Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant calling”

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 415 records · Page 23Linked to original sources
PubMed1999

Two approaches for estimating disease prevalence from population-based registries of incidence and total mortality.

Two approaches are described for estimating the prevalence of a disease that may have developed in a previous restricted age interval among persons of a given age at a particular calendar time. The prevalence for all those who ever developed disease is treated as a special case. The counting method (CM) obtains estimates of prevalence by dividing the estimated number of diseased persons by the total population size, taking loss to follow-up into account. The transition rate method (TRM) uses estimates of transition rates and competing risk calculations to estimate prevalence. Variance calculations are described for CM and TRM as well as for a variant of CM, called counting method times 10 (CM10), that is designed to yield more precise estimates than CM. We compare these three estimators in terms of precision and in terms of the underlying assumptions required to justify the methods. CM makes fewer assumptions but is typically ess precise than TRM or CM10. For common diseases such as breast cancer, CM may be preferred because its precision is excellent even though not as high as for TRM or CM10. For less common diseases, such as brain cancer, however, TRM or CM10 and other methods that make stabilizing assumptions may be preferred to CM.

Adult↗
PubMed2004

The Sup35 domains required for maintenance of weak, strong or undifferentiated yeast [PSI+] prions.

The Sup35 protein can exist in a non-infectious form or in various infectious forms called [PSI+] prion variants (or prion strains). Each of the different [PSI+] prion variants converts non-infectious Sup35 molecules into that prion variant's infectious form. One definition of a 'prion domain' is the minimal fragment of a prion protein that is necessary and sufficient to maintain the prion form. We now demonstrate that the Sup35 N region (residues 1-123), which is frequently referred to as the 'prion domain', is insufficient to maintain the weak or strong [PSI+] variants per se, but appears to maintain them in an 'undifferentiated' [PSI+] state that can differentiate into weak or strong [PSI+] variants when transferred to the full-length Sup35 protein. In contrast, Sup35 residues 1-137 are necessary and sufficient to faithfully maintain weak or strong [PSI+] variants. This implicates Sup35 residues 124-137 in the variant-specific maintenance of the weak or strong [PSI+] forms. Structure predictions indicate that the residues in the 124-137 region form an alpha-helix and that the 1-123 region may have beta structure. In view of these findings, we discuss a plausible molecular basis for the [PSI+] prion variants as well as the inherent difficulties in defining a 'prion domain'.

Animals↗
PubMed1992

An additional exon in the human vinculin gene specifically encodes meta-vinculin-specific difference peptide. Cross-species comparison reveals variable and conserved motifs in the meta-vinculin insert.

We have analyzed the structure, origin and expression of the high-molecular-mass muscle-specific variant of vinculin, called meta-vinculin. The meta-vinculin-specific inserts from the human and avian molecules have been isolated and sequenced and the sequences confirmed via cloning of the corresponding cDNA. Comparison of the human, avian and determined porcine sequences revealed cross-species identity in the C-terminal half of the insert. Human and porcine meta-vinculin were highly similar in the insert region, showing only five amino acid exchanges; avian meta-vinculin showed 22 exchanges in the same region compared to human meta-vinculin and exhibited, in addition, one extra amino acid, making 69 in all. Each insert was flanked by characteristic KWSSK motifs. Evidence for two vinculin mRNA species in human uterus smooth muscle was provided by reverse transcription combined with the polymerase chain reaction, as well as by ribonuclease-mapping analysis of cDNA/mRNA hybrids. One of the mRNA species contained an additional 204-nucleotide insert that precisely encoded the meta-vinculin-specific peptide. Sequence analysis of the appropriate portion of the human vinculin gene showed that the section coding for the meta-vinculin-specific insert is present as a discrete exon. Thus, meta-vinculin and vinculin mRNA are generated by alternative splicing.

Amino Acid Sequence↗
PubMed1989

Psychological aspects of weekend headache sufferers in comparison with migraine patients.

Sometimes the relaxation after stress may trigger a migraine attack. This is the principle that underlies that particular variant of migraine called "weekend headache". We hypothesize the presence in weekend headache prone subjects of a particular psychological background, different from that of common migraine sufferers. In order to detect possible differences supporting our hypothesis, we studied 104 new outpatients: 46 patients suffering from headache only on weekends (23 males and 23 females) and 58 matched common migraineurs (26 males and 32 females) with no weekend predilection. The psychological assessment was performed using the following psychometric tools: MMPI, BDI, STAIX1-X2. A clinical assessment of each patient was also carried out. Significant differences were found after statistically analyzing the test results. Most of the MMPI scales were found to be more elevated in both male and female weekend headache sufferers. From a clinical point of view, the weekend headache attacks proved to be similar to those of common migraine, but with a significantly higher incidence of concomitant symptoms. Our study confirms the important role that psychological factors play in the pathogenesis and clinical development of migraine and leads us to conclude that a psychic tension component is associated with the vascular one in weekend headache.

Adult↗
PubMed1975

Use of a serologically distinct strain of Thermoactinomyces vulgaris in the diagnosis of farmer's lung disease.

During investigations into farmer's lung disease it was noticed that Micropolyspora faeni (MF) was isolated and identified with ease, but difficulty was encountered in the identification of Thermoactinomyces vulgaris (TV), although an organism resembling TV was frequently isolated. Extracts prepared from the isolates resembling TV (called Thermoactinomyces vulgaris variant, TVV) when tested against the standard TV antiserum by double diffusion, did not produce any precipitin lines. When TVV extracts were tested against the serum of a patient from whom TVV had been isolated from the sputum, +++ precipitin lines were observed. With the TVV extracts the authors have demonstrated the existence of a serologically distinct strain of TV, and also that it would be a useful addition to the routine testing of antibodies to farmer's lung disease.

Dust↗
PubMed2001

Celiac-bimesenteric trunk: anatomic and radiologic description--case report.

The authors report the case of a 39-year-old man with a common origin of three arteries-the celiac, superior mesenteric, and inferior mesenteric arteries-that has not been described previously in the literature, to their knowledge. This variant, which they call the celiac-bimesenteric trunk, is documented with a selective angiogram, and an embryologic explanation is offered.

Adult↗
PubMed2002

Identification of T-type alpha1H Ca2+ channels (Ca(v)3.2) in major pelvic ganglion neurons.

Among autonomic neurons, sympathetic neurons of the major pelvic ganglia (MPG) are unique by expressing low-voltage-activated T-type Ca2+ channels. To date, the T-type Ca2+ channels have been poorly characterized, although they are believed to be potentially important for functions of the MPG neurons. In the present study, thus we investigated characteristics and molecular identity of the T-type Ca2+ channels using patch-clamp and RT-PCR techniques. When the external solution contained 10 mM Ca2+ as a charge carrier, T-type Ca2+ currents were first activated at -50 mV and peaked around -20 mV. Besides the low-voltage activation, T-type Ca2+ currents displayed typical characteristics including transient activation/inactivation and voltage-dependent slow deactivation. Overlap of the activation and inactivation curves generated a prominent window current around resting membrane potentials. Replacement of the external Ca2+ with 10 mM Ba2+ did not affect the amplitudes of T-type Ca2+ currents. Mibefradil, a known T-type Ca2+ channel antagonist, depressed T-type Ca2+ currents in a concentration-dependent manner (IC50 = 3 microM). Application of Ni2+ also produced a concentration-dependent blockade of T-type Ca2+ currents with an IC50 of 10 microM. The high sensitivity to Ni2+ implicates alpha1H in generating the T-type Ca2+ currents in MPG neurons. RT-PCR experiments showed that MPG neurons predominantly express mRNAs encoding splicing variants of alpha1H (called pelvic Ta and Tb, short and long forms of alpha1H, respectively). Finally, we tested whether the low-threshold spikes could be generated in sympathetic MPG neurons expressing T-type Ca2+ channels. When hyperpolarizing currents were injected under a current-clamp mode, sympathetic neurons produced postanodal rebound spikes, while parasympathetic neurons were silent. The number of the rebound spikes was reduced by 10 microM Ni2+ that blocked 50% of T-type Ca2+ currents and had a little effect on HVA Ca2+ currents in sympathetic MPG neurons. Furthermore, generation of the rebound spikes was completely prevented by 100 microM Ni2+ that blocked most of the T-type Ca2+ currents. In conclusions, T-type Ca2+ currents in MPG neurons mainly arise from alpha1H among the three isoforms (alpha1G, alpha1H, and alpha1I) and may contribute to generation of low-threshold spikes in sympathetic MPG neurons.

Action Potentials↗
PubMed1978

Reliable classification of six Pi M subtypes by separator isoelectric focusing.

For the first time, segregation of three common PiM alleles in family material is verified by application of separator isoelectric focusing. A new nomenclature system for the Pi M subtypes is used, whereby the common subtypes are designated according to their physicochemical properties; the most anodal type is called Pi M1, the intermediary one Pi M2, and the most cathodal variant Pi M3 (previously called Pi M2). Pi gene frequencies from Finnish, Dutch and Black populations are presented. The PiM2 allele was rather high in Finns (0.12) but low (0.04) in the West African Bozo. The PiM3 was found with a frequency of 0.13 in Dutch, 0.08 in Finns and 0.02 in Bozo. A previous Finnish sample was retested with the new subtyping method and the six-subtype distribution was found to be in good Hardy-Weinberg equilibrium. The validity of the Pi polymorphism for population genetics, linkage analysis and parentage testing is discussed.

Africa, Western↗
PubMed1982

Albumin Vanves: a new fast-moving variant of European origin.

In the course of a study on the albumin variants in 36 unrelated subjects with genetic bisalbuminemia, we have observed, in the serum of a French blood donor, a new fast-moving variant. Cellulose acetate electrophoresis at pH 8.6 showed that this variant, so-called albumin 'Vanves', moved slowlier than albumin Gent and faster than albumin Reading.

Electrophoresis, Polyacrylamide Gel↗
PubMed2005

Estrogen receptor-alpha splice variants in the medial mamillary nucleus of Alzheimer's disease patients: identification of a novel MB1 isoform.

Previously we have reported an increased nuclear estrogen receptor-alpha (ERalpha) in the medial mamillary nucleus (MMN) in Alzheimer's disease (AD). In the present study, we addressed the presence of specific ERalpha mRNA splice variants in this brain area of five AD cases compared with five controls using the RT-PCR and quantitative RT-PCR approach. Indeed, the occurrence of isoforms with the deletion of exons 7 (del.7), 4 (del.4), or 2 (del.2) was determined in all patients. However, there were no significant differences in the relative transcription levels of each of the mentioned splice variants between AD and control cases, although the ratio of the del.7 isoform to the canonical ERalpha mRNA was higher in controls. Given that exons 7 and 4 encode the ligand-binding domain of the ERalpha, whereas exon 2 encodes the DNA-binding domain, abundant expression of these splice variants suggests that much of the available ERalpha in the MMN of AD and elderly control patients is nonfunctional because they will be unable to bind either the ligand (del.7 and del.4 variants) or the estrogen-responsive elements on appropriate DNA (del.2 variant). Yet, the wild-type ERalpha mRNA appeared to be 2- to 3-fold up-regulated in AD, confirming the rise in the nuclear immunocytochemical staining and pointing to the potential for a beneficial effect of estrogen replacement therapy on the MMN-associated cognitive functions in AD because it represents the availability of potentially functional ERalpha in the MMN. Noteworthy, the expression of the wild-type, del.7, and del.2 mRNAs declined with advanced age in both AD and control patients. Interestingly, we have identified in two AD and two control patients a novel ERalpha splice variant that we called MB1 (mamillary body, exon 1) with a 168-nucleotide deletion corresponding to a U2-type intron inside exon 1 encoding the major portion of the transactivation function 1 domain of the receptor.

Aged↗
PubMed1999

Lack of effect of GnRH agonists on final height in girls with advanced puberty: a randomized long-term pilot study.

GnRH agonists improve final height in girls with "true" precocious puberty. To test if a comparable effect can be obtained in older girls, we performed a long-term controlled study in 30 caucasian girls whose puberty started between 8.4 and 10 yr (9.4 +/- 0.1 yr), a variant of normal called "advanced" puberty. At entry into trial, these girls had clinical, biological, and sonographic manifestations of puberty and a bone age greater than 10.9 yr. They were randomized 2:1 to receive 3.75 mg triptorelin im every 4 weeks for 2 yr (n = 20, group I) or no treatment (n = 10, group II). Mean height at inclusion was 135.2 +/- 4.3 cm (+0.6 SDS) in group I, 136.1 +/- 4.2 cm (+0.8 SDS) in group II, with target height 157.6 +/- 4.3 cm (group I) and 157.8 +/- 4.7 cm (group II), and predicted height (Bayley-Pinneau) 154.1 +/- 3.9 cm and 155.2 +/- 3.7 cm. Although GnRH agonists transiently delayed sexual maturation as well as bone age and growth rate, they had no clear-cut long-standing effect, and final height was comparable in treated (157.6 +/- 4.0 cm) and untreated girls (156.1 +/- 5.3 cm) (NS).

Age Determination by Skeleton↗
PubMed1984

Coronary artery spasm--1984.

Coronary artery spasm was virtually unknown not long ago, but the intense, ongoing interest it has generated in the past decade has produced a number of specific diagnostic techniques and therapeutic approaches, as well as considerable insight into mechanisms of coronary vascular tone and various coronary syndromes. There is growing evidence that coronary artery spasm is involved in unstable angina, stable angina, myocardial infarction, and sudden death. It is by no means a benign process and is associated with significant morbidity or mortality if misdiagnosed or untreated. It seems clear that what started as a mere clinical curiosity involving a minority of patients with the so-called Prinzmetal's variant angina is snowballing into a major arena for research, diagnosis, and treatment in the field of ischemic coronary artery disease.

Arrhythmias, Cardiac↗
PubMed2004

New Drosophila transgenic reporters: insulated P-element vectors expressing fast-maturing RFP.

In vivo green fluorescent protein (GFP)/red fluorescent protein (RFP) double-labeling studies have been hampered by several inconvenient properties of DsRed, the first described RFP. These disadvantages include a very slow (> 24 h) maturation time, emission of contaminating green light, and low solubility. A recently developed variant of DsRed, called DsRed.T4, has a much shorter maturation time, no significant green emission, and improved solubility. We have constructed Drosophila P-element transformation vectors encoding DsRed.T4 for promoter/enhancer analysis, labeling of living cells, or RFP tagging of proteins. These new vectors have all of the features of the widely used Pelican/Stinger GFP vectors, including insulator sequences to reduce position effects, an extensive polylinker, and both cytoplasmic and nuclear-localized forms of the reporter. We have also constructed an upstream activating sequence (UAS)-DsRed.T4 vector, for GAL4 activation of the reporter. We find that DsRed.T4 is very easily detected in transgenic flies without contamination of the GFP signal and that it matures to its fluorescent form nearly simultaneously with GFP. This advance in Drosophila reporter technology makes timed double-labeling experiments in developing transgenic animals possible for the first time.

Animals↗
PubMed2001

Localisation of DNA sequences on plant chromosomes using PRINS and C-PRINS.

Localisation of DNA sequences to plant chromosomes in situ has traditionally been accomplished using fluorescence in situ hybridisation (FISH). Although the method is suitable for most applications it is time-consuming and requires labelled probes. Recently, primed in situ labelling (PRINS) has been developed as an alternative to FISH. PRINS is based on annealing of unlabelled oligonucleotide primer(s) to chromosome DNA and its elongation by DNA polymerase in the presence of labelled nucleotide(s). The method was found useful to detect high-copy tandem repeats on plant chromosomes. Low copy repeats were detected after a more sensitive variant of PRINS called cycling PRINS (C-PRINS), which involves a sequence of thermal cycles analogous to polymerase chain reaction. This paper describes protocols of PRINS and C-PRINS, which have been optimised for chromosome spreads and for chromosomes purified using gradient centrifugation and/or flow sorting. The methods result in clear signals with negligible non-specific labelling. Further work is needed to improve the sensitivity to allow for reliable detection of single- copy DNA sequences.

DNA, Plant↗
PubMed1976

[Antibacterial effect of various mycotoxins and fungal metabolites against Bacillus thuringiensis (Berliner) strains sensitive or resistant to aflatoxin B1].

Antimicrobial activity of pure preparations of mycotoxins and fungal metabolites was studied against strains of Bacillus thuringiensis (Berliner). Two resistant strains, called stable-variant, were isolated after treatment with high concentrations of aflatoxin B1. These strains were then resistant also towards compounds with a double furan system (aflatoxins B1, B2, G1, G2, and sterigmatocystin).

Aflatoxins↗
PubMedDate not supplied

Gestational trophoblastic neoplasia in the 1990s.

Major advances have been achieved during the past 40 years in the epidemiology, etiology, pathology, endocrinology, immunology, diagnosis, and treatment of molar pregnancy (MP) and gestational trophoblastic neoplasia (GTN). MP is now recognized as composing two distinct entities--complete and partial, with distinct histopathology, genetics, and clinical presentations. Proper management is dependent on a thorough understanding of each type. Early diagnosis and effective treatment of patients with GTN has resulted in 100 percent cure rates in non-metastatic disease and in the majority of patients with metastases. In most instances, resistant disease leading to death results from delayed diagnosis and overwhelming tumor burden. Moreover, in most instances successful treatment can be accomplished with preservation of fertility and normal pregnancy outcome anticipated. A rare variant of choriocarcinoma called placental site trophoblastic tumor (PSTT) has been described, which, although curable by surgery when localized, is usually fatal when disseminated. It is anticipated that during the decade of the nineties the scientific work in progress will lead to earlier diagnosis and improved survival in resistant cases.

Antineoplastic Agents↗
PubMed1986

[Fibroadenoma of the breast with atypical clear-cell epithelial hyperplasia. Apropos of 7 cases. Immunohistochemical study].

We report 7 cases of unusual fibroadenomas of the breast. They are characterized by an exuberant cellular proliferation within the ductal lumens. They appear in young women from 20 to 40 years old. These lesions are histologically identical to those described by Azzopardi (1979) under the name of "Argyrophilic cells in fibroadenomas" and by Eusebi and Azzopardi (1980) and by Govoni (1981) and called "Lobular endocrine neoplasia in fibroadenoma of the Breast". An immunohistochemical study reveals a major positivity of these cells, in all cases, with Antikeratin Antibody (anti Kl1) and with Epithelial Membrane Antigen (anti EMA) proving the epithelial origin of these cells. There cells cannot yet be regarded as belonging to the neuro-endocrine group, because of the negativity, in all cases of Grimelius and Bodian stains, and of the very heterogeneous positivity observed with Neuron-Specific Enolase antibody (anti NSE) and with anti Human Natural Killer antibody (anti HNK). These cellular proliferations seem to us, on the microscopical point of view related to the atypical epithelial hyperplasias of the breast, and different from the in situ lobular carcinoma. Thus we propose to call these lesions "variant of the breast fibroadenoma" characterized by an atypical epithelial clear cell hyperplasia. The treatment of these lesions merely consists of a lumpectomy. Only one case is associated with an eleven years free of disease follow-up: a follow-up comprised between on to fifteen months is observed in the others cases. The knowledge of these benign lesions appears to us very important, to avoid improper treatment caused by an erroneous diagnosis of carcinoma developing in a breast fibroadenoma.

Adenofibroma↗
PubMed1978

Xeroderma pigmentosum and the role of DNA repair in oncogenesis.

Biochemical and genetic information on xeroderma pigmentosum (XP) has been briefly reviewed. This indicates that 80 to 90 percent of all XP patients are defective in the excision repair of pyrimidine dimers and are unable to perform the first step of this process as shown, for example, by their inability to undergo the DNA superhelical changes which accompany the initiation of excision repair in normal cells. However, in spite of its apparent biochemical homogeneity, XP is genetically heterogeneous and many genes appear to be responsible for the function of the factor defective in XP. Ten to 20 percent of all XP patients (called XP-variants) are capable of "dimer excision repair" but have difficulties in replicating UV-damaged DNA. The defects of XP and XP-variant affect also the repair of DNA damage caused by a number of chemical mutagens and carcinogens. This has important theoretical and practical implications since it indicates, for example, that the repair systems defective in XP must have broad specificity and that even XP cells not exposed to the harmful effect of light may suffer from poor repair of DNA damage. With regard to cancer, two questions have been considered. Namely, does XP provide a valid general model for UV-carcinogenesis in man and does it show how DNA damage leads to malignant transformation? The first question was answered in the affirmative in view of some clinical but, mainly, of cell biological data indicating that normal and excision defective XP cells differ, more quantitatively than qualitatively, in their response to UV-light. With regard to the second question XP seems to provide some support for various theories on carcinogenesis and, DNA repair defects may favour actinic carcinogenesis in a complex, non-univocous manner. Possibly the most important lesson imparted by XP is that, in man, the stability of the genetic material is dependent on the function of repair systems whose failure may predispose to cancer. In addition, the study of XP has stressed the fact that many genes control DNA metabolism and new evidence is accumulating to show that defects in such genes may contribute significantly to the genetic predisposition to cancer.

Carcinogens↗