Lack of clonal BCRA2 gene deletion on chromosome 13in chronic lymphocytic leukaemia
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Abstract:
Chromosome 13q deletion is among the most common cytogenetic abnormalities in chronic lymphocytic leukaemia (CLL). We investigated the 13q14.3 deletion in 44 CLL patients by Southern blotting following purification of clonal B CLL cells to >90%. Two sets of probes were used to investigate the site of clonal deletion, the D13S25 and D13S319 markers (at 13q14.3) and probes for exons 11 and 26–27 of the BRCA2 gene (at 13q12). Homozygous and heterozygous deletion at the 13q14.3 region was found in five and 17 patients, respectively. Despite the recent report of the BRCA2 gene involvement in >80% of CLL patients, we failed to detect a single case of homozygous or heterozygous deletion involving the 13q12 region. Our data support previous findings that the 13q14.3, and not the 13q12 region, is the major site of candidate tumour suppressor gene(s) in CLL.Keywords:
Chromosome 13
Gene deletion
Hereditary multiple exostoses
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Objective: To locate lost region of tumor suppressor gene on chromosome 13q in squamous cell carcinoma of the larynx (LSCC) and to provide clues and evidence for discovering and locating new suppressor gene. Methods: Loss of heterozygosity (LOH) on chromosome 13q was analyzed in 58 LSCC patients by microsatellite polymorphic sequences in loci D13S765 (13q13), RBI.20 (13q14.2), D13S133 (13q14.3) and D13S318 (13q21) on chromosome 13 by PCR. Results: There weren’t any LOH on chromosome 13q in 3 cases with preinvasive LSCC. Forty-five percentage (24/53) of the 53 invasive LSCC cases showed LOH at one or more loci on chromosome 13q region. The highest percentage of LOH on chromosome 13q was 52% (22/53) at D13S765 locus. Conclusion: The deletion region on chromosome 13q was located near by D13S765 locus which is centromeric to RBI. In this region there is suppressor gene, which is related to the genesis and development of LSCC, possibly including RBI. The inactivation of these suppressor genes may be related to the genesis and development of invasive LSCC.
Chromosome 13
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Hunter disease or mucopolysaccharidosis type II is an X-linked disease caused by the deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS). The IDS gene (24 kb) contains nine exons and has been completely sequenced. A pseudogene (IDS-2 locus) distal to the functional IDS gene has recently been identified. This work reports the characterization of IDS gene alterations in two severely affected patients. Patient 1 has a partial deletion that removes exons I to VI and extends about 200 kb upstream of the IDS gene. Patient 2 has an internal deletion of exons IV, V, VI, and VII, which results from an IDS gene-pseudogene exchange between highly homologous regions. In the rearranged gene, the junction intron contains pseudogene intron 3- and intron 7-related sequences. An interchromosomal recombination is probably the cause of this rearranged X chromosome. © 1996 Wiley-Liss, Inc.
Pseudogene
Mucopolysaccharidosis type II
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Chromosome 13
Human genetics
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We have characterized two intragenic polymorphisms in the neurofibromatosis type 1 (NF1) gene by direct sequencing of PCR products. The variants for these polymorphisms were initially detected on Hydrolink gels. One of the polymorphisms involves a G to A transition in intron 41 at the 28th base upstream of exon 42 with an observed 'G'/'A' heterozygosity of 0.42. The other polymorphism is a T to C transition in intron 16 at the 16th base upstream of exon 17 with an observed 'T'/'C' heterozygosity of 0.09. In combination with other documented polymorphisms in the NF1 gene, these variants should assist in genetic analysis of NF1 families.
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Epidermoid carcinoma
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Hunter disease or mucopolysaccharidosis type II is an X-linked disease caused by the deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS). The IDS gene (24 kb) contains nine exons and has been completely sequenced. A pseudogene (IDS-2 locus) distal to the functional IDS gene has recently been identified. This work reports the characterization of IDS gene alterations in two severely affected patients. Patient 1 has a partial deletion that removes exons I to VI and extends about 200 kb upstream of the IDS gene. Patient 2 has an internal deletion of exons IV, V, VI, and VII, which results from an IDS gene-pseudogene exchange between highly homologous regions. In the rearranged gene, the junction intron contains pseudogene intron 3- and intron 7-related sequences. An interchromosomal recombination is probably the cause of this rearranged X chromosome. © 1996 Wiley-Liss, Inc.
Pseudogene
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Journal Article Viral K-ras detects two TaqI polymorphisms, one for KRAS1 on chromosome 6 and the other for KRAS2 on chromosome 12 Get access M. Okamoto, M. Okamoto Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Sato, C. Sato Search for other works by this author on: Oxford Academic PubMed Google Scholar N. Tsuchida, N. Tsuchida 1Department of Oral Microbiology, Tokyo Medical and Dental UniversityYushima, Tokyo 113, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar M.C. Yoshida, M.C. Yoshida 2Chromosome Research Unit, Hokkaido UniversitySapporo 060, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar C. Ezawa, C. Ezawa Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Miyaki M. Miyaki Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 5, 11 March 1988, Page 2363, https://doi.org/10.1093/nar/16.5.2363 Published: 11 March 1988
TaqI
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A previously undescribed gene, Saitohin (STH), has been discovered in the intron between exons 9 and 10 of the human tau gene. STH is an intronless gene that encodes a 128-aa protein with no clear homologs. The tissue expression of STH is similar to tau , a gene that is implicated in many neurodegenerative disorders. In humans, a single nucleotide polymorphism that results in an amino acid change (Q7R) has been identified in STH and was used in a case control study. The Q7R polymorphism appears to be over-represented in the homozygous state in late onset Alzheimer's disease subjects.
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Natural selection influences synonymous mutations and synonymous codon usage in many eukaryotes to improve the efficiency of translation in highly expressed genes. Recent studies of gene composition in eukaryotes have shown that codon usage also varies independently of expression levels, both among genes and at the intragenic level. Here, we investigate rates of evolution (Ks) and intensity of selection (γs) on synonymous mutations in two groups of genes that differ greatly in the length of their exons, but with equivalent levels of gene expression and rates of crossing-over in Drosophila melanogaster. We estimate γs using patterns of divergence and polymorphism in 50 Drosophila genes (100 kb of coding sequence) to take into account possible variation in mutation trends across the genome, among genes or among codons. We show that genes with long exons exhibit higher Ks and reduced γs compared to genes with short exons. We also show that Ks and γs vary significantly across long exons, with higher Ks and reduced γs in the central region compared to flanking regions of the same exons, hence indicating that the difference between genes with short and long exons can be mostly attributed to the central region of these long exons. Although amino acid composition can also play a significant role when estimating Ks and γs, our analyses show that the differences in Ks and γs between genes with short and long exons and across long exons cannot be explained by differences in protein composition. All these results are consistent with the Interference Selection (IS) model that proposes that the Hill-Robertson (HR) effect caused by many weakly selected mutations has detectable evolutionary consequences at the intragenic level in genomes with recombination. Under the IS model, exon size and exon-intron structure influence the effectiveness of selection, with long exons showing reduced effectiveness of selection when compared to small exons and the central region of long exons showing reduced intensity of selection compared to flanking coding regions. Finally, our results further stress the need to consider selection on synonymous mutations and its variation—among and across genes and exons—in studies of protein evolution.
Synonymous substitution
Silent mutation
Coding region
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