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Richard Anney,
Lambertus Klei,
Dalila Pinto,
Joana Almeida,
Elena Bacchelli,
Gillian Baird,
Nadia Bolshakova,
Sven Bölte,
Patrick F Bolton,
Thomas Bourgeron, [......],
Edwin H Cook,
Louise Gallagher,
Michael Gill,
Joachim Hallmayer, Andrew D Paterson,
James S Sutcliffe,
Peter Szatmari,
Veronica J Vieland,
Hakon Hakonarson,
Bernie Devlin
[show abstract]
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ABSTRACT: While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest.
Human Molecular Genetics 07/2012; 21(21):4781-92. · 7.64 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: Long-term complications of type 1 diabetes, including nephropathy and retinopathy, share diabetes duration and hyperglycemia as major risk factors. Cross-sectional studies of sibpairs, both with type 1 diabetes, have shown familial clustering of specific complications, leading to the hypothesis that there are genetic contributors. However, because of the cross-sectional design of these studies, they were not able to account for the long-term effect of glycemia. Glycemia, measured by HbA1c, is correlated in sibs with type 1 diabetes. Recently, specific genetic loci that are associated with differences in HbA1c between people with type 1 diabetes have been convincingly identified, and they have also been shown to be associated with diabetic complications. This raises the question: how much of the familial clustering of diabetic complications is due to genes that influence risk without acting through the conventional risk factors? Implications for the design of genetic studies of diabetic complications are discussed.
Journal of Cardiovascular Translational Research 06/2012; 5(4):388-98. · 2.61 Impact Factor
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ABSTRACT: We identified genetic predictors of diabetes associated erectile dysfunction using genome-wide and candidate gene approaches in a cohort of men with type 1 diabetes.
We examined 528 white men with type 1 diabetes, including 125 with erectile dysfunction, from DCCT (Diabetes Control and Complications Trial) and its observational followup, the EDIC (Epidemiology of Diabetes Interventions and Complications) study. Erectile dysfunction was identified from a single International Index of Erectile Function item. A Human1M BeadChip (Illumina®) was used for genotyping. A total of 867,125 single nucleotide polymorphisms were subjected to analysis. Whole genome and candidate gene approaches were used to test the hypothesis that genetic polymorphisms may predispose men with type 1 diabetes to erectile dysfunction. Univariate and multivariate models were used, controlling for age, HbA1c, diabetes duration and prior randomization to intensive or conventional insulin therapy during DCCT. A stratified false discovery rate was used to perform the candidate gene approach.
Two single nucleotide polymorphisms located on chromosome 3 in 1 genomic loci were associated with erectile dysfunction with p <1 × 10(-6), including rs9810233 with p = 7 × 10(-7) and rs1920201 with p = 9 ×10(-7). The nearest gene to these 2 single nucleotide polymorphisms is ALCAM. Genetic association results at these loci were similar on univariate and multivariate analysis. No candidate genes met the criteria for statistical significance.
Two single nucleotide polymorphisms, rs9810233 and rs1920101, which are 25 kb apart, are associated with erectile dysfunction, although they do not meet the standard genome-wide association study significance criterion of p <5 × 10(-8). Other studies with larger sample sizes are required to determine whether ALCAM represents a novel gene in the pathogenesis of diabetes associated erectile dysfunction.
The Journal of urology 06/2012; 188(2):514-20. · 4.02 Impact Factor
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Kristen N Stevens,
Sara Lindstrom,
Christopher G Scott,
Deborah Thompson,
Thomas A Sellers,
Xianshu Wang,
Alice Wang,
Elizabeth Atkinson,
David N Rider,
Jeanette E Eckel-Passow, [......],
Jennifer Stone,
Carmel Apicella,
Peter Kraft,
Susan E Hankinson,
Aditi Hazra,
David J Hunter,
Douglas F Easton,
Fergus J Couch,
Rulla M Tamimi,
Celine M Vachon
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ABSTRACT: Percent mammographic density adjusted for age and body mass index (BMI) is one of the strongest risk factors for breast cancer and has a heritable component that remains largely unidentified. We performed a three-stage genome-wide association study (GWAS) of percent mammographic density to identify novel genetic loci associated with this trait. In stage 1, we combined three GWASs of percent density comprised of 1241 women from studies at the Mayo Clinic and identified the top 48 loci (99 single nucleotide polymorphisms). We attempted replication of these loci in 7018 women from seven additional studies (stage 2). The meta-analysis of stage 1 and 2 data identified a novel locus, rs1265507 on 12q24, associated with percent density, adjusting for age and BMI (P = 4.43 × 10(-8)). We refined the 12q24 locus with 459 additional variants (stage 3) in a combined analysis of all three stages (n = 10 377) and confirmed that rs1265507 has the strongest association in the 12q24 region (P = 1.03 × 10(-8)). Rs1265507 is located between the genes TBX5 and TBX3, which are members of the phylogenetically conserved T-box gene family and encode transcription factors involved in developmental regulation. Understanding the mechanism underlying this association will provide insight into the genetics of breast tissue composition.
Human Molecular Genetics 04/2012; 21(14):3299-305. · 7.64 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The detrimental effects of the winner’s curse, including overestimation of the genetic effects of associated variants and
underestimation of sufficient sample sizes for replication studies are well-recognized in genome-wide association studies
(GWAS). These effects can be expected to worsen as the field moves from GWAS into whole genome sequencing. To date, few studies
have reported statistical adjustments to the naive estimates, due to the lack of suitable statistical methods and computational
tools. We have developed an efficient genome-wide non-parametric method that explicitly accounts for the threshold, ranking,
and allele frequency effects in whole genome scans. Here, we implement the method to provide bias-reduced estimates via bootstrap
re-sampling (BR-squared) for association studies of both disease status and quantitative traits, and we report the results
of applying BR-squared to GWAS of psoriasis and HbA1c. We observed over 50% reduction in the genetic effect size estimation for many associated
SNPs. This translates into a greater than fourfold increase in sample size requirements for successful replication studies,
which in part explains some of the apparent failures in replicating the original signals. Our analysis suggests that adjusting
for the winner’s curse is critical for interpreting findings from whole genome scans and planning replication and meta-GWAS
studies, as well as in attempts to translate findings into the clinical setting.
Human Genetics 04/2012; 129(5):545-552. · 5.07 Impact Factor
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Jajini S Varghese,
Deborah J Thompson,
Kyriaki Michailidou,
Sara Lindström,
Clare Turnbull,
Judith Brown,
Jean Leyland,
Ruth M L Warren,
Robert N Luben,
Ruth J Loos, [......],
Jennifer Stone,
Jingmei Li,
Louise Eriksson,
Kamila Czene,
Norman F Boyd,
Per Hall,
John L Hopper,
Rulla M Tamimi,
Nazneen Rahman,
Douglas F Easton
[show abstract]
[hide abstract]
ABSTRACT: Percent mammographic breast density (PMD) is a strong heritable risk factor for breast cancer. However, the pathways through which this risk is mediated are still unclear. To explore whether PMD and breast cancer have a shared genetic basis, we identified genetic variants most strongly associated with PMD in a published meta-analysis of five genome-wide association studies (GWAS) and used these to construct risk scores for 3,628 breast cancer cases and 5,190 controls from the UK2 GWAS of breast cancer. The signed per-allele effect estimates of single-nucleotide polymorphisms (SNP) were multiplied with the respective allele counts in the individual and summed over all SNPs to derive the risk score for an individual. These scores were included as the exposure variable in a logistic regression model with breast cancer case-control status as the outcome. This analysis was repeated using 10 different cutoff points for the most significant density SNPs (1%-10% representing 5,222-50,899 SNPs). Permutation analysis was also conducted across all 10 cutoff points. The association between risk score and breast cancer was significant for all cutoff points from 3% to 10% of top density SNPs, being most significant for the 6% (2-sided P = 0.002) to 10% (P = 0.001) cutoff points (overall permutation P = 0.003). Women in the top 10% of the risk score distribution had a 31% increased risk of breast cancer [OR = 1.31; 95% confidence interval (CI), 1.08-1.59] compared with women in the bottom 10%. Together, our results show that PMD and breast cancer have a shared genetic basis that is mediated through a large number of common variants.
Cancer Research 03/2012; 72(6):1478-84. · 7.86 Impact Factor
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Celia M T Greenwood, Andrew D Paterson,
Linda Linton,
Irene L Andrulis,
Carmel Apicella,
Apostolos Dimitromanolakis,
Valentina Kriukov,
Lisa J Martin,
Ayesha Salleh,
Elena Samiltchuk,
Rashmi V Parekh,
Melissa C Southey,
Esther M John,
John L Hopper,
Norman F Boyd,
Johanna M Rommens
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[hide abstract]
ABSTRACT: Mammographic breast density is a highly heritable (h2 > 0.6) and strong risk factor for breast cancer. We conducted a genome-wide linkage study to identify loci influencing mammographic breast density (MD).
Epidemiological data were assembled on 1,415 families from the Australia, Northern California and Ontario sites of the Breast Cancer Family Registry, and additional families recruited in Australia and Ontario. Families consisted of sister pairs with age-matched mammograms and data on factors known to influence MD. Single nucleotide polymorphism (SNP) genotyping was performed on 3,952 individuals using the Illumina Infinium 6K linkage panel.
Using a variance components method, genome-wide linkage analysis was performed using quantitative traits obtained by adjusting MD measurements for known covariates. Our primary trait was formed by fitting a linear model to the square root of the percentage of the breast area that was dense (PMD), adjusting for age at mammogram, number of live births, menopausal status, weight, height, weight squared, and menopausal hormone therapy. The maximum logarithm of odds (LOD) score from the genome-wide scan was on chromosome 7p14.1-p13 (LOD = 2.69; 63.5 cM) for covariate-adjusted PMD, with a 1-LOD interval spanning 8.6 cM. A similar signal was seen for the covariate adjusted area of the breast that was dense (DA) phenotype. Simulations showed that the complete sample had adequate power to detect LOD scores of 3 or 3.5 for a locus accounting for 20% of phenotypic variance. A modest peak initially seen on chromosome 7q32.3-q34 increased in strength when only the 513 families with at least two sisters below 50 years of age were included in the analysis (LOD 3.2; 140.7 cM, 1-LOD interval spanning 9.6 cM). In a subgroup analysis, we also found a LOD score of 3.3 for DA phenotype on chromosome 12.11.22-q13.11 (60.8 cM, 1-LOD interval spanning 9.3 cM), overlapping a region identified in a previous study.
The suggestive peaks and the larger linkage signal seen in the subset of pedigrees with younger participants highlight regions of interest for further study to identify genes that determine MD, with the goal of understanding mammographic density and its involvement in susceptibility to breast cancer.
Breast cancer research: BCR 12/2011; 13(6):R132. · 5.24 Impact Factor
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ABSTRACT: The implications of the well known sex differences in the prevalence of autism spectrum disorder (ASD) are not well understood. The aim of this paper was to investigate whether these differences might be associated with differences in genetic liability. Individuals with ASD (970 families, 2,028 individuals) were recruited as part of the Autism Genome Project (AGP). The families were differentiated into families containing a female (either female-female or male-female) and those with only males. If the sex with the lower prevalence is associated with a greater genetic liability necessary to cross sex-specific thresholds, the males from female containing families should be more severely affected than males from male only families. Affected subjects from the different types of families with ASD were sampled and compared on the social reciprocity and repetitive behavior scores from the Autism Diagnostic Interview-Revised (ADI-R). In general, females had lower repetitive behavior scores than males. More importantly, males from female containing families had higher repetitive behavior scores than males from male-male families. No such differences were apparent on the social reciprocity scores. These results support the hypothesis of a multiple threshold model of genetic liability of ASD with females having a higher liability for affectation status, at least on the repetitive behavior dimension of the disorder. These data also support the dissociation of the different phenotypic dimensions of ASD in terms of its genetic architecture. The implications of these results for linkage and association studies are discussed.
American Journal of Medical Genetics Part B Neuropsychiatric Genetics 11/2011; 159B(1):5-12. · 3.70 Impact Factor
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ABSTRACT: To investigate the underlying phenotypic constructs in autism spectrum disorders (ASD) and to identify genetic loci that are linked to these empirically derived factors.
Exploratory factor analysis was applied to two datasets with 28 selected Autism Diagnostic Interview-Revised (ADI-R) algorithm items. The first dataset was from the Autism Genome Project (AGP) phase I (1,236 ASD subjects from 618 families); the second was from the AGP phase II (804 unrelated ASD subjects). Variables derived from the factor analysis were then used as quantitative traits in genome-wide variance components linkage analyses.
Six factors, namely, joint attention, social interaction and communication, nonverbal communication, repetitive sensory-motor behavior, peer interaction, and compulsion/restricted interests, were retained for both datasets. There was good agreement between the factor loading patterns from the two datasets. All factors showed familial aggregation. Suggestive evidence for linkage was obtained for the joint attention factor on 11q23. Genome-wide significant evidence for linkage was obtained for the repetitive sensory-motor behavior factor on 19q13.3.
This study demonstrates that the underlying phenotypic constructs based on the ADI-R algorithm items are replicable in independent datasets, and that the empirically derived factors are suitable and informative in genetic studies of ASD.
Journal of the American Academy of Child and Adolescent Psychiatry 07/2011; 50(7):687-696.e13. · 4.98 Impact Factor
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Veronica J Vieland,
Joachim Hallmayer,
Yungui Huang,
Alistair T Pagnamenta,
Dalila Pinto,
Hameed Khan,
Anthony P Monaco, Andrew D Paterson,
Stephen W Scherer,
James S Sutcliffe,
Peter Szatmari
[show abstract]
[hide abstract]
ABSTRACT: The Autism Genome Project has assembled two large datasets originally designed for linkage analysis and genome-wide association analysis, respectively: 1,069 multiplex families genotyped on the Affymetrix 10 K platform, and 1,129 autism trios genotyped on the Illumina 1 M platform. We set out to exploit this unique pair of resources by analyzing the combined data with a novel statistical method, based on the PPL statistical framework, simultaneously searching for linkage and association to loci involved in autism spectrum disorders (ASD). Our analysis also allowed for potential differences in genetic architecture for ASD in the presence or absence of lower IQ, an important clinical indicator of ASD subtypes. We found strong evidence of multiple linked loci; however, association evidence implicating specific genes was low even under the linkage peaks. Distinct loci were found in the lower IQ families, and these families showed stronger and more numerous linkage peaks, while the normal IQ group yielded the strongest association evidence. It appears that presence/absence of lower IQ (LIQ) demarcates more genetically homogeneous subgroups of ASD patients, with not just different sets of loci acting in the two groups, but possibly distinct genetic architecture between them, such that the LIQ group involves more major gene effects (amenable to linkage mapping), while the normal IQ group potentially involves more common alleles with lower penetrances. The possibility of distinct genetic architecture across subtypes of ASD has implications for further research and perhaps for research approaches to other complex disorders as well.
Journal of Neurodevelopmental Disorders 06/2011; 3(2):113-23. · 3.06 Impact Factor
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Carsten A Böger,
Ming-Huei Chen,
Adrienne Tin,
Matthias Olden,
Anna Köttgen,
Ian H de Boer,
Christian Fuchsberger,
Conall M O'Seaghdha,
Cristian Pattaro,
Alexander Teumer, [......],
Peter P Pramstaller,
L Adrienne Cupples,
Jacques S Beckmann,
Qiong Yang,
Iris M Heid,
Rainer Rettig,
Albert W Dreisbach,
Murielle Bochud,
Caroline S Fox,
W H L Kao
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ABSTRACT: Identification of genetic risk factors for albuminuria may alter strategies for early prevention of CKD progression, particularly among patients with diabetes. Little is known about the influence of common genetic variants on albuminuria in both general and diabetic populations. We performed a meta-analysis of data from 63,153 individuals of European ancestry with genotype information from genome-wide association studies (CKDGen Consortium) and from a large candidate gene study (CARe Consortium) to identify susceptibility loci for the quantitative trait urinary albumin-to-creatinine ratio (UACR) and the clinical diagnosis microalbuminuria. We identified an association between a missense variant (I2984V) in the CUBN gene, which encodes cubilin, and both UACR (P = 1.1 × 10(-11)) and microalbuminuria (P = 0.001). We observed similar associations among 6981 African Americans in the CARe Consortium. The associations between this variant and both UACR and microalbuminuria were significant in individuals of European ancestry regardless of diabetes status. Finally, this variant associated with a 41% increased risk for the development of persistent microalbuminuria during 20 years of follow-up among 1304 participants with type 1 diabetes in the prospective DCCT/EDIC Study. In summary, we identified a missense CUBN variant that associates with levels of albuminuria in both the general population and in individuals with diabetes.
Journal of the American Society of Nephrology 02/2011; 22(3):555-70. · 9.66 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The detrimental effects of the winner's curse, including overestimation of the genetic effects of associated variants and underestimation of sufficient sample sizes for replication studies are well-recognized in genome-wide association studies (GWAS). These effects can be expected to worsen as the field moves from GWAS into whole genome sequencing. To date, few studies have reported statistical adjustments to the naive estimates, due to the lack of suitable statistical methods and computational tools. We have developed an efficient genome-wide non-parametric method that explicitly accounts for the threshold, ranking, and allele frequency effects in whole genome scans. Here, we implement the method to provide bias-reduced estimates via bootstrap re-sampling (BR-squared) for association studies of both disease status and quantitative traits, and we report the results of applying BR-squared to GWAS of psoriasis and HbA1c. We observed over 50% reduction in the genetic effect size estimation for many associated SNPs. This translates into a greater than fourfold increase in sample size requirements for successful replication studies, which in part explains some of the apparent failures in replicating the original signals. Our analysis suggests that adjusting for the winner's curse is critical for interpreting findings from whole genome scans and planning replication and meta-GWAS studies, as well as in attempts to translate findings into the clinical setting.
Human Genetics 01/2011; 129(5):545-52. · 5.07 Impact Factor
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Sara Lindström,
Celine M Vachon,
Jingmei Li,
Jajini Varghese,
Deborah Thompson,
Ruth Warren,
Judith Brown,
Jean Leyland,
Tina Audley,
Nicholas J Wareham, [......],
Louise Eriksson,
Fergus J Couch,
Jennifer Stone,
Carmel Apicella,
Kamila Czene,
Peter Kraft,
Per Hall,
Douglas F Easton,
Norman F Boyd,
Rulla M Tamimi
[show abstract]
[hide abstract]
ABSTRACT: High-percent mammographic density adjusted for age and body mass index is one of the strongest risk factors for breast cancer. We conducted a meta analysis of five genome-wide association studies of percent mammographic density and report an association with rs10995190 in ZNF365 (combined P = 9.6 × 10(-10)). Common variants in ZNF365 have also recently been associated with susceptibility to breast cancer.
Nature Genetics 01/2011; 43(3):185-7. · 35.53 Impact Factor
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Proton Rahman,
Nicole M Roslin,
Fawnda J Pellett,
Mathieu Lemire,
Celia M T Greenwood,
Joseph Beyene,
Angela Pope,
Lynette Peddle, Andrew D Paterson,
Mohammed Uddin,
Dafna D Gladman
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ABSTRACT: Psoriatic arthritis (PsA) has a clear familial predisposition, the major histocompatibility complex (MHC) region being the strongest genetic locus. The study primary objective was to identify single nucleotide polymorphisms (SNPs) independent of known human leucocyte antigen (HLA) alleles within the MHC region that are associated with PsA using a high-density SNP map.
In all, 914 samples were assessed, including 427 PsA cases from 2 well established PsA cohorts and 487 controls from Canada. The genotype data consisted of 2521 SNPs from 2 Illumina Goldengate MHC panels, spanning 4.9 Mb of chromosome 6 with an average spacing of 2 kb. Classical HLA alleles were genotyped in all subjects using sequence-specific oligonucleotide probes or sequence-specific primers. A conditioning approach was used to distinguish between new associations and those in linkage disequilibrium (LD) with known HLA alleles.
Unconditional association analysis revealed 43 markers with p<7.26×10(-5) (calculated experiment-wide significance threshold). In the conditional analysis, 10 SNPs showed statistically significant association at a threshold of p<7.26×10(-5). Seven SNPs were in strong LD in the study data (pairwise r(2) >0.77 in the controls) reflecting one association signal. These SNPs spanned a 1.6 Mb region. SNP rs1150735 is 1.5 kb upstream from ring finger protein 39 (RNF39). RNF39 SNPs have been associated with HIV1 disease progression and set point CD4 T cell count.
Four new loci for either psoriasis or PsA in the MHC region that are independent of known HLA alleles have been identified. The effect size of these variants is modest. Replication of these variants in multiple larger populations is necessary.
Annals of the rheumatic diseases 01/2011; 70(4):690-4. · 8.11 Impact Factor
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Richard Anney,
Lambertus Klei,
Dalila Pinto,
Regina Regan,
Judith Conroy,
Tiago R Magalhaes,
Catarina Correia,
Brett S Abrahams,
Nuala Sykes,
Alistair T Pagnamenta, [......],
Gerard D Schellenberg,
Stephen W Scherer,
James S Sutcliffe,
Peter Szatmari,
Astrid M Vicente,
Veronica J Vieland,
Ellen M Wijsman,
Bernie Devlin,
Sean Ennis,
Joachim Hallmayer
[show abstract]
[hide abstract]
ABSTRACT: Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
Human Molecular Genetics 10/2010; 19(20):4072-82. · 7.64 Impact Factor
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Alistair T Pagnamenta,
Hameed Khan,
Susan Walker,
Dianne Gerrelli,
Kirsty Wing,
Maria Clara Bonaglia,
Roberto Giorda,
Tom Berney,
Elisa Mani,
Massimo Molteni,
Dalila Pinto,
Ann Le Couteur,
Joachim Hallmayer,
James S Sutcliffe,
Peter Szatmari, Andrew D Paterson,
Stephen W Scherer,
Veronica J Vieland,
Anthony P Monaco
[show abstract]
[hide abstract]
ABSTRACT: Autism spectrum disorder (ASD) is characterised by impairments in social communication and by a pattern of repetitive behaviours, with learning disability (LD) typically seen in up to 70% of cases. A recent study using the PPL statistical framework identified a novel region of genetic linkage on chromosome 16q21 that is limited to ASD families with LD.
In this study, two families with autism and/or LD are described which harbour rare >1.6 Mb microdeletions located within this linkage region. The deletion breakpoints are mapped at base-pair resolution and segregation analysis is performed using a combination of 1M single nucleotide polymorphism (SNP) technology, array comparative genomic hybridisation (CGH), long-range PCR, and Sanger sequencing. The frequency of similar genomic variants in control subjects is determined through analysis of published SNP array data. Expression of CDH8, the only gene disrupted by these microdeletions, is assessed using reverse transcriptase PCR and in situ hybridisation analysis of 9 week human embryos.
The deletion of chr16: 60 025 584-61 667 839 was transmitted to three of three boys with autism and LD and none of four unaffected siblings, from their unaffected mother. In a second family, an overlapping deletion of chr16: 58 724 527-60 547 472 was transmitted to an individual with severe LD from his father with moderate LD. No copy number variations (CNVs) disrupting CDH8 were observed in 5023 controls. Expression analysis indicates that the two CDH8 isoforms are present in the developing human cortex.
Rare familial 16q21 microdeletions and expression analysis implicate CDH8 in susceptibility to autism and LD.
Journal of Medical Genetics 10/2010; 48(1):48-54. · 6.36 Impact Factor
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Michelle Liu,
Sally Shi,
Sean Senthilnathan,
Julie Yu,
Elliot Wu,
Carsten Bergmann,
Klaus Zerres,
Nadja Bogdanova,
Eliecer Coto,
Constantinos Deltas, [......],
Riccardo Magistroni,
Patrick Parfrey,
Martijn Breuning,
Dorien J M Peters,
Roser Torra,
Christopher G Winearls,
Vicente E Torres,
Peter C Harris, Andrew D Paterson,
York Pei
[show abstract]
[hide abstract]
ABSTRACT: Significant variation in the course of autosomal dominant polycystic kidney disease ( ADPKD) within families suggests the presence of effect modifiers. Recent studies of the variation within families harboring PKD1 mutations indicate that genetic background may account for 32 to 42% of the variance in estimated GFR (eGFR) before ESRD and 43 to 78% of the variance in age at ESRD onset, but the genetic modifiers are unknown. Here, we conducted a high-throughput single-nucleotide polymorphism (SNP) genotyping association study of 173 biological candidate genes in 794 white patients from 227 families with PKD1. We analyzed two primary outcomes: (1) eGFR and (2) time to ESRD (renal survival). For both outcomes, we used multidimensional scaling to correct for population structure and generalized estimating equations to account for the relatedness among individuals within the same family. We found suggestive associations between each of 12 SNPs and at least one of the renal outcomes. We genotyped these SNPs in a second set of 472 white patients from 229 families with PKD1 and performed a joint analysis on both cohorts. Three SNPs continued to show suggestive/significant association with eGFR at the Dickkopf 3 (DKK3) gene locus; no SNPs significantly associated with renal survival. DKK3 antagonizes Wnt/beta-catenin signaling, which may modulate renal cyst growth. Pending replication, our study suggests that genetic variation of DKK3 may modify severity of ADPKD resulting from PKD1 mutations.
Journal of the American Society of Nephrology 09/2010; 21(9):1510-20. · 9.66 Impact Factor
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Dalila Pinto,
Alistair T Pagnamenta,
Lambertus Klei,
Richard Anney,
Daniele Merico,
Regina Regan,
Judith Conroy,
Tiago R Magalhaes,
Catarina Correia,
Brett S Abrahams, [......], Andrew D Paterson,
Margaret A Pericak-Vance,
Gerard D Schellenberg,
Peter Szatmari,
Astrid M Vicente,
Veronica J Vieland,
Ellen M Wijsman,
Stephen W Scherer,
James S Sutcliffe,
Catalina Betancur
[show abstract]
[hide abstract]
ABSTRACT: The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
Nature 07/2010; 466(7304):368-72. · 36.28 Impact Factor
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ABSTRACT: Height, weight, and body mass index (BMI) are partly heritable, known to be associated with chronic diseases, and are linked to circulating insulin-like growth factor I (IGF-I) concentrations. IGF-I concentrations are also partly heritable and thus genetic variation at IGF1 could influence height, weight, BMI and the risk of developing chronic diseases. Our objective was to examine the association of genetic variation at IGF1 with height, weight and BMI using a sample of premenopausal women. A family-based study design was used to investigate the association of three IGF1 CA repeat variants at 5' (5'CA), intron 2 (In2CA) and 3' (3'CA) with these anthropometric measures. We analyzed the data for 827 families of different sizes and configurations, which included 1520 premenopausal women. Nominally significant associations (P<or=0.05) were found for a rare 3' variant allele (3'CA-193) and BMI (P=0.05), and for the more common 3'CA-187 allele and weight (P=0.04). These associations did not remain significant when adjusted for multiple comparisons. Haplotype analysis did not support an association between these variants and anthropometric measures. This study does not support an association between IGF1 and these anthropometric measures. Study limitations, including sample size and capturing genetic variation at IGF1 with these markers, could mean associations were missed.
Journal of Human Genetics 03/2010; 55(4):255-8. · 2.57 Impact Factor
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Miralem Mrkonjic,
Nicole M Roslin,
Celia M Greenwood,
Stavroula Raptis,
Aaron Pollett,
Peter W Laird,
Vaijayanti V Pethe,
Theodore Chiang,
Darshana Daftary,
Elizabeth Dicks, [......],
Patrick S Parfrey,
H Banfield Younghusband,
John D Potter,
Thomas J Hudson,
John R McLaughlin,
Roger C Green,
Brent W Zanke,
Polly A Newcomb, Andrew D Paterson,
Bharati Bapat
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ABSTRACT: We previously identified an association between a mismatch repair gene, MLH1, promoter SNP (rs1800734) and microsatellite unstable (MSI-H) colorectal cancers (CRCs) in two samples. The current study expanded on this finding as we explored the genetic basis of DNA methylation in this region of chromosome 3. We hypothesized that specific polymorphisms in the MLH1 gene region predispose it to DNA methylation, resulting in the loss of MLH1 gene expression, mismatch-repair function, and consequently to genome-wide microsatellite instability.
We first tested our hypothesis in one sample from Ontario (901 cases, 1,097 controls) and replicated major findings in two additional samples from Newfoundland and Labrador (479 cases, 336 controls) and from Seattle (591 cases, 629 controls). Logistic regression was used to test for association between SNPs in the region of MLH1 and CRC, MSI-H CRC, MLH1 gene expression in CRC, and DNA methylation in CRC. The association between rs1800734 and MSI-H CRCs, previously reported in Ontario and Newfoundland, was replicated in the Seattle sample. Two additional SNPs, in strong linkage disequilibrium with rs1800734, showed strong associations with MLH1 promoter methylation, loss of MLH1 protein, and MSI-H CRC in all three samples. The logistic regression model of MSI-H CRC that included MLH1-promoter-methylation status and MLH1 immunohistochemistry status fit most parsimoniously in all three samples combined. When rs1800734 was added to this model, its effect was not statistically significant (P-value = 0.72 vs. 2.3×10(-4) when the SNP was examined alone).
The observed association of rs1800734 with MSI-H CRC occurs through its effect on the MLH1 promoter methylation, MLH1 IHC deficiency, or both.
PLoS ONE 01/2010; 5(10):e13314. · 4.09 Impact Factor
