651
|
Bi J, Gelernter J, Sun J, Kranzler HR. Comparing the utility of homogeneous subtypes of cocaine use and related behaviors with DSM-IV cocaine dependence as traits for genetic association analysis. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:148-56. [PMID: 24339190 PMCID: PMC4152729 DOI: 10.1002/ajmg.b.32216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 11/20/2013] [Indexed: 11/08/2022]
Abstract
Because DSM-IV cocaine dependence (CD) is heterogeneous, it is not an optimal phenotype to identify genetic variation contributing to risk for cocaine use and related behaviors (CRBs). We used a cluster analytic method to differentiate homogeneous, highly heritable subtypes of CRBs and to compare their utility with that of the DSM-IV CD as traits for genetic association analysis. Clinical features of CRBs and co-occurring disorders were obtained via a poly-diagnostic interview administered to 9,965 participants in genetic studies of substance dependence. A subsample of subjects (N = 3,443) were genotyped for 1,350 single nucleotide polymorphisms (SNPs) selected from 130 candidate genes related to addiction. Cluster analysis of clinical features of the sample yielded five subgroups, two of which were characterized by heavy cocaine use and high heritability: a heavy cocaine use, infrequent intravenous injection group and an early-onset, heavy cocaine use, high comorbidity group. The utility of these traits was compared with the CD diagnosis through association testing of 2,320 affected subjects and 480 cocaine-exposed controls. Analyses examined both single SNP (main) and SNP-SNP interaction (epistatic) effects, separately for African-Americans and European-Americans. The two derived subtypes showed more significant P values for 6 of 8 main effects and 7 of 8 epistatic effects. Variants in the CLOCK gene were significantly associated with the heavy cocaine use, infrequent intravenous injection group, but not with the DSM-IV diagnosis of CD. These results support the utility of subtypes based on CRBs to detect risk variants for cocaine addiction.
Collapse
Affiliation(s)
- Jinbo Bi
- Department of Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, Connecticut,Department of Psychiatry, VA CT Healthcare Center, West Haven, Connecticut
| | - Jiangwen Sun
- Department of Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut
| | - Henry R. Kranzler
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania,VISN 4 Mental Illness Research, Education, and Clinical Center, Philadelphia, Pennsylvania,Correspondence to: Henry R. Kranzler, M.D., Department of Psychiatry, Treatment Research Center, University of Pennsylvania Perelman School of Medicine, 3900 Chestnut Street, Philadelphia, PA 19104-6178.
| |
Collapse
|
652
|
Guay SP, Brisson D, Lamarche B, Gaudet D, Bouchard L. Epipolymorphisms within lipoprotein genes contribute independently to plasma lipid levels in familial hypercholesterolemia. Epigenetics 2014; 9:718-29. [PMID: 24504152 DOI: 10.4161/epi.27981] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gene polymorphisms associated so far with plasma lipid concentrations explain only a fraction of their heritability, which can reach up to 60%. Recent studies suggest that epigenetic modifications (DNA methylation) could contribute to explain part of this missing heritability. We therefore assessed whether the DNA methylation of key lipoprotein metabolism genes is associated with high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglyceride levels in patients with familial hypercholesterolemia (FH). Untreated FH patients (61 men and 37 women) were recruited for the measurement of blood DNA methylation levels at the ABCG1, LIPC, PLTP and SCARB1 gene loci using bisulfite pyrosequencing. ABCG1, LIPC and PLTP DNA methylation was significantly associated with HDL-C, LDL-C and triglyceride levels in a sex-specific manner (all P<0.05). FH subjects with previous history of coronary artery disease (CAD) had higher LIPC DNA methylation levels compared with FH subjects without CAD (P = 0.02). Sex-specific multivariable linear regression models showed that new and previously reported epipolymorphisms (ABCG1-CpGC3, LIPC-CpGA2, mean PLTP-CpGC, LPL-CpGA3, CETP-CpGA2, and CETP-CpGB2) significantly contribute to variations in plasma lipid levels (all P<0.001 in men and P<0.02 in women), independently of traditional predictors such as age, waist circumference, blood pressure, fasting plasma lipids and glucose levels. These results suggest that epigenetic perturbations of key lipoprotein metabolism genes are associated with plasma lipid levels, contribute to the interindividual variability and might partially explain the missing heritability of plasma lipid levels, at least in FH.
Collapse
Affiliation(s)
- Simon-Pierre Guay
- Department of Biochemistry; Université de Sherbrooke; Sherbrooke, QC Canada; ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada
| | - Diane Brisson
- ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada; Department of Medicine; Université de Montréal; Montréal, QC Canada
| | - Benoit Lamarche
- Institute of Nutrition and Functional Foods; Université Laval; Québec, QC Canada
| | - Daniel Gaudet
- ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada; Department of Medicine; Université de Montréal; Montréal, QC Canada
| | - Luigi Bouchard
- Department of Biochemistry; Université de Sherbrooke; Sherbrooke, QC Canada; ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada
| |
Collapse
|
653
|
Ghelardini L, Berlin S, Weih M, Lagercrantz U, Gyllenstrand N, Rönnberg-Wästljung AC. Genetic architecture of spring and autumn phenology in Salix. BMC Plant Biol 2014; 14:31. [PMID: 24438179 PMCID: PMC3945485 DOI: 10.1186/1471-2229-14-31] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/03/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa. RESULTS All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized. CONCLUSIONS This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.
Collapse
Affiliation(s)
- Luisa Ghelardini
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
- Present address: Institute for Plant Protection, Italian National Research Council CNR, 50019 Sesto fiorentino, Italy
| | - Sofia Berlin
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Ulf Lagercrantz
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Niclas Gyllenstrand
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| | - Ann Christin Rönnberg-Wästljung
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-750 07 Uppsala, Sweden
| |
Collapse
|
654
|
Langford DJ, West C, Elboim C, Cooper BA, Abrams G, Paul SM, Schmidt BL, Levine JD, Merriman JD, Dhruva A, Neuhaus J, Leutwyler H, Baggott C, Sullivan CW, Aouizerat BE, Miaskowski C. Variations in potassium channel genes are associated with breast pain in women prior to breast cancer surgery. J Neurogenet 2014; 28:122-35. [PMID: 24392765 DOI: 10.3109/01677063.2013.856430] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Preoperative breast pain in women with breast cancer may result from a number of causes. Previous work from our team found that breast pain occurred in 28.2% of women (n = 398) who were about to undergo breast cancer surgery. The occurrence of preoperative breast pain was associated with a number of demographic and clinical characteristics, as well as variation in two cytokine genes. Given that ion channels regulate excitability of sensory neurons, we hypothesized that variations in potassium channel genes would be associated with preoperative breast pain in these patients. Therefore, in this study, we evaluated for associations between single-nucleotide polymorphisms and inferred haplotypes among 10 potassium channel genes and the occurrence of preoperative breast pain in patients scheduled to undergo breast cancer surgery. Multivariable logistic regression analyses were used to identify those genetic variations that were associated with the occurrence of preoperative breast pain while controlling for age and genomic estimates of and self-reported race/ethnicity. Variations in four potassium channel genes: (1) potassium voltage-gated channel, delayed rectifier, subfamily S, member 1 (KCNS1); (2) potassium inwardly rectifying channel, subfamily J, member 3 (KCNJ3); (3) KCNJ6; and (4) potassium channel, subfamily K, member 9 (KCNK9) were associated with the occurrence of breast pain. Findings from this study warrant replication in an independent sample of women who report breast pain following one or more breast biopsies.
Collapse
|
655
|
Abstract
Candidate gene (CG) approaches provide a strategy for identification and characterization of major genes underlying complex phenotypes such as production traits and susceptibility to diseases, but the conclusions tend to be inconsistent across individual studies. Meta-analysis approaches can deal with these situations, e.g., by pooling effect-size estimates or combining P values from multiple studies. In this paper, we evaluated the performance of two types of statistical models, parametric and non-parametric, for meta-analysis of CG effects using simulated data. Both models estimated a “central” effect size while taking into account heterogeneity over individual studies. The empirical distribution of study-specific CG effects was multi-modal. The parametric model assumed a normal distribution for the study-specific CG effects whereas the non-parametric model relaxed this assumption by posing a more general distribution with a Dirichlet process prior (DPP). Results indicated that the meta-analysis approaches could reduce false positive or false negative rates by pooling strengths from multiple studies, as compared to individual studies. In addition, the non-parametric, DPP model captured the variation of the “data” better than its parametric counterpart.
Collapse
Affiliation(s)
- Xiao-Lin Wu
- 1. Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA; ; 2. Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Gianola
- 1. Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA; ; 2. Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA; ; 3. Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Guilherme J M Rosa
- 2. Department of Animal Sciences, University of Wisconsin, Madison, WI 53706, USA; ; 3. Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Kent A Weigel
- 1. Department of Dairy Science, University of Wisconsin, Madison, WI 53706, USA
| |
Collapse
|
656
|
Abstract
Flowering time is an important trait in wheat breeding as it affects adaptation and yield potential. The aim of this study was to investigate the genetic architecture of flowering time in European winter bread wheat cultivars. To this end a population of 410 winter wheat varieties was evaluated in multi-location field trials and genotyped by a genotyping-by-sequencing approach and candidate gene markers. Our analyses revealed that the photoperiod regulator Ppd-D1 is the major factor affecting flowering time in this germplasm set, explaining 58% of the genotypic variance. Copy number variation at the Ppd-B1 locus was present but explains only 3.2% and thus a comparably small proportion of genotypic variance. By contrast, the plant height loci Rht-B1 and Rht-D1 had no effect on flowering time. The genome-wide scan identified six QTL which each explain only a small proportion of genotypic variance and in addition we identified a number of epistatic QTL, also with small effects. Taken together, our results show that flowering time in European winter bread wheat cultivars is mainly controlled by Ppd-D1 while the fine tuning to local climatic conditions is achieved through Ppd-B1 copy number variation and a larger number of QTL with small effects.
Collapse
Affiliation(s)
| | | | - Tobias Würschum
- *Correspondence: Tobias Würschum, State Plant Breeding Institute, University of Hohenheim, Fruwirthstrasse 21, Stuttgart 70593, Germany e-mail:
| |
Collapse
|
657
|
Clark LN, Liu X, Parmalee NL, Hernandez N, Louis ED. The microtubule associated protein tau H1 haplotype and risk of essential tremor. Eur J Neurol 2013; 21:1044-8. [PMID: 24372973 DOI: 10.1111/ene.12335] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/18/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND PURPOSE Two recent studies investigated the association of the microtubule associated protein tau (MAPT) H1 haplotype, a known risk factor for neurodegenerative disease including progressive supranuclear palsy and Parkinson's disease (PD), with essential tremor (ET). METHODS To confirm this association in a different population the distribution of allele and genotype frequencies for the MAPT H1/H2 tagging single-nucleotide polymorphism (SNP) rs1052553 in ET cases and controls enrolled in a clinical-epidemiological study of ET at Columbia University was analyzed. RESULTS Overall, no association was observed between ET and the MAPT H1 haplotype. The analysis was also restricted to clinical subtypes including early-onset (≤40 years of age), Ashkenazi Jewish ancestry, white non-Ashkenazi, or ET cases with a 'definite' or 'probable/possible' diagnosis; none of these stratified analyses showed evidence of association with ET. A meta-analysis of the H1/H2 tagging SNP rs1052553 in published data sets and the H1 haplotype with risk for ET in the current study was also performed and did not find evidence for association. CONCLUSIONS The inconsistent reports of association of MAPT H1 in three emerging studies (our own and two published studies) may reflect sampling issues and/or clinical heterogeneity in these populations.
Collapse
Affiliation(s)
- L N Clark
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY, USA; Center for Human Genetics, Columbia University, New York, NY, USA
| | | | | | | | | |
Collapse
|
658
|
Sahebjada S, Schache M, Richardson AJ, Snibson G, MacGregor S, Daniell M, Baird PN. Evaluating the association between keratoconus and the corneal thickness genes in an independent Australian population. Invest Ophthalmol Vis Sci 2013; 54:8224-8. [PMID: 24265017 DOI: 10.1167/iovs.13-12982] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE A recent genome-wide association study (GWAS) identified six loci associated with central corneal thickness that also conferred associated risk of keratoconus (KC). We aimed to assess whether genetic associations existed for these loci with KC or corneal curvature in an independent cohort of European ancestry. METHODS In total, 157 patients with KC were recruited from public and private clinics in Melbourne, Australia, and 673 individuals without KC were identified through the Genes in Myopia study from Australia. The following six single-nucleotide polymorphisms (SNPs) that showed a statistically significant association with KC in a recent GWAS study were selected for genotyping in our cohort: rs4894535 (FNDC3B), rs1324183 (MPDZ-NF1B), rs1536482 (RXRA-COL5A1), rs7044529 (COL5A), rs2721051 (FOXO1), and rs9938149 (BANP-ZNF469). The SNPs were assessed for their association with KC or corneal curvature using logistic or linear regression methods, with age and sex included as covariates. Bonferroni corrections were applied to account for multiple testing. RESULTS Genotyping data were available for five of the SNPs. Statistically significant associations with KC were found for the SNPs rs1324183 (P = 0.001; odds ratio [OR], 1.68) and rs9938149 (P = 0.010; OR, 1.47). Meta-analysis of previous studies yielded genome-wide significant evidence of an association for rs1324183, firmly establishing it as a KC risk variant. None of the SNPs were significantly associated with corneal curvature. CONCLUSIONS The SNPs rs1324183 in the MPDZ-NF1B gene and rs9938149 (between BANP and ZNF4659) were associated with KC in this independent cohort, but their association was via a non-corneal curvature route.
Collapse
Affiliation(s)
- Srujana Sahebjada
- Ocular Genetics Unit, Centre for Eye Research Australia, East Melbourne, Australia
| | | | | | | | | | | | | |
Collapse
|
659
|
Pu Y, Gao J, Guo Y, Liu T, Zhu L, Xu P, Yi B, Wen J, Tu J, Ma C, Fu T, Zou J, Shen J. A novel dominant glossy mutation causes suppression of wax biosynthesis pathway and deficiency of cuticular wax in Brassica napus. BMC Plant Biol 2013; 13:215. [PMID: 24330756 PMCID: PMC3881019 DOI: 10.1186/1471-2229-13-215] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 12/05/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND The aerial parts of land plants are covered with cuticular waxes that limit non-stomatal water loss and gaseous exchange, and protect plants from ultraviolet radiation and pathogen attack. This is the first report on the characterization and genetic mapping of a novel dominant glossy mutant (BnaA.GL) in Brassica napus. RESULTS Transmission electron microscopy revealed that the cuticle ultrastructure of GL mutant leaf and stem were altered dramatically compared with that of wide type (WT). Scanning electron microscopy corroborated the reduction of wax on the leaf and stem surface. A cuticular wax analysis of the GL mutant leaves further confirmed the drastic decrease in the total wax content, and a wax compositional analysis revealed an increase in aldehydes but a severe decrease in alkanes, ketones and secondary alcohols. These results suggested a likely blockage of the decarbonylation step in the wax biosynthesis pathway. Genetic mapping narrowed the location of the BnaA.GL gene to the end of A9 chromosome. A single-nucleotide polymorphism (SNP) chip assay in combination with bulk segregant analysis (BSA) also located SNPs in the same region. Two SNPs, two single sequence repeat (SSR) markers and one IP marker were located on the flanking region of the BnaA.GL gene at a distance of 0.6 cM. A gene homologous to ECERIFERUM1 (CER1) was located in the mapped region. A cDNA microarray chip assay revealed coordinated down regulation of genes encoding enzymes of the cuticular wax biosynthetic pathway in the glossy mutant, with BnCER1 being one of the most severely suppressed genes. CONCLUSIONS Our results indicated that surface wax biosynthesis is broadly affected in the glossy mutant due to the suppression of the BnCER1 and other wax-related genes. These findings offer novel clues for elucidating the molecular basis of the glossy phenotype.
Collapse
Affiliation(s)
- Yuanyuan Pu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingting Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lixia Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jitao Zou
- National Research Council Canada, Saskatoon, Saskatchewan S7N 0 W9, Canada
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
660
|
Tayeh N, Bahrman N, Sellier H, Bluteau A, Blassiau C, Fourment J, Bellec A, Debellé F, Lejeune-Hénaut I, Delbreil B. A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genomics 2013; 14:814. [PMID: 24261852 PMCID: PMC4046650 DOI: 10.1186/1471-2164-14-814] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/04/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Freezing provokes severe yield losses to different fall-sown annual legumes. Understanding the molecular bases of freezing tolerance is of great interest for breeding programs. Medicago truncatula Gaertn. is an annual temperate forage legume that has been chosen as a model species for agronomically and economically important legume crops. The present study aimed to identify positional candidate genes for a major freezing tolerance quantitative trait locus that was previously mapped to M. truncatula chromosome 6 (Mt-FTQTL6) using the LR3 population derived from a cross between the freezing-tolerant accession F83005-5 and the freezing-sensitive accession DZA045-5. RESULTS The confidence interval of Mt-FTQTL6 was narrowed down to the region comprised between markers MTIC153 and NT6054 using recombinant F7 and F8 lines. A bacterial-artificial chromosome (BAC) clone contig map was constructed in an attempt to close the residual assembly gap existing therein. Twenty positional candidate genes including twelve C-repeat binding factor (CBF)/dehydration-responsive element binding factor 1 (DREB1) genes were identified from BAC-derived sequences and whole-genome shotgun sequences (WGS). CBF/DREB1 genes are organized in a tandem array within an approximately 296-Kb region. Eleven CBF/DREB1 genes were isolated and sequenced from F83005-5 and DZA045-5 which revealed high polymorphism among these accessions. Unique features characterizing CBF/DREB1 genes from M. truncatula, such as alternative splicing and large tandem duplication, are elucidated for the first time. CONCLUSIONS Overall, twenty genes were identified as potential candidates to explain Mt-FTQTL6 effect. Their future functional characterization will uncover the gene(s) involved in freezing tolerance difference observed between F83005-5 and DZA045-5. Knowledge transfer for breeding improvement of crop legumes is expected. Furthermore, CBF/DREB1 related data will certainly have a large impact on research studies targeting this group of transcriptional activators in M. truncatula and other legume species.
Collapse
Affiliation(s)
- Nadim Tayeh
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
| | - Nasser Bahrman
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Hélène Sellier
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Aurélie Bluteau
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Christelle Blassiau
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
| | - Joëlle Fourment
- />INRA, Centre National de Ressources Génomiques Végétales (CNRGV), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Arnaud Bellec
- />INRA, Centre National de Ressources Génomiques Végétales (CNRGV), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Frédéric Debellé
- />INRA/CNRS, UMR 441/2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Isabelle Lejeune-Hénaut
- />INRA, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Estrées-Mons, BP 50136, F-80203 Péronne Cedex, France
| | - Bruno Delbreil
- />Université Lille 1, UMR 1281 Stress Abiotiques et Différenciation des Végétaux cultivés (SADV), Bâtiment SN2, F-59655 Villeneuve d’Ascq Cedex, France
| |
Collapse
|
661
|
Ahsan M, Li X, Lundberg AE, Kierczak M, Siegel PB, Carlborg O, Marklund S. Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data. Front Genet 2013; 4:226. [PMID: 24204379 PMCID: PMC3817360 DOI: 10.3389/fgene.2013.00226] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/17/2013] [Indexed: 11/13/2022] Open
Abstract
Mapping of chromosomal regions harboring genetic polymorphisms that regulate complex traits is usually followed by a search for the causative mutations underlying the observed effects. This is often a challenging task even after fine mapping, as millions of base pairs including many genes will typically need to be investigated. Thus to trace the causative mutation(s) there is a great need for efficient bioinformatic strategies. Here, we searched for genes and mutations regulating growth in the Virginia chicken lines - an experimental population comprising two lines that have been divergently selected for body weight at 56 days for more than 50 generations. Several quantitative trait loci (QTL) have been mapped in an F2 intercross between the lines, and the regions have subsequently been replicated and fine mapped using an Advanced Intercross Line. We have further analyzed the QTL regions where the largest genetic divergence between the High-Weight selected (HWS) and Low-Weight selected (LWS) lines was observed. Such regions, covering about 37% of the actual QTL regions, were identified by comparing the allele frequencies of the HWS and LWS lines using both individual 60K SNP chip genotyping of birds and analysis of read proportions from genome resequencing of DNA pools. Based on a combination of criteria including significance of the QTL, allele frequency difference of identified mutations between the selected lines, gene information on relevance for growth, and the predicted functional effects of identified mutations we propose here a subset of candidate mutations of highest priority for further evaluation in functional studies. The candidate mutations were identified within the GCG, IGFBP2, GRB14, CRIM1, FGF16, VEGFR-2, ALG11, EDN1, SNX6, and BIRC7 genes. We believe that the proposed method of combining different types of genomic information increases the probability that the genes underlying the observed QTL effects are represented among the candidate mutations identified.
Collapse
Affiliation(s)
- Muhammad Ahsan
- Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
662
|
Kuhn K, Schwenk K, Both C, Canal D, Johansson US, van der Mije S, Töpfer T, Päckert M. Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change. Ecol Evol 2013; 3:4799-814. [PMID: 24363905 PMCID: PMC3867912 DOI: 10.1002/ece3.855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 11/11/2022] Open
Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
Collapse
Affiliation(s)
- Kerstin Kuhn
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Ecology and Evolution, Johann Wolfgang Goethe-UniversitätMax-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Institute of Environmental Sciences, University of Koblenz-LandauFortstraße 7, Landau in der Pfalz, 76829, Germany
| | - Christiaan Both
- Centre for Ecological and Evolutionary Studies (CEES), University of GroningenPO Box 11103, Groningen, 9700 CC, The Netherlands
| | - David Canal
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSICAv. Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural HistoryPO Box 50007, Stockholm, SE 10405, Sweden
| | | | - Till Töpfer
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| | - Martin Päckert
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| |
Collapse
|
663
|
Stephens K, Cooper BA, West C, Paul SM, Baggott CR, Merriman JD, Dhruva A, Kober KM, Langford DJ, Leutwyler H, Luce JA, Schmidt BL, Abrams GM, Elboim C, Hamolsky D, Levine JD, Miaskowski C, Aouizerat BE. Associations between cytokine gene variations and severe persistent breast pain in women following breast cancer surgery. J Pain 2013; 15:169-80. [PMID: 24411993 DOI: 10.1016/j.jpain.2013.09.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/21/2013] [Accepted: 09/03/2013] [Indexed: 01/02/2023]
Abstract
UNLABELLED Persistent pain following breast cancer surgery is a significant clinical problem. Although immune mechanisms may play a role in the development and maintenance of persistent pain, few studies have evaluated for associations between persistent breast pain following breast cancer surgery and variations in cytokine genes. In this study, associations between previously identified extreme persistent breast pain phenotypes (ie, no pain vs severe pain) and single nucleotide polymorphisms (SNPs) spanning 15 cytokine genes were evaluated. In unadjusted analyses, the frequency of 13 SNPs and 3 haplotypes in 7 genes differed significantly between the no pain and severe pain classes. After adjustment for preoperative breast pain and the severity of average postoperative pain, 1 SNP (ie, interleukin [IL] 1 receptor 2 rs11674595) and 1 haplotype (ie, IL10 haplotype A8) were associated with pain group membership. These findings suggest a role for cytokine gene polymorphisms in the development of persistent breast pain following breast cancer surgery. PERSPECTIVE This study evaluated for associations between cytokine gene variations and the severity of persistent breast pain in women following breast cancer surgery. Variations in 2 cytokine genes were associated with severe breast pain. The results suggest that cytokines play a role in the development of persistent postsurgical pain.
Collapse
Affiliation(s)
- Kimberly Stephens
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Bruce A Cooper
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Claudia West
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Steven M Paul
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Christina R Baggott
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - John D Merriman
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Anand Dhruva
- School of Medicine, University of California, San Francisco, San Francisco, California
| | - Kord M Kober
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Dale J Langford
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Heather Leutwyler
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Judith A Luce
- School of Medicine, University of California, San Francisco, San Francisco, California
| | - Brian L Schmidt
- Department of Oral Maxillofacial Surgery, New York University College of Dentistry, New York, New York
| | - Gary M Abrams
- School of Medicine, University of California, San Francisco, San Francisco, California
| | | | - Deborah Hamolsky
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Jon D Levine
- Department of Oral and Maxillofacial Surgery, University of California, San Francisco, San Francisco, California
| | - Christine Miaskowski
- School of Nursing, University of California, San Francisco, San Francisco, California
| | - Bradley E Aouizerat
- School of Nursing, University of California, San Francisco, San Francisco, California; Institute for Human Genetics, University of California, San Francisco, San Francisco, California.
| |
Collapse
|
664
|
Osoegawa K, Iovannisci DM, Lin B, Parodi C, Schultz K, Shaw GM, Lammer EJ. Identification of novel candidate gene loci and increased sex chromosome aneuploidy among infants with conotruncal heart defects. Am J Med Genet A 2013; 164A:397-406. [PMID: 24127225 DOI: 10.1002/ajmg.a.36291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHDs) are common malformations, affecting four to eight per 1,000 total births. Conotruncal defects are an important pathogenetic subset of CHDs, comprising nearly 20% of the total. Although both environmental and genetic factors are known to contribute to the occurrence of conotruncal defects, the causes remain unknown for most. To identify novel candidate genes/loci, we used array comparative genomic hybridization to detect chromosomal microdeletions/duplications. From a population base of 974,579 total births born during 1999-2004, we screened 389 California infants born with tetralogy of Fallot or d-transposition of the great arteries. We found that 1.7% (5/288) of males with a conotruncal defect had sex chromosome aneuploidy, a sevenfold increased frequency (relative risk = 7.0; 95% confidence interval 2.9-16.9). We identified eight chromosomal microdeletions/duplications for conotruncal defects. From these duplications and deletions, we found five high priority candidate genes (GATA4, CRKL, BMPR1A, SNAI2, and ZFHX4). This is the initial report that sex chromosome aneuploidy is associated with conotruncal defects among boys. These chromosomal microduplications/deletions provide evidence that GATA4, SNAI2, and CRKL are highly dosage sensitive genes involved in outflow tract development. Genome wide screening for copy number variation can be productive for identifying novel genes/loci contributing to non-syndromic common malformations.
Collapse
Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland, Oakland, California
| | | | | | | | | | | | | |
Collapse
|
665
|
Santin I, Eizirik DL. Candidate genes for type 1 diabetes modulate pancreatic islet inflammation and β-cell apoptosis. Diabetes Obes Metab 2013; 15 Suppl 3:71-81. [PMID: 24003923 DOI: 10.1111/dom.12162] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/17/2013] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have identified more than 50 loci associated with genetic risk of type 1 diabetes (T1D). Several T1D candidate genes have been suggested or identified within these regions, but the molecular mechanisms by which they contribute to insulitis and β-cell destruction remain to be clarified. More than 60% of the T1D candidate genes are expressed in human pancreatic islets, suggesting that they contribute to T1D by regulating at least in part pathogenic mechanisms at the β-cell level. Recent studies by our group indicate that important genetically regulated pathways in β-cells include innate immunity and antiviral activity, involving RIG-like receptors (particularly MDA5) and regulators of type I IFNs (i.e. PTPN2 and USP18), and genes related to β-cell phenotype and susceptibility to pro-apoptotic stimuli (i.e. GLIS3). These observations reinforce the concept that the early pathogenesis of T1D is characterized by a dialogue between the immune system and pancreatic β-cells. This dialogue is probably influenced by polymorphisms in genes expressed at the β-cell and/or immune system level, leading to inadequate responses to environmental cues such as viral infections. Further studies are needed to clarify how these disease-associated variants affect pancreatic β-cell responses to inflammation and the subsequent triggering of autoimmune responses and progressive β-cell loss.
Collapse
Affiliation(s)
- I Santin
- Laboratory of Experimental Medicine, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium.
| | | |
Collapse
|
666
|
Short AD, Boag A, Catchpole B, Kennedy LJ, Massey J, Rothwell S, Husebye E, Ollier B. A candidate gene analysis of canine hypoadrenocorticism in 3 dog breeds. J Hered 2013; 104:807-20. [PMID: 23997205 DOI: 10.1093/jhered/est051] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Canine hypoadrenocorticism is believed to be an immune-related condition. It is rare in the overall dog population but shows a breed-related predisposition with Standard poodles and Portuguese water dogs having a greater prevalence of the condition. It shares many similarities with human primary adrenal insufficiency and is believed to be a naturally occurring, spontaneous model for the human condition. Short haplotype blocks and low levels of linkage disequilibrium in the human genome mean that the identification of genetic contributors to the condition requires large sample numbers. Pedigree dogs have high linkage disequilibrium and long haplotypes within a breed, increasing the potential of identifying novel genes that contribute to canine genetic disease. We investigated 222 SNPs from 42 genes that have been associated or may be implicated in human Addison's disease. We conducted case-control analyses in 3 pedigree dog breeds (Labrador retriever: affected n = 30, unaffected = 76; Cocker Spaniel: affected n = 19, unaffected = 53; Springer spaniel: affected n = 26, unaffected = 46) and identified 8 associated alleles in genes COL4A4, OSBPL9, CTLA4, PTPN22, and STXBP5 in 3 pedigree breeds. Association with immune response genes PTPN22 and CTLA4 in certain breeds suggests an underlying immunopathogenesis of the disease. These results suggest that canine hypoadrenocorticism could be a useful model for studying comparative genetics relevant to human Addison's disease.
Collapse
Affiliation(s)
- Andrea D Short
- the Centre for Integrated Genomic Medical Research, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, UK
| | | | | | | | | | | | | | | |
Collapse
|
667
|
Alberto FJ, Derory J, Boury C, Frigerio JM, Zimmermann NE, Kremer A. Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea. Genetics 2013; 195:495-512. [PMID: 23934884 DOI: 10.1534/genetics.113.153783] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We explored single nucleotide polymorphism (SNP) variation in candidate genes for bud burst from Quercus petraea populations sampled along gradients of latitude and altitude in Western Europe. SNP diversity was monitored for 106 candidate genes, in 758 individuals from 32 natural populations. We investigated whether SNP variation reflected the clinal pattern of bud burst observed in common garden experiments. We used different methods to detect imprints of natural selection (FST outlier, clinal variation at allelic frequencies, association tests) and compared the results obtained for the two gradients. FST outlier SNPs were found in 15 genes, 5 of which were common to both gradients. The type of selection differed between the two gradients (directional or balancing) for 3 of these 5. Clinal variations were observed for six SNPs, and one cline was conserved across both gradients. Association tests between the phenotypic or breeding values of trees and SNP genotypes identified 14 significant associations, involving 12 genes. The results of outlier detection on the basis of population differentiation or clinal variation were not very consistent with the results of association tests. The discrepancies between these approaches may reflect the different hierarchical levels of selection considered (inter- and intrapopulation selection). Finally, we obtained evidence for convergent selection (similar for gradients) and clinal variation for a few genes, suggesting that comparisons between parallel gradients could be used to screen for major candidate genes responding to natural selection in trees.
Collapse
|
668
|
Liu X, Cheng R, Ye X, Verbitsky M, Kisselev S, Mejia-Santana H, Louis E, Cote L, Andrews H, Waters C, Ford B, Fahn S, Marder K, Lee J, Clark L. Increased Rate of Sporadic and Recurrent Rare Genic Copy Number Variants in Parkinson's Disease Among Ashkenazi Jews. Mol Genet Genomic Med 2013; 1:142-154. [PMID: 24073418 PMCID: PMC3782064 DOI: 10.1002/mgg3.18] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
To date, only one genome-wide study has assessed the contribution of copy number variants (CNVs) to Parkinson's disease (PD). We conducted a genome-wide scan for CNVs in a case–control dataset of Ashkenazi Jewish (AJ) origin (268 PD cases and 178 controls). Using high-confidence CNVs, we examined the global genome wide burden of large (≥100 kb) and rare (≤1% in the dataset) CNVs between cases and controls. A total of 986 such CNVs were observed in our dataset of 432 subjects. Overall global burden analyses did not reveal significant differences between cases and controls in CNV rate, distribution of deletions or duplications or number of genes affected by CNVs. Overall deletions (total CNV size and ≥2× frequency) were found 1.4 times more often in cases than in controls (P = 0.019). The large CNVs (≥500 kb) were also significantly associated with PD (P = 0.046, 1.24-fold higher in cases than in controls). Global burden was elevated for rare CNV regions. Specifically, for OVOS2 on Chr12p11.21, CNVs were observed only in PD cases (n = 7) but not in controls (P = 0.028) and this was experimentally validated. A total of 81 PD cases carried a rare genic CNV that was absent in controls. Ingenuity pathway analysis (IPA) identified ATXN3, FBXW7, CHCHD3, HSF1, KLC1, and MBD3 in the same disease pathway with known PD genes.
Collapse
Affiliation(s)
- X Liu
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
669
|
Ferguson JF, Matthews GJ, Townsend RR, Raj DS, Kanetsky PA, Budoff M, Fischer MJ, Rosas SE, Kanthety R, Rahman M, Master SR, Qasim A, Li M, Mehta NN, Shen H, Mitchell BD, O'Connell JR, Shuldiner AR, Ho WK, Young R, Rasheed A, Danesh J, He J, Kusek JW, Ojo AO, Flack J, Go AS, Gadegbeku CA, Wright JT, Saleheen D, Feldman HI, Rader DJ, Foulkes AS, Reilly MP. Candidate gene association study of coronary artery calcification in chronic kidney disease: findings from the CRIC study (Chronic Renal Insufficiency Cohort). J Am Coll Cardiol 2013; 62:789-98. [PMID: 23727086 DOI: 10.1016/j.jacc.2013.01.103] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/16/2013] [Accepted: 01/20/2013] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This study sought to identify loci for coronary artery calcification (CAC) in patients with chronic kidney disease (CKD). BACKGROUND CKD is associated with increased CAC and subsequent coronary heart disease (CHD), but the mechanisms remain poorly defined. Genetic studies of CAC in CKD may provide a useful strategy for identifying novel pathways in CHD. METHODS We performed a candidate gene study (∼2,100 genes; ∼50,000 single nucleotide polymorphisms [SNPs]) of CAC within the CRIC (Chronic Renal Insufficiency Cohort) study (N = 1,509; 57% European, 43% African ancestry). SNPs with preliminary evidence of association with CAC in CRIC were examined for association with CAC in the PennCAC (Penn Coronary Artery Calcification) (N = 2,560) and AFCS (Amish Family Calcification Study) (N = 784) samples. SNPs with suggestive replication were further analyzed for association with myocardial infarction (MI) in the PROMIS (Pakistan Risk of Myocardial Infarction Study) (N = 14,885). RESULTS Of 268 SNPs reaching p < 5 × 10(-4) for CAC in CRIC, 28 SNPs in 23 loci had nominal support (p < 0.05 and in same direction) for CAC in PennCAC or AFCS. Besides chr9p21 and COL4A1, known loci for CHD, these included SNPs having reported genome-wide association study association with hypertension (e.g., ATP2B1). In PROMIS, 4 of the 23 suggestive CAC loci (chr9p21, COL4A1, ATP2B1, and ABCA4) had significant associations with MI, consistent with their direction of effect on CAC. CONCLUSIONS We identified several loci associated with CAC in CKD that also relate to MI in a general population sample. CKD imparts a high risk of CHD and may provide a useful setting for discovery of novel CHD genes and pathways.
Collapse
Affiliation(s)
- Jane F Ferguson
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
670
|
Towler DA. Chronic kidney disease: the "perfect storm" of cardiometabolic risk illuminates genetic diathesis in cardiovascular disease. J Am Coll Cardiol 2013; 62:799-801. [PMID: 23727212 DOI: 10.1016/j.jacc.2013.04.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 11/18/2022]
|
671
|
Pau C, Saxena R, Welt CK. Evaluating reported candidate gene associations with polycystic ovary syndrome. Fertil Steril 2013; 99:1774-8. [PMID: 23375202 PMCID: PMC3722586 DOI: 10.1016/j.fertnstert.2012.12.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 12/20/2012] [Accepted: 12/20/2012] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To replicate variants in candidate genes associated with polycystic ovary syndrome (PCOS) in a population of European women with PCOS and control subjects. DESIGN Case-control association analysis and meta-analysis. SETTING Major academic hospital. PATIENT(S) Women of European ancestry with PCOS (n = 525) and controls (n = 472), aged 18-45 years. INTERVENTION(S) Variants previously associated with PCOS in candidate gene studies were genotyped (n = 39). Metabolic, reproductive, and anthropomorphic parameters were examined as a function of the candidate variants. All genetic association analyses were adjusted for age, body mass index, and ancestry and were reported after correction for multiple testing. MAIN OUTCOME MEASURE(S) Association of candidate gene variants with PCOS. RESULT(S) Three variants, rs3797179 (SRD5A1), rs12473543 (POMC), and rs1501299 (ADIPOQ), were nominally associated with PCOS. However, they did not remain significant after correction for multiple testing, and none of the variants replicated in a sufficiently powered meta-analysis. Variants in the FBN3 gene (rs17202517 and rs73503752) were associated with smaller waist circumferences, and variant rs727428 in the SHBG gene was associated with lower sex hormone-binding globulin levels. CONCLUSION(S) Previously identified variants in candidate genes do not seem to be associated with PCOS risk. CLINICAL TRIAL REGISTRATION NUMBER NCT00166569.
Collapse
Affiliation(s)
- Cindy Pau
- Reproductive Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.
| | | | | |
Collapse
|
672
|
Dunner S, Sevane N, Garcia D, Levéziel H, Williams JL, Mangin B, Valentini A. Genes involved in muscle lipid composition in 15 European Bos taurus breeds. Anim Genet 2013; 44:493-501. [PMID: 23611291 DOI: 10.1111/age.12044] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2013] [Indexed: 11/29/2022]
Abstract
Consumers demand healthy and palatable meat, both factors being affected by fat composition. However, red meat has relatively high concentration of saturated fatty acids and low concentration of the beneficial polyunsaturated fatty acids. To select animals prone to produce particular fat types, it is necessary to identify the genes influencing muscle lipid composition. This paper describes an association study in which a large panel of candidate genes involved in adipogenesis, lipid metabolism and energy homoeostasis was tested for effects on fat composition in 15 European cattle breeds. Sixteen genes were found to have significant effects on different lipid traits, and among these, CFL1 and MYOZ1 were found to have large effects on the ratio of 18:2/18:3, CRI1 on the amount of neutral adrenic acid (22:4 n-6), MMP1 on docosahexaenoic acid (22:6 n-3) and conjugated linoleic acid, PLTP on the ratio of n-6:n-3 and IGF2R on flavour. Several genes - ALDH2, CHRNE, CRHR2, DGAT1, IGFBP3, NEB, SOCS2, SUSP1, TCF12 and FOXO1 - also were found to be associated with both lipid and organoleptic traits although with smaller effect. The results presented here help in understanding the genetic and biochemical background underlying variations in fatty acid composition and flavour in beef.
Collapse
Affiliation(s)
- S Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain.
| | | | | | | | | | | | | | | |
Collapse
|
673
|
Muñoz-Fambuena N, Mesejo C, González-Mas MC, Primo-Millo E, Agustí M, Iglesias DJ. Use or abuse of bioinformatic tools: a response to Samach. Ann Bot 2013; 111:335-336. [PMID: 23388880 PMCID: PMC3579452 DOI: 10.1093/aob/mct020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 01/14/2013] [Indexed: 06/01/2023]
Abstract
In a recent paper, we described for the first time the effects of fruit on the expression of putative homologues of genes involved in flowering pathways. It was our aim to provide insight into the molecular mechanisms underlying alternate bearing in citrus. However, a bioinformatics-based critique of our and other related papers has been given by Samach in the preceding Viewpoint article in this issue of Annals of Botany. The use of certain bioinformatic tools in a context of structural rather than functional genomics can cast doubts about the veracity of a large amount of data published in recent years. In this response, the contentions raised by Samach are analysed, and rebuttals of his criticisms are presented.
Collapse
Affiliation(s)
- Natalia Muñoz-Fambuena
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, E-46022 Valencia, Spain
| | - Carlos Mesejo
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, E-46022 Valencia, Spain
| | - María C. González-Mas
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, E-46113 Moncada, Valencia, Spain
| | - Eduardo Primo-Millo
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, E-46113 Moncada, Valencia, Spain
| | - Manuel Agustí
- Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia, E-46022 Valencia, Spain
| | - Domingo J. Iglesias
- Departamento de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, E-46113 Moncada, Valencia, Spain
| |
Collapse
|
674
|
Raskind WH, Peter B, Richards T, Eckert MM, Berninger VW. The genetics of reading disabilities: from phenotypes to candidate genes. Front Psychol 2013; 3:601. [PMID: 23308072 PMCID: PMC3538356 DOI: 10.3389/fpsyg.2012.00601] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/18/2012] [Indexed: 12/19/2022] Open
Abstract
This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationships; and (d) current understanding of epigenetic mechanisms whereby environmental events may alter behavioral expression of genetic variations. A glossary of genetic terms (denoted by bold font) is provided for readers not familiar with the technical terms.
Collapse
Affiliation(s)
- Wendy H Raskind
- Department of Medicine, University of Washington Seattle, WA, USA ; Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA, USA
| | | | | | | | | |
Collapse
|
675
|
Roschanski AM, Fady B, Ziegenhagen B, Liepelt S. Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae). Appl Plant Sci 2013; 1:apps1200179. [PMID: 25202477 PMCID: PMC4105350 DOI: 10.3732/apps.1200179] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/30/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. • METHODS AND RESULTS A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA. • CONCLUSIONS The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in A. alba.
Collapse
Affiliation(s)
- Anna M. Roschanski
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
| | - Bruno Fady
- INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon, France
| | - Birgit Ziegenhagen
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
| | - Sascha Liepelt
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
| |
Collapse
|
676
|
Genro JP, Roman T, Rohde LA, Hutz MH. The Brazilian contribution to Attention-Deficit/Hyperactivity Disorder molecular genetics in children and adolescents. Genet Mol Biol 2012; 35:932-8. [PMID: 23411749 PMCID: PMC3571428 DOI: 10.1590/s1415-47572012000600007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Attention-Deficit/Hyperactivity Disorder (ADHD) is a common psychiatric condition of children worldwide. This disorder is defined by a combination of symptoms of inattention and hyperactivity/impulsivity. Diagnosis is based on a sufficient number of symptoms causing impairment in these two domains determining several problems in personal and academic life. Although genetic and environmental factors are important in ADHD etiology, how these factors influence the brain and consequently behavior is still under debate. It seems to be consensus that a frontosubcortical dysfunction is responsible, at least in part, for the ADHD phenotype spectrum. The main results from association and pharmacogenetic studies performed in Brazil are discussed. The investigations performed so far on ADHD genetics in Brazil and elsewhere are far from conclusive. New plausible biological hypotheses linked to neurotransmission and neurodevelopment, as well as new analytic approaches are needed to fully disclose the genetic component of the disorder.
Collapse
Affiliation(s)
- Júlia Pasqualini Genro
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | | | | | | |
Collapse
|
677
|
Rodríguez-Suárez C, Atienza SG. Hordeum chilense genome, a useful tool to investigate the endosperm yellow pigment content in the Triticeae. BMC Plant Biol 2012; 12:200. [PMID: 23122232 PMCID: PMC3534404 DOI: 10.1186/1471-2229-12-200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 10/30/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND The wild barley Hordeum chilense fulfills some requirements for being a useful tool to investigate the endosperm yellow pigment content (YPC) in the Triticeae including its diploid constitution, the availability of genetic resources (addition and deletion stocks and a high density genetic map) and, especially, its high seed YPC not silenced in tritordeums (amphiploids derived from H. chilense and wheat). Thus, the aim of this work was to test the utility of the H. chilense genome for investigating the YPC in the Triticeae. RESULTS Twelve genes related to endosperm carotenoid content and/or YPC in grasses (Dxr, Hdr [synonym ispH], Ggpps1, Psy2, Psy3, Pds, Zds, e-Lcy, b-Lcy, Hyd3, Ccd1 and Ppo1) were identified, and mapped in H. chilense using rice genes to identify orthologs from barley, wheat, sorghum and maize. Macrocolinearity studies revealed that gene positions were in agreement in H. vulgare and H. chilense. Additionally, three main regions associated with YPC were identified in chromosomes 2Hch, 3Hch and 7Hch in H. chilense, the former being the most significant one. CONCLUSIONS The results obtained are consistent with previous findings in wheat and suggest that Ggpps1, Zds and Hyd3 on chromosome 2Hch may be considered candidate genes in wheat for further studies in YPC improvement. Considering the syntenic location of carotenoid genes in H. chilense, we have concluded that the Hch genome may constitute a valuable tool for YPC studies in the Triticeae.
Collapse
Affiliation(s)
| | - Sergio G Atienza
- Instituto de Agricultura Sostenible, IAS-CSIC, Apdo 4084, Córdoba, E-14080, Spain
| |
Collapse
|
678
|
Abstract
A genetic contribution to develop chronic obstructive pulmonary disease (COPD) is well established. However, the specific genes responsible for enhanced risk or host differences in susceptibility to smoke exposure remain poorly understood. The goal of this review is to provide a comprehensive literature overview on the genetics of COPD, highlight the most promising findings during the last few years, and ultimately provide an updated COPD gene list. Candidate gene studies on COPD and related phenotypes indexed in PubMed before January 5, 2012 are tabulated. An exhaustive list of publications for any given gene was looked for. This well-documented COPD candidate-gene list is expected to serve many purposes for future replication studies and meta-analyses as well as for reanalyzing collected genomic data in the field. In addition, this review summarizes recent genetic loci identified by genome-wide association studies on COPD, lung function, and related complications. Assembling resources, integrative genomic approaches, and large sample sizes of well-phenotyped subjects is part of the path forward to elucidate the genetic basis of this debilitating disease.
Collapse
Affiliation(s)
- Yohan Bossé
- Centre de recherche Institut universitaire de cardiologie et de pneumologie de Québec, Quebec, Canada.
| |
Collapse
|
679
|
Seifuddin F, Mahon PB, Judy J, Pirooznia M, Jancic D, Taylor J, Goes FS, Potash JB, Zandi PP. Meta-analysis of genetic association studies on bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:508-18. [PMID: 22573399 PMCID: PMC3582382 DOI: 10.1002/ajmg.b.32057] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Accepted: 04/10/2012] [Indexed: 01/05/2023]
Abstract
Numerous candidate gene association studies of bipolar disorder (BP) have been carried out, but the results have been inconsistent. Individual studies are typically underpowered to detect associations with genes of small effect sizes. We conducted a meta-analysis of published candidate gene studies to evaluate the cumulative evidence. We systematically searched for all published candidate gene association studies of BP. We then carried out a random-effects meta-analysis on all polymorphisms that were reported on by three or more case-control studies. The results from meta-analyses of these genes were compared with the findings from a recent mega-analysis of eleven genome-wide association studies (GWAS) in BP performed by the Psychiatric GWAS Consortium (PGC). A total of 487 articles were included in our review. Among these, 33 polymorphisms in 18 genes were reported on by three or more case-control studies and included in the random-effects meta-analysis. Polymorphisms in BDNF, DRD4, DAOA, and TPH1, were found to be nominally significant with a P-value < 0.05. However, none of the findings were significant after correction for multiple testing. Moreover, none of these polymorphisms were nominally significant in the PGC-BP GWAS. A number of plausible candidate genes have been previously associated with BP. However, the lack of robust findings in our review of these candidate genes highlights the need for more atheoretical approaches to study the genetics of BP afforded by GWAS. The results of this meta-analysis and from other on-going genomic experiments in BP are available online at Metamoodics (http://metamoodics.igm.jhmi.edu).
Collapse
Affiliation(s)
- Fayaz Seifuddin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Pamela Belmonte Mahon
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Jennifer Judy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Dubravka Jancic
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Jacob Taylor
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Fernando S. Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James B. Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Peter P. Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland,Correspondence to: Peter P. Zandi, Ph.D., Johns Hopkins School of Medicine, Baltimore, MD 21287; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.
| |
Collapse
|
680
|
Pottorff M, Ehlers JD, Fatokun C, Roberts PA, Close TJ. Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species. BMC Genomics 2012; 13:234. [PMID: 22691139 PMCID: PMC3431217 DOI: 10.1186/1471-2164-13-234] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/29/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. RESULTS Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, Hls (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding Hls locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the Hls region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic Hls region in Medicago truncatula and Glycine max. One syntenic locus for Hls was identified on Medicago chromosome 7 while syntenic regions for Hls were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the Hls locus. The Hls locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25. CONCLUSIONS This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.
Collapse
Affiliation(s)
- Marti Pottorff
- Department of Botany & Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Jeffrey D Ehlers
- Department of Botany & Plant Sciences, University of California Riverside, Riverside, CA, USA
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Christian Fatokun
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Philip A Roberts
- Department of Nematology, University of California Riverside, Riverside, CA, USA
| | - Timothy J Close
- Department of Botany & Plant Sciences, University of California Riverside, Riverside, CA, USA
| |
Collapse
|
681
|
Sehgal D, Rajaram V, Armstead IP, Vadez V, Yadav YP, Hash CT, Yadav RS. Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci. BMC Plant Biol 2012; 12:9. [PMID: 22251627 PMCID: PMC3287966 DOI: 10.1186/1471-2229-12-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 01/17/2012] [Indexed: 05/21/2023]
Abstract
BACKGROUND Identification of genes underlying drought tolerance (DT) quantitative trait loci (QTLs) will facilitate understanding of molecular mechanisms of drought tolerance, and also will accelerate genetic improvement of pearl millet through marker-assisted selection. We report a map based on genes with assigned functional roles in plant adaptation to drought and other abiotic stresses and demonstrate its use in identifying candidate genes underlying a major DT-QTL. RESULTS Seventy five single nucleotide polymorphism (SNP) and conserved intron spanning primer (CISP) markers were developed from available expressed sequence tags (ESTs) using four genotypes, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. A total of 228 SNPs were obtained from 30.5 kb sequenced region resulting in a SNP frequency of 1/134 bp. The positions of major pearl millet linkage group (LG) 2 DT-QTLs (reported from crosses H 77/833-2 × PRLT 2/89-33 and 841B × 863B) were added to the present consensus function map which identified 18 genes, coding for PSI reaction center subunit III, PHYC, actin, alanine glyoxylate aminotransferase, uridylate kinase, acyl-CoA oxidase, dipeptidyl peptidase IV, MADS-box, serine/threonine protein kinase, ubiquitin conjugating enzyme, zinc finger C- × 8-C × 5-C × 3-H type, Hd3, acetyl CoA carboxylase, chlorophyll a/b binding protein, photolyase, protein phosphatase1 regulatory subunit SDS22 and two hypothetical proteins, co-mapping in this DT-QTL interval. Many of these candidate genes were found to have significant association with QTLs of grain yield, flowering time and leaf rolling under drought stress conditions. CONCLUSIONS We have exploited available pearl millet EST sequences to generate a mapped resource of seventy five new gene-based markers for pearl millet and demonstrated its use in identifying candidate genes underlying a major DT-QTL in this species. The reported gene-based markers represent an important resource for identification of candidate genes for other mapped abiotic stress QTLs in pearl millet. They also provide a resource for initiating association studies using candidate genes and also for comparing the structure and function of distantly related plant genomes such as other Poaceae members.
Collapse
Affiliation(s)
- Deepmala Sehgal
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3 EB, UK
| | - Vengaldas Rajaram
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ICRISAT-Patencheru, Hyderabad 502 324, Andhra Pradesh, India
| | - Ian Peter Armstead
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3 EB, UK
| | - Vincent Vadez
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ICRISAT-Patencheru, Hyderabad 502 324, Andhra Pradesh, India
| | - Yash Pal Yadav
- Chaudhary Charan Singh Haryana Agricultural University (CCSHAU), Bawal 123 501, Haryana, India
| | - Charles Thomas Hash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), ICRISAT-Patencheru, Hyderabad 502 324, Andhra Pradesh, India
| | - Rattan Singh Yadav
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion SY23 3 EB, UK
| |
Collapse
|
682
|
Walsh N, Dale J, McGraw KJ, Pointer MA, Mundy NI. Candidate genes for carotenoid coloration in vertebrates and their expression profiles in the carotenoid-containing plumage and bill of a wild bird. Proc Biol Sci 2012; 279:58-66. [PMID: 21593031 PMCID: PMC3223654 DOI: 10.1098/rspb.2011.0765] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 04/28/2011] [Indexed: 12/13/2022] Open
Abstract
Carotenoid-based coloration has attracted much attention in evolutionary biology owing to its role in honest, condition-dependent signalling. Knowledge of the genetic pathways that regulate carotenoid coloration is crucial for an understanding of any trade-offs involved. We identified genes with potential roles in carotenoid coloration in vertebrates via (i) carotenoid uptake (SR-BI, CD36), (ii) binding and deposition (StAR1, MLN64, StAR4, StAR5, APOD, PLIN, GSTA2), and (iii) breakdown (BCO2, BCMO1). We examined the expression of these candidate loci in carotenoid-coloured tissues and several control tissues of the red-billed quelea (Quelea quelea), a species that exhibits a male breeding plumage colour polymorphism and sexually dimorphic variation in bill colour. All of the candidate genes except StAR1 were expressed in both the plumage and bill of queleas, indicating a potential role in carotenoid coloration in the quelea. However, no differences in the relative expression of any of the genes were found among the quelea carotenoid phenotypes, suggesting that other genes control the polymorphic and sexually dimorphic variation in carotenoid coloration observed in this species. Our identification of a number of potential carotenoid genes in different functional categories provides a critical starting point for future work on carotenoid colour regulation in vertebrate taxa.
Collapse
Affiliation(s)
- N. Walsh
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 ITN, UK
| | - J. Dale
- Max Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany
| | - K. J. McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - M. A. Pointer
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 ITN, UK
| | - N. I. Mundy
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 ITN, UK
| |
Collapse
|
683
|
Fritsche S, Wang X, Li J, Stich B, Kopisch-Obuch FJ, Endrigkeit J, Leckband G, Dreyer F, Friedt W, Meng J, Jung C. A candidate gene-based association study of tocopherol content and composition in rapeseed (Brassica napus). Front Plant Sci 2012; 3:129. [PMID: 22740840 PMCID: PMC3382996 DOI: 10.3389/fpls.2012.00129] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/30/2012] [Indexed: 05/06/2023]
Abstract
Rapeseed (Brassica napus L.) is the most important oil crop of temperate climates. Rapeseed oil contains tocopherols, also known as vitamin E, which is an indispensable nutrient for humans and animals due to its antioxidant and radical scavenging abilities. Moreover, tocopherols are also important for the oxidative stability of vegetable oils. Therefore, seed oil with increased tocopherol content or altered tocopherol composition is a target for breeding. We investigated the role of nucleotide variations within candidate genes from the tocopherol biosynthesis pathway. Field trials were carried out with 229 accessions from a worldwide B. napus collection which was divided into two panels of 96 and 133 accessions. Seed tocopherol content and composition were measured by HPLC. High heritabilities were found for both traits, ranging from 0.62 to 0.94. We identified polymorphisms by sequencing selected regions of the tocopherol genes from the 96 accession panel. Subsequently, we determined the population structure (Q) and relative kinship (K) as detected by genotyping with genome-wide distributed SSR markers. Association studies were performed using two models, the structure-based GLM + Q and the PK-mixed model. Between 26 and 12 polymorphisms within two genes (BnaX.VTE3.a, BnaA.PDS1.c) were significantly associated with tocopherol traits. The SNPs explained up to 16.93% of the genetic variance for tocopherol composition and up to 10.48% for total tocopherol content. Based on the sequence information we designed CAPS markers for genotyping the 133 accessions from the second panel. Significant associations with various tocopherol traits confirmed the results from the first experiment. We demonstrate that the polymorphisms within the tocopherol genes clearly impact tocopherol content and composition in B. napus seeds. We suggest that these nucleotide variations may be used as selectable markers for breeding rapeseed with enhanced tocopherol quality.
Collapse
Affiliation(s)
- Steffi Fritsche
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Xingxing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Friedrich J. Kopisch-Obuch
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Jessica Endrigkeit
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Gunhild Leckband
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KGHohenlieth, Germany
| | - Felix Dreyer
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KGHohenlieth, Germany
| | - Wolfgang Friedt
- Faculty of Agricultural Sciences, Nutritional Sciences and Environmental Management, Institute of Agronomy and Plant Breeding I, Justus-Liebig-UniversityGiessen, Germany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Christian Jung
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
- *Correspondence: Christian Jung, Plant Breeding Institute, Christian-Albrechts-University, Olshausenstrasse 40, 24118 Kiel, Germany. e-mail:
| |
Collapse
|
684
|
Luijk MPCM, Roisman GI, Haltigan JD, Tiemeier H, Booth-LaForce C, van IJzendoorn MH, Belsky J, Uitterlinden AG, Jaddoe VW, Hofman A, Verhulst FC, Tharner A, Bakermans-Kranenburg MJ. Dopaminergic, serotonergic, and oxytonergic candidate genes associated with infant attachment security and disorganization? In search of main and interaction effects. J Child Psychol Psychiatry 2011; 52:1295-307. [PMID: 21749372 PMCID: PMC3202071 DOI: 10.1111/j.1469-7610.2011.02440.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND METHODS In two birth cohort studies with genetic, sensitive parenting, and attachment data of more than 1,000 infants in total, we tested main and interaction effects of candidate genes involved in the dopamine, serotonin, and oxytocin systems (DRD4, DRD2, COMT, 5-HTT, OXTR) on attachment security and disorganization. Parenting was assessed using observational rating scales for parental sensitivity (Ainsworth, Bell, & Stayton, 1974), and infant attachment was assessed with the Strange Situation Procedure. RESULTS We found no consistent additive genetic associations for attachment security and attachment disorganization. However, specific tests revealed evidence for a codominant risk model for COMT Val158Met, consistent across both samples. Children with the Val/Met genotype showed higher disorganization scores (combined effect size d = .22, CI = .10-.34, p < .001). Gene-by-environment interaction effects were not replicable across the two samples. CONCLUSIONS This unexpected finding might be explained by a broader range of plasticity in heterozygotes, which may increase susceptibility to environmental influences or to dysregulation of emotional arousal. This study is unique in combining the two largest attachment cohorts with molecular genetic and observed rearing environment data to date.
Collapse
Affiliation(s)
- Maartje P. C. M. Luijk
- Center for Child and Family Studies, Leiden University, The Generation R Study Group, Erasmus University Medical Center, Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital
| | - Glenn I. Roisman
- Department of Psychology, University of Illinois at Urbana-Champaign
| | - John D. Haltigan
- Department of Psychology, University of Illinois at Urbana-Champaign
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital, Department of Epidemiology, Erasmus University Medical Center
| | | | - Marinus H. van IJzendoorn
- Center for Child and Family Studies, Leiden University, Erasmus School of Pedagogical and Educational Sciences, Erasmus University Rotterdam
| | - Jay Belsky
- Department of Human and Community Development, University of California, Davis, Davis, CA 95616
| | - Andre G. Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Department of Internal Medicine, Erasmus Medical Center, Department of Clinical Genetics, Erasmus Medical Center, Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA)
| | - Vincent W.V. Jaddoe
- The Generation R Study Group, Erasmus University Medical Center, Department of Epidemiology, Erasmus University Medical Center, Department of Pediatrics, Erasmus University Medical Center
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center
| | - Frank C. Verhulst
- Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital
| | - Anne Tharner
- Center for Child and Family Studies, Leiden University, The Generation R Study Group, Erasmus University Medical Center, Department of Child and Adolescent Psychiatry, Erasmus University Medical Center-Sophia Children's Hospital
| | | |
Collapse
|
685
|
de Miguel-Yanes JM, Manning AK, Shrader P, McAteer JB, Goel A, Hamsten A, Fox CS, Florez JC, Dupuis J, Meigs JB. Variants at the endocannabinoid receptor CB1 gene (CNR1) and insulin sensitivity, type 2 diabetes, and coronary heart disease. Obesity (Silver Spring) 2011; 19:2031-7. [PMID: 21633404 PMCID: PMC3686489 DOI: 10.1038/oby.2011.135] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inhibition of the endocannabinoid receptor CB1 improves insulin sensitivity, lowers glycemia, and slows atherosclerosis. We analyzed whether common variants in the gene encoding CB1, CNR1, are associated with insulin resistance, risk of type 2 diabetes (T2D) or coronary heart disease (CHD). We studied 2,411 participants of the Framingham Offspring Study (mean age 60 years, 52% women) for quantitative traits and CHD, and the Framingham SHARe database for T2D risk. We genotyped 19 single-nucleotide polymorphisms (SNPs) that tagged 85% (at r(2) = 0.8) of common (>5%) CNR1 SNPs. Fasting blood glucose and insulin at the 7th (1999-2001) exam were collected. We used age-, sex-, BMI-adjusted models to test additive associations of genotype with homeostasis model assessment of insulin resistance (HOMA(IR)) (linear mixed-effect models), T2D, or CHD. To account for multiple tests of SNPs, we generated empirical P values. The C allele at SNP rs806365 (frequency, 57.4%), ~4.1 kb 3' from CNR1, was associated with increased HOMA(IR) (n = 2,261, β = 0.05 per C, empirical P = 0.01), risk of T2D (674 cases, odds ratio = 1.19 per C, nominal P = 0.01) and CHD (237 cases, hazard ratio = 1.23 per C, nominal P = 0.04). The association of rs806365 with HOMA(IR) was replicated in a meta-analysis of two independent cohorts (National Health and Nutrition Examination Survey III genetic cohort (NHANES-III) plus Partners Case-Control Diabetes Study; 2,540 white individuals, β = 0.037, nominal P = 0.007), but not in the large Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) Consortium (n = 29,248, nominal P = 0.74). The association of rs806365 was not replicated either with T2D in Diabetes Genetics Replication and Meta-analysis (DIAGRAM) (n = 10,128, nominal P = 0.31), or with CHD in PROCARDIS (n = 13,614, nominal P = 0.37). Although supported by initial results, we found no reproducible statistical association of common variation at CNR1 with insulin resistance, T2D, or CHD.
Collapse
|
686
|
Abstract
This commentary focuses on the issues of statistical power, the usefulness of hypothesis-free approaches such as in genome-wide association explorations, the necessity of expanding the research beyond common DNA variants, the advantage of combining transcriptomics with genomics, and the complexities inherent to the search for links between genotype and phenotype in exercise genomics research.
Collapse
Affiliation(s)
- Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, 6400 Perkins Road, Baton Rouge, LA 70808, USA.
| |
Collapse
|
687
|
Tiwari HK, Patki A, Lieberman J, Stroup TS, Allison DB, Leibel RL, Chung WK. Association of Allelic Variation in Genes Mediating Aspects of Energy Homeostasis with Weight Gain during Administration of Antipsychotic Drugs (CATIE Study). Front Genet 2011; 2:56. [PMID: 22039372 PMCID: PMC3202977 DOI: 10.3389/fgene.2011.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 08/13/2011] [Indexed: 11/28/2022] Open
Abstract
Antipsychotic drugs are widely used in treating schizophrenia, bipolar disorder, and other psychiatric disorders. Many of these drugs, despite their therapeutic advantages, substantially increase body weight. We assessed the association of alleles of 31 genes implicated in body weight regulation with weight gain among patients being treated with specific antipsychotic medications in the clinical antipsychotic trials in intervention effectiveness study, we found that rs2237988 in Potassium Channel Inwardly Rectifying Subfamily J Member 11 (KCNJ11), rs13269119 in Solute carrier family 30 member 8 (SLC30A8), and rs9922047 in fat mass and obesity associated (FTO) were associated with percent weight gain. We also observed the significant interaction of rs11643744 by treatment effect on the weight gain.
Collapse
Affiliation(s)
- Hemant K Tiwari
- Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham Birmingham, AL, USA
| | | | | | | | | | | | | |
Collapse
|
688
|
Abstract
Complexity of multifactorial diseases as Parkinson's disease (PD) often complicate identifying causal genetic factors by traditional approaches such as positional cloning and candidate gene analyses. PD is etiologically and genetically complex disease and second most common neurodegenerative disorder after Alzheimer's disease. The most cases of PD are idiopathic and small growing subset of individuals have single gene defect as the cause. The main goal of this research was to identify the potential candidate genes for idiopathic PD by using biomedical discovery support system (BITOLA). For detecting the potential candidate genes for PD was used opened system of bioinformatics tool BITOLA. Data of chromosome location, tissue specific expression of potential candidate genes and their potential association with PD were obtained from Medline, Locus Link, Gene Cards and OMIM. By using BITOLA system is identified 17 genes as potential candidate genes for PD. The role of three genes (MAPT, PARK2, UCHL1) in PD were confirmed earlier. Discovering the novel candidate genes for multifactiorial diseases by using specially mentioned bioinformatics tool BITOLA could offer the new opportunity for researching genetics base of PD without using tissue samples of patients.
Collapse
Affiliation(s)
- Amela Karić
- Division of Genetics, University of Tuzla, Bosnia and Herzegovina.
| | | |
Collapse
|
689
|
Sarup P, Sørensen P, Loeschcke V. Flies selected for longevity retain a young gene expression profile. Age (Dordr) 2011; 33:69-80. [PMID: 20607427 PMCID: PMC3063640 DOI: 10.1007/s11357-010-9162-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/15/2010] [Indexed: 05/29/2023]
Abstract
We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were differentially expressed between selected and control flies when measured at the same chronological age. The longevity-selected flies consistently showed expression profiles more similar to control flies one age class younger than control flies of the same age. This finding is in accordance with a younger gene expression profile in longevity-selected lines. Among the genes down-regulated in longevity-selected lines, we found a clear over-representation of genes involved in immune functions, supporting the hypothesis of a life-shortening effect of an overactive immune system, known as inflammaging. We judged the physiological age as the level of cumulative mortality. Eighty-four genes were differentially expressed between the control and longevity-selected lines at the same physiological age, and the overlap between the same chronological and physiological age gene lists included 40 candidate genes for increased longevity. Among these candidates were genes with roles in starvation resistance, immune response regulation, and several that have not yet been linked to longevity. Investigating these genes would provide new knowledge of the pathways that affect life span in invertebrates and, potentially, mammals.
Collapse
Affiliation(s)
- Pernille Sarup
- Aarhus Centre for Environmental Stress Research (ACES), Department of Biological Sciences, Aarhus University, Ny Munkegade 114, Aarhus C, Denmark.
| | | | | |
Collapse
|
690
|
Rizzi TS, Arias-Vasquez A, Rommelse N, Kuntsi J, Anney R, Asherson P, Buitelaar J, Banaschewski T, Ebstein R, Ruano D, Van der Sluis S, Markunas CA, Garrett ME, Ashley-Koch AE, Kollins SH, Anastopoulos AD, Hansell NK, Wright MJ, Montgomery GW, Martin NG, Harris SE, Davies G, Tenesa A, Porteous DJ, Starr JM, Deary IJ, St. Pourcain B, Smith GD, Timpson NJ, Evans DM, Gill M, Miranda A, Mulas F, Oades RD, Roeyers H, Rothenberger A, Sergeant J, Sonuga-Barke E, Steinhausen HC, Taylor E, Faraone SV, Franke B, Posthuma D. The ATXN1 and TRIM31 genes are related to intelligence in an ADHD background: evidence from a large collaborative study totaling 4,963 subjects. Am J Med Genet B Neuropsychiatr Genet 2011; 156:145-57. [PMID: 21302343 PMCID: PMC3085124 DOI: 10.1002/ajmg.b.31149] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 10/26/2010] [Indexed: 11/30/2022]
Abstract
Intelligence is a highly heritable trait for which it has proven difficult to identify the actual genes. In the past decade, five whole-genome linkage scans have suggested genomic regions important to human intelligence; however, so far none of the responsible genes or variants in those regions have been identified. Apart from these regions, a handful of candidate genes have been identified, although most of these are in need of replication. The recent growth in publicly available data sets that contain both whole genome association data and a wealth of phenotypic data, serves as an excellent resource for fine mapping and candidate gene replication. We used the publicly available data of 947 families participating in the International Multi-Centre ADHD Genetics (IMAGE) study to conduct an in silico fine mapping study of previously associated genomic locations, and to attempt replication of previously reported candidate genes for intelligence. Although this sample was ascertained for attention deficit/hyperactivity disorder (ADHD), intelligence quotient (IQ) scores were distributed normally. We tested 667 single nucleotide polymorphisms (SNPs) within 15 previously reported candidate genes for intelligence and 29451 SNPs in five genomic loci previously identified through whole genome linkage and association analyses. Significant SNPs were tested in four independent samples (4,357 subjects), one ascertained for ADHD, and three population-based samples. Associations between intelligence and SNPs in the ATXN1 and TRIM31 genes and in three genomic locations showed replicated association, but only in the samples ascertained for ADHD, suggesting that these genetic variants become particularly relevant to IQ on the background of a psychiatric disorder.
Collapse
Affiliation(s)
- Thais S Rizzi
- Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam, VU University and VU Medical Center, Amsterdam, the Netherlands.
| | - Alejandro Arias-Vasquez
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands,Department of Human Genetics, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands
| | - Nanda Rommelse
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands
| | - Jonna Kuntsi
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, United Kingdom
| | - Richard Anney
- Department of Psychiatry, Trinity Centre for Health Sciences, St. James's HospitalDublin, Ireland
| | - Philip Asherson
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, United Kingdom
| | - Jan Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands
| | - Tobias Banaschewski
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, University of HeidelbergMannheim, Germany
| | - Richard Ebstein
- Departments of Psychology, National University of Singapore and Hebrew UniversityJerusalem, Israel
| | - Dina Ruano
- Section Medical Genomics, VUMCAmsterdam, the Netherlands
| | - Sophie Van der Sluis
- Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam,VU University and VU Medical CenterAmsterdam, the Netherlands
| | | | - Melanie E Garrett
- Center for Human Genetics, Duke University Medical CenterDurham, North Carolina
| | | | - Scott H Kollins
- Department of Psychiatry, Duke University Medical CenterDurham, North Carolina
| | | | | | | | | | | | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, Medical Genetics Section, University of EdinburghEdinburgh, UK,Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of EdinburghEdinburgh, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of EdinburghEdinburgh, UK
| | - Albert Tenesa
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General HospitalEdinburgh, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, Medical Genetics Section, University of EdinburghEdinburgh, UK
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Geriatric Medicine Unit, University of Edinburgh, Royal Victoria HospitalEdinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of EdinburghEdinburgh, UK
| | - Beate St. Pourcain
- School of Social and Community Medicine and Medical Research Council and Medical Research Council Centre for Causal Analyses in Translational Epidemiology, University of BristolBristol, UK
| | - George Davey Smith
- School of Social and Community Medicine and Medical Research Council and Medical Research Council Centre for Causal Analyses in Translational Epidemiology, University of BristolBristol, UK
| | - Nicholas J Timpson
- School of Social and Community Medicine and Medical Research Council and Medical Research Council Centre for Causal Analyses in Translational Epidemiology, University of BristolBristol, UK
| | - David M Evans
- School of Social and Community Medicine and Medical Research Council and Medical Research Council Centre for Causal Analyses in Translational Epidemiology, University of BristolBristol, UK
| | - Michael Gill
- Department of Psychiatry, Trinity Centre for Health Sciences, St. James's HospitalDublin, Ireland
| | - Ana Miranda
- Department of Developmental and Educational Psychology, University of ValenciaValencia, Spain
| | - Fernando Mulas
- Department of Neuropaediatrics, La Fe University HospitalValencia, Spain
| | - Robert D Oades
- University Clinic for Child and Adolescent PsychiatryEssen, Germany
| | - Herbert Roeyers
- Department of Experimental Clinical and Health Psychology, Ghent UniversityGhent, Belgium
| | | | - Joseph Sergeant
- Department of Clinical Neuropsychology, Vrije UniversiteitAmsterdam, the Netherlands
| | - Edmund Sonuga-Barke
- Department of Experimental Clinical and Health Psychology, Ghent UniversityGhent, Belgium,Institute for Disorder on Impulse and Attention, School of Psychology, University of SouthamptonSouthampton, UK
| | - Hans Christoph Steinhausen
- Department of Child and Adolescent Psychiatry, University of ZurichZurich, Switzerland,Child and Adolescent Clinical Psychology, Institute of Psychology, University of BaselBasel, Switzerland,Child and Adolescent Psychiatry, Region Nordjylland Aalborg Psychiatric Hospital Aarhus, University Hospital AalborgAalborg, Denmark
| | - Eric Taylor
- MRC Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, United Kingdom
| | - Stephen V Faraone
- Department of Neuroscience, SUNY Upstate Medical UniversitySyracuse, New York,Department of Psychiatry, SUNY Upstate Medical UniversitySyracuse, New York
| | - Barbara Franke
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands,Department of Human Genetics, Radboud University Nijmegen Medical CenterNijmegen, the Netherlands
| | - Danielle Posthuma
- Department of Functional Genomics, CNCR, Neuroscience Campus Amsterdam,VU University and VU Medical CenterAmsterdam, the Netherlands,Section Medical Genomics, VUMCAmsterdam, the Netherlands
| |
Collapse
|
691
|
Abstract
Autism is a neurodevelopmental disorder that is currently diagnosed by the presence of three behavioral criteria (1) qualitative impairments in reciprocal social interactions, (2) deficits in communication, including delayed language and noninteractive conversation, and (3) motor stereotypies, repetitive behaviors, insistence on sameness, and restricted interests. This chapter describes analogous behavioral assays that have been developed for mice, including tests for social approach, reciprocal social interactions, olfactory communication, ultrasonic vocalizations, repetitive and perseverative behaviors, and motor stereotypies. Examples of assay applications to genetic mouse models of autism are provided. Robust endophenotypes that are highly relevant to the core symptoms of autism are enabling the search for the genetic and environmental causes of autism, and the discovery of effective treatments.
Collapse
Affiliation(s)
- Florence I. Roullet
- Laboratory of Behavioral Neuroscience, Intramural Research Program, National Institute of Mental Health, Building 35 Room 1C-903/909, Mail Code 3730, Bethesda, MD 20892-3730, USA
| | - Jacqueline N. Crawley
- Laboratory of Behavioral Neuroscience, Intramural Research Program, National Institute of Mental Health, Building 35 Room 1C-903/909, Mail Code 3730, Bethesda, MD 20892-3730, USA
| |
Collapse
|
692
|
Abstract
Dissecting evolutionary dynamics of ecologically important traits is a long-term challenge for biologists. Attempts to understand natural variation and molecular mechanisms have motivated a move from laboratory model systems to non-model systems in diverse natural environments. Next generation sequencing methods, along with an expansion of genomic resources and tools, have fostered new links between diverse disciplines, including molecular biology, evolution, and ecology, and genomics. Great progress has been made in a few non-model wild plants, such as Arabidopsis relatives, monkey flowers, and wild sunflowers. Until recently, the lack of comprehensive genomic information has limited evolutionary and ecological studies to larger QTL regions rather than single gene resolution, and has hindered recognition of general patterns of natural variation and local adaptation. Further efforts in accumulating genomic data and developing bioinformatic and biostatistical tools are now poised to move this field forward. Integrative national and international collaborations and research communities are needed to facilitate development in the field of evolutionary and ecological genomics.
Collapse
Affiliation(s)
- Bao-Hua Song
- Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina 27708
| | | |
Collapse
|
693
|
Abstract
A large body of evidence indicates that the risk for developing chronic diabetic complications is under the control of genetic factors. Previous studies using a candidate gene approach have uncovered a number of genetic loci that may shape this risk, such as the VEGF gene for retinopathy, the ELMO1 gene for nephropathy, and the ADIPOQ gene for coronary artery disease. Recently, a new window has opened on identifying these genes through genome-wide association studies. Such systematic approach has already led to the identification of a major locus for coronary artery disease on 9p21 as well three potential genes for nephropathy on 7p, 11p, and 13q. Further insights are expected from a broader application of this strategy. It is anticipated that the identification of these genes will provide novel insights on the etiology of diabetic complications, with crucial implications for the development of new drugs to prevent the adverse effects of diabetes.
Collapse
Affiliation(s)
- Alessandro Doria
- Section on Genetics & Epidemiology, Joslin Diabetes Center, One Joslin Place, Boston, MA 02215, USA.
| |
Collapse
|
694
|
Abstract
Functional gastrointestinal disorders are complex symptom-based disorders without agreed upon biomarkers or pathophysiology. A better understanding of the genetic architecture of these disorders would help to better identify their complex biology and explain the common comorbidity with other disorders of persistent pain, mood, and affect, as well as possibly make it possible to identify subgroups of patients who respond to customized therapies. In contrast to monogenic diseases, polygenic diseases and traits are characterized by the contribution of common variants in a large number of genes, as well as environmental factors, to the vulnerability of an individual. Family and twin studies have clearly established a genetic component in irritable bowel syndrome. Although candidate gene studies have identified a few gene polymorphisms that may be correlated with the syndrome, small sample size, lack of reproducibility in large data sets, and the unreliability of the clinical phenotype require caution when extrapolating to a major role of any of the reported polymorphisms in the pathophysiology of irritable bowel syndrome. Future progress in this area will require better characterization of intermediate phenotypes with large effect size for the clinical phenotype, as well as consideration of gene-gene, environment-gene (epigenetics), and sex-gene interactions, genome-wide association, and whole genome sequencing approaches in large data sets.
Collapse
Affiliation(s)
- Yuri A Saito
- C.E.N.T.E.R., Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | |
Collapse
|
695
|
Abstract
A cattle database of candidate genes and genetic markers for milk production and mastitis has been developed to provide an integrated research tool incorporating different types of information supporting a genomic approach to study lactation, udder development and health. The database contains 943 genes and genetic markers involved in mammary gland development and function, representing candidates for further functional studies. The candidate loci were drawn on a genetic map to reveal positional overlaps. For identification of candidate loci, data from seven different research approaches were exploited: (i) gene knockouts or transgenes in mice that result in specific phenotypes associated with mammary gland (143 loci); (ii) cattle QTL for milk production (344) and mastitis related traits (71); (iii) loci with sequence variations that show specific allele-phenotype interactions associated with milk production (24) or mastitis (10) in cattle; (iv) genes with expression profiles associated with milk production (207) or mastitis (107) in cattle or mouse; (v) cattle milk protein genes that exist in different genetic variants (9); (vi) miRNAs expressed in bovine mammary gland (32) and (vii) epigenetically regulated cattle genes associated with mammary gland function (1). Fourty-four genes found by multiple independent analyses were suggested as the most promising candidates and were further in silico analysed for expression levels in lactating mammary gland, genetic variability and top biological functions in functional networks. A miRNA target search for mammary gland expressed miRNAs identified 359 putative binding sites in 3'UTRs of candidate genes.
Collapse
Affiliation(s)
- J Ogorevc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | | | | | | |
Collapse
|
696
|
McGough JJ, McCracken JT, Loo SK, Manganiello M, Leung MC, Tietjens JR, Trinh T, Baweja S, Suddath R, Smalley SL, Hellemann G, Sugar CA. A candidate gene analysis of methylphenidate response in attention-deficit/hyperactivity disorder. J Am Acad Child Adolesc Psychiatry 2009; 48:1155-64. [PMID: 19858760 PMCID: PMC2888980 DOI: 10.1097/chi.0b013e3181bc72e3] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
OBJECTIVE This study examines the potential role of candidate genes in moderating treatment effects of methylphenidate (MPH) in attention-deficit/hyperactivity disorder (ADHD). METHOD Eighty-two subjects with ADHD aged 6 to 17 years participated in a prospective, double-blind, placebo-controlled, multiple-dose, crossover titration trial of immediate release MPH three times daily. The subjects were assessed on a variety of parent and clinician ratings and a laboratory math test. Data reduction based on principal components analysis identified statistically derived efficacy and side effect outcomes. RESULTS Attention-deficit/hyperactivity disorder symptom response was predicted by polymorphisms at the serotonin transporter (SLC6A4) intron 2 VNTR (p = .01), with a suggested trend for catechol-O-methyltransferase (COMT) (p = .04). Gene × dose interactions were noted on math test outcomes for the dopamine D4 receptor (DRD4) promoter (p = .008), DRD4 exon 3 VNTR (p = .006), and SLC6A4 promoter insertion/deletion polymorphism (5HTTLPR) (p = .02). Irritability was predicted by COMT (p = .02). Vegetative symptoms were predicted by 5HTTLPR (p = .003). No significant effects were noted for the dopamine transporter (SLC6A3) or synaptosomal-associated protein 25 (SNAP25). CONCLUSIONS This article confirms and expands previous studies suggesting that genes moderate ADHD treatment response. The ADHD outcomes are not unitary but reflect both behavioral and learning domains that are likely influenced by different genes. Future research should emphasize candidate gene and genome-wide association studies in larger samples, symptom reduction as well as side effects outcomes, and responses over full therapeutic dose ranges to assess differences in both gene and gene × dose interactive effects.
Collapse
Affiliation(s)
- James J McGough
- Semel Institute for Neuroscience & Human Behavior and David Geffen School of Medicine, University of California, Los Angeles, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
697
|
Matarin M, Brown WM, Dena H, Britton A, De Vrieze FW, Brott TG, Brown RD, Worrall BB, Case LD, Chanock SJ, Metter EJ, Ferrucci L, Gamble D, Hardy JA, Rich SS, Singleton A, Meschia JF. Candidate gene polymorphisms for ischemic stroke. Stroke 2009; 40:3436-42. [PMID: 19729601 PMCID: PMC2784015 DOI: 10.1161/strokeaha.109.558015] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 07/28/2009] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND PURPOSE Ischemic stroke (IS) is a multifactorial disorder with strong evidence from twin, family, and animal model studies suggesting a genetic influence on risk and prognosis. Several candidate genes for IS have been proposed, but few have been replicated. We investigated the contribution of 67 candidate genes (369 single nucleotide polymorphisms [SNPs]) on the risk of IS in a North American population of European descent. METHODS Two independent studies were performed. In the first, 342 SNPs from 52 candidate genes were genotyped in 307 IS cases and 324 control subjects. The SNPs significantly associated with IS were tested for replication in another cohort of 583 IS cases and 270 control subjects. In the second study, 212 SNPs from 62 candidate genes were analyzed in 710 IS cases with subtyping available and 3751 control subjects. RESULTS None of the candidate genes (SNPs) were significantly associated with IS risk independent of known stroke risk factors after correction for multiple hypotheses testing. CONCLUSIONS These results are consistent with previous meta-analyses that demonstrate an absence of genetic association of variants in plausible candidate genes with IS risk. Our study suggests that the effect of the investigated SNPs may be weak or restricted to specific populations or IS subtypes.
Collapse
Affiliation(s)
- Mar Matarin
- Molecular Genetics Section, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
698
|
Daniels TF, Killinger KM, Michal JJ, Wright RW, Jiang Z. Lipoproteins, cholesterol homeostasis and cardiac health. Int J Biol Sci 2009; 5:474-88. [PMID: 19584955 PMCID: PMC2706428 DOI: 10.7150/ijbs.5.474] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 06/19/2009] [Indexed: 12/22/2022] Open
Abstract
Cholesterol is an essential substance involved in many functions, such as maintaining cell membranes, manufacturing vitamin D on surface of the skin, producing hormones, and possibly helping cell connections in the brain. When cholesterol levels rise in the blood, they can, however, have dangerous consequences. In particular, cholesterol has generated considerable notoriety for its causative role in atherosclerosis, the leading cause of death in developed countries around the world. Homeostasis of cholesterol is centered on the metabolism of lipoproteins, which mediate transport of the lipid to and from tissues. As a synopsis of the major events and proteins that manage lipoprotein homeostasis, this review contributes to the substantial attention that has recently been directed to this area. Despite intense scrutiny, the majority of phenotypic variation in total cholesterol and related traits eludes explanation by current genetic knowledge. This is somewhat disappointing considering heritability estimates have established these traits as highly genetic. Thus, the continued search for candidate genes, mutations, and mechanisms is vital to our understanding of heart disease at the molecular level. Furthermore, as marker development continues to predict risk of vascular illness, this knowledge has the potential to revolutionize treatment of this leading human disease.
Collapse
Affiliation(s)
- Tyler F Daniels
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
| | | | | | | | | |
Collapse
|
699
|
Suryapriya P, Snehalatha A, Kayalvili U, Krishna R, Singh S, Ulaganathan K. Genome-wide analyses of rice root development QTLs and development of an online resource, Rootbrowse. Bioinformation 2009; 3:279-81. [PMID: 19255649 PMCID: PMC2646863 DOI: 10.6026/97320630003279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 12/19/2008] [Accepted: 12/29/2008] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles. Intensive data mining of literature resulted in the identification 861 root development QTLs and associated microsatellite markers located on different chromosomes. The QTL and marker data generated and the genome sequence of rice were used for construction of a relational database, Rootbrowse, using MySQL relational database management system and Bio::DB::GFF schema. The data is viewed using GBrowse visualization tool. It graphically displays a section of the genome and all features annotated on it including the QTLs. The QTLs can be displayed along with SSR markers, protein coding genes and/or known root development genes for prediction of probable candidate genes. AVAILABILITY Rootbrowse is freely available at http://www.ricebrowse.org.
Collapse
Affiliation(s)
- Pala Suryapriya
- Centre for Plant Molecular Biology, Osmania University, Hyderabad 500 007, India.
| | | | | | | | | | | |
Collapse
|
700
|
Liang X, Slifer M, Martin ER, Schnetz-Boutaud N, Bartlett J, Anderson B, Züchner S, Gwirtsman H, Gilbert JR, Pericak-Vance MA, Haines JL. Genomic convergence to identify candidate genes for Alzheimer disease on chromosome 10. Hum Mutat 2009; 30:463-71. [PMID: 19241460 PMCID: PMC2713862 DOI: 10.1002/humu.20953] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A broad region of chromosome 10 (chr10) has engendered continued interest in the etiology of late-onset Alzheimer Disease (LOAD) from both linkage and candidate gene studies. However, there is a very extensive heterogeneity on chr10. We converged linkage analysis and gene expression data using the concept of genomic convergence that suggests that genes showing positive results across multiple different data types are more likely to be involved in AD. We identified and examined 28 genes on chr10 for association with AD in a Caucasian case-control dataset of 506 cases and 558 controls with substantial clinical information. The cases were all LOAD (minimum age at onset > or = 60 years). Both single marker and haplotypic associations were tested in the overall dataset and 8 subsets defined by age, gender, ApoE and clinical status. PTPLA showed allelic, genotypic and haplotypic association in the overall dataset. SORCS1 was significant in the overall data sets (p=0.0025) and most significant in the female subset (allelic association p=0.00002, a 3-locus haplotype had p=0.0005). Odds Ratio of SORCS1 in the female subset was 1.7 (p<0.0001). SORCS1 is an interesting candidate gene involved in the Abeta pathway. Therefore, genetic variations in PTPLA and SORCS1 may be associated and have modest effect to the risk of AD by affecting Abeta pathway. The replication of the effect of these genes in different study populations and search for susceptible variants and functional studies of these genes are necessary to get a better understanding of the roles of the genes in Alzheimer disease.
Collapse
Affiliation(s)
- Xueying Liang
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Michael Slifer
- Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL 33136, USA
| | - Eden R. Martin
- Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL 33136, USA
| | - Nathalie Schnetz-Boutaud
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Jackie Bartlett
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Brent Anderson
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Stephan Züchner
- Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL 33136, USA
| | - Harry Gwirtsman
- Department of Psychiatry, VA Hospital Medical Center, TN 37232, USA
| | - John R. Gilbert
- Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL 33136, USA
| | - Margaret A. Pericak-Vance
- Miami Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami FL 33136, USA
| | - Jonathan L. Haines
- Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| |
Collapse
|