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Results for “mutational profiling”

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At least 433 records · Page 24Linked to original sources

PubMed2001

Expression profiles of betaTRCP1 and betaTRCP2, and mutation analysis of betaTRCP2 in gastric cancer.

betaTRCP1 and betaTRCP2, components of the beta-catenin-ubiquitin ligase complex, are negative regulators of the WNT signaling pathway. We have previously isolated the betaTRCP2 gene, and detected betaTRCP2 in all gastric cancer cell lines examined. Here, expression profiles of betaTRCP1 and betaTRCP2 in various normal tissues and in primary gastric cancer were investigated. betaTRCP1 was predominant in small intestine, while betaTRCP2 was predominant in stomach. betaTRCP1 was expressed in gastric cancer cell lines MKN28, MKN45, MKN74, and KATO-III, but not in any cases of primary gastric cancer. betaTRCP2 was expressed in most cases of primary gastric cancer at almost the equal level in tumor and in non-cancerous portion of gastric mucosa. As betaTRCP2 was found to be the major betaTRCP expressed in gastric cancer, genetic alterations of betaTRCP2 in 7 gastric cancer cell lines and 12 cases of primary gastric cancer were investigated. A nucleotide substitution (Tright curved arrow C) at the nucleotide position 1486 of betaTRCP2 was identified in OKAJIMA cells, which lead to F462S amino acid substitution in the seventh WD-repeat domain. F462 was conserved among betaTRCPs derived from human, mouse, Xenopus laevis, and Drosophila melanogaster. As WD-repeats of betaTRCPs are the substrate-recognition motif of the beta-catenin-ubiquitin ligase, F462S amino-acid substitution might lead to beta-catenin stabilization, and might be implicated in carcinogenesis through activation of the WNT signaling pathway. This is the first report on comprehensive expression analyses of betaTRCP1 and betaTRCP2, and also on mutation analysis of betaTRCP2.

Blotting, Northern↗

PubMed2003

Mutational patterns of paired blood and rectal biopsies in HIV-infected patients on HAART.

Blood and concurrent rectal biopsy samples of human immunodeficiency virus type 1 (HIV-1)-positive highly active antiretroviral therapy (HAART)-treated patients were tested for genotypic resistance by direct sequencing of reverse transcriptase (RT) and protease (PR) regions to compare the patterns of resistance in these compartments. Fourteen subjects (five with undetectable plasma viral load (pVL) and nine persistently viremic) were studied. Four of five patients with undetectable pVL also had undetectable mucosal HIV RNA; sequence analyses from proviral DNA (PBMCs and rectal biopsy) were obtained with none or few resistance-associated mutations and no alteration of susceptibility profile. All viremic patients, and one with negative pVL, had detectable levels of mucosal HIV RNA (1.93-4.21 log(10) copies/mg); sequences of HIV RNA (plasma and/or rectal biopsy) were also obtained, and multiple mutations generally compatible with current/past medications were detected. Overall, 40 HIV-1 PR and 42 RT sequences were analyzed, yielding a total of 42 PR and 47 RT sequence pairs (plasma/tissue-RNA; plasma-RNA/tissue-DNA; PBMC/tissue-DNA; tissue-DNA/RNA; tissue-RNA/PBMC-DNA; PBMC-DNA/plasma-RNA), which almost always differed at the total amino acid level (median percentage discordance 8.08% in the PR, 4.8% in RT). The median percentage of resistance position discordance equaled 88.8% (IQR = 20-100) in the PR and 74.55% (IQR = 31.75-100%) in the RT pairs, respectively. Different resistance levels were detected by means of a computer-assisted interpretation of mutational profiles. The results support the multiform evolution of HIV genotype in various body compartments and emphasize the participation of intestinal mucosa in HIV genotype selection. Samples from diverse tissues should be used for resistance evaluation to obtain a complete picture of drug resistance for antiretroviral-treated patients.

Adult↗

PubMed2001

Gastrointestinal stromal tumors with KIT mutations exhibit a remarkably homogeneous gene expression profile.

Gastrointestinal stromal tumors (GISTs), the most common mesenchymal tumors of the digestive tract, are believed to arise from the interstitial cells of Cajal. GISTs are characterized by mutations in the proto-oncogene KIT that lead to constitutive activation of its tyrosine kinase activity. The tyrosine kinase inhibitor STI571, active against the BCR-ABL fusion protein in chronic myeloid leukemia, was recently shown to be highly effective in GISTs. We used 13,826-element cDNA microarrays to define the expression patterns of 13 KIT mutation-positive GISTs and compared them with the expression profiles of a group of spindle cell tumors from locations outside the gastrointestinal tract. Our results showed a remarkably distinct and uniform expression profile for all of the GISTs. In particular, hierarchical clustering of a subset of 113 cDNAs placed all of the GIST samples into one branch, with a Pearson correlation >0.91. This homogeneity suggests that the molecular pathogenesis of a GIST results from expansion of a clone that has acquired an activating mutation in KIT without the extreme genetic instability found in the common epithelial cancers. The results provide insight into the histogenesis of GIST and the clinical behavior of this therapeutically responsive tumor.

Adult↗

PubMed2005

Clinical profile of four families with arrhythmogenic right ventricular cardiomyopathy caused by dominant desmoplakin mutations.

AIMS: To characterize the clinical profile of patients belonging to families affected with autosomal dominant arrhythmogenic right ventricular cardiomyopathy (ARVC) due to mutations of the gene encoding for the cell-to-cell adhesion protein desmoplakin (DSP). METHODS AND RESULTS: Thirty-eight subjects belonging to four families showing different DSP mutations (three missense and one in the intron-exon splicing region) underwent clinical and genetic investigation, including annual 12-lead ECG, signal averaged ECG, 24 h Holter ECG, and two-dimensional echocardiography. Twenty-six family members (11 males and 15 females) were found to carry a DSP mutation. After a follow-up of 1-24 years, median 6, 14 (54%) fulfilled (mean age at diagnosis 33+/-15 years) and 12 (mean age 43+/-24 years at the last follow-up) did not fulfil the established diagnostic criteria of ARVC, although five of them had some cardiac abnormalities. Clinical presentations were palpitations in six, sudden death (SD) in three, syncope in one, and chest pain with increased myocardial enzymes in two. Abnormal 12-lead ECG findings were present in 15 cases (58%), ventricular arrhythmias in 12 (46%), and late potentials in 11 (42%). Fourteen (54%) had abnormal echocardiographic findings, with left ventricular involvement in seven of them. SD occurred in six subjects and in three it was the first symptom of the disease; moreover, one subject died due to heart failure. The annual disease-related death and SD/aborted SD were 0.028 and 0.023 patient/year, respectively. CONCLUSION: Familial ARVC caused by DSP mutations is characterized by a high occurrence of SD even as first clinical manifestation. Left ventricular involvement is not a rare feature of the disease, which frequently escapes clinical diagnosis by applying the currently available criteria. Genetic screening is mandatory for early identification of asymptomatic carriers and preventive strategies within a family with a genotyped index case.

Adolescent↗

PubMed2003

Clinical outcome and virologic profiles of severe hepatitis B exacerbation due to YMDD mutations.

BACKGROUND/AIMS: To study the outcome and the virologic profiles of severe hepatitis exacerbations due to YMDD mutants in lamivudine-treated patients. METHODS: Eighteen lamivudine-treated patients with severe hepatitis exacerbations due to YMDD mutants were recruited. Laboratory and clinical parameters were monitored. Viral genotypes and YMDD mutations were determined. RESULTS: None of the 18 patients had YMDD wild-type during exacerbations. Three (17%) and 15 (83%) patients had genotypes B and C, respectively. Elevated bilirubin levels and prolonged prothrombin time were found in 11 (61%) and six patients (33%) respectively. Three patients (17%) had adverse outcome with the development of ascites and/or encephalopathy. One of these patients required liver transplantation and one died. Both patients had evidence of cirrhosis before treatment and hepatitis B e antigen (HBeAg) seroreversion from anti-HBe positivity. The remaining 16 patients (89%) have no evidence of pre-existing cirrhosis. Thirty seven percent of patients had normal alanine aminotransferase levels at the last follow-up. The median HBV DNA level at the last follow-up was significantly lower than the pre-treatment level (P=0.009). CONCLUSIONS: Though the majority of patients with severe hepatitis exacerbations due to YMDD mutants had uneventful course, early liver transplantation should be considered in patients with pre-existing cirrhosis and HBeAg seroreversion.

Adult↗

PubMed2005

Cloning and characterization of the glucosidase II alpha subunit gene of Trichoderma reesei: a frameshift mutation results in the aberrant glycosylation profile of the hypercellulolytic strain Rut-C30.

We describe isolation and characterization of the gene encoding the glucosidase II alpha subunit (GIIalpha) of the industrially important fungus Trichoderma reesei. This subunit is the catalytic part of the glucosidase II heterodimeric enzyme involved in the structural modification within the endoplasmic reticulum (ER) of N-linked oligosaccharides present on glycoproteins. The gene encoding GIIalpha (gls2alpha) in the hypercellulolytic strain Rut-C30 contains a frameshift mutation resulting in a truncated gene product. Based on the peculiar monoglucosylated N-glycan pattern on proteins produced by the strain, we concluded that the truncated protein can still hydrolyze the first alpha-1,3-linked glucose residue but not the innermost alpha-1,3-linked glucose residue from the Glc2Man9GlcNAc2 N-glycan ER structure. Transformation of the Rut-C30 strain with a repaired T. reesei gls2alpha gene changed the glycosylation profile significantly, decreasing the amount of monoglucosylated structures and increasing the amount of high-mannose N-glycans. Full conversion to high-mannose carbohydrates was not obtained, and this was probably due to competition between the endogenous mutant subunit and the introduced wild-type GIIalpha protein. Since glucosidase II is also involved in the ER quality control of nascent polypeptide chains, its transcriptional regulation was studied in a strain producing recombinant tissue plasminogen activator (tPA) and in cultures treated with the stress agents dithiothreitol (DTT) and brefeldin A (BFA), which are known to block protein transport and to induce the unfolded protein response. While the mRNA levels were clearly upregulated upon tPA production or BFA treatment, no such enhancement was observed after DTT addition.

Amino Acid Sequence↗

PubMed2001

Profile of cognitive functioning in women with the fragile X mutation.

Two studies tested the specificity of the neurocognitive profile of women with fragile X syndrome (FXS). First, women with an FXS full mutation were compared with women with a premutation and women without FXS who grew up in FXS families. Women with FXS had a significantly lower IQ than the other groups, and analyses of subtest profiles showed they had a relative weakness on Arithmetic and strength on Picture Completion. Women with FXS performed worse than the other groups on executive function, spatial ability, and visual memory. Next, women with FXS were compared with women without FXS matched on age and IQ. A similar IQ profile was found, but women with FXS were worse than controls only on executive function. The authors also examined which neurocognitive indices were related to the underlying biology of the disorder. Overall, the results indicated that executive rather than visuospatial deficits were primary in the neurocognitive profile of FXS.

Adolescent↗

PubMed2026

Genomic Profiling of Epidermal Growth Factor Receptor Mutation-Positive Non-Small Cell Lung Cancer after Progression on First-line Osimertinib: Phase II ORCHARD Study.

PURPOSE: Osimertinib is the standard of care for first-line treatment for epidermal growth factor receptor-mutated (EGFRm) non-small cell lung cancer (NSCLC). Understanding the tumor molecular profile of patients following progression on osimertinib could help inform optimal second-line treatment. PATIENTS AND METHODS: ORCHARD (NCT03944772), a phase II biomarker-directed study, enrolled patients with EGFRm NSCLC who progressed on first-line osimertinib to receive treatment based on their tumor molecular profile after progression. The study comprised three groups into which patients were allocated based on the molecular profile of their tumor, determined via next-generation sequencing (NGS) of a tumor biopsy. We report results from a prespecified, exploratory analysis of baseline tumor tissue and plasma samples to evaluate mechanisms of resistance to first-line osimertinib identified by tissue and plasma NGS. Agreement between tissue and plasma NGS data was also assessed. RESULTS: This study provided a comprehensive dataset exploring tissue (n = 400) and plasma (n = 191) genomics, enabling characterization of the histogenomic landscape after first-line osimertinib treatment. TP53 and MDM2/4 alterations were mutually exclusive and occurred in 86% of tumors. When combining tissue and plasma genomics, resistance alterations were detected in 87% of samples, with multiple resistance alterations in 46%. Alterations in the PI3K pathway, SOX2, and MYC were frequently detected in histologically transformed tumors. Additionally, differential patterns of co-occurring EGFR mutations in tumors with L858R versus exon 19 deletion were observed. CONCLUSIONS: This comprehensive analysis highlights potential heterogeneous resistance to first-line osimertinib treatment, providing a rationale for combining treatments with broad activity to improve patient outcomes. See related commentary by Gupta et al., p. 3718.

Humans↗

PubMed1999

Longitudinal assessment of adaptive and maladaptive behaviors in fragile X males: growth, development, and profiles.

As young fully mutated fragile X [fra(X)] males age, cognitive levels (IQ scores) and adaptive behavior levels (DQ scores) decline. Given the variable behavioral profiles reported previously, we wondered whether changes in specific attributes of adaptive behavior are related to declines in composite adaptive behavior levels. We also examined maladaptive behavior to determine if changes are related to age. Therefore, we evaluated three areas of adaptive behavior, as well as maladaptive behavior, in 28 fully mutated fra(X) males, ages 4-14 years. To develop a profile of adaptive behavior, we analyzed nine subscale scores from the Vine-land Adaptive Behavior Scale (VABS). To assess maladaptive behavior, we graded part I of the VABS Maladaptive Behavior Scale. Subjects were sorted into three age cohorts, according to their initial test age: younger than 6 years; 6 to 9 years; older than 9 years. Results indicate that, in all age groups, the communications domain is the most severely impacted compared with either the socialization domain or daily living skills and that, in all age groups, the socialization domain is a relative strength compared with either the communications domain or daily living skills. The youngest cohort manifested significant increases in age-equivalent community living skills. Significant differences in age-equivalent scores between cohorts were observed in written language and play skills. Maladaptive behavior scores were available from cross-sectional data only. Twenty males (74%) showed significantly higher maladaptive scores than expected from other children their age. Our data analysis also revealed a moderate and significant negative correlation between maladaptive behavior levels and age (r = -0.54; P < 0.01). Curiously, adaptive and maladaptive behaviors did not correlate with each other.

Adaptation, Psychological↗

PubMed1997

Analysis of helicase gene mutations in Japanese Werner's syndrome patients.

The profile of helicase gene mutations was studied in 89 Japanese Werner's syndrome (WRN) patients by examining the previously described mutations 1-4 as well as a new mutation found during this study, designated mutation 5. Of 178 chromosomes (89 patients), 89 chromosomes (50%) had mutation 4, 11 (6.2%) chromosomes had mutation 1, and two chromosomes (1.1%) contained mutation 5. Mutations 2 and 3 were not observed in this patient population. The remaining 76 (42.7%) chromosomes had none of these mutations. A significant fraction of all patients (22 total patients, 24.7%) appear to be compound heterozygotes, including those carrying mutations of both types 1 and 4. The genotypes analysis of the markers surrounding the. WRN helicase gene strongly suggests that most of the chromosomes carrying either mutation 1 or 4 were derived from two single founders.

DNA Helicases↗

PubMed1996

Identification of putative beneficial mutations for lipid transport.

To determine the effect of a common mutation (Ser447-Ter) of the human LPL gene upon serum lipid and lipoprotein levels and coronary artery disease (CAD) within a representative adult male population, we analyzed subjects from the Caerphilly Prospective Heart Disease Study (n = 1273). The possession of this mutation associates with protective lipid and lipoprotein profiles. Subjects possessing the mutation have significantly higher HDL-C (p = 0.002) and apo AI (p < 0.04) levels, lower triglycerides (p = < 0.04) and total cholesterol/HDL-C ratios (p < 0.02); all established previously to reduce risk of CAD. We also find that this mutation is significantly less frequent amongst CAD subjects (p < 0.05). These associations provide evidence for a common mutation that appears to confer beneficial lipid and lipoprotein profiles amongst an adult male population with regard to risk of CAD.

Adult↗

PubMed1999

Molecular characterization of phenylalanine hydroxylase deficiency in Chile. Mutations in brief no. 243. Online.

Both the haplotype distribution and the mutational spectrum of the phenylalanine hydroxylase (PAH) gene has been defined for the Chilean phenylketonuria (PKU) population. Mutation analysis was performed using a combined approach of screening for common European and Oriental mutations and application of the DGGE scanning method in the remaining uncharacterized alleles. A total of 16 different mutations have been identified, including two novel ones, Q232X and IVS11nt5. The most frequent mutations were IVS10nt-11 and V388M present both in the 13% of the mutant chromosomes. The rest of the mutations are rare. The haplotype association including VNTR and STR alleles, was examined to investigated the origin and distribution of PAH alleles in Chile. Our results are consistent with Southern Europeans as the major source of PAH mutations in Latin America. However, we have also detected mutations from East and Central Europe, such IVS12nt1, R408W and R252W. It is clear that the PKU mutation present in each Latin American country varies with the demographic profile and specific mutation scanning is necessary in each population both for diagnostic and prognostic purposes. The correlation between the genotypes and the phenotypes is consistent with the emerging pattern of mutation severity deduced from previous studies in related populations.

Chile↗

PubMed2025

Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns.

Effective identification of oncogenic mutations is essential for diagnosis, forecasting resistance, and metastasis in remission. It is required for an optimal drug regimen. We develop a framework to discover mutations that co-exist in different oncoproteins, and those that are excluded, likely encoding oncogene-induced senescence. First, mapping the proteins onto pathways assists combinatorial drug selections and helps to detect metastases. Second, it provides the molecular basis for synthetic lethality, to date investigated at the genome level. Our pan-cancer profiles of ~60,000 tumor sequences, detect 3424 co-existing tumor-specific mutations. Mapping them onto pathways indicates that they preferentially promote specific primary tumors. We uncover metastatic mutations and provide metastatic breast-cancer markers. This work not only clarifies the mechanistic basis of intratumor mutational diversity but usefully reveals markers for metastasis in patients' genomes and introduces a novel computational framework for detecting metastasis based on tumor mutational profiles. Mapping the mutations onto pathways provides an invaluable metastasis-targeting resource, guiding drug combinations.

Humans↗

PubMed1996

Antigenic variation of SIV: mutations in V4 alter the neutralization profile.

Antigenic variation is a characteristic feature of lentiviral infection. The SIV/macaque model of AIDS provides an ideal system in which to investigate the molecular basis of antigenic variation. The purpose of this study was to genetically map the nucleotide changes in env that alter the neutralization phenotype of SIV. Serum taken from an SIVmac239-infected macaque (2D) at 30 weeks postinoculation was found to neutralize the input virus (SIVmac239) and an isolate, P9, obtained at 10 weeks p.i., but did not neutralize two other isolates, P13 and P23, obtained at 20 and 52 weeks, respectively. Sequence analysis of these virus variants revealed clustered amino acid changes in V1 and single base pair changes in V2-V4 of P13 and P23. Infectious recombinant viruses in which the V1 and V1-V3 sequences of SIVmac239 were replaced with those of P13 or P23 retained the neutralization profile of SIVmac239; both were neutralized by macaque 2D serum. Recombinants containing the entire surface glycoprotein (gp120) (V1-V5) and the 5' portion of gp41 of P13 and P23 and those containing gp120 sequences from V4 through the 5' portion of the transmembrane glycoprotein (gp41) were not neutralized by 2D serum. Using a panel of monoclonal antibodies in radioimmunoprecipitation assays, P23 and recombinants containing V4 and V5 of P23 were shown to be antigenically distinct from P13 and SIVmac239. The majority of the amino acid changes in the antigenically distinct viruses were clustered in V4 (amino acids 413-418) and these changes created new potential N-linked glycosylation sites. This study demonstrates that a small number of specific amino acid changes (amino acids 412 to 418 in the env gene) in the V4 region of the SIV envelope glycoprotein can alter antibody recognition and neutralization and that these phenotypic changes may be associated with altered glycosylation of the envelope.

Amino Acid Sequence↗

PubMed2026

Spinal low-grade ependymal tumors harboring telomerase reverse transcriptase promoter mutation and chromosome 7 gain with methylation profile of spinal subependymoma.

Spinal intramedullary tumors comprise a heterogeneous group of entities with diverse histopathological features, making their diagnosis particularly challenging. With the introduction of DNA methylation profiling, the underlying biological diversity of these tumors has been increasingly clarified and systematized; however, owing to the rarity of these tumors, case accumulation remains limited, and significant challenges persist. In this study, we identified two cases of spinal ependymal tumors exhibiting a methylation profile of spinal (SP-) subependymoma (SEPN). Both cases occurred in elderly patients and demonstrated circumscribed growth consistent with low-grade ependymal tumors; however, these tumors did not exhibit the typical histopathological features required for a diagnosis of SEPN in the 2021 WHO classification of central nervous system (CNS) tumors, showing indistinct cluster formation, an astrocytic immunohistochemical profile suggested by Olig2 expression, and relatively elevated Ki-67 labeling indices of 4.5% and 3.1%. At the molecular level, both cases harbored telomerase reverse transcriptase promoter mutations and whole chromosome 7 gain. On two-dimensional t-distributed stochastic neighbor embedding analysis, both clustered within the SP-SEPN methylation class at its periphery, with low classifier calibration scores (0.70 and 0.69). According to the current WHO classification, these cases are designated as low-grade ependymal tumors (CNS WHO grade 2) with methylation profile of SP-SEPN because they do not meet the essential WHO histopathological criteria. Ependymal tumors exhibiting a methylation profile consistent with SEPN, but discordant histopathological features have been increasingly recognized, and the appropriate classification of such tumors remains a subject of ongoing debate. These cases provide important insights into the histopathological diversity of ependymal tumors and contribute to establishing a more comprehensive and systematic classification of ependymal tumors.

Aged↗

PubMed2004

Genomic modulation of diabetes (db/db) and obese (ob/ob) mutation-induced hypercytolipidemia: cytochemical basis of female reproductive tract involution.

Infertility and hypercytolipidemic utero-ovarian involution are recognized consequences of the diabetes-obesity syndrome (DOS) in C57BL mice with either obese (ob/ob) or diabetes (db/db) single gene mutations. We have evaluated the interdependent deleterious influences of both mutation types and differences in the genomic background on utero-ovarian dysfunction in C57BL mice. Control ( +/?) C57BL mice were matched with littermate ob/ob and db/db mutants expressed on either the /KsJ or /6 background. Both ob/ob and db/db mutations increased body weights of /KsJ and /6 background strains relative to +/? groups. In contrast, uterine and ovarian weights were depressed by ob/ob and db/db mutations relative to +/?, regardless of the background strain, but especially when expressed on the /KsJ background. Functionally, both ob/ob and db/db mutations induced hyperglycemic-hyperinsulinemic states coupled with depressed serum estradiol-17-beta and progesterone concentrations when expressed on a /KsJ background. Microscopic analysis of utero-ovarian tissue samples revealed marked hypercytolipidemia in the follicular granulosa and endometrial epithelial tissue layers of both ob/ob and db/db mutant groups relative to normal +/? cytoarchitecture. The db/db mutation consistently promoted more severe hypercytolipidemic profiles than the ob/ob mutation, regardless of background strain. Thus, the severity of utero-ovarian hypercytolipidemia following the expression of ob/ob and db/db mutations in C57BL mice is influenced, or moderated, by the genomic background on which the mutation is expressed.

Animals↗

PubMed2003

The association of Pro12Ala polymorphism in PPARgamma2 with lower carotid artery IMT in Japanese.

In this study, the association of the Pro12Ala peroxisome proliferator-activated receptor gamma2 (PPARgamma2) polymorphism with atherosclerosis was examined in a Japanese Type 2 diabetic population. PPARgamma has been identified as a key regulator of adipogenesis. Recently, some studies reported that the Pro12Ala polymorphism was associated with resistance to Type 2 diabetes. It is well-known that Type 2 diabetes is closely related with disorder of lipid metabolism as well as impaired glucose homeostasis, resulting in atherosclerosis. We aimed to evaluate the association between carriers of the Pro12Ala PPARgamma2 mutation and clinical profiles concerning atherosclerosis besides plasma glucose and lipid concentrations. Screening for the mutation was performed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method among 154 Type 2 diabetic patients. The homozygotes of the Pro12 allele were 143 (93%), the heterozygotes of the Pro12 and Ala12 allele were 11 (7%) and the homozygote of the Ala12 allele was not detected. The group with the Ala12 allele had a significantly lower value of carotid artery intima-media thickness (IMT) than that without it, although there was no difference between two groups in sex, age or other clinical variables we examined. The Pro12Ala PPARgamma2 polymorphism may be associated with carotid artery IMT values in Type 2 diabetes mellitus.

Adult↗

PubMed2006

Discrete profile comparison using information bottleneck.

Sequence homologs are an important source of information about proteins. Amino acid profiles, representing the position-specific mutation probabilities found in profiles, are a richer encoding of biological sequences than the individual sequences themselves. However, profile comparisons are an order of magnitude slower than sequence comparisons, making profiles impractical for large datasets. Also, because they are such a rich representation, profiles are difficult to visualize. To address these problems, we describe a method to map probabilistic profiles to a discrete alphabet while preserving most of the information in the profiles. We find an informationally optimal discretization using the Information Bottleneck approach (IB). We observe that an 80-character IB alphabet captures nearly 90% of the amino acid occurrence information found in profiles, compared to the consensus sequence's 78%. Distant homolog search with IB sequences is 88% as sensitive as with profiles compared to 61% with consensus sequences (AUC scores 0.73, 0.83, and 0.51, respectively), but like simple sequence comparison, is 30 times faster. Discrete IB encoding can therefore expand the range of sequence problems to which profile information can be applied to include batch queries over large databases like SwissProt, which were previously computationally infeasible.

Algorithms↗