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PubMed2006

A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification.

BACKGROUND: In spite of the recognized diagnostic potential of biomarkers, the quest for squelching noise and wringing in information from a given set of biomarkers continues. Here, we suggest a statistical algorithm that--assuming each molecular biomarker to be a diagnostic test--enriches the diagnostic performance of an optimized set of independent biomarkers employing established statistical techniques. We validated the proposed algorithm using several simulation datasets in addition to four publicly available real datasets that compared i) subjects having cancer with those without; ii) subjects with two different cancers; iii) subjects with two different types of one cancer; and iv) subjects with same cancer resulting in differential time to metastasis. RESULTS: Our algorithm comprises of three steps: estimating the area under the receiver operating characteristic curve for each biomarker, identifying a subset of biomarkers using linear regression and combining the chosen biomarkers using linear discriminant function analysis. Combining these established statistical methods that are available in most statistical packages, we observed that the diagnostic accuracy of our approach was 100%, 99.94%, 96.67% and 93.92% for the real datasets used in the study. These estimates were comparable to or better than the ones previously reported using alternative methods. In a synthetic dataset, we also observed that all the biomarkers chosen by our algorithm were indeed truly differentially expressed. CONCLUSION: The proposed algorithm can be used for accurate diagnosis in the setting of dichotomous classification of disease states.

Algorithms↗
PubMed2006

Differential DNA methylation patterns of small B-cell lymphoma subclasses with different clinical behavior.

Non-Hodgkin's lymphoma (NHL) is a group of malignancies of the immune system with variable clinical behaviors and diverse molecular features. Despite the progress made in classification of NHLs based on classical methods, molecular classifications are a work in progress. Toward this goal, we used an array-based technique called differential methylation hybridization (DMH) to study small B-cell lymphoma (SBCL) subtypes. A total of 43 genomic DMH experiments were performed. From these results, several statistical methods were used to generate a set of differentially methylated genes for further validation. Methylation of LHX2, POU3F3, HOXC10, NRP2, PRKCE, RAMP, MLLT2, NKX6.1, LRP1B and ARF4 was validated in cell lines and patient samples and demonstrated subtype-related preferential methylation patterns. For LHX2 and LRP1B, bisulfite sequencing, real-time reverse transcriptase-polymerase chain reaction and induction of gene expression following treatment with the demethylating agent, 5'-aza-2'-deoxycytidine, were confirmed. This new epigenetic information is helping to define molecular portraits of distinct subtypes of SBCL that are not recognized by current classification systems and provides valuable potential insights into the biology of these tumors.

Adult↗
PubMed2004

Congenital abnormalities of cranial nerve development: overview, molecular mechanisms, and further evidence of heterogeneity and complexity of syndromes with congenital limitation of eye movements.

PURPOSE: The clinical and molecular genetic classification of syndromes with congenital limitation of eye movements and evidence of cranial nerve dysgenesis continues to evolve. This monograph details clinical and molecular genetic data on a number of families and isolated patients with congenital fibrosis of the extraocular muscles (CFEOM) and related disorders, and presents an overview of the mechanisms of abnormal patterns of motor and sensory cranial nerve development in these rare syndromes. METHODS: Clinical examination of one patient with CFEOM1, one family with clinical features of CFEOM2, one family with recessive CFEOM3, one family with horizontal gaze palsy and progressive scoliosis (HGPPS), and four patients with various combinations of congenital cranial nerve abnormalities. Genotyping of families with CFEOM and HGPPS for polymorphic markers in the regions of the three known CFEOM loci and in the HGPPS region, and mutation analysis of the ARIX and KIF21A genes in patients with CFEOM were performed according to standard published protocols. RESULTS: The patient with CFEOM1 had the second most common mutation in KIF21A, a 2861 G>A mutation that resulted in an R954Q substitution. The family with CFEOM2 phenotype did not map to the CFEOM2 locus. The family with recessive CFEOM3 did not map to any of the known loci. The HGPPS family mapped to 11q23-q25. One patient had optic nerve hypoplasia and fifth nerve dysfunction. Two patients had the rare combination of Möbius syndrome and CFEOM. One patient had Möbius syndrome and fifth nerve dysfunction. CONCLUSIONS: There is genetic heterogeneity in CFEOM2 and CFEOM3. Abnormalities in sensory nerves can also accompany abnormalities of motor nerves, further substantiating the effect of individual mutations on developing motor as well as sensory cranial nerve nuclei.

Adenine↗
PubMed2001

A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts.

Infection with the endosymbiotic bacteria Wolbachia is widespread in filarial nematodes. Previous studies have suggested concordance between the phylogeny of Wolbachia with that of their nematode hosts. However, there is only one published molecular phylogenetic study of filarial species, based on the 5S rRNA gene spacer. The phylogeny proposed by this study is partially incongruent with previous classifications of filarial nematodes, based on morphological characters. Furthermore, both traditional classifications and molecular phylogenies are, in part, inconsistent with the phylogeny of Wolbachia. Here we report mitochondrial cytochrome oxidase I (COI) gene sequences for 11 species of filaria and for another spirurid nematode which was included as an outgroup. In addition, 16S rRNA, wsp and ftsZ gene sequences were generated for the Wolbachia of several filarial species, in order to complete the available data sets and further resolve the phylogeny of Wolbachia in nematodes. We used these data to evaluate whether nematode and Wolbachia phylogenies are concordant. Some of the possible phylogenetic reconstructions based on COI gene were congruent with the phylogeny of Wolbachia and supported the grouping of the rodent filaria Litomosoides sigmodontis with the lymphatic filariae (i.e. Brugia spp. and Wuchereria spp.) and the sister group relationship of Dirofilaria spp. and Onchocerca spp. However, the placement of the Wolbachia-free filaria Acanthocheilonema viteae is ambiguous and dependent on the phylogenetic methods used.

Animals↗
PubMed1994

Mitochondrial encephalomyopathies: clinical and molecular analysis.

The classification of mitochondrial encephalomyopathies relied upon clinical, biochemical, and histological features until the discovery of mitochondrial DNA defects in 1988. Since then, an outburst of molecular genetic information has aided our understanding of the pathogenesis and the classification of these heterogeneous disorders. Novel concepts of maternal inheritance, mitochondrial DNA (mtDNA) heteroplasmy, tissue distribution, and threshold have explained many of the clinical characteristics. The discovery of point mutations, large-scale mtDNA deletions, duplications, and autosomally inherited disorders with multiple mtDNA deletions have revealed new genetic phenomena. Despite our rapidly expanding understanding of the molecular genetic defects, many questions remain to be explored to fill the gap in our knowledge of the relationship between genotype and clinical phenotype.

DNA, Mitochondrial↗
PubMed2005

Molecular prognostic factors in diffuse large B-cell lymphoma.

The treatment of patients with diffuse large B-cell lymphoma (DLBCL) has been guided traditionally by clinical parameters such as the Ann Arbor Staging Classification for Hodgkin's disease. Although the International Prognostic Index (IPI) represents the most widely accepted prognostic model, there is still a marked variability in outcome within identical IPI subgroups, reflecting the heterogeneity of this malignancy. Use of DNA microarray, real-time reverse transcription polymerase chain reaction, and tissue array immunohistochemistry methodologies makes the development of new classifications possible based on molecular profiling. The molecular classification of DLBCL may lead to the grouping of specific disease entities sharing similar biologic features, clinical behavior, and outcome. Once tested and validated, this new generation of prognostic models should become an integral part of the daily practice, providing valuable additional information to the currently existing clinically based predictive models. To accomplish these goals and to be in a position in which existing or new prognostic models can be easily tested and validated, there is a strong need to collect frozen and paraffin-embedded material that can be used for RNA extraction and construction of tissue arrays, respectively. Such materials should be gathered as an integral part of any planned study.

Biomarkers, Tumor↗
PubMed2001

Quantification of human telomerase RNA (hTR) and human telomerase reverse transcriptase (hTERT) mRNA in testicular tissue of infertile patients.

AIM: To evaluate the quantitative detection of human telomerase RNA (hTR) and human telomerase reverse transcriptase (hTERT) mRNA as diagnostic parameters in the workup of testicular tissue specimens from patients presenting with non-obstructive azoospermia. METHODS: hTR and hTERT mRNA expression were quantified in 38 cryopreserved testicular tissue specimens by fluorescence real-time reverse transcription-polymerase chain reaction (RT-PCR) in a LightCycler(r). This was paralleled by conventional histological workup in all tissue specimens and additional semithin sectioning preparation in cases with maturation arrest (n = 12) and Sertoli-cell-only syndrome (n = 12). RESULTS: The average normalized hTERT expression (N(hTERT)) was 131.9 +/- 48.0 copies (mean +/- SD) in tissue specimens with full spermatogenesis, N(hTERT) = 51.2 +/- 17.2 copies in those with maturation arrest and N(hTERT) = 2.7 +/- 2.4 copies in those with Sertoli-cell-only syndrome (SCOS). The discriminant analysis showed that detection of N(hTERT) (N(hTR)) had a predictive value of 86.8% (55.3%) for correct classification in one of the three histological subgroups. CONCLUSION: Our results demonstrate that quantitative detection of hTERT mRNA expression in testicular tissue enables a molecular-diagnostic classification of gametogenesis. Quantitative detection of hTERT in testicular biopsies is thus well suited for supplementing the histopathological evaluation.

DNA-Binding Proteins↗
PubMed1992

Biodiversity: molecular biological domains, symbiosis and kingdom origins.

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still behave as if there were only two important kingdoms (plants and animals).

Animal Population Groups↗
PubMed2003

From rare gas atoms to fullerenes: spherical aromaticity studied from the point of view of atomic structure theory.

The characteristic features of molecules like polyhedra and fullerenes, which follow the 2(N+1)(2) rule of spherical aromaticity, can be related to energetically stable closed-shell configurations of (pseudo-)atoms. This unifying view relies on a thought experiment, which produces a polyhedron in a two-step process and which can, in turn, relate the electronic configuration of any spherical polyhedron to the one of a corresponding closed-shell atom. In the first step, the electronic ground-state configuration is identified. In the second step, a group theoretical analysis can be carried out; this relates the spherically symmetric atomic orbitals to the molecular orbitals classified according to the irreducible representations of the point group of the polyhedron under consideration. This procedure explains and justifies the pseudo-l classification of molecular orbitals, which is the basis of the 2(N+1)(2) rule. For the transition from the electronic configuration of the rare gas Eka-Rn (Uuo) to the icosahedral fullerene C(20) (2+), we show how a change in the ground-state configuration leads to the phenomenologically found 2(N+1)(2) rule for spherically aromatic fullerenes.

Journal Article↗
PubMed2025

A functional assay to classify RB1 variants of uncertain significance.

PURPOSE: The RB1 gene encodes the retinoblastoma protein (pRB) playing a major role in cell cycle control, particularly by its interaction with E2F transcription factors. Familial forms of retinoblastoma are caused by germline pathogenic variants in the RB1 gene predisposing to retinoblastoma and other tumors. By analyzing the RB1 gene in patients with retinoblastoma, we found that missense variants often remain variants of uncertain significance (VUS). METHODS: To classify RB1 VUS, we developed a functional assay evaluating their impact on the ability of pRB to inhibit the activity of the E2F1 promoter, with a luciferase reporter gene. A set of 14 pathogenic/likely pathogenic and benign/likely benign RB1 variants was used for validation. RESULTS: We tested 16 VUS detected in patients with retinoblastoma and found that 9 VUS reduced the ability of pRB to inhibit E2F1 promoter. Among them, the (RB1) c.2263T>G p.(Phe755Val) variant showed a reduced level of pRB on Western blot, suggesting a defect in pRB stability. By applying the criterion PS3_moderate of the American College of Medical Genetics and Genomics/Association for Molecular Pathology classification to this functional assay, 5 of the 9 VUS with functional impact could be classified as likely pathogenic. CONCLUSION: This functional assay can improve the molecular diagnosis of retinoblastoma predisposition by a better determination of pathogenic/likely pathogenic RB1 variants.

Humans↗
PubMed2005

Serrated polyps of the large intestine.

Serrated polyps of the large intestine comprise a family of lesions bearing some histological similarities, including an overall serrated configuration caused at least in part by inhibition of apoptosis by mutations in one of two genes. Over the past decade, it has become apparent that these lesions can be subdivided by histological criteria into lesions with differing degrees of relationship to the development of carcinoma, including sporadic microsatellite instable (MSI) carcinomas and probably carcinomas demonstrating the CpG island methylator phenotype (CIMP), which includes both MSI and microsatellite stable tumors. These differing histological subtypes can in part predict some of the molecular features of these lesions, and the combination of histological and molecular features is beginning to give us better insight into the potential natural history and therefore management of these lesions. This review will present the histological classification of these lesions, relate that histological classification to molecular aspects of the lesions, and present recommendations for management.

Colorectal Neoplasms↗
PubMed1988

[Molecular weight and restriction mapping of the DNA of cholera phages].

Molecular masses of cholera bacteriophages 493, 7226 and Eltor II were defined by electron microscopic technique. DNA of these bacteriophages was digested by the restriction endonucleases PstI, BglI, MluI and SalI. The number and molecular masses of the obtained restricts were identified. The physical map of bacteriophage 493 was constructed using three restriction endonucleases. The obtained data can be used for classification and molecular biology research of cholera bacteriophages.

Bacteriophages↗
PubMed2005

Molecular clonality determination of ipsilateral recurrence of invasive breast carcinomas after breast-conserving therapy: comparison with clinical and biologic factors.

We established clonality relationships between invasive ipsilateral breast failures (IBFs; local recurrences) and initial invasive carcinomas using a molecular polymerase chain reaction loss of heterozygosity (LOH) assay for 26 patients treated with breast-conserving therapy for invasive carcinoma with no distant metastases (DMs) before the IBE LOH was +/- 50% allelic loss. Eighteen IBFs (69%) were related clonally to initial carcinomas; 8 (31%) were clonally distinct, second primary carcinomas. IBFs and initial invasive carcinomas were morphologically similar in 6 (75%) of 8 clonally different cases. Clinical IBF classification and molecular assay results differed in 11 cases (42%). The mean intervals to IBF were 4.7 years in related and 8.7 years in different cases (P = .013). In 6 patients, DMs developed; 5 had related IBFs. In related IBF cases, the mean increase in fractional allelic loss (FAL) of IBFs associated with DMs was 18.9% compared with 7.6% in cases unassociated with DMs (P = .004). Molecular assays can accurately establish the clonality of most IBFs. Morphologic comparison and clinical IBF classification are unreliable methods of determining clonality. Clonally related IBFs occurred sooner than clonally different IBFs. Patients with clonally related IBFs are the main pool in which DMs occur Not all clonally related IBFs have the same DM association; those with large FAL gains were associated with DMs. Molecular clonality assays may provide a reliable means of identifying patients who might benefit from systemic chemotherapy at the time of IBF.

Adenocarcinoma↗
PubMed2006

Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny.

The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classification and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classification. Data sets with different compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleotia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales.

Ascomycota↗
PubMed2003

Molecular pathogenesis of vascular anomalies: classification into three categories based upon clinical and biochemical characteristics.

Vascular tumors and malformations can be challenging to diagnose. Although they can resemble one another, their classification into tumors, such as hemangiomas of infancy, and malformations, such as venous or arteriovenous malformations, is based not only on their divergent biological behavior, but also on their pathogenesis. This review examines the molecular pathobiology of the processes involved in the development of these vascular birthmarks as they are currently understood. The terms hemangioma, hemangiosarcoma, and vascular proliferation are often used interchangeably, even though these entities are clinically and biochemically distinct. A more precise classification is necessary to facilitate communication between basic scientists and clinicians. Vasculogenesis, the in situ differentiation of blood vessels, occurs very early in the developing embryo. In vivo and in vitro studies, as well as knockout models, seem to indicate that this mechanism is unlikely to be involved in the development of either vascular malformations or hemangiomas of infancy. Recent advances in embryonic angiogenesis, especially explorations of mechanisms of vascular remodeling, have brought new understanding of the pathogenesis of vascular malformations. Vascular remodeling, an integral part of angiogenesis that centers upon the interactions between pericytes and endothelial cells, has been shown to be defective in certain experimental models and in some familial cases of vascular malformation. The occurrences of arteriovenous malformations in territories susceptible to increased remodeling also point towards epigenetic events in the development of vascular malformations.

Animals↗
PubMed2002

Real-time PCR technology for cancer diagnostics.

BACKGROUND: Advances in the biological sciences and technology are providing molecular targets for diagnosing and treating cancer. Current classifications in surgical pathology for staging malignancies are based primarily on anatomic features (e.g., tumor-node-metastasis) and histopathology (e.g., grade). Microarrays together with clustering algorithms are revealing a molecular diversity among cancers that promises to form a new taxonomy with prognostic and, more importantly, therapeutic significance. The challenge for pathology will be the development and implementation of these molecular classifications for routine clinical practice. APPROACH: This article discusses the benefits, challenges, and possibilities for solid-tumor profiling in the clinical laboratory with an emphasis on DNA-based PCR techniques. CONTENT: Molecular markers can be used to provide accurate prognosis and to predict response, resistance, or toxicity to therapy. The diversity of genomic alterations involved in malignancy necessitates a variety of assays for complete tumor profiling. Some new molecular classifications of tumors are based on gene expression, requiring a paradigm shift in specimen processing to preserve the integrity of RNA for analysis. More stable markers (i.e., DNA and protein) are readily handled in the clinical laboratory. Quantitative real-time PCR can determine gene duplications or deletions. Furthermore, melting curve analysis immediately after PCR can identify small mutations, down to single base changes. These techniques are becoming easier and faster and can be multiplexed. Real-time PCR methods are a favorable option for the analysis of cancer markers. SUMMARY: There is a need to translate recent discoveries in oncology research into clinical practice. This requires objective, robust, and cost-effective molecular techniques for clinical trials and, eventually, routine use. Real-time PCR has attractive features for tumor profiling in the clinical laboratory.

Biomarkers, Tumor↗
PubMed1987

[Molecular genetics of the pathogenesis and classification of chronic myelocytic leukemia].

The Philadelphia (Ph) translocation in CML is molecular-genetically characterized by a rearrangement of the c-abl oncogene with sequences of the bcr gene on the Ph chromosome. In leukemic cells this recombination results in the transcription of a 8.5 kb bcr/c-abl hybrid RNA which is translated into a p210 abl protein. The p210 abl protein contains, in contrast to its normal 145 abl counterpart, associated tyrosine kinase activity which is not physiologically controlled. Both genes do not participate in the acceleration of CML from chronic state into blast crisis. The majority of CML patients without cytogenetically detectable Ph chromosome also lack a bcr/abl rearrangement. However, some cases of Ph-negative CML could be reclassified into the group of Ph-positive CML by demonstration of a bcr gene rearrangement. One patient exhibited a bcr gene recombination without translocation of c-abl sequences. A similar heterogenous pattern is observed in Ph-positive acute leukemias. About 50% of cases are characterized by a bcr/abl rearrangement, as is likewise observed in Ph-positive CML. It is tempting to speculate that these patients represent Ph-positive CML cases that initially presented themselves for treatment with CML blast crisis. Particularly in pediatric Ph-positive ALL, the majority of cases show a c-abl oncogene translocation without bcr rearrangement. Precise molecular-genetic analyses of those cases are still pending. Molecular-genetic analyses have already been proven to be of clinical value 1) in the diagnosis of Ph-positive CML in the absence of cytogenetic methods, 2) in the subclassification of Ph-negative CML or Ph-positive acute leukemias.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosomes, Human, Pair 22↗