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At least 127 records · Page 7Linked to original sources
PubMed2000

Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of H19-associated CTCF-binding sites in colorectal cancer.

We hypothesize that loss of imprinting (LOI) of the insulin-like growth factor II (IGF2) gene is associated with a predisposition to sporadic colorectal cancer. We confirmed a previously known strong correlation between LOI and microsatellite instability and showed that LOI was not a consequence of microsatellite instability or mismatch repair deficiency. LOI of IGF2 correlated strongly with biallelic hypermethylation of a core of five CpG sites in the insulator region of IGF2/H19, which is a known CTCF-binding element. As this methylation-dependent LOI was present in both tumors and normal colonic mucosa, it is possible that hypermethylation creates a field defect predisposing to cancer.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Comparison of the power and accuracy of biallelic and microsatellite markers in population-based gene-mapping methods.

Because of their great abundance and amenability to fully automated genotyping, single-nucleotide polymorphisms (SNPs) and simple insertion/deletion are emerging as a new generation of markers for positional cloning. Although the efficiency and cost associated with the markers are important in the mapping of human disease genes, the power to detect the linkage between the marker and the disease locus, as well as the accuracy of the estimation of the map location of the disease gene, dictate the selection of the markers. Both the power and the accuracy depend not only on the type of the markers but also on other factors, such as the age of the disease mutation, the magnitude of the genetic effect, the marker-allele distribution in the population, mutation rates of marker loci, the frequency of the disease allele, the recombination fraction, and the methods for mapping the human disease genes. In this article, we develop a mathematical framework and the analytical formulas for calculation of the power and the accuracy and investigate the impact that the aforementioned factors have on the power and the accuracy, by using two population-based gene-mapping methods-likelihood-based linkage-disequilibrium mapping and the transmission/disequilibrium test, for both biallelic SNPs and microsatellites. These studies provide not only guidance in selection of the markers and in the design of the sample scheme for positional cloning but also insight into the biological bases of the mapping of human disease genes.

Alleles↗
PubMed2000

Linkage disequilibrium analysis of biallelic DNA markers, human quantitative trait loci, and threshold-defined case and control subjects.

Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to more complex human quantitative traits have not been straightforward. In this article, we consider the analysis of biallelic DNA marker loci and human quantitative trait loci in settings that involve sampling individuals from opposite ends of the trait distribution. The purpose of this sampling strategy is to enrich samples for individuals likely to possess (and not possess) trait-influencing alleles. Simple statistical models for detecting LD between a trait-influencing allele and neighboring marker alleles are derived that make use of this sampling scheme. The power of the proposed method is investigated analytically for some hypothetical gene-effect scenarios. Our studies indicate that LD mapping of loci influencing human quantitative trait variation should be possible in certain settings. Finally, we consider possible extensions of the proposed methods, as well as areas for further consideration and improvement.

Alleles↗
PubMed2002

Biallelic germline mutations in MYH predispose to multiple colorectal adenoma and somatic G:C-->T:A mutations.

We have recently demonstrated that inherited defects of the base excision repair gene MYH predispose to multiple colorectal adenomas and carcinoma. Three affected siblings from a single British family were identified as Y165C/G382D compound heterozygotes and both missense mutations were shown to be functionally compromised. Here, we report the identification of seven further unrelated patients with >100 colorectal adenomas (six with colorectal cancer) and biallelic germline mutations in MYH: four were homozygous for truncating mutations, two were homozygous for Y165C and one was a Y165C/G382D compound heterozygote. As predicted from studies of the bacterial and yeast orthologues of MYH, colorectal tumours from affected individuals displayed a significant excess of somatic G:C-->T:A mutations in APC, as compared to sporadic ( chi(2)=242.96, P<10(-20)) or FAP-associated ( chi(2)=194.85, P<10(-20)) colorectal tumours. The sequence immediately downstream of the somatic G:C-->T:A mutations was predominantly AA, irrespective of the nature of the germline MYH mutations. These findings confirm the role of MYH in colorectal adenoma and carcinoma predisposition.

Adenoma↗
PubMed1994

Monoallelic expression of normal mRNA in the PIT1 mutation heterozygotes with normal phenotype and biallelic expression in the abnormal phenotype.

The combined deficiency of thyrotropin, growth hormone and prolactin, caused by PIT1 abnormality manifests in the homozygous or heterozygous state. We studied a patient having an allele with Arg271Trp mutation, which produces clinical symptoms in heterozygotes by a dominant-negative effect. However, in the family, her father, grandmother and aunts had the same mutation without clinical symptoms, although the proband had typical phenotypic expression. We analyzed the PIT1 transcript in peripheral lymphocytes by reverse transcription-polymerase chain reaction and found monoallelic expression of normal allele in the father and grandmother and skewed pattern of biallelic expression in the proband. The phenotypic expression of PIT1 abnormality may depend on different transcription of the PIT1 gene.

Alleles↗
PubMed1995

A novel L23-related gene 40 kb downstream of the imprinted H19 gene is biallelically expressed in mid-fetal and adult human tissues.

The closely linked IGF2 and H19 genes on human chromosome 11p15.5 are monoallelically expressed as a result of genomic imprinting and show altered expression in Wilms' tumors (WTs). To map regional imprinting we have sought to isolate additional human genes close to IGF2/H19 and to characterize their allelic expression patterns. Here we report a novel gene, provisionally named L23MRP [L23 (mitochondrial)-related protein], which is oriented 'tail-to-tail' with H19 and is transcribed to within 40 kb of the last H19 exon. L23MRP is expressed biallelically in many mid-fetal and adult human tissues. This gene is also expressed at normal levels in WTs which have lost expression of H19 either via loss of the maternal chromosome 11p15.5 or via an epigenetic pathway involving site-specific DNA hypermethylation. These data indicate that, at least in post-embryonic stages, L23MRP is functionally insulated from the IGF2/H19 imprinted domain.

Adult↗
PubMed1996

A novel human homologue of yeast nucleosome assembly protein, 65 kb centromeric to the p57KIP2 gene, is biallelically expressed in fetal and adult tissues.

Three genes on 11p15.5 are known to undergo genomic imprinting. The gene for insulin-like growth factor II (IGF2) is normally expressed from the paternal allele, while H19 and p57KIP2, a cyclin-dependent kinase inhibitor, are expressed from the maternal allele. Five germline balanced chromosomal rearrangement breakpoints from patients with Beckwith-Wiedemann syndrome (BWS) have been mapped to 11p15.5 between p57KIP2 and IGF2, and all are derived from the maternal chromosome. By positional cloning from BWS breakpoints, we have isolated a gene 100 kb and 65 kb centromeric to the proximal end of this BWS breakpoint cluster and p57KIP2, respectively. This gene is homologous to yeast nucleosome assembly protein (NAP1) and to a human homologue of NAP1, and we designate it hNAP2 (human nucleosome assembly protein 2). hNAP2 diverges in its expression pattern from IGF2, H19, and p57KIP2, and it shows biallelic expression in all tissues tested. Thus, hNAP2 is functionally insulated from the imprinting domain of 11p15.

Adult↗
PubMed1994

Biallelic expression of the H19 and IGF2 genes in human testicular germ cell tumors.

BACKGROUND: Genomic imprinting, resulting in the nonequivalence of expression of homologue genes depending on their parental origin, is an important determinant of the developmental potential of embryonic cells. The expression of two genes, one termed H19 and the other IGF2, has been found to be necessary for proper embryonal development in humans. Both the murine and human H19 and IGF2 genes are normally characterized by monoallelic expression. PURPOSE: Because testicular germ cell tumors of adults originate from an early germ cell and, to a certain extent, mimic normal embryonal development, we investigated the patterns of allelic expression of the H19 and IGF2 genes in these tumors to determine if genomic imprinting, or a disturbance of it, is involved in their pathogenesis. METHODS: Specimens of normal tissue and tumor tissue were obtained from 20 patients with testicular germ cell tumors; 10 of the patients had seminomas and 10 had nonseminomatous germ cell tumors. To determine if there was heterozygosity of the Alu I and Apa I restriction site polymorphism in the H19 and IGF2 genes, respectively, DNA was isolated from cells of the peripheral blood of these patients, then subjected to polymerase chain reaction (PCR) amplification, restriction enzyme digestion, and electrophoresis in agarose gels. If heterozygosity was determined, a similar analysis was performed on complementary DNA (cDNA) obtained from matched tumor RNA by reverse transcription and subsequent PCR amplification (RT-PCR). If monoallelic expression was found, matched tumor DNA was studied for possible deletions. RESULTS: Tumor samples from 14 of 20 and 11 of 20 patients were informative for allelic expression patterns of the H19 and IGF2 genes, respectively. Analysis of the products of RT-PCR showed biallelic expression of the H19 gene in 12 testicular germ cell tumors (patients numbered 6, 8-13, 15, 16, and 18-20) and of the IGF2 gene in 10 testicular germ cell tumors (patients numbered 1, 3, 6, 8-13, and 15-20). The three remaining tumors (patients numbered 2, 4, and 5) had lost the nonexpressed allele. CONCLUSIONS: In contrast to normally developing embryos, testicular germ cell tumors show a consistent expression of both parental alleles of the H19 and IGF2 genes. IMPLICATIONS: Testicular germ cell tumors of adults may develop from precursor cells in which the imprinting has been either erased or subjected to a consistent relaxation of its effect.

Alleles↗
PubMed2000

Maternal chromosome 7 hetero/isodisomy in Silver-Russell syndrome and PEG1 biallelic expression.

Silver-Russell syndrome (SRS) is characterized by a severe intrauterine and postnatal growth retardation, relative macrocephaly associated with 'mild' facial anomalies. The diagnostic importance of skeletal asymmetry remains controversial. The aetiology of the syndrome is heterogeneous. Maternal uniparental disomy of chromosome 7 (mUPD7) has been reported in approximately 7% of patients, but two carriers of chromosomal abnormalities involving the band 17q25 have also been described. We investigated a clinically selected sample of 20 SRS patients for the presence of mUPD7 using polymorphic microsatellite markers spanning the whole chromosome. Maternal UPD7 was found in only one patient corresponding to an incidence of 5%. The allelic distribution in this patient was consistent with heterodisomy. Segregation analysis of chromosome 14 and 16 showed a biparental contribution in all the 20 patients. Blood RNA from the mUPD7 patient and a normal donor were evaluated for the expression of Paternally Expressed Gene (PEG1), an imprinted gene on chromosome 7q32. Biallelic expression of the gene in adult blood tissues was found in both samples. Our results confirm the causal role of mUPD7 in a minority of SRS patients.

Abnormalities, Multiple↗
PubMedDate not supplied

Asynchronous replication of biallelically expressed loci: a new phenomenon in Turner syndrome.

PURPOSE: Transcriptional activity of genes is related to their replication timing; alleles showing the common biallelic mode of expression replicate synchronously, whereas those with a monoallelic mode of expression replicate asynchronously. Here the level of synchronization in replication timing of alleles was determined in subjects with Turner syndrome. METHODS: Fluorescence in situ hybridization was used for three loci not linked to X chromosome, in lymphocytes derived from 12 controls, 3 individuals with Turner, and 4 with mosaic Turner syndrome. RESULTS: In cells derived from controls, each pair of alleles replicated synchronously; yet these same alleles replicated asynchronously in cells monosomic for X chromosome derived from Turner and mosaic Turner patients. When the level of 45,X was low in the mosaic samples, the replication pattern of the 46,XX cells was normal. However, in samples with a high level of mosaicism, a significantly increased asynchronous replication was detected in the 46,XX cells. CONCLUSION: An altered temporal replication control in Turner syndrome affecting the aneuploid and euploid cells is shown. This alteration may potentially be involved in the determination of the syndrome.

Alleles↗
PubMed1995

Biallelic expression of imprinted genes in the mouse germ line: implications for erasure, establishment, and mechanisms of genomic imprinting.

Genomic imprinting in mammals determines parental-specific (monoallelic) expression of a relatively small number of genes during development. Imprinting must logically be imparted in the germ line, where inherited maternal and paternal imprinting is erased and new imprinting established according to the individual's sex. We have assessed the allele-specific expression of four imprinted genes, two of which exhibit maternal-specific (H19 and Igf2r) and two of which exhibit paternal-specific (Igf2 and Snrpn) monoallelic somatic expression, in the germ line of F1 hybrid mice utilizing quantitative RT-PCR single-nucleotide primer extension assays. The expression of each gene was biallelic in the female and male germ line from the time that migratory mitotic PGCs entered the embryonic genital ridge and throughout gametogenesis, except that H19 RNA was not detected late in gametogenesis. These findings demonstrate that inherited imprinting is erased, or not recognized, in germ cells by the time of genital ridge colonization; also that new imprinting may not be established until late in gametogenesis, or that it is incomplete or not recognized at this stage. Regardless of imprinting status, a generalized neutralization of imprinting is evident in the germ line, associated with the totipotent state of this unique cell lineage.

Alleles↗
PubMed2026

Biallelic Variants in ATP1A4 Are Associated with Oligoasthenoteratozoospermia and Male Infertility.

Male infertility, often caused by structural and functional sperm defects, remains genetically unexplained in a substantial proportion of cases. ATP1A4 encodes a testis-specific isoform of the Na+, K+-ATPase, a membrane enzyme crucial for maintaining cellular ionic homeostasis. Previous studies on Atp1a4 knockout mice have demonstrated severe defects in sperm motility and flagellar architecture; however, the contribution of ATP1A4 variants to human male reproduction remains to be elucidated. In this study, we identified compound biallelic variants in ATP1A4, a missense variant (c.2578&#x2009;T>A, p.Tyr860Asn) and a frameshift variant (c.2582del, p.Gly861Aspfs*5), in a patient presenting with severe oligoasthenoteratozoospermia. Both variants markedly affected ATP1A4 protein expression. Morphological analyses revealed coiled and folded flagella, disrupted mitochondrial sheaths, and irregular head morphology in the patient's spermatozoa. Expression profiling revealed that ATP1A4 was highly enriched in post-meiotic spermatids and localized along the entire flagellum of mature sperm in both humans and mice, indicating a critical role in flagellar assembly and structural integrity. Notably, intracytoplasmic sperm injection (ICSI) in this patient resulted in low fertilization efficiency and failed implantation, suggesting a potential adverse impact of ATP1A4 deficiency on sperm functional competence beyond motility. These findings broaden the genetic spectrum of oligoasthenoteratozoospermia and highlight ATP1A4 as a potential gene associated with human male infertility.

Male↗
PubMed1995

Biallelic DNA rearrangements and deletions within the BCL-6 gene in B-cell non-Hodgkin's lymphoma.

Chromosomal translocations involving band 3q27 are recently described common specific cytogenetic abnormalities in B-cell neoplasms, and the BCL-6 gene, identified on 3q27, was shown to be disrupted and over-expressed in lymphoma cells having these chromosomal translocations. In the present study we found rearrangements within the BCL-6 gene in seven out of 35 cases with B-cell non-Hodgkin's lymphoma (NHL). Further analysis revealed that three of these patients with BCL-6 abnormality had multiple rearranged bands hybridized with probes from a single restriction fragment within the major translocation cluster (MTC), suggesting that independent DNA rearrangements would occur on both alleles. Additionally, Southern blot analysis indicated that three patients carry deletions encompassing the area containing the first exon of the BCL-6 gene. Our results suggest that biallelic DNA rearrangements and deletions would occasionally occur in NHL patients with BCL-6 abnormality.

Adult↗
PubMed2007

Dissecting the genetic history of São Tomé e Príncipe: a new window from Y-chromosome biallelic markers.

Twenty biallelic Y chromosome markers were analyzed in Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. While most male lineages belonged to sub-Saharan haplogroups, the component of European origin added up 23.9% in the archipelago. This contrasts with the reported absence of European mtDNA lineages, and the combined findings testify to a strong sex-biased admixture process during the long-lasting colonial period in São Tomé e Príncipe. Furthermore, the male mediated European component was clearly found to be out of proportion to the small demographic impact of the Portuguese on the islands, reflecting high variance in the reproductive success of the individuals that contributed to its peopling. The male portion of European ancestry was 33.3% in Forros, 27.3% in Tongas and approximately two-fold less, 14.5%, in Angolares. The Angolares also showed the lowest haplogroup diversity and the most reduced number of different haplogroups. The current results reinforce our previous evidence pointing to remarkable restrictions in gene flow between Angolares and other São Tomean inhabitants, in agreement with their considerable isolation and confinement to the south-eastern tip of São Tomé until recently.

Africa↗
PubMed2002

Biallelic inactivation of BRCA2 in Fanconi anemia.

Fanconi anemia (FA) is a rare autosomal recessive cancer susceptibility disorder characterized by cellular hypersensitivity to mitomycin C (MMC). Six FA genes have been cloned, but the gene or genes corresponding to FA subtypes B and D1 remain unidentified. Here we show that cell lines derived from FA-B and FA-D1 patients have biallelic mutations in BRCA2 and express truncated BRCA2 proteins. Functional complementation of FA-D1 fibroblasts with wild-type BRCA2 complementary DNA restores MMC resistance. Our results link the six cloned FA genes with BRCA1 and BRCA2 in a common pathway. Germ-line mutation of genes in this pathway may result in cancer risks similar to those observed in families with BRCA1 or BRCA2 mutations.

Alleles↗
PubMed2025

Biallelic loss-of-function variants in C19orf44 lead to retinal degeneration.

BACKGROUND: Inherited retinal diseases (IRDs) are a group of disorders often resulting in progressive vision loss, ultimately leading to blindness. A significant portion of their genetic causes remain unresolved, partly due to undiscovered disease-associated genes or variants. This study aimed to identify novel genetic links to IRDs. METHODS: All patients underwent comprehensive ophthalmological evaluation, including retinal imaging (fundus autofluorescence and macular optical coherence tomography) and electroretinogram testing. Whole exome sequencing and whole genome sequencing were performed on patients with clinically unsolved IRD, and data were analysed using an in-house pipeline to identify causal variants. Subsequently, Sanger sequencing was performed to confirm identified variants. RESULTS: Three unrelated patients from Europe, Middle East and East Asia were identified with unique late-onset retinal degeneration (Stargardt-like phenotype) associated with biallelic loss-of-function (LoF) variants in C19orf44 (HGNC: 26141), a gene of unknown function. The homozygous variant NM_032207.2:c.549_550del;p.Ser185Profs*2 was identified in two unrelated patients (European and Middle Eastern). Moreover, an East Asian patient had likely compound heterozygous LoF variants (NM_032207.2:c.1168C>T;p.Gln390*/c.976_977del;p.Leu326Lysfs*15). CONCLUSIONS: Our findings establish C19orf44 as a novel disease-causing gene for IRD with Stargardt-like phenotype, expanding the genetic landscape of retinal degeneration.

Humans↗
PubMed2001

Reconsideration of biallelic inactivation of the VHL tumour suppressor gene in hemangioblastomas of the central nervous system.

OBJECTIVES: Cerebellar haemangioblastoma occurs sporadically or as a component tumour of autosomal dominant von Hippel-Lindau disease. Biallelic inactivation of the VHL tumour suppressor gene, which is located on chromosome 3p, has been shown to be involved in the pathogenesis of both tumour entities. Mechanisms of VHL inactivation are intragenic mutations, mitotic recombination events, and hypermethylation of the promoter region. The systematic and complete examination of these genetic and epigenetic phenomena in large series of von Hippel-Lindau disease related and sporadic hemangioblastomas has, thus far, not been performed. METHODS: In the largest series to date, 29 von Hippel-Lindau disease associated and 13 sporadic haemangioblastomas were investigated for all suggested inactivating mechanisms of the VHL gene using single strand conformational polymorphism (SSCP), loss of heterozygosity (LOH), and methylation analyses. Additionally, corresponding blood samples of all patients were screened for VHL germline mutations by SSCP and Southern blotting. RESULTS: Germline mutations were identified in 94% of patients with von Hippel-Lindau disease and their tumours and 62% of these hemangioblastomas showed LOH of chromosome 3p. Of the 13 sporadic tumours, 23% showed a single somatic mutation of the VHL gene that was not present in the germline. 3p LOH was identified in 50% of informative sporadic tumours. No von Hippel-Lindau disease related or sporadic tumour demonstrated VHL promoter hypermethylation. CONCLUSIONS: For most von Hippel-Lindau disease related haemangioblastomas, the inactivation or loss of both alleles of the VHL gene, as predicted by the Knudson two hit theory, is required. However, in a subset of tumours including most sporadic haemangioblastomas, the genetic pathways involved in tumorigenesis have yet to be defined and may represent alterations of a different pathway or pathways.

Adolescent↗
PubMed2005

Targeted biallelic inactivation of Pten in the mouse prostate leads to prostate cancer accompanied by increased epithelial cell proliferation but not by reduced apoptosis.

The PTEN tumor suppressor gene is frequently inactivated in human tumors, including prostate cancer. Based on the Cre/loxP system, we generated a novel mouse prostate cancer model by targeted inactivation of the Pten gene. In this model, Cre recombinase was expressed under the control of the prostate-specific antigen (PSA) promoter. Conditional biallelic and monoallelic Pten knock-out mice were viable and Pten recombination was prostate-specific. Mouse cohorts were systematically characterized at 4 to 5, 7 to 9, and 10 to 14 months. A slightly increased proliferation rate of epithelial cells was observed in all prostate lobes of monoallelic Pten knock-out mice (PSA-Cre;Pten-loxP/+), but minimal pathologic changes were detected. All homozygous knock-out mice (PSA-Cre;Pten-loxP/loxP) showed an increased size of the luminal epithelial cells, large areas of hyperplasia, focal prostate intraepithelial neoplasia lesions and an increased prostate weight at 4 to 5 months. More extensive prostate intraepithelial neoplasia and focal microinvasion occurred at 7 to 9 months; invasive prostate carcinoma was detected in all male PSA-Cre;Pten-loxP/loxP mice at 10 to 14 months. At 15 to 16 months, a rare lymph node metastasis was found. In hyperplastic cells and in tumor cells, the expression of phospho-AKT was up-regulated. In hyperplastic and tumor cells, expression of luminal epithelial cell cytokeratins was up-regulated; tumor cells were negative for basal epithelial cell cytokeratins. Androgen receptor expression remained detectable at all stages of tumor development. The up-regulation of phospho-AKT correlated with an increased proliferation rate of the epithelial cells, but not with a reduced apoptosis.

Age Factors↗