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PubMed2001

Stratification analysis of MICA triplet repeat polymorphisms and HLA antigens associated with ulcerative colitis in Japanese.

We previously reported a conserved haplotype of HLA B52-DR2 and a significantly high frequency of the major histocompatibility complex (MHC) class I chain-related gene A (MICA) transmembrane-short tandem repeat (TM-STR) 6 allele in Japanese patients with ulcerative colitis (UC). To examine the predominance of the MICA TM-STR 6 allele as a marker of the susceptibility to UC within the susceptible haplotype, the association of each allele with UC was estimated following stratification of the patients to control for any possible confounding effects of other alleles positively associated with UC. Sixty-four patients with UC and 236 unrelated healthy controls were included in this study. All subjects were Japanese. HLA-A, -B, -C, and -DR antigens were determined serologically. A triplet repeat polymorphism of the MICA was determined by direct sequencing. To control for the effect of linkage disequilibrium, Mantel-Haenszel weighed odds ratios were calculated. Significantly higher phenotype frequencies of B52, MICA TM-STR 6, and DR2 were observed in patients with UC. Linkage disequilibria among alleles associated with UC revealed that a B52 - MICA TM-STR 6 - DR2 haplotype was conserved in patients with UC, as in controls. When the association of HLA-B52 was estimated after patient stratification for the possible confounding effect of MICA TM-STR 6 or DR2, a strong significant association of B52 with UC was still observed. In contrast, no association with UC was observed for MICA TM-STR 6 or DR2, after stratification of the possible confounding effect of HLA-B52. These results imply that the significant increase in MICA TM-STR 6 in Japanese patients with UC is attributable to linkage disequilibrium with HLA-B52.

Colitis, Ulcerative↗
PubMed2001

STR typing of human telogen hairs--a new approach.

A new approach to short tandem repeat (STR) typing of DNA extracted from telogen shed hairs is presented. Newly designed primer pairs with annealing positions close to the repeat units of the STR loci HUMFES, HUMTH01 and HUMTPOX were used for amplification. The typing results were compared to those obtained by the commonly used primer pairs by means of success rates. The primer pairs capable of producing very short amplicons (< 106 bp with HUMFES, < 86 bp with HUMTH01 and < 87 bp with HUMTPOX) described in this study significantly increased the success rates when typing telogen hairs.

DNA Fingerprinting↗
PubMed1994

Infection of donor lymphocytes with human T lymphotrophic virus type 1 (HTLV-I) following allogeneic bone marrow transplantation for HTLV-I positive adult T-cell leukaemia.

Human T lymphotrophic virus type 1 (HTLV-I) associated leukaemia has a poor prognosis even with chemotherapy. We describe a patient with adult T-cell leukaemia treated with allogeneic bone marrow transplantation from an HTLV-I negative identical sibling donor. During follow-up after bone marrow transplantation, HTLV-I could be repeatedly isolated inspite of anti-viral prophylaxis. The patient died of an acute encephalitis and HTLV-I could be detected in autopsy material from the brain. By a PCR-based technique using short tandem repeats (STRs) it was shown that the patient's haemopoiesis was of donor origin. This shows the infection of donor cells in vivo by an aetiological agent which has been implicated in the leukaemogenic process for adult T-cell leukaemia.

Bone Marrow↗
PubMed1987

Tandemly repeated sequences are present at the ends of the DNA of raccoonpox virus.

The DNA of raccoonpox virus (RCN) has been characterized by restriction enzyme analysis. DNA hybridization studies showed that all HindIII fragments of the 215-kbp RCN DNA share some nucleotide sequence similarity with fragments of the DNA of cowpox virus (CPV). This information was used to construct a HindIII restriction map of the RCN DNA. The nucleotide sequence of the 2.2-kbp Sal 1 end fragment of the RCN DNA has been determined from a cloned copy of the HindIII O fragment. Of this 2.2-kb region 75% consists of short, tandemly repeated sequences. It does not contain any open reading frames capable of encoding polypeptide chains of more than 62 amino acids. There are six related types of repeated sequence, and these are arranged into two separate sets, each flanked by nonrepeated sequences. The nucleotide sequences of both repeated and nonrepeated sequences within this Sal 1 fragment are extremely similar to those of the Sal 1-generated end fragments of the DNas of CPV and vaccinia virus. The arrangements of the repeated and nonrepeated sequences are also similar in the DNAs of these three viruses. In contrast, the remainder of the RCN DNA is markedly different from the DNAs of other orthopoxviruses. The high degree of similarity between the ends of the RCN DNA and the ends of the other orthopoxvirus DNAs suggest that the complex arrays of repeated and nonrepeated sequences have been conserved because they have a role in virus multiplication.

Animals↗
PubMed1998

A novel TP53 germ-line mutation identified in a girl with a primitive neuroectodermal tumor and her father.

A search of TP53 mutations was undertaken in a series of 51 pediatric brain tumors. The only germ-line mutation was detected in a 9-year-old girl with a PNET. Her family history was unremarkable for neoplastic disease, except for the paternal grandfather, who died of a gallbladder carcinoma at an advanced age. The mutation was a thymine deletion at the first base of codon 241, leading to termination codon at position 246 that has not previously been reported. This mutation was found to be inherited from the proband's father, who was healthy at age 40. In the tumoral sample, loss of heterozygosity in several 17p markers was found, the only TP53 allele preserved in the tumor was the mutated one. The presence of two short tandem repeats and two different palindromic sequences spanning the deletion lead us to propose the predisposition of this region to forming a complex secondary structure during replication. Consequently, it could have facilitated the present deletion. Furthermore, six other short deletions affecting--partially or totally--the region implicated in the folding model that we propose have been described in the literature. These findings confirm that this sequence represents a hotspot of deletion in the TP53 gene.

Child↗
PubMed2004

Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding.

Although microsatellites with functional effects have been described, generally, these repeats are considered as "junk" DNA in the same way as other repetitive sequences. Our aim was to investigate if certain microsatellites can have a functional role as cis-regulatory elements. A database was created of all short tandem repeats, from 2 to 10 bases, located in the first 10-kb 5' of the transcription start sites of all annotated genes of the human genome. Of 114 microsatellites selected based on their size and location in the promoter, 51 were found to be polymorphic. Using electrophoretic mobility shift assay (EMSA), we studied five repetitive motifs and three displayed specific protein binding which were found in 12 of the polymorphic microsatellites. An interesting microsatellite is the CTC/GAG repeat which, as double-stranded (DS) DNA, bound specificity protein 1 (SP1) with high affinity, formed triplexes in vitro and displayed differences in SP1 binding and triplex formation capacity for repeats with distinct numbers of repeat units. Interestingly, the polypyrimidine strand of the repeat (CTC) bound other proteins such as polypyrimidine tract-binding protein 1 (PTBP1) as single-stranded (SS) DNA, and a model with two alternative DNA conformations is proposed for these repeats. Distinct protein binding to DS DNA was also observed for different numbers of AAACA and AAAAT repeats. Our results suggest that certain microsatellites may act as cis-regulatory elements, controlling gene expression through transcription factor binding and/or secondary DNA structure formation. Due to their high polymorphism and abundance, they might represent an important source of quantitative genetic variation.

Base Sequence↗
PubMed1993

DNA polymorphism in cytokine genes based on length variation in simple-sequence tandem repeats.

The possibility of the involvement of cytokines in the genetic predisposition to various diseases has been suggested by a large variety of studies. However, the study of potential disease linkage of cytokine genes has been hampered by a lack of sufficiently polymorphic markers at the restriction fragment length polymorphism (RFLP) level. We have investigated the distribution, the length polymorphism, the informativeness, and the efficiency of analysis, of simple-sequence tandem repeats in the mouse cytokine genes. Highly polymorphic sequences have been identified in the IL-1 beta, IL-1ra, IL-2, IL-4, IL-5, IL-6, IL-7, and IFN-gamma genes. The utility and the value of these sequences as gene markers is exemplified by mapping the IL-7 gene to mouse chromosome 3 close to pgk-1ps3 and Car-2 loci and the IFN-gamma gene to chromosome 10 near the pg locus. Advantages of short tandemly repeated sequences as genetic markers are discussed in comparison with RFLPs.

Animals↗
PubMed1983

Structure and evolution of a mouse tRNA gene cluster encoding tRNAAsp, tRNAGly and tRNAGlu and an unlinked, solitary gene encoding tRNAAsp.

We have sequenced mouse tRNA genes from two recombinant lambda phage. An 1800 bp sequence from one phage contains 3 tRNA genes, potentially encoding tRNAAsp, tRNAGly, and tRNAGlu, separated by spacer sequences of 587 bp and 436 bp, respectively. The mouse tRNA gene cluster is homologous to a rat sequence (Sekiya et al., 1981, Nucleic Acids Res. 9, 2239-2250). The mouse and rat tRNAAsp and tRNAGly coding regions are identical. The tRNAGlu coding regions differ at two positions. The flanking sequences contain 3 non-homologous areas: a c. 100 bp insertion in the first mouse spacer, short tandemly repeated sequences in the second spacers and unrelated sequences at the 3' ends of the clusters. In contrast, most of the flanking regions are homologous, consisting of strings of consecutive, identical residues (5-17 bp) separated by single base differences and short insertions/deletions. The latter are often associated with short repeats. The homology of the flanking regions is c. 75%, similar to other murine genes. The second lambda clone contains a solitary mouse tRNAAsp gene. The coding region is identical to that of the clustered tRNAAsp gene. The 5' flanking regions of the two genes contain homologous areas (10-25 bp) separated by unrelated sequences. Overall, the flanking regions of the two mouse tRNAAsp genes are less homologous than those of the mouse and rat clusters.

Animals↗
PubMed2000

Expansion of mouse involucrin by intra-allelic repeat addition.

Involucrin, loricrin and the small proline-rich proteins (SPRRs) are precursors of the cornified envelope of terminally differentiated keratinocytes. The genes for these proteins are closely linked on mouse chromosome 3. Each of the proteins is encoded by a single exon and is largely composed of a segment of short tandem repeats. No size polymorphism of either loricrin or the SPRRs was observed. In contrast, involucrin was found in at least eight polymorphic forms of different size with molecular weights ranging from 51 to 82kDa. Two classes of involucrin alleles were identified. Size polymorphism of involucrin has resulted from the recent expansion of the segment of repeats in one class of alleles, but not in the other. In expanding alleles, repeats were added at a precise location within the segment of repeats, in a 5'-to-3' direction. A study of a large number of allele-specific markers, located on both sides of the site of repeat addition, revealed no evidence for recombination between any of the alleles examined. Expansion of the segment of repeats of the gene for mouse involucrin must result from an intra-allelic process controlled by a cis-acting element, active in one class of alleles, and inactive in the other.

Alleles↗
PubMed1999

Survey for CAG repeat polymorphisms in the human MAP-2 gene.

Microtubule-associated protein-2 (MAP-2) expression is altered in response to a number of physiological insults such as Alzheimer's disease, schizophrenia, stroke and AIDS-dementia. Changes include alteration in MAP-2 transcription, translation, and state of phosphorylation. Multiple MAP-2 transcripts exist within the nervous system and, as noted for a number of genes expressed in the central nervous system, MAP-2 contains a region of trinucleotide repeats located in exon 1 of the 5' untranslated region (5' UTR). Since expansion of CAG repeats are found in several neurodegenerative disorders, we analysed the CAG repeats in MAP-2 for polymorphisms in 31 controls, 35 chronic schizophrenics, and 20 with other neuropsychiatric illnesses. Genomic DNA samples from 86 individuals were used as templates in PCR amplifications with primers within exon 1. Sequencing of the PCR products, or short tandem repeat polymorphism (STRP) analysis, demonstrated consistency in the size of the CAG repeats. This study demonstrates that the seven copies of the CAG repeat located in the 5' UTR of the MAP-2 gene are highly conserved in the general population, and that there is no evidence for expansion of the CAG repeat.

DNA↗
PubMed1995

DNA typing for bone marrow engraftment follow-up after allogeneic transplant: a comparative study of current technologies.

DNA typing is widely used to document engraftment after allogeneic bone marrow transplantation (BMT). Most DNA typing procedures discriminate allogeneic engraftment on the basis of DNA length polymorphisms or sequence variations found in variable number of tandem repeat (VNTR) loci, or the presence of Y chromosome-specific DNA We have compared 3 types of VNTR analysis, their respective mode of allele detection and Y chromosome DNA detection in order to assess the strengths and limitations of each approach. Chimerism was assessed in 8 recipients after allogeneic BMT. Samples were subjected to 6 restriction fragment length polymorphism (RFLP) loci-analysis using radioactivity, 2 amplified fragment length polymorphism (AmpFLP) loci-analysis using a silver-stain mode of detection, 12 short tandem repeat (STR) loci-analysis using fluorescence detection and Y chromosome analysis. We evaluated each procedure for its ability to (1) discriminate sibling donor-recipient pairs in our samples; (2) generate a concordant chimerism diagnosis; and (3) detect and assess the contribution of minority components in mixed-chimera situations. In sex-mismatched BMTs with a female graft donor, Y chromosome probing has proven most efficient. In all other cases, AmpFLPs proved to be a rapid and efficient procedure with sufficient discriminating capability and sensitivity to warrant their use in clinical settings. STRs are rapid as well but require a larger loci complement to discriminate efficiently and they do not currently detect, under our conditions, all mixed chimeras. RFLPs are clearly superior at discriminating siblings but are time-consuming and serve best in cases where AmpFLP and STR analyses fail.

Alleles↗
PubMed1996

Linkage of autosomal dominant radial drusen (malattia leventinese) to chromosome 2p16-21.

OBJECTIVE: To identify the chromosomal location of the gene involved in the pathogenesis of autosomal dominant radial drusen (malattia leventinese). PATIENTS: Eighty-six members of four families affected with radial drusen; one family of American origin and three families of Swiss origin. METHODS: Family members were clinically examined for the presence of radial drusen. Affected patients and potentially informative spouses were genotyped with short tandem repeat polymorphisms distributed across the autosomal genome. The clinical and genotypic data were subjected to linkage analysis. RESULTS: Fifty-six patients were found to be clinically affected. Significant linkage was observed between the disease phenotype and markers known to lie on the short arm of chromosome 2. The maximum two-point lod score (Zmax) observed for all four families combined was 10.5 and was obtained with marker D2S378. Multipoint analysis yielded a Zmax of 12, centered on marker D2S378. The lod-1 confidence interval was 8 cM, while the disease interval defined by observed recombinants was 14 cM. CONCLUSIONS: The gene responsible for autosomal dominant radial drusen has been mapped to the short arm of chromosome 2. This is an important step toward actually isolating the disease-causing gene. In addition, this information can be used to evaluate other familial drusen phenotypes such as Doyne's macular dystrophy for a possible allelic relationship.

Adolescent↗
PubMed2001

Maternal isodisomy for chromosome 2p causing severe congenital hypothyroidism.

Severe congenital hypothyroidism (CH) due to a total iodide organification defect (TIOD) is usually due to mutations in the thyroid peroxidase (TPO) gene located at chromosome 2p25. A homozygous deletion [DeltaT2512 (codon 808)] in exon 14 was identified in a patient with classical TIOD. The transmission pattern of the TPO gene in this family was anomalous; the mother was heterozygous for the deletion; and the mutation was absent in the father. Polymorphic short tandem repeat (STR) markers confirmed paternity and demonstrated on chromosome 2 that the propositus was homozygous for most markers on chromosome 2p and that these were identical to one of the maternal 2p homologs. A normal karyotype was found in the propositus, his parents and sister. We conclude that the homozygosity in the patient is due to partial maternal isodisomy of the short arm of chromosome 2, carrying a defective TPO gene. The patient, born small for gestational age, develops and grows well and appears healthy (while being treated with thyroxine) and has a normal phenotype except for a unilateral preauricular skin tag. This shows that partial maternal isodisomy for chromosome 2p (2pter - 2p12) is compatible with a minimal influence on normal development.

Base Sequence↗
PubMed1999

Biased amino acid composition in repeat regions of Plasmodium antigens.

Many malarial antigens contain extensive arrays of tandemly repeated short amino acid sequences, and much of the antibody response induced by malaria infections is directed against these repeats. Indeed, it has been hypothesized that these repeats function to elicit a relatively ineffective T-cell-independent antibody response by the host. In order to test this hypothesis, tandem repeats of Plasmodium species were examined for a bias in composition favoring amino acids likely to form epitopes for the antibody. The genome of Plasmodium is very A+T-rich, and nucleotide compositional bias will, in itself, lead to a high proportion of hydrophilic amino acids. When this bias was controlled for, Plasmodium antigens did not show a higher proportion of hydrophilic amino acids than expected, but there was a significant reduction in the proportion of hydrophobic amino acids in the repeats of the antigens. The amino acid composition of the repeats was thus strikingly different from those seen both in the remainder of the antigens and in a sample of Plasmodium falciparum housekeeping genes.

Amino Acid Sequence↗
PubMed1998

[Recent developments of genetic markers in legal practice].

The human identification in forensic science is currently based upon the study of highly polymorphic systems with mendelian transmission: the STRs (Short Tandem Repeats). These genetic markers are three to seven bases repetitive sequences spread all over the genome. They are detected by using the Polymerase Chain Reaction (PCR). This analysis method makes it possible to amplify several different loci from very low quantities of genomic DNA (Desoxyribonucleic Acid) in very short periods of time without using any radioactive substances. Interpretation of the results is simple because the amplified fragments are of a known size. The alleles known in each system with discrete values allow the calibration of the revealing gel and the populations studies; moreover, they may be entered into a database. The fragility of this test implies specific precautions with the Laboratory's organization in order to avoid any kind of contamination. Both the establishment of a quality assurance responding to the ISO 9002 standard together with internal quality controls would ensure that these tests are reliable and repeatable in the opinion of the Courts. Only authorized laboratories may perform DNA testing on the occasion of legal proceedings.

Chromosome Mapping↗
PubMed1990

Cloning and characterization of the white and topaz eye color genes from the sheep blowfly Lucilia cuprina.

Clones carrying the white and topaz eye color genes have been isolated from genomic DNA libraries of the blowfly Lucilia cuprina using cloned DNA from the homologous white and scarlet genes, respectively, of Drosophila melanogaster as probes. On the basis of hybridization studies using adjacent restriction fragments, homologous fragments were found to be colinear between the genes from the two species. The nucleotide sequence of a short region of the white gene of L. cuprina has been determined, and the homology to the corresponding region of D. melanogaster is 72%; at the derived amino acid level the homology is greater (84%) due to a marked difference in codon usage between the species. A major difference in genome organization between the two species is that whereas the DNA encompassing the D. melanogaster genes is free of repeated sequences, that encompassing their L. cuprina counterparts contains substantial amounts of repeated sequences. This suggests that the genome of L. cuprina is organized on the short period interspersion pattern. Repeated sequence DNA elements, which appear generally to be short (less than 1 kb) and which vary in repetitive frequency in the genome from greater than 10(4) copies to less than 10(2) copies, are found in at least two different locations in the clones carrying these genes. One type of repeat structure, found by sequencing, consists of tandemly repeating short sequences. Restriction site and restriction fragment length polymorphisms involving both the white and topaz gene regions are found within and between populations of L. cuprina.

Amino Acid Sequence↗
PubMed2006

Significant linkage to airway responsiveness on chromosome 12q24 in families of children with asthma in Costa Rica.

Although asthma is a major public health problem in certain Hispanic subgroups in the United States and Latin America, only one genome scan for asthma has included Hispanic individuals. Because of small sample size, that study had limited statistical power to detect linkage to asthma and its intermediate phenotypes in Hispanic participants. To identify genomic regions that contain susceptibility genes for asthma and airway responsiveness in an isolated Hispanic population living in the Central Valley of Costa Rica, we conducted a genome-wide linkage analysis of asthma (n = 638) and airway responsiveness (n = 488) in members of eight large pedigrees of Costa Rican children with asthma. Nonparametric multipoint linkage analysis of asthma was conducted by the NPL-PAIR allele-sharing statistic, and variance component models were used for the multipoint linkage analysis of airway responsiveness as a quantitative phenotype. All linkage analyses were repeated after exclusion of the phenotypic data of former and current smokers. Chromosome 12q showed some evidence of linkage to asthma, particularly in nonsmokers (P < 0.01). Among nonsmokers, there was suggestive evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 2.33 at 146 cM). After genotyping 18 additional short-tandem repeat markers on chromosome 12q, there was significant evidence of linkage to airway responsiveness on chromosome 12q24.31 (LOD = 3.79 at 144 cM), with a relatively narrow 1.5-LOD unit support interval for the observed linkage peak (142-147 cM). Our results suggest that chromosome 12q24.31 contains a locus (or loci) that influence a critical intermediate phenotype of asthma (airway responsiveness) in Costa Ricans.

Adolescent↗
PubMed2003

Corticotroph carcinoma presenting as a silent corticotroph adenoma.

Malignant pituitary tumours are rare and their pathogenesis is not fully understood. We have performed genetic analyses on tissues arising from a pituitary carcinoma that initially presented as a silent corticotroph adenoma but which failed to respond to repeated, aggressive surgical and medical therapy. Loss of heterozygosity (LOH) of known or putative tumour suppressor genes (TSG) was assessed by microsatellite analysis of microdissected tumour and matched patient blood DNA. Clonality of the pituitary tumour samples was analysed by two PCR-based techniques; one employing the highly polymorphic short tandem repeat (STR) within the human androgen receptor allele (HUMARA), another based on a restriction fragment length polymorphism of the X chromosome phosphoglycerokinase (PGK-1) gene. Screening with 9 microsatellite markers demonstrated allelic loss at 3 sites (D1S190, D3S1283 and D10S297) in all tumour samples except the presenting pituitary tumour. X chromosome inactivation analysis demonstrated polyclonality in the original presenting tumour and a metastatic deposit but monoclonality in tissue samples from a second and third transsphenoidal resection. In these cases of tumour recurrence both LOH and X chromosome inactivation suggest that monoclonality arose from preferential clonal growth from the original polyclonal tumour. Polyclonality of the metastatic deposit suggests that this was derived from the presenting tumour, although the LOH pattern indicates that a single clone dominates. The data are consistent with increasing allelic loss associated with tumour dedifferentiation and malignant transformation.

Adenoma↗