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Results for “Genotyping performance”

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At least 19 recordsLinked to original sources
PubMed1991

The role of gene rearrangements for antigen receptors in the diagnosis of lymphoma obtained by fine-needle aspiration. A study of 63 cases with concomitant immunophenotyping.

To assess the efficacy of performing genotyping in addition to immunophenotyping as an adjunct to cytologic diagnosis, 63 consecutive patients with fine-needle aspirates of lymphoproliferative lesions who had concurrent immunophenotyping and genotyping performed on fine-needle aspirate cell suspensions were studied. Thirty-nine of 63 specimens (62%) that appeared to contain non-Hodgkin's lymphoma and that proved to be of B-cell lineage by genotyping were accurately phenotyped and shown to be monotypic for immunoglobulin light chains by cell suspension immunocytochemistry. Genotyping facilitated lineage assignment and/or confirmed clonality in 17 of 63 specimens (27%) that were difficult to determine based on morphologic data. These include cases of atypical lymphoid proliferations with polyclonal or inconclusive markers (n = 6), peripheral T-cell lymphoma (n = 3), extracutaneous mycosis fungoides (n = 1), lymphoblastic lymphoma (n = 4), null cell lymphoma (n = 1), and specimens with equivocal or technically unsatisfactory markers (n = 2). Based on these results, it is proposed that genotyping for lineage assignment and/or clonality be performed to include cases of atypical lymphoid proliferations, T-cell malignant neoplasms, lymphoid malignant neoplasms with equivocal markers, and differentiation of lymphoid from nonlymphoid neoplasms. Genotyping by antigen-receptor gene rearrangement appears to be redundant in cases with mature B-cell phenotypes that demonstrate monoclonality by immunophenotyping.

Adult↗
PubMed1976

[Genetic-statistical analysis of multiple births in humans. I. Genetic analysis of predisposition to multiple birth].

Genetico-statistical analysis was made to check various hypotheses of the tendency to multiple birth inheritance. The material involved was comprised of 115 MZ and 228 DZ twin families burdened by recurrent cases of multiple births in their genealogy. Test data included 516 single birth probands, 5 from which had twins among sibs; this results in p = 0,97% for the evaluation of population frequency of the "affected" couples having twins). Vienberg proband method was applied to check monogenous-autosomal model and Edward & Smith approximating formulae to check additive-polygenous model with liminal results (manifestation). It is shown: 1) that the degree of genetical determination of MZ and DZ twinning is approximately the same for both multiple birth types; H-61 and 53% respectively; 2) in MZ twinning both mother's and father's genotypes perform as multiple birth factors; H-76% for the group of mother's sisters and 64% for that of father's brothers; 3) in case of DZ twinning mother's genotype is much more valid as a multiple birth factor as compared to the father's one; H-68% for the group of mother's sisters and H-25% for father's brothers; 4) at least some genetical factors, involved in multiple birth determination, are common for MZ and DZ twins; the rate of DZ twinning (of different sexes) among sibs of parents of MZ twins is reliable and more than 5-fold increases that in common population. It is suggested that the contradiction of literary data on multiple birth genetics is due to unadequate methods in many early investigations: calculations have been carried out on the basis of twin birth rate, and not on the rate of "affected" (couples having twins); differential Veinberg's method has been used, which is adequate in populational analysis and is unsuitable for genealogical studies for the estimation of MZ and DZ twinning frequency; cases of "sporadic" multiple birth have not been excluded from summary family material. On the basis of the authors' and literary data it is suggested also that the number of main genetic factors determining the tendency to multiple births is more than 2 (probably 3) and does not exceed 5, and their interaction approximated by oligenic-complementary model, which does not exclude the presence of genocopying loci in a total system.

Adolescent↗
PubMed1992

Sampling methods in behavior research.

Animals perform a continuous stream of behavior throughout their lives. Because their behavior is not random, appropriate sampling methods can be used to obtain data that accurately reflect the actual behavior and are valid for answering research questions. Answering questions related to several variables assists in narrowing the choices of sampling methods. First, a determination must be made of what behaviors to measure. If the behaviors are few and easily measured, then All Occurrences Sampling is the method of choice because it generates accurate frequency and duration data through continuous recording. Sequence and Sociometric Matrix Sampling are specialized types of All Occurrences Sampling that are restricted to sampling intra- or interindividual sequences and social interactions (e.g., agonistic), respectively. Second, if who (e.g., specific individual, sex, or genotype) performs the behavior is a major component of the research question, then consideration should be given to Focal Animal (Pair, Group) Sampling. Third, if when or where the behavior is performed is of interest (e.g., activity budget), then Instantaneous or Scan Sampling can often be effective. Ad libitum Sampling does not produce valid data for analyses, but it is useful when formulating and fine-tuning research questions. One-Zero Sampling is not recommended except when the research question relates to the presence or absence of behaviors only. Other factors to consider in selecting a sampling method are duration of the behavior (event or state), desired scale of measurement (nominal, ordinal, interval, or ratio), and logistics (e.g., time, and equipment and facilities available).

Animals↗
PubMed1976

[Genetico-statistical analysis of multiple birth factors in man. III. Component analysis of multiple birth factors].

Based on the component analysis of correlation matrices for five indicies (parents' age by the moment of twin birth, the number of proband's pregnancy, the beginning of mother's coitus and menarche) characterizing four specified family groups (MZ and DZ load multiple birth and MZ and DZ sporadic multiple birth) at least 6 independent trends of multiple birth factors influence have been revealed. Gases of burdened and sporadic multiple birth turned out to differ in some of the specific trends. At the same time while cases of MZ and DZ load multiple birth differ in some of the trends, they appear to be much more similar to one another than those of MZ and DZ sporadic multiple birth. The data obtained make it possible to assert that first, according to the mechanism of the appearance, there exist at least four main multiple birth groups, specified above, and second, there are multiple birth factors being both common to all groups and specific to each of them separately. At this some of the defined factors influence mainly as implementing hereditary determined trend to multiple burth, while the others in the absence of predisposing genotype perform apparently as casual. The present study data confirm the concept, formed on the basis of genealogical analysis, that genetical factors involved in the determination of MZ and DZ multiple birth are of definitely common character. In addition to that the results of the study make it possible to conclude that multiple aproach in the statistical analysis of quantitative characteristics (multiple birth factors in the present case) is extremely sensitive and results in non-routine conclusions the effects of which can be directly changed.

Age Factors↗
PubMed1991

Female genotype influences the behavioral performance of mice selected for reproductive traits.

The behavioral performance of mice that differ in regularity of the estrous cycle and litter size was studied after female exposure to a male of the same or a different strain. Emotional reactivity was measured using the pole, straightaway and open field tests. Factor interpretations of emotionality included motor discharge, autonomic imbalance and acrophobia. Mice characterized by regular estrous cycles and large litters (line E) were more explorative and emotionally reactive with respect to motor discharge and autonomic imbalance. In contrast, mice with less regular estrous cycles and small litter size (line CN-) were more acrophobic. These strain differences in behavioral performance were influenced by the genotype of the female rather than the cohabitating male.

Animals↗
PubMed1990

Multilobated lymphoma of B cell type: a multiparameter investigation.

Multilobated lymphomas were originally described as T-cell neoplasms, but many of B-cell type have subsequently been reported. A case of B-cell origin is reported in which both immunophenotypic and genotypic studies performed on a cell suspension of the lymphoma gave inconclusive and potentially misleading information, while paraffin and frozen section immunohistologic studies, as well as genotypic studies performed on DNA obtained from snap-frozen tissue, were definitive. Thus, this case illustrates some of the problems that may be encountered using cell suspensions as a source for immunophenotypic, and even the much more sensitive genotypic, studies.

Antigens, CD↗
PubMed2026

Influence of IFNG rs2069709 on the severity of varicella in children.

OBJECTIVE: Aim: To assess the association between IFNG rs2069709 genotypes (CC, AC), as well as demographic factors such as sex and age, with the risk of complicated varicella in children. PATIENTS AND METHODS: Materials and Methods: The study included 132 children with confirmed varicella. Genotyping was performed using PCR with the TaqMan Genotyping Assay. Statistical analysis comprised the χ2 test, allele frequency evaluation, and logistic regression to determine the effects of genotype, sex, and age on disease severity. RESULTS: Results: The AC genotype was detected in 67.2% of children, while the CC genotype accounted for 20.3%; samples lacking genotype data (12.5%) were excluded from analysis. The C allele predominated in the uncomplicated group (64.2%), whereas the A allele was more frequent among children with complicated varicella (41.3%). Logistic regression demonstrated a tendency toward increased risk of complicated disease in AC carriers (OR=2.05; p=0.10). Sex and age showed no significant association with disease severity (p>0.05). Although statistical significance was not reached, the findings indicate that variability in the IFNG locus may influence individual immune responses to varicella-zoster virus. CONCLUSION: Conclusions: The IFNG rs2069709 C allele may act as a protective factor against severe varicella, while the A allele may increase susceptibility to complications. The observed trend for the AC genotype highlights the potential role of genetic markers in predicting disease course. Larger studies are required to confirm these associations and clarify their underlying mechanisms.

Humans↗
PubMed2025

PopGLen-a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods.

SUMMARY: PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for raw sequence processing of both historical and modern DNA, quality control, multiple filtering schemes, and population genomic analysis. Currently, the population genomic analyses included allow for estimating linkage disequilibrium, kinship, genetic diversity, genetic differentiation, population structure, inbreeding, and allele frequencies. Through Snakemake, it is highly scalable, and all steps of the workflow are automated, with results compiled into an HTML report. PopGLen provides an efficient, customizable, and reproducible option for analyzing population genomic datasets across a wide variety of organisms. AVAILABILITY AND IMPLEMENTATION: PopGLen is available under GPLv3 with code, documentation, and a tutorial at https://github.com/zjnolen/PopGLen. An example HTML report using the tutorial dataset is included in the Supplementary Material.

Software↗
PubMed1985

Genotyping with DNA probes in combined immunodeficiency syndrome with defective expression of HLA.

We performed HLA genotyping by using restriction-enzyme fragments hybridized with specific HLA probes instead of traditional immunologic methods in two patients whose lymphocytes expressed so few HLA antigens on the cell surface that serologic methods failed. Segregation of restriction-fragment-length polymorphism permitted identification of the genotypes. In addition, known correlations between serologically determined antigens and restriction-fragment-length polymorphism were confirmed. We applied this approach in making therapeutic decisions regarding bone marrow transplantation.

Bone Marrow Transplantation↗
PubMed2025

DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

Adolescent↗
PubMed1975

H-2-associated quantitative traits; statistical analysis of the relative contributions of the H-2 linked genes and the residual genotype.

Several associations have been recently reported of the kind that a certain H-2 haplotype tends to be accompanied by a low value and another H-2 haplotype by a high value of some quantitative traits. This includes also the weights of lymphoid and reproductive organs. In order to throw more light on the seeming clustering within the H-2 gene complex of the genetic determinants of such traits, statistical analysis of the relative contributions of the H-2 and the total residual genotypes to the variations in the weight of the thymus, spleen, lymph nodes, testes, seminal vesicles and ovaries was performed. Ten genotypically uniform populations of 2-month-old mice, each consisting of 31 males and 31 females, were analyzed using two different statistical procedures. Four of them were mice of the inbred strains A (H-2a), B10 (H-2b), A.BY (H-2b) and B10.A (H-2a) and six were various F1 hybrids derived from these four strains. The conclusion based on both approaches was that the relative contribution to the variations in the weight of the tested organs from the H-2 haplotype is much smaller or maximally not greater than the contribution from the total residual genotype.

Animals↗
PubMed2025

A Complete Picture of the CYP2D6 Heterogeneity in Northeastern Italian Genetic Isolates.

The CYP2D6 gene is a highly polymorphic pharmacogene involved in the metabolism of 25% of commonly used drugs. We aim to assess the feasibility of extracting relevant pharmacogenomic information from Whole Genome Sequencing (WGS) data and to highlight any difference in CYP2D6 allele frequencies between the northeastern Italian and European populations. To achieve this aim, WGS was performed on two cohorts: 664 individuals from six different isolated communities (FIC) and 123 outbred Italian individuals (FOP). In silico CYP2D6 genotyping was performed and allele frequencies from the FIC cohort were compared to those of FOP and European individuals from 1000 Genomes. Interestingly, 18 alleles identified in FIC were absent in the control cohorts. In particular, 13 individuals carried the extremely rare CYP2D6*28x2 allele, whose activity is unknown. Moreover, we identified a carrier of the CYP2D6*34x2 allele, which has never been described before. The population structure and genetic differentiation of the cohorts were investigated, revealing that the genetic isolates differ only slightly from the outbred and the European populations, but still offer new insight into CYP2D6 heterogeneity. The findings described here will be relevant to tailoring the treatments in the northeastern Italian population.

Cytochrome P-450 CYP2D6↗
PubMed2026

Characterization of DPYD pharmacogenetic variation in Mexican patients with gastrointestinal malignancies.

PURPOSE: Fluoropyrimidines are among the most widely used chemotherapeutic agents for gastrointestinal malignancies, but interindividual variability in dihydropyrimidine dehydrogenase (DPD) activity, encoded by DPYD, can lead to severe or lethal toxicities. Most pharmacogenetic data on DPYD originates from European populations, limiting the applicability of current guidelines in admixed groups. METHODS: We evaluated DPYD pharmacogenetic variation and its association with fluoropyrimidine-related adverse events in Mexican patients with gastrointestinal cancers. Adverse events were prospectively assessed using CTCAE v5.0. Genotyping was performed with the Illumina Global Screening Array and analyzed using PLINK and R. RESULTS: A total of 208 patients were enrolled, and 192 samples passed genotyping quality control; 156 patients received fluoropyrimidines. Only three patients (1.5%) carried actionable DPYD variants (rs3918290, rs67376798 and rs75017182), yielding allele frequencies of 0.26%, approximately ten-fold lower than those reported in European cohorts. Genome-wide analyses did not reveal significant genotype-phenotype associations, though suggestive variants in SDK1, ZPBP, and FGF12 were observed. Pharmacodynamic analyses identified frequent variation in TYMS rs2847153 and MTHFR rs1801133, both previously associated with fluoropyrimidine toxicity. Overall, patients exhibited a predominantly Native Mexican ancestry (56.5%), which may explain the markedly low frequency of actionable DPYD alleles commonly found in European populations. CONCLUSIONS: These findings highlight the limited representation of admixed populations in pharmacogenetic research and underscore the need for population-specific data to inform safe and equitable fluoropyrimidine dosing.

Humans↗
PubMed2025

Genomic Epidemiology of Resurgent Hepatitis A in Florida, 2018-2022.

During 2018-2022, a resurgence of hepatitis A occurred in Florida, with 5491 cases reported. Genotyping was performed on a convenience sample of cases through amplification and sequencing of the hepatitis A virus VP1-P2B junction region. Virus isolates from 1190 cases (22%) were genotyped; 69% were subgenotype IB, 30% were subgenotype IA, and 1% were subgenotype IIIA. Subgenotype IB was more common among patients reporting recent drug use or homelessness, whereas IA was more common among those reporting recent international travel and among men who have sex with men. Genotype IB infection was associated with a more than 4-fold greater odds of death compared to IA infection. A network analysis revealed 11 genomic clusters of ≥10 cases, with distinct temporal and spatial distributions. Case reports in 2023 decreased to below pre-2018 numbers, likely due to high population immunity following natural infection and extensive vaccination activities in the highest-risk groups.

Humans↗
PubMed1986

First trimester prenatal diagnosis of 21-hydroxylase deficiency by linkage analysis to HLA-DNA probes and by 17-hydroxyprogesterone determination.

The close genetic linkage between the gene for congenital adrenal hyperplasia due to 21-hydroxylase (21-OH) deficiency and HLA genes allowed us to use the polymorphism of this system as a marker of the disease. HLA genotyping can be performed by using restriction enzyme fragments hybridized with specific probes instead of serologic methods. In seven pregnancies at risk for 21-OH deficiency, a first trimester prenatal diagnosis has been performed by determining the fetal genotype by linkage analysis of DNA from chorionic villi using HLA class I and class II probes. In four of these pregnancies, determination of 17-OH progesterone in first trimester amniotic fluid afforded a complementary approach to the diagnosis.

17-alpha-Hydroxyprogesterone↗