Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “clonal analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed1994

Investigation of methylation at Hha I sites using the hypervariable probe M27 beta allows improved clonal analysis in myeloid leukaemia and demonstrates differences in methylation between leukaemic and remission samples.

The methylation-sensitive enzyme Hha I has been used to assess the differentially methylated patterns on active and inactive X-chromosomes at the DXS255 locus recognized by the hypervariable probe M27 beta. The X-chromosome inactivation ratios obtained from 37 haematologically normal females using PstI and HhaI and correlated well with results obtained using PstI Hpa II (r = 0.97), and in 19 individuals with values obtained probing for either phosphoglycerate kinase or hypoxanthine phosphoribosyl transferase (r = 0.92). At least one Hha I site was found to be unmethylated on all alleles on inactive X-chromosomes. A monoclonal or oligoclonal pattern could be obtained by digestion with Hha I in 18/22 (82%) patients with acute myeloid leukaemia who had previously shown hypermethylation of both alleles using Hpa II, although in six of these patients differences in methylation could still be demonstrated between leukaemic and remission samples.

Acute Disease↗
PubMed1998

Clonal analysis of a human antibody response. III. Nucleotide sequences of monoclonal IgM, IgG, and IgA to rabies virus reveal restricted V kappa gene utilization, junctional V kappa J kappa and V lambda J lambda diversity, and somatic hypermutation.

In previous work, we generated four IgM, five IgG1, and one IgA1 mAbs to rabies virus using B cells from four subjects vaccinated with inactivated rabies virus, a thymus-dependent (TD) mosaic Ag, and sequenced the mAb V(H)DJ(H) genes. Here, we have cloned the V kappa J kappa and V lambda J lambda genes to complete the primary structure of the Ag-binding site of these mAbs. While the anti-rabies virus mAb selection of VA genes (2e.2.2 twice, DPL11, and DPL23) reflected the representation of the V lambda genes in the human haploid genome (stochastic utilization), that of V kappa genes (O2/O12 twice, O8/O18, A3/A19, A27, and L2) did not (p = 0.0018) (nonstochastic utilization). Furthermore, the selection of both V kappa and V lambda genes by the anti-rabies virus mAbs vastly overlapped with that of 557 assorted V kappa J kappa rearrangements, that of 253 V lambda J lambda rearrangements in lambda-type gammopathies, and that of other Abs to thymus-dependent Ags, including 23 anti-HIV mAbs and 51 rheumatoid factors, but differed from that of 43 Abs to Haemophilus influenzae type b polysaccharide, a prototypic thymus-independent (TI) Ag. The anti-rabies virus mAb V kappa J kappa and V lambda J lambda segments displayed variable numbers of somatic mutations, which, in mAb58 and the virus-neutralizing mAb57, entailed a significant concentration of amino acid replacements in the complementarity-determining regions (p = 0.0028 and p = 0.0023, respectively), suggesting a selection by Ag. This Ag-dependent somatic selection process was superimposed on a somatic diversification process that occurred at the stage of B cell receptor for Ag rearrangement, and that entailed V gene 3' truncation and N nucleotide additions to yield heterogeneous CDR3s.

Amino Acid Sequence↗
PubMed1999

Molecular analysis of clonality in ovarian endometrial cysts.

Ovarian endometrial cysts, one of the typical manifestations of endometriosis, are classified as tumor-like lesions rather than as neoplasms. Clonality analysis provides important information on the histogenesis and progression of neoplastic diseases. It is generally accepted that most neoplasms are monoclonal in origin, while the clonality of endometrial cysts remains uncertain. In our study, the clonality of endometrial cysts was analyzed by means of polymerase chain reaction (PCR) based on restriction fragment length polymorphism of the X chromosome-linked human androgen receptor gene (HUMARA) and on random inactivation of the gene by methylation. We separated 21 fresh epithelial cell samples from 11 endometrial cysts and found that all were monoclonal in the methylation pattern of the human androgen receptor alleles. Moreover, in each of the five cysts where epithelial cells were sampled from multiple areas, the methylation patterns of all samples from a single cyst were identical. These data indicate that endometrial cysts are monoclonal in origin and suggest their neoplastic potential.

Adult↗
PubMed2001

Carcinosarcoma of the uterus: immunohistochemical and genetic analysis of clonality of one case.

BACKGROUND: Carcinosarcomas of the uterus are characterized by admixtures of malignant epithelial and stromal cells, and their histogenesis remains controversial. CASE: An operated case of carcinosarcoma of the uterus in a 49-year-old woman is reported with clonal analysis. The tumor was composed of carcinomatous, sarcomatous, and transitional elements in the frontal wall of the uterine body and therefore was diagnosed as a carcinosarcoma. On immunohistochemical analysis, the sarcomatous component proved negative for epithelial membrane antigen and keratin while both components were positive for vimentin. Analysis of X-chromosome inactivation showed the same pattern throughout and additionally, the same K-ras and p53 mutations were homogeneously detected. Microsatellite instability analysis showed loss of heterozygosity at D5S346 in the sarcomatous but not the carcinomatous component. CONCLUSIONS: This tumor appears monoclonal in line with the combination tumor theory, with late divergence in genetic alteration in the sarcomatous elements.

Carcinosarcoma↗
PubMed2003

Rabbit model for human EBV-associated hemophagocytic syndrome (HPS): sequential autopsy analysis and characterization of IL-2-dependent cell lines established from herpesvirus papio-induced fatal rabbit lymphoproliferative diseases with HPS.

Epstein-Barr virus-associated hemophagocytic syndrome (EBV-AHS) is often associated with fatal infectious mononucleosis or T-cell lymphoproliferative diseases (LPD). To elucidate the true nature of fatal LPD observed in Herpesvirus papio (HVP)-induced rabbit hemophagocytosis, reactive or neoplastic, we analyzed sequential development of HVP-induced rabbit LPD and their cell lines. All of the seven Japanese White rabbits inoculated intravenously with HVP died of fatal LPD 18 to 27 days after inoculation. LPD was also accompanied by hemophagocytic syndrome (HPS) in five of these seven rabbits. Sequential autopsy revealed splenomegaly and swollen lymph nodes, often accompanied by bleeding, which developed in the last week. Atypical lymphoid cells infiltrated many organs with a "starry sky" pattern, frequently involving the spleen, lymph nodes, and liver. HVP-small RNA-1 expression in these lymphoid cells was clearly demonstrated by a newly developed in situ hybridization (ISH) system. HVP-ISH of immunomagnetically purified lymphoid cells from spleen or lymph nodes revealed HVP-EBER1+ cells in each CD4+, CD8+, or CD79a+ fraction. Hemophagocytic histiocytosis was observed in the lymph nodes, spleen, bone marrow, and thymus. HVP-DNA was detected in the tissues and peripheral blood from the infected rabbits by PCR or Southern blot analysis. Clonality analysis of HVP-induced LPD by Southern blotting with TCR gene probe revealed polyclonal bands, suggesting polyclonal proliferation. Six IL-2-dependent rabbit T-cell lines were established from transplanted scid mouse tumors from LPD. These showed latency type I/II HVP infection and had normal karyotypes except for one line, and three of them showed tumorigenicity in nude mice. These data suggest that HVP-induced fatal LPD in rabbits is reactive polyclonally in nature.

Animals↗
PubMed2001

[Development and preliminary analysis for EBV clonality using non-RI probe].

We develop a method for EBV clonality analysis by southern blot hybridization using Non-RI probes directed to EBV genome. We also tried to use newly developed method for several cells, which have been known as EBV genome carrier, and for a clinically diagnosed specimen from patients of infectious mononucleosis (IM) and chronic active EBV infection(CAEBV). Non-RI probe(directed to terminal repeat of EBV genome, TR probe) were made by following ways; The Xho I fragment(1.9 Kb) of B95-8 cells(carrier of EBV genome) was amplified by PCR, and the product was cloned into pBluescript, and cloned DNA were labeled by digoxigenin(Dig) after purification. The TR probes did not hybridize with DNA from other herpes viruses and Ramos cells(EBV-free cell line). When TR probe used against peripheral blood mononuclear cells(PBMCs) from a CAEBV patient, pattern was monoclonal as same as the case of Raji cells. In the case of B95-8 cells and PBMCs of IM patient, patterns were polyclonal. These results were the same as those of previously reported. This method was possible to detect about 0.3% target Raji's DNA from the mixture of Raji and Ramos cells. Above results indicated that this newly developed method was considered to be superior method in specificity and sensitivity, and also suggested that it was useful for analyzing the clonality of EBV infected cells in daily clinical examinations without radiological equipment and facilities.

Blotting, Southern↗
PubMed2003

Analysis of the clonality of ectopic glands in peritoneal endometriosis using laser microdissection.

OBJECTIVE: To investigate the clonality of ectopic gland cells in peritoneal endometriosis. DESIGN: Prospective study. University hospital. PATIENT(S): Seventeen women with surgically diagnosed endometriosis. INTERVENTION(S): Samples of peritoneal endometriotic lesions were obtained from patients during laparoscopic surgery. MAIN OUTCOME MEASURE(S): Clonality analysis used the laser microdissection technique, a phosphoglycerate kinase (PGK) gene polymorphism assay, and an androgen receptor (AR) gene polymorphism assay after digestion of the DNA with methylation-sensitive endonuclease. RESULT(S): Each ectopic gland of the peritoneal endometriotic lesion showed a monoclonal pattern in both the PGK gene and AR gene assays, but the methylation pattern of the PGK gene and/or AR gene was divergent among adjacent glands in the lesion. These data indicate that the peritoneal endometriotic lesions are multicellular in origin, although individual glands of the lesion are derived from single precursor cells. CONCLUSION(S): The colored peritoneal endometriotic lesion in the present study was multicellular in origin. Peritoneal endometriotic lesions may thus be initiated by transplantation of a cluster of eutopic endometrial tissues into the pelvis.

Clone Cells↗
PubMed2001

Analysis of clonality in cutaneous T cell lymphoma and associated diseases.

The T cell receptor (TCR) is the antigen-specific receptor for T cells. During its differentiation, each T cell undergoes rearrangement of its TCR genes. This results in novel nucleotide sequences that constitute a unique signature or fingerprint for each T cell and all its clonal progeny. Analysis of TCR gene rearrangements in cutaneous T cell lymphoma (CTCL) has lead to several findings concerning CTCL tumor biology. First, like most other lymphomas, CTCL is a monoclonal lymphoproliferative disorder. Second, rather than being truly a cutaneous lymphoma, CTCL is actually a lymphoma of the skin-associated lymphoid tissue (SALT). Even when disease appears confined to the skin clinically, there can be low-level trafficking of tumor cells through the peripheral lymph nodes via the lymphatics and blood vessels. Furthermore, CTCL is a mature SALT lymphoma capable of trafficking to sites of cutaneous inflammation analogous to normal SALT T cells. Third, the earliest manifestation of CTCL may be "clonal dermatitis." This is a form of chronic dermatitis that harbors a dominant T cell clone but lacks histologic features diagnostic for CTCL. About 25% of clonal dermatitis cases progress to overt CTCL within five years. Fourth, other lymphoproliferative disorders that are associated with CTCL share the same TCR gene rearrangements and therefore arise as subclones of the original tumor. These include lymphomatoid papulosis, large-cell lymphoma, and Hodgkin's disease.

Clone Cells↗
PubMed1994

Analysis of clonality by amplification of short tandem repeats. Carcinomas of the female reproductive tract.

The clonal composition of cancers of the female reproductive tract was evaluated by analysis of patterns of X-chromosome inactivation. Using DNA extracted from frozen tissues or paraffin-embedded archival specimens as template, polymerase chain reaction (PCR) was performed to generate amplified DNA fragments of exon 1 of the X-linked androgen receptor gene, which contains a highly polymorphic trinucleotide repeat. Predigestion of tumor DNA with methylation-sensitive restriction endonuclease Hha I or Hpa II permitted selective PCR amplification from the methylated (uncleaved) allele. Of a total of 54 tumors analyzed, 50 cases showed heterozygosity (93%) and were therefore informative for clonal analysis. Monoclonal composition of the tumors was suggested in a total of 49 of 50 cases, including 12 adenocarcinomas of the uterine endometrium, 13 squamous cell carcinomas of the uterine cervix, 6 adenocarcinomas of the uterine endocervix, and 18 epithelial tumors of the ovary. However, polyclonal composition was observed in one mucinous carcinoma of the ovary, in which we previously showed that both GGT-->GAT and GGT-->GTT mutations are present in > 20% of total K-ras copies in the tissue. Our studies demonstrate the utility of PCR amplification of highly polymorphic repetitive sequences for analysis of patterns of X-chromosome inactivation. This approach is practical for the analysis of clonal cell composition in a high proportion of both formalin-fixed and frozen archival tissues.

Carcinoma↗
PubMed2026

Clonal haematopoiesis of indeterminate potential and epigenetic age acceleration: Systematic review and meta-analysis.

Clonal haematopoiesis of indeterminate potential (CHIP) represents somatic mutations in haematopoietic stem cells that drive clonal expansion. Epigenetic age acceleration (EAA), estimated from DNA methylation (DNAm) clocks, may capture age-related changes in haematopoiesis. This systematic review and meta-analysis was conducted to synthesise evidence on associations between CHIP and EAA and explore shared biological mechanisms that may underlie this relationship. Six databases were searched from January 1, 2011, to June 6, 2025, adhering to PRISMA 2020. Random-effects meta-analyses were performed. Five studies comprising 7483 individuals (ages 55-79, 67.1% female) assessing associations between CHIP and DNAm clocks were included. Across studies, CHIP individuals had higher EAA than no-CHIP individuals, and larger clones were associated with higher EAA. Meta-analysis of three cross-sectional studies (n = 6946) showed that CHIP had higher EAA versus no-CHIP for Horvath1Age IEAA (mean difference, MD=2.84 years, 95% confidence interval, CI: 1.49-4.19), HannumAge EEAA (MD=2.31 years, 95% CI: 1.14-3.49), PhenoAge (MD=1.84 years, 95% CI: 0.96-2.71), and GrimAge (MD=1.20 years, 95% CI: 0.80-1.61). Both DNMT3A- and TET2-mutated CHIP were associated with higher EAA with TET2-mutated CHIP showing larger effect sizes and more consistent associations than DNMT3A-mutated CHIP across DNAm clocks tested. Higher EAA may also act as an effect modifier for morbidity and mortality in CHIP. Larger longitudinal studies are needed to verify a temporal relationship and determine whether EAA provides incremental prognostic value for morbidity and mortality in CHIP.

Humans↗
PubMed1990

Clonal repertoire analysis of murine B cells specific for repeat sequence antigens of Plasmodium falciparum.

Clonal analysis of the murine B-cell repertoire has been used to investigate the possible role of tandem repeat sequence epitopes of Plasmodium falciparum in immune evasion. A limiting dilution culture system was used whereby murine spleen cells were stimulated with the B-cell mitogen lipopolysaccharide (LPS) in the presence of 3T3 fibroblast filler cells. One in three B cells were shown to produce clones secreting immunoglobulin measurable by an ELISA. The frequency of antibody forming cell precursors (AFCp) specific for the 3' repeat epitopes of the ring injected erythrocyte surface antigen (RESA) was estimated in non-primed mice and found to be low. However, an accurate frequency determination was not possible using this method since the detection of the few positive cultures was found to depend on the presence of more than one AFCp or its products. Limiting dilution analysis was used to assess the frequency and repertoire of splenic AFCp at various times after immunization with a synthetic peptide of the RESA 3' repeat epitope (8 x 4-mer), presented in various ways. There was no marked increase in LPS-responsive AFCp specific for this antigen at the level of either IgM or IgG secretion. This was in marked contrast to the antibody response in vivo, where moderate IgG antibody titres, normally indicative of a secondary response, were seen in the serum of the same mice used for AFCp assay. This discrepancy between serum titre and AFCp frequency following immunization was not apparent with a non-malarial antigen, keyhole limpet haemocyanin (KLH). It was concluded that the LPS-stimulated limiting dilution culture system was not registering RESA-specific memory AFCp. These results raise the possibility that the malarial antigens are deficient in memory B-cell generation, or that secondary responses to these determinants may arise from a distinct B-cell progenitor which is non-responsive to LPS in vitro.

Adjuvants, Immunologic↗
PubMed1996

Demonstration of monoclonal origin of human parotid gland pleomorphic adenoma.

BACKGROUND: Parotid gland pleomorphic adenoma is histologically comprised of epithelial and mesenchymal elements. It remains to be established whether this neoplasm arises from epithelial and mesenchymal elements, or solely from the epithelial element. METHODS: In an attempt to resolve this issue, we have conducted clonal analysis on five pleomorphic adenomas. The method for clonal analysis was based on the trinucleotide repeat polymorphism of the x-chromosome-linked androgen receptor gene and on random inactivation of this gene by methylation. The epithelial and mesenchymal elements were obtained separately from the paraffin sections of the pleomorphic adenomas using a microdissection technique and then subjected to clonal analysis. RESULTS: Clonal analysis revealed that both epithelial and mesenchymal elements were monoclonal. In addition, the same allele of the androgen receptor gene was inactivated in both elements in every case. CONCLUSIONS: It is unlikely that the epithelial and mesenchymal elements of different origin happen to inactivate the same allele of the androgen receptor gene in all five tumors. Rather, it is more reasonable to consider that these two elements have a common single cell origin.

Adenoma, Pleomorphic↗
PubMed1997

Analysis of clonality in cytologic material using the polymerase chain reaction (PCR).

Immunoglobulin heavy chain (IgH) gene rearrangement analysis was performed on 27 fine needle aspiration (FNA) specimens (13 reactive hyperplasia, 11 B cell non-Hodgkin's lymphoma (B-NHL), one Hodgkin's disease and two suspicious of non-Hodgkin's lymphoma). Satisfactory amplification was achieved in 23/27 cases. A polyclonal pattern was seen in 14 cases (11 reactive hyperplasia, one B-NHL, one suspicious of lymphoma, one Hodgkin's disease). A monoclonal band was seen in nine cases (eight B-NHL, one reactive hyperplasia). Amplification was unsuccessful in four cases. Clonal analysis by PCR-based IgH gene rearrangement analysis can be successfully applied to FNA material and can be useful in diagnosis, but the results must be interpreted in conjunction with morphology and other ancillary information.

Biopsy, Needle↗
PubMed2003

Clonal tracking of autoaggressive T cells in polymyositis by combining laser microdissection, single-cell PCR, and CDR3-spectratype analysis.

Clonal expansions of CD8+ T cells have been identified in muscle and blood of polymyositis patients by PCR techniques, including T cell receptor (TCR) complementarity-determining region (CDR)3 length analysis (spectratyping). To examine a possible pathogenic role of these clonally expanded T cells, we combined CDR3 spectratyping with laser microdissection and single-cell PCR of individual myocytotoxic T cells that contact, invade, and destroy a skeletal muscle fiber. First, we screened cDNA from muscle biopsy specimens by CDR3 spectratyping for expanded TCR beta chain variable region (BV) sequences. To pinpoint the corresponding T cells in tissue, we stained cryostat sections with appropriate anti-TCR BV mAbs, isolated single BV+ T cells that directly contacted or invaded a muscle fiber by laser-assisted microdissection, and amplified their TCR BV chain sequences from rearranged genomic DNA. In this way, we could relate the oligoclonal peaks identified by CDR3-spectratype screening to morphologically characterized microdissected T cells. In one patient, a large fraction of the microdissected T cells carried a common TCR-BV amino acid CDR3 motif and conservative nucleotide exchanges in the CDR3 region, suggesting an antigen-driven response. In several cases, we tracked these T cell clones for several years in CD8+ (but not CD4+) blood lymphocytes and in two patients also in consecutive muscle biopsy specimens. During immunosuppressive therapy, oligoclonal CDR3-spectratype patterns tended to revert to more polyclonal Gaussian distribution-like patterns. Our findings demonstrate that CDR3 spectratyping and single-cell analysis can be combined to identify and track autoaggressive T cell clones in blood and target tissue. This approach should be applicable to other inflammatory and autoimmune disorders.

Adult↗
PubMed1995

Analysis of clonality by polymerase chain reaction for phosphoglycerate kinase-1. Heteroduplex generator.

Polymerase chain reaction (PCR) amplification has been used to determine the clonal composition of tissues based on analysis of the pattern of X-chromosome inactivation, but its use has been limited by technical difficulties. This report presents an expedited method to use PCR in the analysis of clonality. The method uses gel electrophoresis of heteroduplexes formed with an artificial heteroduplex generator (HG) and PCR products from the phosphoglycerate kinase-1 (PGK-1) gene from the tissue sections. Amplification was successful in 36 of 37 cases originally diagnosed as endometrial adenocarcinoma. HG analysis of 36 cases confirmed heterozygosity in 12 cases (33.3%). PGK-1 PCR amplification product was obtained from both control and lesional tissue in 10 of the 12 heterozygous cases. Of these 10 cases, seven were shown to consist of clonal cell populations by HG analysis. Two of three cases diagnosed as well-differentiated endometrioid adenocarcinoma were found to be comprised of polyclonal populations of cells. One case produced an anomalous pattern with HG analysis and was shown to be aneuploid by fluorescence in situ hybridization (FISH) with a chromosome X alpha-satellite probe. It is concluded that HG is a useful alternative to restriction fragment length polymorphism (RFLP) analysis of X-chromosome inactivation as a marker of tissue clonality in cases in women.

Adult↗