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PubMed1987

Three additional DNA polymorphisms in the met gene and D7S8 locus: use in prenatal diagnosis of cystic fibrosis.

We have used cloned DNA sequences from the 5' end of the met locus and the D7S8 locus to locate new restriction fragment length polymorphisms. TaqI and MspI polymorphisms with frequencies of 0.34/0.66 and 0.10/0.90, respectively, for met and a PvuII polymorphism (0.15/0.85) at D7S8 are described. We used these new markers to analyze our reference panel of cystic fibrosis pedigrees and found that they provided additional information in several families. No evidence for recombination was observed between the 5' end of met and previously described met markers. We present examples of the use of the met markers in the clinical diagnosis of cystic fibrosis and summarize our analysis of 29 clinical cases including eight prenatal diagnoses. We conclude that DNA-based prediction of cystic fibrosis is an effective clinical diagnostic procedure.

Alleles↗

PubMed2001

Causes of microsatellite instability in colorectal tumors: implications for hereditary non-polyposis colorectal cancer screening.

Microsatellite instability (MSI) analysis was performed using a "reference panel" of microsatellite markers in 345 unselected primary colorectal cancers (CRC). Thirty-five (10%) tumors were classified as high MSI (MSI-H). We identified 6 (17%) MSI-H tumors with germline mutations in mismatch repair (MMR) genes (tumors from patients with hereditary non-polyposis colorectal cancer (HNPCC) syndrome) and 29 (83%) MSI-H tumors without germline MMR mutations (sporadic MSI-H tumors). Hypermethylation of the hMLH1 promoter was found in 26/29 (90%) sporadic MSI-H tumors but only in 1/6 (17%) HNPCC tumors (P<.001). Somatic alterations were identified in both MMR genes in HNPCC tumors but mainly in the hMSH2 gene in sporadic MSI-H tumors. LOH at MMR loci was detected in 3/6 (50%) HNPCC tumors and in 4/26 (15%) informative sporadic MSI-H tumors. These results together indicate different mode of inactivation of MMR genes in sporadic MSI-H tumors versus MSI-H tumors in HNPCC patients. We therefore propose that MSI analysis of newly diagnosed primary CRC followed by methylation analysis of hMLH1 promoter in MSI-H tumors and mutational analysis of MMR genes in MSI-H tumors lacking hMLH1 promoter methylation might be an efficient molecular genetic approach for HNPCC screening.

Adaptor Proteins, Signal Transducing↗

PubMed1997

Evaluation of four PCR systems amplifying different genomic regions for molecular diagnosis of GB virus C infections.

Diagnosis of GB virus C (GBV-C) infection is based on RT-PCR methodology that detects genomic viral RNA. Four sets of primers located in different genomic regions were compared. These primers were used to amplify a reference panel of sera used by the French blood banks, including five positive sera, five negative sera and 10-fold serial dilutions of one positive serum. Three sets of primers located in the 5'UTR, NS3 and NS5a genomic regions gave comparable results with undiluted sera. When diluted sera were tested, the most sensitive protocol was that using a set of primers and a probe selected within the 5'UTR, together with a colorimetric detection based on DNA enzyme immunoassay.

Evaluation Studies as Topic↗

PubMed1998

Ultrarapid hepatitis C virus clearance by daily high-dose interferon in non-responders to standard therapy.

BACKGROUND/AIMS: To analyze the kinetics of the hepatitis C virus and the patterns of resistance to interferon alpha, we assessed HCV RNA levels early during retreatment with high-dose interferon in patients who did not respond to standard treatment. METHODS: Eleven non-responders to previous therapy with 3-6 MU interferon three times a week were retreated with daily 10 MU. Plasma was sampled at days 0, 1, 2, 3, 14 and 28; all samples were prepared within 2 h and stored at -70 degrees C without thawing until analysis. The quantitative HCV RNA level was assessed by the Superquant assay (NGI, USA). The Eurohep reference panel, tested blindly, confirmed the linearity of the assay with a detection limit for genotypes 1 and 3 between 10(2) and 10(3) copies/ml. RESULTS: All patients showed a fall in viral load between week 0 and week 2 (2.6 log, i.e. 99.7%, range 1.3-4.7 log), whereas no fall was detected after week 2. Closer examination in nine patients revealed that all had a dramatic fall in the first 2 days (first day 1.8 log, 0.8-3.5; second day 0.8 log, -0.2-1.3), without any significant fall thereafter. The calculated half-life of viral decay in plasma was 5 (2-8.9) h, corresponding to a clearance of 2.4 (0.2-13.7) x 10(11) virions per day. Sustained responders showed a significantly greater fall in viral load in the first day (3.2 log, 2.8-3.5) than those who did not respond (1.4 log, 0.8-2.1, p=0.001). All three sustained responders had undetectable plasma HCV RNA at day 14. CONCLUSION: In patients without a response to standard interferon, the hepatitis C virus has a high daily turnover rate similar to that reported in naive patients. Our findings suggest that an early clearance of HCV RNA from the circulation is the key to a sustained response, which might be induced in about 25% of these patients by treatment with high (10 MU) daily doses of interferon. These findings have important implications for the concept of treatment of hepatitis C, which should shift its focus from long-term mild treatment towards aggressive therapy aiming at a fast viral disappearance within the first few days.

Adult↗

PubMed1996

Performance of HTLV-1 screening assays in Brazil.

In recent years a variety of studies have been carried out to compare the accuracy (generally expressed in terms of sensitivity and specificity) of commercially available anti-HTLV tests. None of these studies were performed in Brazil or in any other South American country. During the characterization of our Brazilian reference panel we evaluated the sensitivities and specificities of the Abbott HTLV EIA (100%; 89.7%) and the Biochrom HTLV-1/-2 ELISA (100%; 42.4%). Our conclusion was that both assays may be problematic in terms of correctly identifying HTLV-negative sera. We therefore adjusted the cut-off values using receiver operating characteristics (ROC). ROC analysis, which involves calculating sensitivity and specificity for several cut-off values, can be used to ascertain the co-variation in the specificity and sensitivity of any assay giving quantitative results. The optimum cut-off value for the assay in a given study population is the point that gives highest possible sensitivity in conjunction with a small false-positive fraction. Using the HTLV-1/-2 Western blot as the "gold standard", we were able to improve the specificity of the Biochrom HTLV-1/-2 assay to 95% without affecting its sensitivity of 100%. However, it seems that when using the Biochrom HTLV-1/-2 ELISA, there may be problems in separating positive and negative sera. In the case of the Abbott HTLV EIA, our ROC analysis revealed that the cut-off value suggested by the manufacturer was nearly identical to the optimum cut-off value. Adjustment will affect neither sensitivity nor specificity. However, a slight adjustment of the cut-off value result in a clearer separation of the positive and negative populations. Furthermore, we assume that this adjustment will help to avoid false-positive results when larger serum panels are investigated. Further investigations will show whether or not this problem is linked to the geographical regions where the test is performed (e.g. polyclonal stimulation due to parasitic infections in tropical countries).

Blood Donors↗

PubMed1992

CEPH maps.

There are CEPH genetic maps on each homologous human chromosome pair. Genotypes for these maps have been generated in 88 laboratories that receive DNA from a reference panel of large nuclear pedigrees/families supplied by the Centre d'Etude du Polymorphisme Humain. These maps serve as useful tools for the localization of both disease genes and other genes of interest.

Academies and Institutes↗

PubMed2000

Flexsim-X: a method for the detection of molecules with similar biological activity

We describe the development of the method Flexsim-X, which can be used to detect molecules with similar biological activity. This procedure is based on comparing virtual affinity fingerprints made up from docking scores of the molecules with respect to a reference set of binding sites. Using a test data set consisting of ligands from five different activity classes and randomly chosen compounds, the reference panel of binding sites was optimized in terms of size and composition. Systematic approaches as well as genetic algorithm based (GA) optimization procedures have been evaluated. Additionally, the effectiveness of the method is illustrated.

Journal Article↗

PubMed1996

Molecular similarity based on DOCK-generated fingerprints.

An alternative method for defining molecular similarity is presented. By using the docking program DOCK and a reference panel of protein binding sites, fingerprints for a set of molecules have been generated, based on calculated interaction energies. These binding patterns allowed us to calculate matrices of similarity coefficients which subsequently were used for nearest-neighbor searches within the database. Our results indicate that the method is suitable for finding significant similarities of compounds of the same biological activity. Although the overall performance of a traditional 2D similarity method is better in the test systems investigated, our 3D approach can be regarded as complementary since it is able to detect similarities independent of the covalent structure of the compounds. Thus it should be a useful 3D database-searching tool for rational lead discovery.

Amino Acid Sequence↗

PubMed2002

Flexsim-R: a virtual affinity fingerprint descriptor to calculate similarities of functional groups.

Methods to describe the similarity of fragments occurring in drug-like molecules are of fundamental importance in computational drug design. In the early phase of lead discovery, they can help to select diverse building blocks for combinatorial compound libraries intended for broad screening. In lead optimization, such methods can guide bioisosteric replacements of one functional group by another or serve as descriptors for QSAR calculations. In this paper, we outline the development of a novel 3D descriptor, termed Flexsim-R, which is a further extension of our virtual affinity fingerprint idea. Descriptors are calculated based on docking of small fragments such as building blocks for combinatorial chemistry or functional groups of drug-like molecules into a reference panel of protein binding sites. The method is validated by examining the neighborhood behavior of the affinity fingerprints and by deriving predictive QSAR models for a couple of literature peptide data sets.

Algorithms↗

PubMed2001

Detection of microsatellite instability by real time PCR and hybridization probe melting point analysis.

Microsatellite alterations can be found in a number of tumors. There are two types of alterations: loss of heterozygosity (LOH), which can be detected in the majority of colorectal cancers (CRC), and microsatellite instability (MSI). MSI occurs in about 15% of CRC with a mutator phenotype and are the hallmark of hereditary nonpolyposis colorectal cancers (HNPCC). Furthermore, MSI can also be detected in other tumors which are part of the HNPCC tumor spectrum (eg, gastric, ovarian, and endometrial carcinomas). Usually, a set of microsatellite markers is amplified by PCR followed by gel or capillary electrophoresis to separate PCR amplicons and by detection of the markers using autoradiography (Thibodeau et al, 1993), silver staining (Schlegel et al, 1996), or fluorescence techniques (Gyapay et al, 1996; Mansfield et al, 1994). We have established a technique to detect MSI by LightCycler PCR and melting point analysis using sequence-specific hybridization probes (HyProbes) labeled with LightCycler dyes, LCRed640 and LCRed705. Amplification of microsatellites by real-time PCR is followed by melting point analysis to display alterations in the length of repetitive sequences, thereby avoiding any electrophoretical separation of amplified DNA. Two mononucleotide markers (BAT25 and BAT26) were tested in 81 formalin-fixed and paraffin-embedded colorectal cancer samples with matched normal tissues from 21 MSI tumors and 60 tumors with microsatellite stability. Amplification and melting point determination of BAT26 and BAT25 was possible in 129/162 (80%) and 123/162 (76%) formalin-fixed and paraffin-embedded tissue samples, respectively. MSI could be detected specifically with both BAT25 and BAT26 markers only in MSI-high tumors (> or =40% MSI rate, determined with microsatellite reference panel, BAT25, BAT26, D5S346, D2S123, D17S250; Boland et al, 1998; Dietmaier et al, 1997). This new technique allows MSI detection within less than a hour and provides a basis for fast, high-throughput MSI analysis.

Animals↗

PubMed2004

The Collaborative Cross, a community resource for the genetic analysis of complex traits.

The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

Animals↗

PubMed2026

Mapping the regulatory architecture of circadian clock adaptation: A genome-wide eQTL analysis in Drosophila melanogaster.

The circadian clock enables organisms to align internal daily rhythms with environmental cues, with major consequences for survival and fitness. Although the molecular framework of this system in Drosophila melanogaster is well characterized through transcription translation feedback loops involving ten core clock genes, the genetic basis of natural variation in their expression remains poorly understood. Here, we used natural expression variation to identify expression quantitative trait loci (eQTLs) through genome-wide association mapping. Using the Drosophila Genetic Reference Panel, we measured relative expression of all core clock genes at a single time point two hours after light onset. We identified 109 significant SNPs and 28 indels associated with expression variation across the clock network. Expression levels varied widely, with Pdp1ε showing the greatest variation (an 86-fold difference between extreme lines) and cyc the least (11.3-fold). Only three significant SNPs were located within clock genes themselves, all in Clk, whereas most associations represented trans-eQTLs in genes with diverse molecular functions. Candidate regulators included transcription factors such as Abd-B, tai, and E5; RNA binding proteins including Pum, Bru-3, and Mbl; and several long noncoding and antisense RNAs. Variants were also detected in gbb and the BMP pathway transcription factor Mad. Consistent with this, Mad knockdown reduced vri expression. Together, these results reveal a complex regulatory architecture underlying natural variation in circadian gene expression.

Journal Article↗

PubMed2026

Archaic ancestry inference in imputed ancient human genomes.

When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This introgression shaped human evolution, yet most insights have been gained from present-day genomes, leaving little known about how archaic variants evolved after interbreeding. Ancient genomes offer a direct view of this process, but low coverage and poor quality have limited their use. Recent advances in genotype imputation offer a way to overcome these challenges by reconstructing missing information from reference panels and recovering evolutionary signals from low-coverage data. Here, we show that imputation enables accurate detection and quantification of archaic introgression in ancient genomes, improves local archaic ancestry inference, and that regions of archaic ancestry are imputed with especially high accuracy. We further demonstrate that imputed genomes can reconstruct the trajectories of introgressed haplotypes, distinguish populations across time and geography, and identify both known and additional candidates for adaptive introgression.

Humans↗

PubMed2004

An automated turbidimetric method for the identification of certain antibiotic groups in incurred kidney samples.

An automated turbidimetric method was developed for group level identification of penicillinase sensitive penicillins, tetracyclines and fluoroquinolones in kidney samples. A sample pretreatment procedure was elaborated for the extraction of incurred residues from kidney tissue in a translucent solution to enable the measurement of changes in optical density. The method was comprised of three pairs, one for each antibiotic group: a sensitive test bacterium strain and a resistant strain for the identification of fluoroquinolones and tetracyclines, and a sensitive strain with and without penicillinase for the identification of penicillinase sensitive penicillins. The algorithm employed compared the areas under the OD vs. time curves; threshold values and experimentally observed intra-test criteria were also included in the algorithm. Antibiotics were reliably identified to group level, and no false identifications were obtained with antibiotics belonging to groups not included in the reference panel. Incurred penicillin G, oxytetracycline and enrofloxacin-ciprofloxacin residues were identified at or below the MRL levels for kidney tissue. The graphically determined shortest possible identification times varied between 2 and 7 h. The method developed could furthermore easily be diversified to include other antibiotic groups by adding new "sensitive-resistant" bacterium and medium combinations.

Algorithms↗

PubMed1999

Five new linkage groups in the canine linkage map.

Nineteen further polymorphic loci were typed on the DogMap reference panel. Five new linkage groups were identified. Additionally, five markers were added to earlier defined linkage groups. Three of the new linkage groups contain markers mapped earlier to specific dog chromosomes by physical mapping. These results make a further contribution to the canine genome map and provides more linkage groups physically assigned to known chromosomes.

Animals↗

PubMed2001

Cattle MHC genes DOA and DOB: sequence polymorphisms and assignments to the class IIb region.

In a study of the genetic polymorphism of the second exons of the cattle DOA and DOB genes, two and four allelic variants were detected, respectively. In the predicted amino acid sequence, the DOA polymorphism corresponded to variation at the respective residue position, whereas the nucleotide substitutions in the DOB gene were non-informative. PCR-RFLP assays were developed for DOA and DOB typing, and both loci were genetically mapped to the BoLA class IIb region by linkage analysis in the International Bovine Reference Panel. The single nucleotide polymorphisms detected in the BoLA-DOA and -DOB genes enable these loci to be used as markers in genetic trait analyses.

Alleles↗

PubMed1992

Cytochrome-P450-dependent hydroxylation in cluster headache.

Two isozymes of the cytochrome-P450-dependent drug oxidizing system exhibit polymorphism. Five to 10% of a Caucasian population are deficient in debrisoquine-hydroxylase activity and about 3% in mephenytoin-hydroxylase activity (poor metabolizers). We tested the hypothesis of a possible over-representation of poor metabolizers among patients with cluster headache. The individual metabolic capacity was determined in 30 cluster headache patients after administration of a test dose of 10 mg of debrisoquine and 100 mg of mephenytoin. Two patients (6.7%) were poor metabolizers of debrisoquine and one (3.3%) a poor metabolizer of mephenytoin. This was no different from the rate of poor metabolizers, 7.1% and 3.3% respectively, in a reference panel of healthy Swedish volunteers.

Adult↗

PubMed1989

The detection of an antibody against IgA allotype A2M 2 and a study of the Am genetic marker among the Han Chinese population.

The serum of a woman was found by the Ouchterlony double-diffusion and the hemagglutination inhibition (HAI) methods to have immunoglobulin A (IgA) deficiency. Further investigation using the hemagglutination (HA) test with red cells coated with IgA myeloma proteins of different specificities showed that the serum agglutinated only IgA2-, A2M-1, and A2M 2-coated cells. The patterns of the HAI test with a reference panel confirmed the presence of two specificities. One was anti-IgA2 and the other was a rare antibody against the allotype A2M 2. The anti-A2M 2 was used for population studies. Testing of the Han Chinese population, including family studies, confirms that A2M.1 and A2M.2 have an autosomal dominant mode of inheritance and are controlled by a codominant allele. The distribution of the two Am genetic markers among the Han Chinese population demonstrated A2M.1 with a gene frequency of 0.553 and A2M.2 with a gene frequency of 0.447 (chi 2 = 0.145, 0.80 greater than p greater than 0.70).

Alleles↗