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PubMed2026

Optical genome mapping enhanced by refined variant interpretation in pediatric acute lymphoblastic leukemia.

Reliable detection of structural variants (SVs) and copy number variations (CNVs) is crucial in the contemporary diagnostics of pediatric B-cell acute lymphoblastic leukemia (B-ALL). However, limitations of commonly used conventional and molecular cytogenetic methods may hinder the accurate genetic characterization of patients. Optical genome mapping (OGM) offers a reliable alternative by enabling high-resolution, genome-wide detection of CNVs and SVs. Chromosomal aberrations were screened using OGM in 51 children with B-ALL. The results were compared with those of karyotyping, fluorescence in situ hybridization (FISH), digital multiplex ligation-dependent probe amplification (digitalMLPA), and targeted RNA sequencing (RNA-seq). OGM data showed high congruency with karyotyping and FISH findings, detecting clinically relevant variants beyond G-banding results and unraveling a complex KMT2A fusion undetected by FISH. Gene fusions involved in complex ETV6::RUNX1 translocations, but not detected by RNA-seq, were confirmed using FISH. Normalization of OGM copy number values with DNA-index-improved concordance with FISH-derived copy numbers in near-tri/tetraploid cases. In the peripheral regions of OGM variants (fringe-zones), a novel evaluation strategy called 'FriZone' was applied, which significantly improved the concordance between OGM and digitalMLPA. In addition, a co-segregation analysis revealed strong associations between ETV6::RUNX1 fusion and deletions of ETV6, RAG2, and NR3C2. OGM uncovered complex rearrangements undetected by widely used methods in 15% of cases, improving genetic classification and risk stratification in 10% of the patients. The FriZone analysis and normalization by DNA-index provide a refined, more accurate approach to OGM variant interpretation, facilitating the efficient application of OGM in clinical diagnostics. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Humans↗
PubMed2000

Modulation of X-ray-induced damage recognition and repair in ageing human peripheral blood mononuclear cells by an interleukin-6-type cytokine.

We have investigated the effects of an interleukin (IL)-6-type cytokine on the DNA-binding activity of ku and on unscheduled DNA repair in X-ray-treated peripheral blood mononuclear cells (PBMC) from human subjects of different ages. The cytokine used, called K-7/D-6, is an IL-6 variant with increased in vivo and in vitro biological activity compared to the wild type molecule. Ku is the DNA-binding component of the DNA-dependent protein kinase (DNA-PK). It binds the ends of various types of DNA discontinuity and is involved in the repair of DNA breaks caused by V(D)J recombination, isotype switching, physiological oxidation reactions, ionizing radiation and some chemotherapeutic drugs. The ku-dependent repair process, called non-homologous end joining, is the main DNA double strand break repair mechanism in irradiated mammalian cells. Results show that K-7/D-6 significantly increases DNA-binding activity of ku in irradiated PBMC from young but not from elderly subjects. However, K-7/D-6 is able to induce unscheduled DNA repair in irradiated PBMC from both young and elderly subjects. These effects of K-7/D-6 are relevant to the mechanisms of the cellular response to DNA damage.

Adult↗
PubMed2000

Combined space-variant maps for optical-flow-based navigation.

A robot navigating in an unstructured environment needs to avoid obstacles in its way and determine free spaces through which it can safely pass. We present here a set of optical-flow-based behaviors that allow a robot moving on a ground plane to perform these tasks. The behaviors operate on a purposive representation of the environment called the "virtual corridor" which is computed as follows: the images captured by a forward-facing camera rigidly attached to the robot are first remapped using a space-variant transformation. Then, optical flow is computed from the remapped image stream. Finally, the virtual corridor is extracted from the optical flow by applying simple but robust statistics. The introduction of a space-variant image preprocessing stage is inspired by biological sensory processing, where the projection and remapping of a sensory input field onto higher-level cortical areas represents a central processing mechanism. Such transformations lead to a significant data reduction, making real-time execution possible. Additionally, they serve to "re-present" the sensory data in terms of ecologically relevant features, thereby simplifying the interpretation by subsequent processing stages. In accordance with these biological principles we have designed a space-variant image transformation, called the polar sector map, which is ideally suited to the navigational task. We have validated our design with simulations in synthetic environments and in experiments with real robots.

Animals↗
PubMed1999

Does learning affect the structure of vocalizations in chimpanzees?

We recorded 'pant-hoot' vocalizations from male chimpanzees, Pan troglodytes, housed in two captive facilities in the U.S.A., Lion Country Safari and North Carolina Zoological Park. Acoustic analysis revealed significant differences between the two groups in the temporal patterning of the calls. Because the captive males within each group are from diverse origins, within-group similarity in pant-hoot structure could not have resulted from genetic similarity of the callers. In addition, there were no obvious differences in housing conditions that could have caused the between-group differences. Instead, the results suggest that the calls in each group converged in structure as a consequence of vocal learning. Within-group variation in call structure of the captive groups was similar to that found in a group of wild Ugandan chimpanzees (Kanyawara study group, Kibale National Park), suggesting the presence of species-specific constraints on this call within which different populations can converge on local variants. In addition, an acoustically novel pant-hoot variant that was introduced by one male to the Lion County Safari colony spread to five other males in the same colony. This suggests that chimpanzees may also be able to modify the frequency parameters of their calls through learning. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1994

Rearrangements of the blood group RhD gene associated with the DVI category phenotype.

The Rh (Rhesus) blood group antigens, D, Cc, and Ee, are carried by three unglycosylated membrane proteins of the human erythrocytes encoded by two highly related genes, D and CcEe. The major antigen, D, is a mosaic composed of at least nine determinants (epD1 through epD9). The lack of expression of some of these D epitopes at the surface of variant red blood cells defines the so-called D category phenotypes. In this report, we have determined the molecular basis of the DVI category phenotype characterized by the lack of epitopes D1, D2, D5, D6/7, and D8. Southern blot analysis and mRNA sequencing showed that the DVI phenotype is associated with two types of rearrangement of the D gene. Of 10 DVI genomes investigated, 8 exhibited a segmental DNA replacement (gene conversion) between the D fragment encompassing exons 4, 5, and 6 and the equivalent region of the CcEe gene. In the two other variants, these three exons are deleted. In both cases, the genomic rearrangement did not alter the reading frame of the variant RhD transcripts that are translated in 417 and 266 amino acid polypeptides, respectively. A heterogeneity of category DVI samples based on variable reactivity of the red blood cells with anti-D antibodies was previously found to be associated with the CDVIe or cDVIE haplotypes. Interestingly, our present results indicated that this serologic subdivision of the DVI category is correlated to two types of genomic rearrangements of the D gene.

Amino Acid Sequence↗
PubMed2001

Comparison of PowerPlex 16, PowerPlex1.1/2.1, and ABI AmpfISTR Profiler Plus/COfiler for forensic use.

AIM: Several amplification and detection formats for the analysis of short tandem repeat loci are readily available to the forensic laboratory. Careful consideration must be given to the throughput, sensitivity, concordance, data interpretation, facility requirements, and costs of operation. The Pennsylvania State Police DNA Laboratory sought to establish that of any of the amplification or detection formats generally used in the United States generates concordant results and that the use of several formats within one laboratory provides a solution to the interpretation of difficult evidentiary samples. METHODS: Validation work consisting of sensitivity, precision, mixture, and substrate studies was performed by use of each of three detection formats (ABI Prism(r)310 Genetic Analyzer, ABI Prism(r)377 DNA Sequencer, and the Hitachi FMBIO(r)II Fluorescent Scanner) and three amplification systems (GenePrint(r) PowerPlex 16, GenePrint(r) PowerPlex 1.1/2.1, and AmpflSTR ProfilerPlus/COfiler). The results generated in each of the formats were compared, along with the problems incurred. RESULTS: All allele calls were concordant, with the exception of primer region variants, and all detection systems were sensitive and reliable. Even with the use of multiple formats, a general protocol can be written with only one set of interpretation guidelines. CONCLUSION: National databases can be used with input data from any of these formats. The use of several detection formats allowed the forensic scientist to select a system, based on sample quality, quantity, and throughput requirements. Interpretation issues resulting from complex mixtures, degraded samples, rare microvariants, internal primer variants, unusual heterozygote ratios, above or below ladder alleles, and potential tri-alleles can be verified.

Criminology↗
PubMed2006

Complete replication cycle and acquisition of tegument in nucleus of human herpesvirus 6A in astrocytes and in T-cells.

The ultrastructural replication cycle of human herpesvirus 6A and 6B, both T-lymphotropic viruses, with tropism for the central nervous system, was compared by electron microscopy in the same cells, that is, in the T-lymphoblastoid cell line SupT-1 and in human astrocytes. Both HHV-6A and HHV-6B replicated efficiently in SupT-1 and formed viral particles. The tegument is the least characterized structure of the herpesviral particle and both variants were able to form intranuclear membrane compartments called tegusomes in SupT-1 where tegumentation occurred. Also, tegumentation occurred in HHV-6A infected cells in the nucleoplasm without the presence of a tegusome. This suggests that there is more than one possible route of tegumentation. Differences in the replication cycles between HHV-6A and HHV-6B were also observed in the cytoplasm. One such difference was that prominent annulate lamellae were only found in the cytoplasm of HHV-6A infected cells. In astrocytes a successful formation of viral particles was only seen with the HHV-6A variant. The HHV-6A virus life cycle in astrocytes resembled the life cycle in the T-cell line SupT-1, except that no annulate lamellae were found. Complete viral particles were found extracellularly around the astrocytes and the supernatant of infected astrocytes were able to re-infect SupT-1 cells. This suggests that HHV-6A infection in astrocytes can generate complete, viable, and infectious viral particles. The HHV-6 variants behave differently in the same type of cells and have different tropisms for astrocytes, supporting the notion that the variants might induce different diseases.

Astrocytes↗
PubMed2001

Analysis of DsRed Mutants. Space around the fluorophore accelerates fluorescence development.

Earlier mutagenesis of the red fluorescent protein drFP583, also called DsRed, resulted in a mutant named Fluorescent Timer (Terskikh, A., Fradkov, A., Ermakova, G., Zaraisky, A., Tan, P., Kajava, A. V., Zhao, X., Lukyanov, S., Matz, M., Kim, S., Weissman, I., and Siebert, P. (2000) Science 290, 1585--1588). Further mutagenesis generated variants with novel and improved fluorescent properties. The mutant called AG4 exhibits only green fluorescence. The mutant, called E5up (V105A), shows complete fluorophore maturation, eventually eliminating residual green fluorescence present in DsRed. Finally, the mutant, called E57 (V105A, I161T, S197A), matures faster than DsRed as demonstrated in vitro with purified protein and in vivo with recombinant protein expressed in Escherichia coli and Xenopus leavis. Comparative analysis of the mutants in the context of the crystal structure of DsRed suggests that mutants with free space around the fluorophore mature faster and more completely.

Animals↗
PubMed1987

Three new orosomucoid (ORM) variants revealed by isoelectric focusing and print immunofixation.

Phenotypes of orosomucoid (ORM) in human sera have been analysed by isoelectric focusing and print immunofixation. After neuraminidase treatment the band patterns indicated that the polymorphism of the structural locus ORM1 is controlled by three autosomal codominant alleles. According to the previous nomenclature they were called ORM1F1, ORM1F2, and ORM1S. In a study of 272 unrelated individuals from southern Germany, five of the six expected common ORM1 subtypes were observed. Furthermore, we found three ORM variant phenotypes which have not been reported previously. These variants were characterized by additional bands in a cathodal position. One variant had additional double bands and presumably represents a rare ORM1 variant named ORM1S1. Two variants had additional single bands. They were assigned tentatively to the ORM2 gene locus. While the common gene product of ORM2 may be called ORM2A, the two variants are named ORM2B1 and ORM2B2, respectively. ORM2B1 has, thus far, been found only in a single individual; the variants ORM1S1 and ORM2B2 were found in a father-child pair and a mother-child pair, respectively. The frequency for variants tentatively assigned to the ORM2 locus is very low and was calculated to be 0.0037.

Alleles↗
PubMed2004

Functional characterization of telomerase RNA variants found in patients with hematologic disorders.

Human telomerase uses a specific cellular RNA, called hTERC, as the template to synthesize telomere repeats at chromosome ends. Approximately 10% to 15% of patients with aplastic anemia or other bone marrow failure syndromes are carriers of hTERC sequence variants whose functional significance, in most cases, is unknown. We screened 10 reported and 2 newly discovered hTERC variants from such patients and found that 10 of these negatively affected telomerase enzymatic function when they were used to reconstitute telomerase enzymatic function in human cells. Most functional deficits were due to perturbations of hTERC secondary structure and correlated well with the degrees of telomere shortening and reduced telomerase activity observed in peripheral blood lymphocytes of the representative patients. We also found no evidence of dominant-negative activity in any of the mutants. Therefore, loss of telomerase activity and of telomere maintenance resulting from inherited hTERC mutations may limit marrow stem cell renewal and predispose some patients to bone marrow failure.

Anemia, Aplastic↗
PubMed1981

Membrane-associated alterations detected in poorly tumorigenic lectin-resistant variant sublines of a highly malignant and metastatic murine tumor.

A number of wheat germ agglutinin-resistant (WGAR) variants of a highly malignant and metastatic mouse tumor (called MDAY-D2) were selected. Two of these, MDW1 and MDW3, were poorly tumorigenic in the normal DBA/2 host but grew well in highly immunosuppressed recipients. In contrast, MDAY-D2, MDW4, and MDW5 were all highly tumorigenic in both normal and immunosuppressed hosts. Analysis of the WGAR variants by cytotoxic T-cell testing did not reveal any evidence for the acquisition of new tumor antigens by the MDW1 or MDW3 variant sublines, although they provoked a significantly stronger T killer cell response than did MDAY-D2, MDW4, or MDW5. Further studies indicated that the rate of tumor cell surface shedding in vitro correlated strongly with relative tumorigenicity and, furthermore, that changes in the cytoskeletal structure of MDW1 and MDW3 may have contributed to their reduced rate of shedding.

Agglutinins↗
PubMed1994

"Silent" hepatitis B virus mutants are responsible for non-A, non-B, non-C, non-D, non-E hepatitis.

Since the recent introduction of diagnostic kits for hepatitis C and E, some cases of non-A, non-B, non-C, non-D, non-E hepatitis (so-called hepatitis F) have been revealed. We attempted to demonstrate that so-called hepatitis F is caused by hepatitis B virus (HBV) variants. Polymerase chain reaction (PCR) was used to amplify serum HBV DNAs from 20 patients with acute hepatitis and 20 patients with chronic hepatitis who had been diagnosed as having so-called hepatitis F on the basis of conventional serological markers. The PCR technique successfully amplified HBV DNAs in 18 (90%) cases of acute hepatitis and 17 (85%) cases of chronic hepatitis. Sequencing of HBV DNAs of six patients (acute 3, chronic 3) revealed equally a T-to-C mutation of DR2 and an 8-nucleotide deletion of the 3'-terminus of the X gene coding region, giving rise to the generation of a C-terminally truncated X protein and probable damage to the enhancer II/core promoter elements. These mutations of the X gene coding region may lead to suppression of replication and expression of HBV DNAs. Thus virtually all cases of so-called hepatitis F appear to be caused by "silent" HBV mutants, at least in Japan.

Acute Disease↗
PubMed1994

ATF-a0, a novel variant of the ATF/CREB transcription factor family, forms a dominant transcription inhibitor in ATF-a heterodimers.

We have isolated a cDNA encoding a variant of the transcription factor ATF-a (called ATF-a0) by screening a HeLa cDNA expression library with a regulatory element of the E-selectin promoter, NF-ELAM1/delta A. Relative to full-length ATF-a, the ATF-a0 cDNA contains a large in-frame deletion of 525 base pairs that removes the P/S/T-rich putative transactivation domain. Using reverse-transcription-polymerase chain reaction and Northern blot hybridization to characterize ATF-a0 expression, we found that putative mRNAs for ATF-a0 and ATF-a are present at varying ratios in different tissues. Full-length ATF-a is a transcriptional activator for the NF-ELAM1/delta A site of the E-selectin promoter. In contrast, we show ATF-a0 has no measurable transactivating function on this element. Moreover, we demonstrate that co-expressed ATP-a0 and ATF-a preferentially heterodimerize. In the heterodimer ATF-a0 is a dominant inhibitor that completely blocks the transactivating activity of ATF-a. Both forms of ATF-a bind the p50 subunit of NF-kappa B as shown by affinity chromatography. ATF-a0 appears to be a splice variant similar to the one found for ATF-2, its closest homologue in structure and function. Taken together, our results suggest that ATF-a0 is an important member of the ATF family with a negative regulatory role in transactivation.

Activating Transcription Factors↗
PubMed1998

Apparent renal cell carcinomas in tuberous sclerosis are heterogeneous: the identification of malignant epithelioid angiomyolipoma.

Renal epithelial tumors (carcinoma and oncocytoma) have been reported with higher a frequency than expected in patients with the tuberous sclerosis complex. However, the recent identification of a monotypic, epithelioid variant of angiomyolipoma, closely simulating renal cell carcinoma, has cast doubt on the real frequency of carcinoma. Immunohistochemical analysis with a panel of antibodies, including melanogenesis marker HMB45, can discriminate between carcinoma and carcinoma-like angiomyolipoma. We studied five tumors previously reported as carcinoma and found that only one of them showed an immunohistochemical phenotype indicative of an epithelial tumor (Ker+, HMB45-). Three tumors exhibited a phenotype compatible with the monotypic epithelioid variant of angiomyolipoma (HMB45+, Ker-), and two of the three patients died of metastatic disease. The last patient had unusual clinical features, and the tumor was positive both for HMB45 and keratin. It is concluded that (1) renal cell carcinoma is less common in tuberous sclerosis complex than previously believed, (2) some cases called renal cell carcinoma probably represent a monotypic, epithelioid variant of angiomyolipoma, and (3) epithelioid angiomyolipoma is a potentially malignant tumor with invasion and metastases. These findings indicate that all reported renal carcinomas in tuberous sclerosis complex, therefore, must be reevaluated.

Adenoma, Oxyphilic↗
PubMed1983

Plasmodium falciparum: comparison of in vitro growth of knobby and knobless isolates.

Variants (K-) of three strains of Plasmodium falciparum which do not produce the erythrocyte surface alterations that have been called knobs have been compared with their wildtype knobby (K+) parents. The K- variants achieve higher parasitemias, incorporate radiolabeled isoleucine more rapidly, and produce a higher percentage of multiply-infected cells than do their K+ parents. Nevertheless, immune owl monkey sera cause approximately the same percentage inhibition of growth of both K+ and K- organisms when included in the growth medium at a 1% concentration.

Animals↗
PubMed2001

Identification of a novel structural variant of the alpha 6 integrin.

The alpha(6) integrin is a 140-kDa (nonreduced) laminin receptor. We have identified a novel 70-kDa (nonreduced) form of the alpha(6) integrin called alpha(6)p for the latin word parvus, meaning small. The variant was immunoprecipitated from human cells using four different alpha(6)-specific monoclonal antibodies but not with alpha(3) or alpha(5) antibodies. The alpha(6)p integrin contained identical amino acid sequences within exons 13--25, corresponding to the extracellular "stalk region" and the cytoplasmic tail of the alpha(6) integrin. The light chains of alpha(6) and alpha(6)p were identical as judged by alpha(6)A-specific antibodies and electrophoretic properties. The alpha(6)p variant paired with either beta(1) or beta(4) subunits and was retained on the cell surface three times longer than alpha(6). Reverse transcription/polymerase chain reaction analysis revealed a single polymerase chain reaction product. The alpha(6)p variant was found in human prostate (DU145H, LnCaP, PC3) and colon (SW480) cancer cell lines but not in normal prostate (PrEC), breast cancer (MCF-7), or lung cancer (H69) cell lines or a variant of a prostate carcinoma cell line (PC3-N). Protein levels of alpha(6)p increased 3-fold during calcium-induced terminal differentiation in a normal mouse keratinocyte model system. A novel form of the alpha(6) integrin exists on cell surfaces that contains a dramatically altered extracellular domain.

Amino Acid Sequence↗
PubMed1978

An interesting normal variant of the temporal bone.

The purpose of this brief communication is to call attention to a small, rounded bony knob which is infrequently present on the superior margin of the petrous bone. This finding is more often unilateral but may rarely be bilateral. The bony excrescence has the same osseous density as the surrounding dense petrosa from which it arises. Lack of familiarity with this normal variant may lead to the erroneous diagnosis of a petrosal meningioma.

Adult↗
PubMedDate not supplied

[M3 variant leukemia: clinical and diagnostic features].

Acute promyelocytic leukemia represents 5-10% of acute myeloid leukemia cases (AML) recorded in the literature, occurring more frequently in young adults. It has a special clinical and biological behaviour when compared to the other forms of AML, being characterized by a particular morphology of blast cells (M3 in FAB classification), translocation of chromosomes 15;17, and disseminated intravascular coagulation at diagnosis or after the onset of chemotherapy. Within this AML subgroup there are 2 morphological subsets called the hypergranular promyelocytic leukemia and the hypogranular or variant form. We have studied clinical and laboratory aspects of 19 cases of AML M3 out of 217 AML cases, and observed a high incidence of failure to recognize the M3 variant form, although its diagnosis has been mainly based on cytomorphology. Only 4 out of 8 cases of the variant form received in our laboratory were correctly diagnosed, being the other 4 cases wrongly identified as the myelomonocytic subset of AML (M4). Immunophenotyping with monoclonal antibodies using CD2 and CD7 as T cell markers, CD10 and CD19 as B cell markers and CD33, CD13, CD14, CD15 and anti MPO as myeloid markers is a complementary diagnostic tool that permits solving difficult cases. It is important to classify AML correctly because of the special therapeutic and prognostic features of AML M3, which differently from other AML forms, has been successfully treated with cellular differentiating agents.

Adolescent↗