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New Candidate Genes (new + candidate_gene)
Selected AbstractsIntegrative approach for prioritizing cancer genes in sporadic colon cancer,GENES, CHROMOSOMES AND CANCER, Issue 11 2009James F. Reid The current multistep carcinogenesis models of colon cancer do not fully capture the genetic heterogeneity of the disease, which is additionally complicated by the presence of passenger and driver genetic alterations. The aim of this study was to select in the context of this significant heterogeneity additional genes functionally related to colon cancer development. High-throughput copy number and gene expression data of 36 microsatellite stable sporadic colon cancers resected from patients of a single institution characterized for mutations in APC, KRAS, TP53 and loss of 18q were analyzed. Genes whose expression correlated with the underlying copy number pattern were selected, and their association with the above listed mutations and overall survival was evaluated. Gain of 20q was strongly associated with TP53 mutation, and overall survival with alterations on 7p, 8p, 13q, 18q, and 20q. An association with 18q loss and gain of 8q24 was also observed. New candidate genes with a potential role in colon cancer are PLCG1 on 20q, DBC1 on 8q21, and NDGR1 on 8p24. In addition, an unexpected pattern of loss and mutability was found in the region upstream of the KRAS gene. By integrating copy number alterations with gene expression and mutations in colon cancer associated genes, we have developed a strategy that identifies previously known molecular features and additional players in the molecular landscape of colon cancer. © 2009 Wiley-Liss, Inc. [source] Two C-Terminal Variants of NBC4, a New Member of the Sodium Bicarbonate Cotransporter Family: Cloning, Characterization, and LocalizationIUBMB LIFE, Issue 1 2000Alexander Pushkin Abstract We report the cloning, characterization, and chromosomal assignment of a new member of the sodium bicarbonate cotransporter (NBC) family, NBC4. The NBC4 gene was mapped to chromosome 2p13 and is a new candidate gene for Alstrom syndrome. Two variants of the transporter have been isolated from human testis and heart, which differ in their C termini. NBC4a encodes a 1137-residue polypeptide and is widely expressed in various tissues, including liver, testis, and spleen. NBC4b is identical to NBC4a except that it has a 16-nucleotide insert, creating a C-terminal frame shift. NBC4b encodes a 1074-residue polypeptide and is highly expressed in heart. Amino acids 1-1046 are common to both NBC4 variants. NBC4a has two protein-interacting domains that are lacking in NBC4b: a proline-rich sequence, PPPSVIKIP (amino acids 1102-1110), and a consensus PDZ-interacting domain, SYSL (1134-1137). NBC4b lacks the stretch of charged residues present in the C terminus of NBC4a and other members of the NBC family.Unlike other members of the NBC family, both NBC4a and NBC4b have a unique glycine-rich region (amino acids 440- 469). In comparison with other members of the bicarbonate transport superfamily, NBC4a and NBC4b are most similar structurally to the electrogenic sodium bicarbonate cotransporters (NBC1). [source] Linkage and Association Study of Late-Onset Alzheimer Disease Families Linked to 9p21.3ANNALS OF HUMAN GENETICS, Issue 6 2008S. Züchner Summary A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present study we analyzed an expanded clinical sample of 674 late-onset AD families, independently ascertained by three different consortia. Sample subsets were stratified by site and autopsy-confirmation. Linkage analysis of a dense array of SNPs across the chromosomal locus revealed the most significant results in the 166 autopsy-confirmed families of the NIMH sample. Peak HLOD scores of 4.95 at D9S741 and 2.81 at the nearby SNP rs2772677 were obtained in a dominant model. The linked region included the cyclin-dependent kinase inhibitor 2A gene (CDKN2A), which has been suggested as an AD candidate gene. By re-sequencing all exons in the vicinity of CDKN2A in 48 AD cases, we identified and genotyped four novel SNPs, including a non-synonymous, a synonymous, and two variations located in untranslated RNA sequences. Family-based allelic and genotypic association analysis yielded significant results in CDKN2A (rs11515: PDT p = 0.003, genotype-PDT p = 0.014). We conclude that CDKN2A is a promising new candidate gene potentially contributing to AD susceptibility on chromosome 9p. [source] Expression profiling of Wilms tumors reveals new candidate genes for different clinical parametersINTERNATIONAL JOURNAL OF CANCER, Issue 8 2006B. Zirn Abstract Wilms tumor is the most frequent renal neoplasm in children, but our understanding of its genetic basis is still limited. We performed cDNA microarray experiments using 63 primary Wilms tumors with the aim of detecting new candidate genes associated with malignancy grade and tumor progression. All tumors had received preoperative chemotherapy as mandated by the SIOP protocol, which sets this study apart from related approaches in the Unites States that are based on untreated samples. The stratification of expression data according to clinical criteria allowed a rather clear distinction between different subsets of Wilms tumors. Clear-cut differences in expression patterns were discovered between relapse-free as opposed to relapsed tumors and tumors with intermediate risk as opposed to high risk histology. Several differentially expressed genes, e.g.TRIM22, CENPF, MYCN, CTGF, RARRES3 and EZH2, were associated with Wilms tumor progression. For a subset of differentially expressed genes, microarray data were confirmed by real-time RT-PCR on the original set of tumors. Interestingly, we found the retinoic acid pathway to be deregulated at different levels in advanced tumors suggesting that treatment of these tumors with retinoic acid may represent a promising novel therapeutic approach. © 2005 Wiley-Liss, Inc. [source] Genome-wide pleiotropy of osteoporosis-related phenotypes: The framingham studyJOURNAL OF BONE AND MINERAL RESEARCH, Issue 7 2010David Karasik Abstract Genome-wide association studies offer an unbiased approach to identify new candidate genes for osteoporosis. We examined the Affymetrix 500K,+,50K SNP GeneChip marker sets for associations with multiple osteoporosis-related traits at various skeletal sites, including bone mineral density (BMD, hip and spine), heel ultrasound, and hip geometric indices in the Framingham Osteoporosis Study. We evaluated 433,510 single-nucleotide polymorphisms (SNPs) in 2073 women (mean age 65 years), members of two-generational families. Variance components analysis was performed to estimate phenotypic, genetic, and environmental correlations (,P, ,G, and ,E) among bone traits. Linear mixed-effects models were used to test associations between SNPs and multivariable-adjusted trait values. We evaluated the proportion of SNPs associated with pairs of the traits at a nominal significance threshold ,,=,0.01. We found substantial correlation between the proportion of associated SNPs and the ,P and ,G (r,=,0.91 and 0.84, respectively) but much lower with ,E (r,=,0.38). Thus, for example, hip and spine BMD had 6.8% associated SNPs in common, corresponding to ,P,=,0.55 and ,G,=,0.66 between them. Fewer SNPs were associated with both BMD and any of the hip geometric traits (eg, femoral neck and shaft width, section moduli, neck shaft angle, and neck length); ,G between BMD and geometric traits ranged from ,0.24 to +0.40. In conclusion, we examined relationships between osteoporosis-related traits based on genome-wide associations. Most of the similarity between the quantitative bone phenotypes may be attributed to pleiotropic effects of genes. This knowledge may prove helpful in defining the best phenotypes to be used in genetic studies of osteoporosis. © 2010 American Society for Bone and Mineral Research [source] Natural genetic variation in whole-genome expression in Arabidopsis thaliana: the impact of physiological QTL introgressionMOLECULAR ECOLOGY, Issue 5 2006THOMAS E. JUENGER Abstract A long-standing and fundamental question in biology is how genes influence complex phenotypes. Combining near-isogenic line mapping with genome expression profiling offers a unique opportunity for exploring the functional relationship between genotype and phenotype and for generating candidate genes for future study. We used a whole-genome microarray produced with ink-jet technology to measure the relative expression level of over 21 500 genes from an Arabidopsis thaliana near-isogenic line (NIL) and its recurrent parent. The NIL material contained two introgressions (bottom of chromosome II and top of chromosome III) of the Cvi-1 ecotype in a Ler -2 ecotype genome background. Each introgression ,captures' a Cvi allele of a physiological quantitative trait loci (QTL) that our previous studies have shown increases transpiration and reduces water-use efficiency at the whole-plant level. We used a mixed model anova framework for assessing sources of expression variability and for evaluating statistical significance in our array experiment. We discovered 25 differentially expressed genes in the introgression at a false-discovery rate (FDR) cut-off of 0.20 and identified new candidate genes for both QTL regions. Several differentially expressed genes were confirmed with QRT,PCR (quantitative reverse transcription,polymerase chain reaction) assays. In contrast, we found no statistically significant differentially expressed genes outside of the QTL introgressions after controlling for multiple tests. We discuss these results in the context of candidate genes, cloning QTL, and phenotypic evolution. [source] Epidemiology underpinning research in the aetiology of orofacial clefts,ORTHODONTICS & CRANIOFACIAL RESEARCH, Issue 3 2007Peter Mossey Structured Abstract Author,,, Mossey P Introduction,,, Epidemiological information gathered through birth defects surveillance is an important adjunct to carrying out clinical and aetiological research. Information on the incidence in the population, causative risk factors and providing baseline data prior to intervention are all important elements. Under the auspices of the World Health Organisation, it was agreed that a global registry and database on craniofacial anomalies should be created and this, the International Database on Craniofacial Anomalies (ICDFA) was designed to gather information on craniofacial abnormalities from existing birth defects registries and databases around the world to become a resource underpinning research. There are currently 62 registries covering 2 million births per year contributing to a database along with information on the size and type of studies used to collect the information, any variation in ascertainment and on the inclusion of syndromes and associated abnormalities. Generation of hypotheses,,, From the epidemiological data collected it is possible to carry out meta-analysis and to search for trends and consistencies in the data that enable hypothesis to be generated. Issues such as geographical distribution, ethnicity, gender, associated abnormalities and clefts in stillbirths can all be examined in a meta-analytical approach. Collection of information on risk factors such as maternal illnesses, medications, lifestyle factors, nutrition and perhaps occupational exposures enables investigation into environmental contribution to causality and genetic predisposition. A range of techniques are currently being used to identify new candidate genes and ultimately it will be necessary to test genetic and environmental hypothesis in the context of human population studies. Conclusions,,, It is only by consistency of association between different populations with different gene pools and maternal exposures, lifestyles, nutrition etc that conclusive evidence regarding causality will be found. It is therefore essential, and a major objective of the WHO that international multicentre collaborative studies are setup to gather the appropriate evidence and improve knowledge and the cause of birth defects in general and orofacial clefts in particular, with the ultimate humanitarian and scientific objective of the WHO being primary prevention. Clinical utility and implications,,, This IDCFA project fulfils three basic objectives namely to enable global surveillance of CFA; to create online access to those who wish to contribute to the IDCFA, and to develop an online directory of resources on craniofacial anomalies for the support of research and improving quality of care. The next sttif for IPDTOC are to expand the number of participating registries and to actively collect data on other craniofacial birth defects. [source] | |||||||||||||