABO Blood-Group System↗
PubMedDate not supplied

Confirmation of linkage of Van der Woude syndrome to chromosome 1q32: evidence of association with STR alleles suggests possible unique origin of the disease mutation.

Van der Woude syndrome (VWS) is an autosomal dominant craniofacial disorder with high penetrance and variable expression. Its clinical features are variably expressed, but include cleft lip and/or cleft palate, lip pits and hypodontia. All VWS families studied to date map the disease gene to a < 2 cM region of chromosome 1q32, with no evidence of locus heterogeneity. The aim of this study is to refine the localization of the VWS gene and to further assess possible heterogeneity. We analyzed four multiplex VWS families. All available members were clinically assessed and genotyped for 19 short tandem repeat markers on chromosome 1 in the VWS candidate gene region. We performed two-point and multipoint limit of detection (LOD) score analyses using a high penetrance autosomal dominant model. All families showed positive LOD scores without any recombination in the candidate region. The largest two-point LOD score was 5.87. Our assay method for short tandem repeat (STR) markers provided highly accurate size estimation of marker allele fragment sizes, and therefore enabled us to determine the specific alleles segregating with the VWS gene in each of our four families. We observed a striking pattern of STR allele sharing at several closely linked loci among our four Caucasian VWS families recruited at three different locations in the US. These results suggest the possibility of a unique origin for a mutation responsible for many or most cases of VWS.

Alleles↗