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Auteur Judith A. BADNER |
Documents disponibles écrits par cet auteur (2)
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Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci / Lea K. DAVIS in Molecular Autism, (May 2012)
[article]
Titre : Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci Type de document : Texte imprimé et/ou numérique Auteurs : Lea K. DAVIS, Auteur ; Eric R. GAMAZON, Auteur ; Emily KISTNER-GRIFFIN, Auteur ; Judith A. BADNER, Auteur ; Chunyu LIU, Auteur ; Edwin H. Jr COOK, Auteur ; James S. SUTCLIFFE, Auteur ; Nancy J. COX, Auteur Année de publication : 2012 Article en page(s) : 25 p. Langues : Anglais (eng) Index. décimale : PER Périodiques Résumé : Background
Autism spectrum disorder is a severe early onset neurodevelopmental disorder with high heritability but significant heterogeneity. Traditional genome-wide approaches to test for an association of common variants with autism susceptibility risk have met with limited success. However, novel methods to identify moderate risk alleles in attainable sample sizes are now gaining momentum.
Methods
In this study, we utilized publically available genome-wide association study data from the Autism Genome Project and annotated the results (P <0.001) for expression quantitative trait loci present in the parietal lobe (GSE35977), cerebellum (GSE35974) and lymphoblastoid cell lines (GSE7761). We then performed a test of enrichment by comparing these results to simulated data conditioned on minor allele frequency to generate an empirical P-value indicating statistically significant enrichment of expression quantitative trait loci in top results from the autism genome-wide association study.
Results
Our findings show a global enrichment of brain expression quantitative trait loci, but not lymphoblastoid cell line expression quantitative trait loci, among top single nucleotide polymorphisms from an autism genome-wide association study. Additionally, the data implicates individual genes SLC25A12, PANX1 and PANX2 as well as pathways previously implicated in autism.
Conclusions
These findings provide supportive rationale for the use of annotation-based approaches to genome-wide association studies.En ligne : http://dx.doi.org/10.1186/2040-2392-3-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=178
in Molecular Autism > (May 2012) . - 25 p.[article] Loci nominally associated with autism from genome-wide analysis show enrichment of brain expression quantitative trait loci but not lymphoblastoid cell line expression quantitative trait loci [Texte imprimé et/ou numérique] / Lea K. DAVIS, Auteur ; Eric R. GAMAZON, Auteur ; Emily KISTNER-GRIFFIN, Auteur ; Judith A. BADNER, Auteur ; Chunyu LIU, Auteur ; Edwin H. Jr COOK, Auteur ; James S. SUTCLIFFE, Auteur ; Nancy J. COX, Auteur . - 2012 . - 25 p.
Langues : Anglais (eng)
in Molecular Autism > (May 2012) . - 25 p.
Index. décimale : PER Périodiques Résumé : Background
Autism spectrum disorder is a severe early onset neurodevelopmental disorder with high heritability but significant heterogeneity. Traditional genome-wide approaches to test for an association of common variants with autism susceptibility risk have met with limited success. However, novel methods to identify moderate risk alleles in attainable sample sizes are now gaining momentum.
Methods
In this study, we utilized publically available genome-wide association study data from the Autism Genome Project and annotated the results (P <0.001) for expression quantitative trait loci present in the parietal lobe (GSE35977), cerebellum (GSE35974) and lymphoblastoid cell lines (GSE7761). We then performed a test of enrichment by comparing these results to simulated data conditioned on minor allele frequency to generate an empirical P-value indicating statistically significant enrichment of expression quantitative trait loci in top results from the autism genome-wide association study.
Results
Our findings show a global enrichment of brain expression quantitative trait loci, but not lymphoblastoid cell line expression quantitative trait loci, among top single nucleotide polymorphisms from an autism genome-wide association study. Additionally, the data implicates individual genes SLC25A12, PANX1 and PANX2 as well as pathways previously implicated in autism.
Conclusions
These findings provide supportive rationale for the use of annotation-based approaches to genome-wide association studies.En ligne : http://dx.doi.org/10.1186/2040-2392-3-3 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=178 A quantitative association study of SLC25A12 and restricted repetitive behavior traits in autism spectrum disorders / Soo-Jeong KIM in Molecular Autism, (May 2011)
[article]
Titre : A quantitative association study of SLC25A12 and restricted repetitive behavior traits in autism spectrum disorders Type de document : Texte imprimé et/ou numérique Auteurs : Soo-Jeong KIM, Auteur ; Raquel M. SILVA, Auteur ; Cindi G. FLORES, Auteur ; Suma JACOB, Auteur ; Stephen GUTER, Auteur ; Gregory VALCANTE, Auteur ; Annette M. ZAYTOUN, Auteur ; Edwin H. Jr COOK, Auteur ; Judith A. BADNER, Auteur Année de publication : 2011 Article en page(s) : 48 p. Langues : Anglais (eng) Index. décimale : PER Périodiques Résumé : Background
SLC25A12 was previously identified in a linkage directed association analysis in autism. In this study, we investigated the relationship between three SLC25A12 single nucleotide polymorphisms (SNPs) (rs2056202, rs908670 and rs2292813) and restricted repetitive behavior (RRB) traits in autism spectrum disorders (ASDs), based on a positive correlation between the G allele of rs2056202 and an RRB subdomain score on the Autism Diagnostic Interview-Revised (ADI-R).
Methods
We used the Repetitive Behavior Scale-Revised (RBS-R) as a quantitative RRB measure, and conducted linear regression analyses for individual SNPs and a previously identified haplotype (rs2056202-rs2292813). We examined associations in our UIC-UF sample (179 unrelated individuals), and then attempted to replicate our findings in the Simons Simplex Collection (SSC) sample (720 families).
Results
In the UIC-UF sample, three RBS-R scores (ritualistic/sameness/sum) showed positive associations with the A allele of rs2292813 (p=0.006-0.012), and with rs2056202-rs2292813 haplotype (omnibus test p=0.025-0.040). The SSC sample revealed positive associations between the A allele of rs2056202 and four RBS-R scores (stereotyped/sameness/restricted/sum, p=0.006-0.010), between the A allele of rs908670 and three RBS-R scores (stereotyped/self-injurious/sum, p=0.003-0.015), and between rs2056202-rs2292813 haplotype and RBS-R scores (stereotyped/self-injurious/compulsive/sameness/restricted/sum, omnibus test p=0.002-0.028). Taken together, the A alleles of rs2056202 and rs2292813 were consistently positively associated with RRB traits in both UIC-UF and SSC samples, but the most significant SNP-phenotype association varied in each dataset.
Conclusions
This study confirmed an association between SLC25A12 and RRB traits in ASDs, but the direction of the association was different from the initial study. This may be because of the examined SLC25A12 SNPs being in linkage disequilibrium (LD) with another risk allele as well as genetic/phenotypic heterogeneity of the ASD samples across studies.En ligne : http://dx.doi.org/10.1186/2040-2392-2-8 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=131
in Molecular Autism > (May 2011) . - 48 p.[article] A quantitative association study of SLC25A12 and restricted repetitive behavior traits in autism spectrum disorders [Texte imprimé et/ou numérique] / Soo-Jeong KIM, Auteur ; Raquel M. SILVA, Auteur ; Cindi G. FLORES, Auteur ; Suma JACOB, Auteur ; Stephen GUTER, Auteur ; Gregory VALCANTE, Auteur ; Annette M. ZAYTOUN, Auteur ; Edwin H. Jr COOK, Auteur ; Judith A. BADNER, Auteur . - 2011 . - 48 p.
Langues : Anglais (eng)
in Molecular Autism > (May 2011) . - 48 p.
Index. décimale : PER Périodiques Résumé : Background
SLC25A12 was previously identified in a linkage directed association analysis in autism. In this study, we investigated the relationship between three SLC25A12 single nucleotide polymorphisms (SNPs) (rs2056202, rs908670 and rs2292813) and restricted repetitive behavior (RRB) traits in autism spectrum disorders (ASDs), based on a positive correlation between the G allele of rs2056202 and an RRB subdomain score on the Autism Diagnostic Interview-Revised (ADI-R).
Methods
We used the Repetitive Behavior Scale-Revised (RBS-R) as a quantitative RRB measure, and conducted linear regression analyses for individual SNPs and a previously identified haplotype (rs2056202-rs2292813). We examined associations in our UIC-UF sample (179 unrelated individuals), and then attempted to replicate our findings in the Simons Simplex Collection (SSC) sample (720 families).
Results
In the UIC-UF sample, three RBS-R scores (ritualistic/sameness/sum) showed positive associations with the A allele of rs2292813 (p=0.006-0.012), and with rs2056202-rs2292813 haplotype (omnibus test p=0.025-0.040). The SSC sample revealed positive associations between the A allele of rs2056202 and four RBS-R scores (stereotyped/sameness/restricted/sum, p=0.006-0.010), between the A allele of rs908670 and three RBS-R scores (stereotyped/self-injurious/sum, p=0.003-0.015), and between rs2056202-rs2292813 haplotype and RBS-R scores (stereotyped/self-injurious/compulsive/sameness/restricted/sum, omnibus test p=0.002-0.028). Taken together, the A alleles of rs2056202 and rs2292813 were consistently positively associated with RRB traits in both UIC-UF and SSC samples, but the most significant SNP-phenotype association varied in each dataset.
Conclusions
This study confirmed an association between SLC25A12 and RRB traits in ASDs, but the direction of the association was different from the initial study. This may be because of the examined SLC25A12 SNPs being in linkage disequilibrium (LD) with another risk allele as well as genetic/phenotypic heterogeneity of the ASD samples across studies.En ligne : http://dx.doi.org/10.1186/2040-2392-2-8 Permalink : https://www.cra-rhone-alpes.org/cid/opac_css/index.php?lvl=notice_display&id=131