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Dalila Pinto,
Alistair Pagnamenta,
Lambertus Klei,
Richard Anney,
Daniele Merico,
Regina Regan,
Judith Conroy,
Tiago Magalhaes,
Catarina Correia,
Brett Abrahams, [......],
Andrew Paterson,
Margaret Pericak-Vance,
Gerard Schellenberg,
Peter Szatmari,
Astrid Vicente,
Veronica Vieland,
Ellen Wijsman,
Stephen Scherer,
James Sutcliffe,
Catalina Betancur
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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 07/2011; 466:368-372. · 36.28 Impact Factor
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Richard Anney,
Lambertus Klei,
Dalila Pinto,
Regina Regan,
Judith Conroy,
Tiago Magalhaes,
Catarina Correia,
Brett Abrahams,
Nuala Sykes,
Alistair Pagnamenta, [......],
Gerard Schellenberg,
Stephen Scherer,
James Sutcliffe,
Peter Szatmari,
Astrid Vicente,
Veronica Vieland,
Ellen Wijsman,
Bernie Devlin,
Sean Ennis,
Joachim Hallmayer
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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 x 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 x 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):4072-4082. · 7.64 Impact Factor
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Federico Innocenti,
Wanqing Liu,
Donna Fackenthal,
Jacqueline Ramírez,
Peixian Chen,
Xin Ye,
Xiaolin Wu,
Wei Zhang,
Snezana Mirkov,
Soma Das, Edwin Cook,
Mark J Ratain
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ABSTRACT: UDP-glucuronosyltransferase 2B7 (UGT2B7) plays a central role in the liver-mediated biotransformation of endogenous and exogenous compounds. The genetic basis of interindividual variability in UGT2B7 function is unknown. This study aimed to discover novel gene variants of functional significance.
Caucasian human livers (n=54) were used. UGT2B7 was resequenced in 12 samples [(six highest and six lowest for the formation of morphine-3-glucuronide (M3G)]. Haplotype-tagging single nucleotide polymorphisms were genotyped in the entire sample set. Samples were phenotyped for mRNA expression.
10 haplotype-tagging single nucleotide polymorphisms were identified and their haplotypes were inferred. Haplotype 4 (-45597G; -6682_-6683A; 372A; IVS1+9_IVS1+10A; IVS1+829T; IVS1+985G; IVS1+999C; IVS1+1250G; 801T; IVS4+185C) (frequency of 0.12) was associated with an increase in enzyme activity and gene expression. The 1/4 and 4/6 diplotypes had higher M3G formation compared with 1/1 (P<0.05) and 2/3 (P<0.01) diplotypes. Diplotypes containing haplotype 4 resulted in a significant 45% average increase in the formation of M3G compared with diplotypes without haplotype 4 (P=0.002). There was also an association between haplotype 4 and increased mRNA expression. IVS1+985A>G, 735A>G, and 1062C>T are the putative functional variants of haplotype 4. We also identified two mRNA splicing variants (UGT2B7_v2 and UGT2B7_v3) splicing out exon 1, 4, 5, and 6 but sharing exons 2 and 3 with the involvement of additional 5' exons. UGT2B7_v2 was detected in all livers tested, but UGT2B7_v3 was present at much lower levels compared with UGT2B7_v2. The UGT2B7 reference sequence mRNA is now named UGT2B7_v1.
UGT2B7 haplotype 4 is functional and its effects on the biotransformation of UGT2B7 substrates should be tested in controlled clinical trials. Biochemical studies should investigate the functional role of the newly discovered mRNA splicing variants.
Pharmacogenetics and Genomics 08/2008; 18(8):683-97. · 3.48 Impact Factor
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Federico Innocenti,
Snezana Mirkov,
Ramamoorthy Nagasubramanian,
Jacqueline Ramírez,
Wanqing Liu,
Wasim K Bleibel,
Sunita J Shukla,
Kathleen Hennessy,
Gary L Rosner, Edwin Cook,
M Eileen Dolan,
Mark J Ratain
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ABSTRACT: Werner's syndrome (WS) is a recessive disorder of premature onset of processes associated with aging. Defective DNA repair has been reported after exposure of cells isolated from WS patients to DNA-damaging agents. The germline 4330T>C (Cys1367Arg) variant in the WS gene (WRN) has been associated with protection from age-related diseases, suggesting it has a functional role. We studied whether the 4330T>C variant confers altered drug sensitivity in vitro.
4330T>C was genotyped in 372 human lymphoblastoid cell lines (LCLs) from unrelated healthy Caucasian individuals using a TaqMan-based method. The study was powered to detect the effect of the 4330T>C genotypes after exposure to camptothecin (based upon preliminary data). The effect of the 4330T>C variant on the cytotoxicity of etoposide, carboplatin, cisplatin and daunorubicin was also tested. WRN expression in 57 LCLs was measured by microarray.
No significant difference between the IC50 of the cells was observed among genotypes (P = 0.46) after exposure to camptothecin. No association was also observed for etoposide, carboplatin, cisplatin, and daunorubicin (ANOVA, P > 0.05). WRN expression also did not vary across genotypes (ANOVA, P = 0.37).
These results suggest that this nonsynonymous variant has relatively normal function at the cellular level.
Cancer Chemotherapy and Pharmacology 08/2008; 63(5):881-7. · 2.83 Impact Factor
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Christa Lese Martin,
Jacqueline A Duvall,
Yesim Ilkin,
Jason S Simon,
M Gladys Arreaza,
Kristin Wilkes,
Ana Alvarez-Retuerto,
Amy Whichello,
Cynthia M Powell,
Kathleen Rao, Edwin Cook,
Daniel H Geschwind
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ABSTRACT: Cytogenetic imbalances are increasingly being realized as causes of autism. Here, we report a de novo translocation between the short arms of chromosomes 15 and 16 in a female with autism, epilepsy, and global developmental delay. FISH analysis identified a cryptic deletion of approximately 160 kb at the boundary of the first exon and first intron of the 1.7 Mb ataxin-2 binding protein-1 (A2BP1) gene, also called FOX1. Quantitative real time PCR (Q-PCR) analysis verified a deletion of exon 1 in the 5' promoter region of the A2BP1 gene. Reverse transcription PCR (qRT-PCR) showed reduced mRNA expression in the individual's lymphocytes, demonstrating the functional consequence of the deletion. A2BP1 codes for a brain-expressed RNA binding or splicing factor. Because of emerging evidence in the role of RNA processing and gene regulation in pervasive developmental disorders, we performed further screening of A2BP1 in additional individuals with autism from the Autism Genetics Resource Exchange (AGRE) collection. Twenty-seven SNPs were genotyped across A2BP1 in 206 parent-child trios and two regions showed association at P < or = 0.008 level. No additional deletions or clear mutations were identified in 88 probands by re-sequencing of all exons and surrounding intronic regions or quantitative PCR (Q-PCR) of exon 1. Although only nominal association was observed, and no obvious causal mutations were identified, these results suggest that A2BP1 may affect susceptibility or cause autism in a subset of patients. Further investigations in a larger sample may provide additional information regarding the involvement of this gene in the autistic phenotype.
American Journal of Medical Genetics Part B Neuropsychiatric Genetics 10/2007; 144B(7):869-76. · 3.70 Impact Factor
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Elizabeth Berry-Kravis,
Sue Ellen Krause,
Sandra S Block,
Steve Guter,
Joanne Wuu,
Sue Leurgans,
Penelope Decle,
Kristina Potanos, Edwin Cook,
Jeff Salt,
Dominick Maino,
Dahlia Weinberg,
Rebecca Lara,
Tristan Jardini,
Jennifer Cogswell,
Steven A Johnson,
Randi Hagerman
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ABSTRACT: A Phase II, 4-week randomized, double-blind, placebo-controlled clinical trial was conducted to evaluate the safety and efficacy of the Ampakine compound CX516 as a potential treatment for the underlying disorder in fragile X syndrome (FXS). After baseline screening, subjects with FXS (n = 49) underwent a 1-week placebo lead-in and then were randomized to study drug or placebo for a 4-week period. Cognitive and behavioral outcome measures were administered prior to treatment, at the end of treatment, and 2 weeks posttreatment. There were minimal side effects, no significant changes in safety parameters, and no serious adverse events. There was a 12.5% frequency of allergic rash in the CX516 group and 1 subject developed a substantial rash. There was also no significant improvement in memory, the primary outcome measure, or in secondary measures of language, attention/executive function, behavior, and overall functioning in CX516-treated subjects compared to placebo. This study did demonstrate that many outcome measures were reproducible in this test-retest setting for the FXS population, yet some were too difficult or variable. Adult subjects with FXS were able to complete an intensive clinical trial, and some valid outcome measures were identified for future FXS trial design. Problems with potency of CX516 in other studies have suggested dosing may have been inadequate for therapeutic effect and thus it remains unclear whether modulation of AMPA-mediated neurotransmission is a viable therapeutic strategy for the treatment of FXS.
Journal of Child and Adolescent Psychopharmacology 11/2006; 16(5):525-40. · 2.88 Impact Factor
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ABSTRACT: Long-term antidepressant drug exposure may regulate its target molecule - the serotonin transporter (SERT). This effect could be related to an individual's genotype for an SERT promoter polymorphism (human serotonin transporter coding [5-HTTLPR]). We aimed to determine the effects of fluoxetine exposure on human platelet SERT levels.
We harvested platelet samples from 21 healthy control subjects. The platelets were maintained alive ex vivo for 24 hours while being treated with 0.1 muM fluoxetine or vehicle. The effects on SERT immunoreactivity (IR) were then compared. Each individual's SERT promoter genotype was also determined to evaluate whether fluoxetine effects on SERT were related to genotype.
Fluoxetine exposure replicably altered SERT IR within individuals. Both the magnitude and the direction of effect were related to a person's SERT genotype. People who were homozygous for the short gene (SS) displayed decreased SERT IR, whereas those who were homozygous for the long gene (LL) demonstrated increased SERT IR. A mechanistic experiment suggested that some individuals with the LL genotype might experience increased conversion of complexed SERT to primary SERT during treatment.
These preliminary results suggest that antidepressant effects after longer-term use may include changes in SERT expression levels and that the type and degree of effect may be related to the 5-HTTLPR polymorphism.
Journal of psychiatry & neuroscience: JPN 10/2006; 31(5):333-9. · 5.34 Impact Factor
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ABSTRACT: The dopamine (DA) system has been implicated in attention deficit hyperactivity disorder (ADHD) based on pharmacologic evidence. Because of an interaction between the serotonin (5-HT) and DA systems, the serotonin transporter gene (SLC6A4) has been considered as a candidate ADHD susceptibility gene. Two common polymorphisms, 5-HTTLPR and the intron 2 VNTR, have been studied for association in ADHD, with both positive (increased frequency of long allele of 5-HTTLPR and decreased frequency of 12 repeats of the intron 2 VNTR) and negative findings. However, there has not been an association study in an East Asian ADHD population. In this study, we examined the genotypes of these two polymorphisms in 126 Korean ADHD families and investigated linkage disequilibrium (LD) between SLC6A4 and ADHD, using the transmission disequilibrium test (TDT) and haplotype analysis. Additionally, association with quantitative measures of inattention, hyperactivity-impulsivity, and overall severity was tested using logistic regression and QTDT analysis. TDT of both polymorphisms and haplotype analysis failed to detect LD. However, after excluding ADHD NOS subtype, TDT revealed nominally significant LD between 5-HTTLPR and ADHD (chi2 = 4.9, P = 0.036). QTDT revealed positive association between 12 repeats of the intron 2 VNTR and attention (P = 0.031), but case-control and TDT logistic regression analyses were negative. These markers have low heterozygosity in the Korean population, which would be expected to reduce the power of association. This result suggests that future studies should include more polymorphic markers and subjects to thoroughly investigate a potential association between SLC6A4 and ADHD in the Korean population.
American Journal of Medical Genetics Part B Neuropsychiatric Genetics 12/2005; 139B(1):14-8. · 3.70 Impact Factor
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Michael B Sawyer,
Federico Innocenti,
Soma Das,
Cheng Cheng,
Jacqueline Ramírez,
Friedl H Pantle-Fisher,
Constance Wright,
Judith Badner,
Deqing Pei,
James M Boyett, Edwin Cook,
Mark J Ratain
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ABSTRACT: We investigated the variation in the uridine diphosphate-glucuronosyltransferase 2B7 (UGT2B7) gene in patients receiving patient-controlled analgesia with morphine. UGT2B7 was sequenced in phenotypic extremes (n = 12) of the distribution of morphine-6-glucuronide/morphine plasma ratios. A new -161C/T promoter variant was in complete linkage disequilibrium with the 802C/T variant and was more frequent in low glucuronidators (P =.039). Both variants were genotyped in all patients (n = 86), and complete linkage disequilibrium was confirmed. Trend analysis showed reduced morphine-6-glucuronide/morphine ratios in patients with T/T, C/T, and C/C genotypes (T/T > C/T > C/C) (P =.031). Morphine levels were lower in T/T patients (median, 18 ng/mL [range, 18-1490 ng/mL]) as compared with C/T and C/C patients combined (median, 66 ng/m; range, 18-3995 ng/mL) (P =.04). Morphine-6-glucuronide and morphine-3-glucuronide concentrations were significantly lower in C/C patients (median, 18 ng/mL; range, 0-66 ng/mL; and median, 152 ng/mL; range, 30-434 ng/mL; respectively) compared with C/T and T/T patients combined (median, 43 ng/mL; range, 0-193 ng/mL; and median, 242 ng/mL; range, 33-1381 ng/mL; respectively) (P =.045 and P =.004, respectively). Interindividual differences in morphine glucuronidation may be the result of genetic variation in UGT2B7, and further studies are indicated.
Clinical Pharmacology & Therapeutics 06/2003; 73(6):566-74. · 6.04 Impact Factor
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ABSTRACT: Recent research suggests that in utero exposure to maternal smoking is a risk factor for conduct disorder and delinquency. We review evidence of causality, a controversial but important public health question.
We analyzed studies of maternal prenatal smoking and offspring antisocial behavior within a causal framework.
The association is (1) independent of confounders, (2) present across diverse contexts, and (3) consistent with basic science. Methodological limitations of existing studies preclude causal conclusions.
Existing evidence provides consistent support for, but not proof of, an etiologic role for prenatal smoking in the onset of antisocial behavior. The possibility of identifying a preventable prenatal risk factor for a serious mental disorder makes further research on this topic important for public health.
American Journal of Public Health 07/2002; 92(6):966-74. · 3.93 Impact Factor
