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PubMed1992

Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation.

The human androgen-receptor gene (HUMARA; GenBank) contains a highly polymorphic trinucleotide repeat in the first exon. We have found that the methylation of HpaII and HhaI sites less than 100 bp away from this polymorphic short tandem repeat (STR) correlates with X inactivation. The close proximity of the restriction-enzyme sites to the STR allows the development of a PCR assay that distinguishes between the maternal and paternal alleles and identifies their methylation status. The accuracy of this assay was tested on (a) DNA from hamster/human hybrid cell lines containing either an active or inactive human X chromosome; (b) DNA from normal males and females; and (c) DNA from females showing nonrandom patterns of X inactivation. Data obtained using this assay correlated substantially with those obtained using the PGK, HPRT, and M27 beta probes, which detect X inactivation patterns by Southern blot analysis. In order to demonstrate one application of this assay, we examined X inactivation patterns in the B lymphocytes of potential and obligate carriers of X-linked agammaglobulinemia.

Animals↗
PubMed1994

Trinucleotide repeat polymorphism within the human antithrombin gene (AT3): allele frequency data for three population groups.

The fifth intron of the human antithrombin gene (AT3) of chromosome 1q23 contains a highly polymorphic short tandem repeat based on the trinucleotide repeat [ATT]. Alleles range in size from [ATT]5 to [ATT]18, and can be typed using the polymerase chain reaction. Here we report allele frequency population data for Caucasians, Blacks and Southeast Asians. Statistical analyses demonstrate consistency with Hardy-Weinberg equilibrium for all three databases, and that the allele frequencies of all three population groups are significantly different from each other. This locus reveals 76% to 87% heterozygosity and therefore may be useful for forensic identity testing and paternity determination.

Alleles↗
PubMed1993

Transposons in place of telomeric repeats at a Drosophila telomere.

We present the first isolation of the terminal DNA of an intact Drosophila telomere. It differs from those isolated from other eukaryotes by the lack of short tandem repeats at the terminus. The terminal 14.5 kb is composed of four tandem elements derived from two families of non-long terminal repeat retrotransposons and is subject to slow terminal loss. One of these transposon families, TART (telomere-associated retrotransposon), is described for the first time here. The other element, HeT-A, has previously been shown to transpose to broken chromosome ends. Our results provide key evidence that these elements also transpose to natural chromosome ends. We propose that the telomere-associated repetitive DNA is maintained by saltatory expansions, including terminal transpositions of specialized retrotransposons, which serve to balance terminal loss.

Animals↗
PubMed2001

A report of the 1997, 1998 and 1999 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Genetics.

We present the results of the 1997, 1998 and 1999 Paternity Testing Workshops of the English Speaking Working Group of the International Society for Forensic Genetics. The numbers of participating laboratories were 24 (1997), 31 (1998) and 32 (1999). In 1997, all laboratories drew the correct conclusion that the alleged father was the biological father of the child. In 1998, the alleged father was the biological brother of the child and all laboratories excluded him. The scenario in 1999 was a deficiency case consisting of mother, child and the parents of the alleged father and all but one laboratory drew the correct conclusion.The percentage of laboratories routinely performing variable number of tandem repeat (VNTR) investigations using single locus probes (SLPs) and restriction fragment length polymorphism (RFLP) decreased from 83% in 1997 to 66% in 1999. In the three workshops, more than 90% of the laboratories used polymerase chain reaction (PCR) based systems. In 1999, 80% of the laboratories performing PCR, used commercially available short tandem repeat (STR) kits. Other commonly used systems were HLA and PolyMarker investigated with PCR. Conventional systems and RFLP investigations of VNTRs with multi loci probes (MLPs) were used routinely by approximately 20% of the participating laboratories. All laboratories submitting results in the three workshops used RFLP-based VNTRs or/and PCR based VNTRs/STRs. Inter-laboratory comparisons of the results showed a very high concordance. The overall coefficients of variation between the laboratories of the results of RFLP typing of the commonly used VNTRs D2S44, D7S21, D7S22 and D12S11 were 1.2-1.3%. Consistent results were obtained in the great majority of the systems investigated by PCR and typing errors counted for less than 0.3% of the PCR based results.

Accreditation↗
PubMed1996

Isolation of tetranucleotide repeat polymorphisms flanking the BRCA1 gene.

Large pools of cosmids from the BRCA1 region of human chromosome 17 were screened for tetranucleotide repeat polymorphisms by hybridizing shotgun subcloned pools with a mixture of 25 oligonucleotides. Identified subclones were PCR amplified and directly sequenced to design PCR primers for short tandem repeat polymorphism (STRP) analysis of family DNAs. With the identification of the BRCA1 gene and the observation that most mutations in this > 100-kb gene are unique, haplotyping and linkage analysis may play a significant role in diagnosis and carrier detection of BRCA1-associated breast and ovarian cancers. We report the characterization of 15 new STRPs flanking the BRCA1 locus.

BRCA1 Protein↗
PubMed1985

Truncated repeated sequences generated by recombination in a specific region.

Structural relationships within a family of long repeated DNA sequences have been determined by molecular cloning of individual family members. About half of the family members are truncated at one end. There is a short, tandemly repeating region flanked by direct repeats associated with truncation. Recombination in a region near the tandemly repeating segment has apparently generated much of the diversity in this family.

Animals↗
PubMed2000

Neurophysiology and molecular genetics of Charcot-Marie-Tooth type 1 neuropathy in Croatian children: follow-up study.

AIM: Longitudinal assessment of clinical and neurophysiological abnormalities in childhood and adolescence and incidence analysis of tandem Charcot-Marie-Tooth disease type 1A gene duplication in Croatian children with Charcot-Marie-Tooth type 1 neuropathy. METHODS: Eight Croatian children with Charcot-Marie-Tooth type 1 neuropathy, aged 4-19 years, were studied clinically, neurophysiologically, and neuropathologically during 1-11 years of follow-up. All children were examined at least once, and in 4 children the measurements were repeated. Molecular genetic analysis was performed in all patients and their family members in order to determine the presence of the Charcot-Marie-Tooth disease type 1A duplication on chromosome 17p11.2-p12, using restriction fragment length polymorphic and short tandem repeat markers. RESULTS: Clubfoot was the most frequently observed clinical feature in children under 10 years of age, whereas muscle hypotrophy, scoliosis, and contractures developed in the second decade of life. All patients showed decreased motor nerve conduction velocity (7-30 m/s) and prolonged distal motor latencies on the first and follow-up examinations. Compound muscle action potential amplitude reduction (0.1-1.25 mV) was recorded in the first and second decade of life. In 6 out of 8 children, molecular genetic studies demonstrated the presence of the 1.5 megabase tandem Charcot-Marie-Tooth disease type 1A duplication in 17p11.2-p12, mostly of paternal origin. CONCLUSION: Pronounced neurographic abnormalities and mild clinical features characterize Charcot-Marie-Tooth type 1 neuropathy in the first decade. There were no significant differences in neurographic abnormalities in the first or second decade of life between Croatian children with and without Charcot-Marie-Tooth type 1A duplication.

Adolescent↗
PubMed2006

A novel method for biodosimetry.

Accurate methods for measuring the biological effects of radiation are critical for estimating an individual's health risk from radiation exposure. We investigated the feasibility of using radiation-induced mutations in repetitive DNA sequences to measure genetic damage caused by radiation exposure. Most repetitive sequences are in non-coding regions of the genome and alterations in these loci are usually not deleterious. Thus, mutations in non-coding repetitive sequences might accumulate, providing a stable molecular record of DNA damage caused by all past exposures. To test this hypothesis, we screened repetitive DNA sequences to identify the loci most sensitive to radiation-induced mutations and then investigated whether these mutations were stable in vivo over time and after multiple exposures. Microsatellite repeat markers were identified that exhibited a linear dose response up to 1 Gy of 1 GeV/nucleon 56Fe ions and 137Cs gamma rays in mouse and human cells. Short tandem repeats on the Y chromosome and mononucleotide repeats on autosomal chromosomes exhibited significant increases in mutations at >or= 0.5 Gy of 56Fe ions with frequencies averaging 4.3-10.3 x 10(-3) mutations/locus/Gy/cell, high enough for direct detection of mutations in irradiated cells. A significant increase in radiation-induced mutations in extended mononucleotide repeats was detectible in vivo in mouse blood and cheek samples 10 and 26 weeks after radiation exposure and these mutations were additive over multiple exposures. This study demonstrates the feasibility of a novel method for biodosimetry that is applicable to humans and other species. This new approach should complement existing methods of biodosimetry and might be useful for measuring radiation exposure in circumstances that are not amenable to current methods.

Biological Assay↗
PubMed2004

A tetranucleotide repeat polymorphism in the CYP19 gene and breast cancer susceptibility in a Greek population exposed and not exposed to pesticides.

Epidemiological studies have suggested that hormones, genetic factors, and environmental agents are significant risk factors in breast carcinogenesis. Some pesticides have the ability to act as xenoestrogens in vivo. The CYP19 gene encodes the aromatase enzyme which is involved in the estrogens biosynthetic pathways. We have assessed the frequency alleles of a (TTTA)(n) repeat of CYP19 gene in breast cancer patients which were either exposed or not exposed to specific pesticides. No differences were observed in the distribution of the alleles between the two groups showing that the polymorphism does not have a significant functional role on the aromatase activity. When compared to healthy control Greek women group, only the (TTTA)(10) repeat variant presented a non-significant increased risk in breast cancer susceptibility [odds ratio (OR): 2.46, P>0.05 ]. Lack of strong association suggests that the polymorphic TTTA short tandem repeat of CYP19 gene may have not a functional effect on the enzyme's activity and thus its role in the development of breast cancer remains unclear.

Adult↗
PubMed1990

The involucrin genes of pig and dog: comparison of their segments of repeats with those of prosimians and higher primates.

The involucrin genes of the dog and the pig have been cloned and sequenced. Like the corresponding genes of the prosimians, each contains a homologous segment of short tandem repeats at the same position in the coding region. However, the codon sequence of the repeats in the prosimians differs significantly from that of the nonprimate mammals. This evolution has been brought about by a combination of genetic modifications (selective deletions, mutations, and gene conversions). In the anthropoids, this segment of repeats was replaced by a modern one differing in location, sequence, and repeat length. In several of its properties the modern segment has continued the prosimian trend away from the nonprimates. The overall direction of the evolution of this segment has therefore been maintained even though there have been sudden changes in the evolutionary processes acting on the gene.

Animals↗
PubMedDate not supplied

A test of allelic independence based on distributions of allele size differences at microsatellite loci.

Thousands of polymorphic microsatellite loci are now mapped in the human genome, most of which exhibit a large number of segregating alleles. For forensic, evolutionary and gene mapping applications, it is important to establish intralocus allelic independence at these loci. We develop a test for intralocus allelic independence based on repeat size differences between alleles within genotypes of individuals, and show its relationship with the intraclass correlation of allele sizes within loci. Applications of this test to 13 short tandem repeat loci in 4 subpopulations indicate that the distribution of size differences of alleles has adequate power to detect intralocus dependence of alleles caused by population substructure. In addition, size differences between randomly chosen alleles provide information regarding heterozygosity and contiguity of allele sizes at the locus, which by themselves do not necessarily indicate the presence of population substructure.

Alleles↗
PubMed2000

Molecular structure of rDNA repeat unit in Magnaporthe grisea.

The 8-kb repeat unit of M. grisea rRNA-encoding DNA (rDNA) was cloned as three subclones, pM50, pM21, and pM86. Nucleotide sequencing of these subclones uncovered the structure of an rDNA repeat unit similar to those of other ascomycetes. The intergenic spacer (IGS) of the rDNA cistron contained a repetitive (R) region, which was rich in two kinds of short tandemly repeated elements.

Base Sequence↗
PubMed2005

Identification of splicing silencers and enhancers in sense Alus: a role for pseudoacceptors in splice site repression.

Auxiliary splicing signals in introns play an important role in splice site selection, but these elements are poorly understood. We show that a subset of serine/arginine (SR)-rich proteins activate a cryptic 3' splice site in a sense Alu repeat located in intron 4 of the human LST1 gene. Utilization of this cryptic splice site is controlled by juxtaposed Alu-derived splicing silencers and enhancers between closely linked short tandem repeats TNFd and TNFe. Systematic mutagenesis of these elements showed that AG dinucleotides that were not preceded by purine residues were critical for repressing exon inclusion of a chimeric splicing reporter. Since the splice acceptor-like sequences are present in excess in exonic splicing silencers, these signals may contribute to inhibition of a large number of pseudosites in primate genomes.

Alternative Splicing↗
PubMed1996

Estimation of mutation rates from parentage exclusion data: applications to STR and VNTR loci.

Nonpaternity is a common source of bias in estimating mutation rates when they are obtained from family data showing discordance of parental and children's genotypes. With the availability of hypervariable DNA markers, this source of bias can be largely eliminated. However, the proportion of cases where parentage exclusion is caused by presumed mutation(s) of parental alleles must be adjusted to obtain a valid mutation rate estimate. The present work derives the basis of this adjustment factor, called the proportional bias. This proportional bias depends upon the allele frequency distribution at the locus. The maximum and minimum bounds of the proportional bias depend on the number of alleles at the locus. Using data from Caucasian populations at tandem repeat loci commonly used for parentage testing and forensic identification purposes, we show that when mutation rates are estimated at these loci, the proportional bias is generally very close to the maximum possible value for the observed number of alleles (or binned fragment sizes) at each locus. The expected proportional bias decreases with increasing mutation rate at a locus. For the short tandem repeat loci, without bias correction, the direct count method can result in an underestimation of up to 60% of their true value. In contrast, for the minisatellite VNTR loci, even with crude measurements on allele sizes, we show that the absolute proportional bias is generally below the coefficient of variation of the direct estimates.

Chromosome Mapping↗
PubMed1997

Rapid sizing of polymorphic microsatellite markers by capillary array electrophoresis.

Genetic mapping and DNA sequencing projects could potentially be completed more rapidly by using capillary array electrophoresis (CAE) systems running 48-96 capillaries simultaneously. Currently, multiplex polymerase chain reaction (PCR) and multicolor fluorescent dye-labeling strategies are used to generate DNA profiles containing 18-24 genotypes per sample. By using 4-color fluorescence detection and these multiplex PCR strategies, a CAE system has the capacity to generate up to 5.5 million genotypes per year. CAE offers extremely fast, high-resolution separation of DNA and more automated sample processing than conventional systems because the labor-intensive slab-gel pouring and sample-loading steps are eliminated. We used a prototype CAE system in an ongoing linkage analysis study of inherited deafness in Mediterranean families. CA-repeat markers linked to deafness susceptibility genes on chromosomes 7, 11 and 13 were analyzed and DNA profiles generated which contain 6 markers per color. Fragment sizes of over 28,000 short tandem repeat alleles and 3200 CA-repeat alleles have been determined by CAE. An average sizing precision of +/- 0.12 base pairs (bp) for fragments up to 350 bp was realized in 1-h runs. In addition, a versatile non-denaturing matrix was used to separate DNA sizing standards, restriction digests, and multiplex PCR samples. Application of this matrix to Duchenne muscular dystrophy exon deletion screening is also described. These CAE approaches should facilitate rapid genotyping of microsatellite markers and subsequent identification of disease-causing mutations.

Base Sequence↗
PubMed1997

The involucrin gene of the tree shrew: recent repeat additions and the relocation of cysteine codons.

The coding region of the involucrin gene of Tupaia glis has been cloned and sequenced. It resembles the involucrin coding region of other non-anthropoid mammals in possessing a segment of related, short tandem repeats at a defined location, but in Tupaia, there has been recent serial duplication of a repeat into which a cysteine codon had earlier been introduced. As a result of the duplication, there is a total of as many as six cysteine codons in the segment of repeats, a number larger than for any other species yet examined. In Ratttus there has been a comparable but independent addition of cysteine codons, and both Tupaia and Rattus have eliminated an otherwise conserved cysteine codon 75 located close to but outside the segment of repeats. In Tupaia, this elimination probably occurred by gene conversion. Also independently, the gene of Canis has added cysteine codons to the segment of repeats but has not yet lost cysteine 75. It is proposed that the gain and the loss of cysteine codons are parts of a multi-stage program of cysteine relocation.

Animals↗
PubMed2006

Genomic copy number changes affecting the thymidylate synthase (TYMS) gene in cancer: a model for patient classification to aid fluoropyrimidine therapy.

Thymidylate synthase (TS) is an important target for 5-fluorouracil (5FU)-based therapy. The TS polymorphic 5'-untranslated region tandem repeat sequence is under investigation to guide 5FU treatment, yet current protocols omit consideration of copy number changes at the TS locus. We surveyed the TS tandem repeat sequence and found copy number changes in gastrointestinal cancers. Ten of 12 informative cases had loss of heterozygosity (LOH), whereas two others and an additional cell line had a novel TS genotype, allelic imbalance at the TS locus due to polysomy. Experimentally, we studied a diploid colorectal cancer line heterozygous at TS to mimic three common TS genotypes of cancers. Using genetic engineering, we deleted the short tandem repeat (two repeats) allele and retained the long (three repeats) allele to produce artificial LOH at the TS gene; the TS(+/-) line had a reduced TS protein expression and was hypersensitive to 5FU and 5-fluoro-2'-deoxyuridine in vitro as compared with syngeneic control lines. We linked this sensitivity directly to the reduced TS expression by introducing exogenous TS cDNA expression into the TS(+/-) line (i.e., increased TS copies). Our model predicts that the 5FU sensitivity of a tumor is modified by aneuploidy producing copy number changes of TS alleles by one or more of the following: LOH, amplification, and, as presented here, copy number changes due to polysomy. The data suggest that TS copy number in a patient's tumor may be a dominating variable affecting 5FU responsiveness.

5' Untranslated Regions↗
PubMed2005

Development, inheritance, and linkage-group assignment of 60 novel microsatellite markers for the gray, short-tailed opossum Monodelphis domestica.

Short-tandem-repeat (SSR) or microsatellite polymorphisms are some of the most extensively employed genetic markers in contemporary linkage mapping studies. To date, only a limited number of microsatellites have been isolated in the gray, short-tailed opossum Monodelphis domestica, a South American marsupial widely used for comparative biological and biomedical research. To increase the number of potentially useful mapping markers, we screened 2 microsatellite-enriched genomic libraries containing alternatively (CA)n or (GA)n repeats. A total of 184 clones were sequenced, from which 60 polymorphic microsatellite markers were successfully optimized. The efficiency of this enrichment protocol for M. domestica microsatellite isolation is discussed, and suggestions to improve the outcome are made. All 60 loci showed high allelic diversity, with allele numbers ranging from 2 to 10 in a subset of 33 unrelated animals. Normal Mendelian inheritance was confirmed for all loci by analyzing allelic segregation in 5 two-generation families. One microsatellite appeared to be X linked, and null alleles were found in 5 others. Two-point linkage analyses were implemented using the data on the 5 families, leading to the assignment of 59 of these loci to the existing linkage groups. The 60 novel microsatellites developed in this study will contribute significantly to the M. domestica linkage map, and further QTL mapping studies.

Animals↗