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PubMed2005

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides.

In mass spectrometry-based proteomics, frequently hundreds of thousands of MS/MS spectra are collected in a single experiment. Of these, a relatively small fraction is confidently assigned to peptide sequences, whereas the majority of the spectra are not further analyzed. Spectra are not assigned to peptides for diverse reasons. These include deficiencies of the scoring schemes implemented in the database search tools, sequence variations (e.g. single nucleotide polymorphisms) or omissions in the database searched, post-translational or chemical modifications of the peptide analyzed, or the observation of sequences that are not anticipated from the genomic sequence (e.g. splice forms, somatic rearrangement, and processed proteins). To increase the amount of information that can be extracted from proteomic MS/MS datasets we developed a robust method that detects high quality spectra within the fraction of spectra unassigned by conventional sequence database searching and computes a quality score for each spectrum. We also demonstrate that iterative search strategies applied to such detected unassigned high quality spectra significantly increase the number of spectra that can be assigned from datasets and that biologically interesting new insights can be gained from existing data.

Alternative Splicing↗

PubMed2005

Tag SNP selection in genotype data for maximizing SNP prediction accuracy.

MOTIVATION: The search for genetic regions associated with complex diseases, such as cancer or Alzheimer's disease, is an important challenge that may lead to better diagnosis and treatment. The existence of millions of DNA variations, primarily single nucleotide polymorphisms (SNPs), may allow the fine dissection of such associations. However, studies seeking disease association are limited by the cost of genotyping SNPs. Therefore, it is essential to find a small subset of informative SNPs (tag SNPs) that may be used as good representatives of the rest of the SNPs. RESULTS: We define a new natural measure for evaluating the prediction accuracy of a set of tag SNPs, and use it to develop a new method for tag SNPs selection. Our method is based on a novel algorithm that predicts the values of the rest of the SNPs given the tag SNPs. In contrast to most previous methods, our prediction algorithm uses the genotype information and not the haplotype information of the tag SNPs. Our method is very efficient, and it does not rely on having a block partition of the genomic region. We compared our method with two state-of-the-art tag SNP selection algorithms on 58 different genotype datasets from four different sources. Our method consistently found tag SNPs with considerably better prediction ability than the other methods. AVAILABILITY: The software is available from the authors on request.

Algorithms↗

PubMed2000

Nucleic acid mutation analysis using catalytic DNA.

The sequence specificity of the '10-23' RNA-cleaving DNA enzyme (deoxyribozyme) was utilised to discriminate between subtle differences in nucleic acid sequence in a relatively conserved segment of the L1 gene from a number of different human papilloma virus (HPV) genotypes. DNA enzymes specific for the different HPV types were found to cleave their respective target oligoribonucleotide substrates with high efficiency compared with their unmatched counterparts, which were usually not cleaved or cleaved with very low efficiency. This specificity was achieved despite the existence of only very small differences in the sequence of one binding arm. As an example of how this methodology may be applied to mutation analysis of tissue samples, type-specific deoxyribozyme cleavable substrates were generated by genomic PCR using a chimeric primer containing three bases of RNA. The RNA component enabled each amplicon to be cleavable in the presence of its matching deoxyribozyme. In this format, the specificity of deoxyribozyme cleavage is defined by Watson-Crick interactions between one substrate-binding domain (arm I) and the polymorphic sequence which is amplified during PCR. Deoxy-ribozyme-mediated cleavage of amplicons generated by this method was used to examine the HPV status of genomic DNA derived from Caski cells, which are known to be positive for HPV16. This method is applicable to many types of nucleic acid sequence variation, including single nucleotide polymorphisms.

Capsid Proteins↗

PubMed2002

Rapid parallel mutation scanning of gene fragments using a microelectronic protein-DNA chip format.

We have developed a method for the de novo discovery of genetic variations, including single nucleotide polymorphisms and mutations, on microelectronic chip devices. The method combines the features of electronically controlled DNA hybridisation on open-format microarrays, with mutation detection by a fluorescence-labelled mismatch- binding protein. Electronic addressing of DNA strands to distinct test sites of the chip allows parallel analysis of several individuals, as demonstrated for mutations in different exons of the p53 gene. This microelectronic chip-based mutation discovery assay may substitute for time-consuming sequencing studies and will complement existing technologies in genomic research.

Adenosine Triphosphatases↗

PubMed2025

β1- and β2-adrenergic Receptor Haplotypes Regulate Therapeutic Responses to Placebo and the Biased Ligand β-blocker Bucindolol.

BACKGROUND: ADRB1 and ADRB2, encoding cardiac myocyte β1- and β2-adrenergic receptors (ARs) that mediate pathologic myocardial remodeling in response to chronically increased signaling, contain N-terminus haplotype variants capable of influencing agonist- or biased ligand-induced receptor internalization that uncouples canonical signaling and initiates EGFR/ERK1/2 cardioprotection. METHODS: In two heart failure (HF) clinical trial genetic substudies we investigated effects of internalizing vs. internalization-resistant ADRB1/ADRB2 haplotypes on clinical or biomarker responses to the biased ligand β-blocker bucindolol vs. placebo or vs. the nonbiased β1-antagonist metoprolol, and in haplotyped isolated human heart preparations we measured ERK1/2 activation in response to these same interventions. RESULTS: In subjects with ≥3 internalizing ADRB1+ADRB2 haplotypes (6.7% subcohort) placebo treatment was associated with fewer clinical events compared to subjects with internalization-resistant haplotypes (Odds Ratio (OR) 0.28, 95% CI (0.10, 0.82)). In contrast, placebo treatment in subjects with ≥3 internalization-resistant haplotypes (70% subcohort) was associated with more clinical events in comparison to subjects with internalizing haplotype counterparts (OR 1.64 (1.46, 1.84)). Bucindolol treatment was equal to placebo in the ≥3 internalizing subcohort, but was superior to placebo in the internalization-resistant subcohort (bucindolol vs. placebo OR 0.49 (0.41, 0.58)). In subjects with all 4 haplotypes internalization-resistant (25% subcohort), bucindolol vs. placebo reduced time to first event rates by 62.3±17.5% (P <0.01, 1.68±0.34 fold > the all-haplotypes parent population and additive to 1.92±0.58 fold when the ADRB1 haplotype contained Arg389 rather than Gly389). The same bucindolol vs. placebo pattern was observed for NT-proBNP or norepinephrine reduction vs. metoprolol. In these comparisons ADRB2 and ADRB1 haplotypes behaved similarly, and although the haplotypes differed in frequency between Black and non-Black subjects, within haplotypes there were no by-race differences in therapeutic effects. Bucindolol but not metoprolol activated ERK1/2 signaling in isolated ventricular preparations with ≥3 internalization-resistant haplotypes. CONCLUSIONS: 1) Both β1- and β2-AR haplotypes regulate therapeutic responses in HF; internalizing species confer protection against clinical events in placebo-treated subjects, while in internalization-resistant haplotypes the biased ligand β-blocker bucindolol but not the non-biased ligand metoprolol is associated with favorable effects. 2) The biased ligand cardioprotective effect may be related to internalization-dependent or -independent ERK1/2 activation.

Beta Adrenergic Receptors↗

PubMed2006

Do host genetic traits in the bacterial sensing system play a role in the development of Chlamydia trachomatis-associated tubal pathology in subfertile women?

BACKGROUND: In women, Chlamydia (C.) trachomatis upper genital tract infection can cause distal tubal damage and occlusion, increasing the risk of tubal factor subfertility and ectopic pregnancy. Variations, like single nucleotide polymorphisms (SNPs), in immunologically important host genes are assumed to play a role in the course and outcome of a C. trachomatis infection. We studied whether genetic traits (carrying multiple SNPs in different genes) in the bacterial sensing system are associated with an aberrant immune response and subsequently with tubal pathology following a C. trachomatis infection. The genes studied all encode for pattern recognition receptors (PRRs) involved in sensing bacterial components. METHODS: Of 227 subfertile women, serum was available for C. trachomatis IgG antibody testing and genotyping (common versus rare allele) of the PRR genes TLR9, TLR4, CD14 and CARD15/NOD2. In all women, a laparoscopy was performed to assess the grade of tubal pathology. Tubal pathology was defined as extensive peri-adnexal adhesions and/or distal occlusion of at least one tube. RESULTS: Following a C. trachomatis infection (i.e. C. trachomatis IgG positive), subfertile women carrying two or more SNPs in C. trachomatis PRR genes were at increased risk of tubal pathology compared to women carrying less than two SNPs (73% vs 33% risk). The differences were not statistically significant (P = 0.15), but a trend was observed. CONCLUSION: Carrying multiple SNPs in C. trachomatis PRR genes tends to result in an aberrant immune response and a higher risk of tubal pathology following a C. trachomatis infection. Larger studies are needed to confirm our preliminary findings.

Antibodies, Bacterial↗

PubMed2004

Genomic approaches to identifying breast cancer susceptibility factors.

The majority of the genetic variants underlying susceptibility to breast cancer are yet to be discovered. Genome-wide linkage analyses, utilizing anonymous genetic markers, have been successful at identifying two genes, BRCA1 and BRCA2, which account for a sizeable fraction of the clearly inherited forms of breast cancer occurring in autosomal dominant Mendellian patterns. Mutations in these genes, however, account for less than (1/4) of the total genetic component of breast cancer susceptibility and the remaining component is likely to be polygenic in nature - the interaction of mutations in multiple genes, each with a weak effect, in combination with environmental influences. The identification of these polygenes will likely require the study of large numbers of unrelated subjects with and without breast cancer in case-control association studies. Until the time when complete genome sequence information is feasible for all study subjects, interim strategies involving a subset of all common genetic variation (primarily single nucleotide polymorphisms, SNPs) are being planned. Assuming the common disease-common variant theory of complex disease susceptibility, studying a very dense set of genetic markers is likely to identify breast cancer susceptibility genes by virtue of including either the biologically relevant variant, or one closely correlated with it due to linkage disequilibrium.

Journal Article↗

PubMed2006

SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms.

Inherited genetic variation plays a critical but largely uncharacterized role in human differentiation. The completion of the International HapMap Project makes it possible to identify loci that may cause human differentiation. We have devised an approach to find such ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database. We selected ESNPs using the nearest shrunken centroid method (NSCM), and performed multiple tests for genetic heterogeneity and frequency spectrum on genes having ESNPs. The function and disease association of the selected SNPs were also annotated. This resulted in the identification of 100 736 SNPs that appeared uniquely in each ethnic group. Of these SNPs, 1009 were within disease-associated genes, and 85 were predicted as damaging using the Sorting Intolerant From Tolerant system. This study resulted in the creation of the SNP@Ethnos database, which is designed to make this type of detailed genetic variation approach available to a wider range of researchers. SNP@Ethnos is a public database of ESNPs with annotation information that currently contains 100 736 ESNPs from 10 138 genes, and can be accessed at http://variome.net and http://bioportal.net/ or directly at http://bioportal.kobic.re.kr/SNPatETHNIC/.

Chromosome Mapping↗

PubMed1998

Genetic analysis of the insulin receptor gene in Chinese patients with extreme insulin resistance.

BACKGROUND: Many patients with extreme insulin resistance in combination with acanthosis nigricans are reported to have defective insulin receptor genes. Because acanthosis nigricans is commonly accompanied by severe hyperinsulinemia and obesity, and obesity is a major factor in insulin resistance, this study was initiated to assess the prevalence of mutations in the insulin receptor gene in Chinese patients with extreme insulin resistance defined by hyperinsulinemia, obesity and acanthosis nigricans. METHODS: Exons 1-22 of the insulin receptor gene were amplified by polymerase chain reaction (PCR) by from genomic DNA from 13 young subjects with clinical and metabolic features of extreme insulin resistance. They were also screened for nucleotide variation using single-strand conformation polymorphism (SSCP) combined with nucleotide sequence analysis. RESULTS: Variant SSCP patterns were detected in exons 1, 3, 6, 11, 12 and 17 of the insulin receptor gene. However, sequencing of amplified DNA fragments revealed that none of the variations were mutations. The SSCP variant in exon 1 was caused by a novel intron polymorphism (G-->T at position 13, 5' intron), while the SSCP variant in exon 12 was caused by a novel silent polymorphism Thr789 (ACG-->ACA). Variants in exons 3 and 17 corresponded to known silent polymorphisms: Gln276 (CAA-->CAG) and His1068 (CAC-->CAT), respectively. Another three variants in exons 3, 6 and 11 were also identified as known polymorphisms in the flanking introns. In addition, two alterations, a silent polymorphism Gly8 (GGA-->GGG) and a polymorphism in the 3' flanking intron (T-->G at position 74), were observed in exon 1 of the insulin receptor gene. CONCLUSIONS: Although the prevalence of insulin receptor gene mutations in this Chinese study population might be underestimated because of the sensitivity of SSCP, these results suggest that mutations at the insulin receptor locus are uncommon in subjects with features of hyperinsulinemia, obesity and acanthosis nigricans.

Adolescent↗

PubMed2004

Single nucleotide polymorphism in CTH associated with variation in plasma homocysteine concentration.

Plasma total homocysteine (tHcy) concentration, an independent risk factor of atherosclerosis, has numerous genetic and environmental determinants. While the thermolabile polymorphism in MTHFR encoding methylenetetrahydrofolate reductase is the best-studied genetic factor associated with variation in plasma tHCy, other candidate genes are being evaluated. Recently, we discovered that cystathioninuria was caused by mutations in the CTH gene encoding cystathionine gamma-lyase, an enzyme that converts cystathionine to cysteine in the trans-sulfuration pathway. We also identified a common single nucleotide polymorphism (SNP), namely c.1364G>T (S403I) in exon 12 of CTH. In the current analysis, we studied the association of genotypes of this SNP with plasma tHcy concentrations in 496 Caucasian subjects. CTH 1364T/T homozygotes had significantly higher mean plasma tHcy concentration than subjects with other genotypes, and the effect sizes of CTH and MTHFR genotypes were similar. The findings suggest that common variation in CTH may be a determinant of plasma tHcy concentrations.

Amino Acid Substitution↗

PubMed2002

Single nucleotide polymorphisms in innate immunity genes: abundant variation and potential role in complex human disease.

Under selective pressure from infectious microorganisms, multicellular organisms have evolved immunological defense mechanisms, broadly categorized as innate or adaptive. Recent insights into the complex mechanisms of human innate immunity suggest that genetic variability in genes encoding its components may play a role in the development of asthma and related diseases. As part of a systematic assessment of genetic variability in innate immunity genes, we have thus far have examined 16 genes by resequencing 93 unrelated subjects from three ethnic samples (European American, African American and Hispanic American) and a sample of European American asthmatics. Approaches to discovering and understanding variation and the subsequent implementation of disease association studies are described and illustrated. Although highly conserved across a wide range of species, the innate immune genes we have sequenced demonstrate substantial interindividual variability predominantly in the form of single nucleotide polymorphisms (SNPs). Genetic variation in these genes may play a role in determining susceptibility to a range of common, chronic human diseases which have an inflammatory component. Differences in population history have produced distinctive patterns of SNP allele frequencies, linkage disequilibrium and haplotypes when ethnic groups are compared. These and other factors must be taken into account in the design and analysis of disease association studies.

Animals↗

PubMed2005

DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L.

Genetic association studies are rapidly becoming the experimental approach of choice to dissect complex traits, including tolerance to drought stress, which is the most common cause of mortality and yield losses in forest trees. Optimization of association mapping requires knowledge of the patterns of nucleotide diversity and linkage disequilibrium and the selection of suitable polymorphisms for genotyping. Moreover, standard neutrality tests applied to DNA sequence variation data can be used to select candidate genes or amino acid sites that are putatively under selection for association mapping. In this article, we study the pattern of polymorphism of 18 candidate genes for drought-stress response in Pinus taeda L., an important tree crop. Data analyses based on a set of 21 putatively neutral nuclear microsatellites did not show population genetic structure or genomewide departures from neutrality. Candidate genes had moderate average nucleotide diversity at silent sites (pi(sil) = 0.00853), varying 100-fold among single genes. The level of within-gene LD was low, with an average pairwise r2 of 0.30, decaying rapidly from approximately 0.50 to approximately 0.20 at 800 bp. No apparent LD among genes was found. A selective sweep may have occurred at the early-response-to-drought-3 (erd3) gene, although population expansion can also explain our results and evidence for selection was not conclusive. One other gene, ccoaomt-1, a methylating enzyme involved in lignification, showed dimorphism (i.e., two highly divergent haplotype lineages at equal frequency), which is commonly associated with the long-term action of balancing selection. Finally, a set of haplotype-tagging SNPs (htSNPs) was selected. Using htSNPs, a reduction of genotyping effort of approximately 30-40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought tolerance in pine.

Base Sequence↗

PubMed2002

Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190,562 genetic variations in the human genome. Single-nucleotide polymorphism.

To construct an infrastructure for genome-wide association studies of common diseases or drug sensitivities, we have been systematically exploring common variants by resequencing genomic regions containing genes in DNA from 24 Japanese individuals. We have analyzed a total of 154 Mb, corresponding to approximately 5% of the human genome, and so far have identified 174,269 single-nucleotide polymorphisms and 16,293 insertion/deletion polymorphisms within gene regions, i.e., one polymorphism in 807 bp on average. Our data are freely available via our web site (http://snp.ims.u-tokyo.ac.jp) and will facilitate studies to identify genes associated with susceptibility to common diseases and genes involved in sensitivity to therapeutic drugs.

Gene Frequency↗

PubMed2003

Human genetic variations in the 5HT2A receptor: a single nucleotide polymorphism identified with altered response to clozapine.

OBJECTIVE: to determine if the agonist serotonin and antagonists loxapine and clozapine have an altered potency for four allelic variants (T25N, I197V, A447V, and H452Y) of the human 5HT2A receptor when compared to the wild-type allele. METHODS: The receptor or its variants are studied in an in-vitro functional assay system consisting of a Sf9 insect cell line that is stably transformed with the human wild-type and mutant alleles. This assay system measures release of calcium stores due to receptor activation by agonists and inhibition of this agonist stimulated response by antagonists. RESULTS: Both loxapine and clozapine exhibit non-competitive antagonism of serotonin stimulation of the human 5HT2A receptor signal transduction system and loxapine is the more potent inhibitor. This study shows that the I197V allele requires a two-fold higher concentration of the atypical neuroleptic clozapine to inhibit serotonin stimulation compared to the wild-type receptor (P = 0.036). The I197V mutation does not affect the inhibition of serotonin stimulation by the typical neuroleptic loxapine nor does it alter the activation of the receptor by serotonin. It is also significant that the results of this study indicate that the T25N, A447V, and H452Y mutations in the human 5HT2A receptor do not significantly alter the response of the receptor to the agonist serotonin or the antagonists loxapine and clozapine.

Animals↗

PubMed2006

Characterization of single nucleotide polymorphisms in sheep and their variation as evidence of selection.

The discovery of SNPs was performed using animals from eight European sheep breeds. Eleven SNPs were further characterized using about 1,700 sheep belonging to 57 breeds. A method for the identification of loci that were likely subject to selection was applied; three of the 11 SNPs lying outside the 95% confidence region of the conditional joint distribution of F(ST) and mean heterozygosity were identified as outliers.

Animals↗

PubMed1994

Molecular analysis of insulin receptor gene in Werner's syndrome.

Werner's syndrome is characterized by premature aging and frequent impaired glucose tolerance or overt diabetes. Insulin resistance may play an important role and may be caused by a post-receptor defect or dysfunctional insulin receptor. The present study was undertaken to investigate the insulin receptor gene mutation in Werner's syndrome. The genomic DNAs were obtained from four patients with Werner's syndrome. Exons 2-22 of the insulin receptor gene except exon 1 were amplified from genomic DNA by the polymerase chain reaction and screened for nucleotide variation by examining for single-stranded conformational polymorphisms. There were no nucleotide variations in exons 2, 4-->7, 9 and 12-->22. Variants were thus found in exons 3, 8, 10 and 11 and each were sequenced. The variant in exon 8 was due to a silent polymorphism (GAT-->GAC/T, Asp519) and other variants in exons 3, 10 and 11 were caused by nucleotide substitutions in introns. These results suggest that the patients with Werner's syndrome express normal insulin receptors and that the primary genetic lesion for insulin resistance is not in the insulin receptor gene. Insulin resistance in Werner's syndrome is thus likely by a post-receptor defect.

Adult↗

PubMed1999

Single-nucleotide polymorphisms, haplotypes, and their relevance to pharmacogenetics.

Recognition that there is a vast quantity of human genetic variation has had a pervasive impact on modern medicine, facilitating the identification of scores of genes that underlie monogenic clinical disorders, as well as genes involved in complex disease processes. The next logical step for human genetics is the exploration and elucidation of genes involved in differential pharmacological response: responders, nonresponders, and those with adverse side effects. An understanding of the role that genes have in pharmacological response is the cornerstone of personalized medicine. Pharmacogenetic activities have swiftly embraced these tenets, leading to a proliferation of resources and approaches meant to enable and expedite targeted drug discovery and development. To realize the potential of these efforts, it will be necessary to incorporate a better understanding of the population genetic and evolutionary processes that have shaped genetic variation in modern humans. This article introduces these concepts to provide context and guidelines for the use of this variation (primarily single-nucleotide polymorphisms and haplotypes) in pharmacogenetics.

Genetics, Population↗

PubMed2001

Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation.

We have developed a formalism and a computational method for analyzing the potential functional consequences of non-synonymous single nucleotide polymorphisms. Our approach uses a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an amino acid polymorphim's effect on function. The feature values can be integrated into a probabilistic assessment of whether an amino acid polymorphism will affect the function or stability of a target protein. The method has been validated with data sets of unbiased mutations in the lac repressor and lysoyzyme. Applying our methodology to recent surveys of genetic variation in the coding regions of clinically important genes, we estimate that approximately 26-32 % of the natural non-synonymous single nucleotide polymorphisms have effects on function. This estimate suggests that a typical person will have about 6240-12,800 heterozygous loci that encode proteins with functional variation due to natural amino acid polymorphism.

Amino Acids↗