An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as risk factors for autistic disorder.

Gene-gene interactions are likely involved in many complex genetic disorders and new statistical approaches for detecting such interactions are needed. We propose a multi-analytic paradigm, relying on convergence of evidence across multiple analysis tools. Our paradigm tests for main and interactive effects, through allele, genotype and haplotype association. We applied our paradigm to genotype data from three GABAA receptor subunit genes (GABRB3, GABRA5, and GABRG3) on chromosome 15 in 470 Caucasian autism families. Previously implicated in autism, we hypothesized these genes interact to contribute to risk. We detected no evidence of main effects by allelic (PDT, FBAT) or genotypic (genotype-PDT) association at individual markers. However, three two-marker haplotypes in GABRG3 were significant (HBAT). We detected no significant multi-locus associations using genotype-PDT analysis or the EMDR data reduction program. However, consistent with the haplotype findings, the best single locus EMDR model selected a GABRG3 marker. Further, the best pairwise genotype-PDT result involved GABRB3 and GABRG3, and all multi-locus EMDR models also selected GABRB3 and GABRG3 markers. GABA receptor subunit genes do not significantly interact to contribute to autism risk in our overall data set. However, the consistency of results across analyses suggests that we have defined a useful framework for evaluating gene-gene interactions.

Identification of significant association and gene-gene interaction of GABA receptor subunit genes in autism.

Autism is a common neurodevelopmental disorder with a significant genetic component. Existing research suggests that multiple genes contribute to autism and that epigenetic effects or gene-gene interactions are likely contributors to autism risk. However, these effects have not yet been identified. Gamma-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the adult brain, has been implicated in autism etiology. Fourteen known autosomal GABA receptor subunit genes were studied to look for the genes associated with autism and their possible interactions. Single-nucleotide polymorphisms (SNPs) were screened in the following genes: GABRG1, GABRA2, GABRA4, and GABRB1 on chromosome 4p12; GABRB2, GABRA6, GABRA1, GABRG2, and GABRP on 5q34-q35.1; GABRR1 and GABRR2 on 6q15; and GABRA5, GABRB3, and GABRG3 on 15q12. Intronic and/or silent mutation SNPs within each gene were analyzed in 470 white families with autism. Initially, SNPs were used in a family-based study for allelic association analysis--with the pedigree disequilibrium test and the family-based association test--and for genotypic and haplotypic association analysis--with the genotype-pedigree disequilibrium test (geno-PDT), the association in the presence of linkage (APL) test, and the haplotype family-based association test. Next, with the use of five refined independent marker sets, extended multifactor-dimensionality reduction (EMDR) analysis was employed to identify the models with locus joint effects, and interaction was further verified by conditional logistic regression. Significant allelic association was found for markers RS1912960 (in GABRA4; P = .01) and HCV9866022 (in GABRR2; P = .04). The geno-PDT found significant genotypic association for HCV8262334 (in GABRA2), RS1912960 and RS2280073 (in GABRA4), and RS2617503 and RS12187676 (in GABRB2). Consistent with the allelic and genotypic association results, EMDR confirmed the main effect at RS1912960 (in GABRA4). EMDR also identified a significant two-locus gene-gene effect model involving RS1912960 in GABRA4 and RS2351299 in GABRB1. Further support for this two-locus model came from both the multilocus geno-PDT and the APL test, which indicated a common genotype and haplotype combination positively associated with disease. Finally, these results were also consistent with the results from the conditional logistic regression, which confirmed the interaction between GABRA4 and GABRB1 (odds ratio = 2.9 for interaction term; P = .002). Through the convergence of all analyses, we conclude that GABRA4 is involved in the etiology of autism and potentially increases autism risk through interaction with GABRB1. These results support the hypothesis that GABA receptor subunit genes are involved in autism, most likely via complex gene-gene interactions.

Ordered-subset analysis of savant skills in autism for 15q11-q13.

Autism is a complex disorder characterized by genetic and phenotypic heterogeneity. Analysis of phenotypically homogeneous subtypes has been used to both confirm and narrow potential autism linkage regions such as the chromosomal region 15q11-q13. Increased evidence for linkage in this region had been found in a subgroup of 21 autism families (total families = 94) stratified based on a savant skill factor (SSF) from the Autism Diagnostic Interview, Revised (ADI-R). We examined the savant phenotypic finding in our sample of 91 multiplex autism families. Using two-point parametric analysis in stratification with a cutoff point of a savant skill score of 0.16, our families failed to demonstrate linkage to 15q11-q13. In addition, ordered subset analysis (OSA) using SSF as a covariate also failed to show evidence for linkage. Our findings do not support savant skills as an informative phenotypic subset for linkage in our sample.

Analysis of the RELN gene as a genetic risk factor for autism.

Several genome-wide screens have indicated the presence of an autism susceptibility locus within the distal long arm of chromosome 7 (7q). Mapping at 7q22 within this region is the candidate gene reelin (RELN). RELN encodes a signaling protein that plays a pivotal role in the migration of several neuronal cell types and in the development of neural connections. Given these neurodevelopmental functions, recent reports that RELN influences genetic risk for autism are of significant interest. The total data set consists of 218 Caucasian families collected by our group, 85 Caucasian families collected by AGRE, and 68 Caucasian families collected at Tufts University were tested for genetic association of RELN variants to autism. Markers included five single-nucleotide polymorphisms (SNPs) and a repeat in the 5'-untranslated region (5'-UTR). Tests for association in Duke and AGRE families were also performed on four additional SNPs in the genes PSMC2 and ORC5L, which flank RELN. Family-based association analyses (PDT, Geno-PDT, and FBAT) were used to test for association of single-locus markers and multilocus haplotypes with autism. The most significant association identified from this combined data set was for the 5'-UTR repeat (PDT P-value=0.002). These analyses show the potential of RELN as an important contributor to genetic risk in autism.

No association between the APOE gene and autism.

Autism is a neurodevelopmental disorder characterized by stereotypic and repetitive behavior and interests, together with social and communicative deficiencies. The results of several genomic screens suggest the presence of an autism susceptibility locus on chromosome 19p13.2-q13.4. The apolipoprotein E (APOE) gene on chromosome 19 encodes for a protein, apoE, whose different isoforms (E2, E3, E4) influence neuronal growth. APOE participates in lipid transport and metabolism, repair, growth, and maintenance of axons and myelin during neuronal development. The APOE protein competes with the Reelin protein for VLDL/APOER2 receptor binding. Several studies have reported evidence for an association between autism and the Reelin gene. Based on these data we tested for association between APOE and autism using family-based association methods in a data set of 322 autism families. Three promoter, one intronic, and one 3' UTR single nucleotide polymorphisms (SNPs) in the APOE gene (-491a/t, -427c/t, -219g/t, 113c/g, and 5361c/t) as well as the APOE functional polymorphism (E2, E3, E4) were examined and failed to reveal significant evidence that autism is associated with APOE.

Fine mapping of autistic disorder to chromosome 15q11-q13 by use of phenotypic subtypes.

Autistic disorder (AutD) is a complex genetic disease. Available evidence suggests that several genes contribute to the underlying genetic risk for the development of AutD. However, both etiologic heterogeneity and genetic heterogeneity confound the discovery of AutD-susceptibility genes. Chromosome 15q11-q13 has been identified as a strong candidate region on the basis of both the frequent occurrence of chromosomal abnormalities in that region and numerous suggestive linkage and association findings. Ordered-subset analysis (OSA) is a novel statistical method to identify a homogeneous subset of families that contribute to overall linkage at a given chromosomal location and thus to potentially help in the fine mapping and localization of the susceptibility gene within a chromosomal area. For the present analysis, a factor that represents insistence on sameness (IS)--derived from a principal-component factor analysis using data on 221 patients with AutD from the repetitive behaviors/stereotyped patterns domain in the Autism Diagnostic Interview-Revised--was used as a covariate in OSA. Analysis of families sharing high scores on the IS factor increased linkage evidence for the 15q11-q13 region, at the GABRB3 locus, from a LOD score of 1.45 to a LOD score of 4.71. These results narrow our region of interest on chromosome 15 to an area surrounding the gamma-aminobutyric acid-receptor subunit genes, in AutD, and support the hypothesis that the analysis of phenotypic homogeneous subtypes may be a powerful tool for the mapping of disease-susceptibility genes in complex traits.

Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder.

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain, acting via the GABAA receptors. The GABAA receptors are comprised of several different homologous subunits, forming a group of receptors that are both structurally and functionally diverse. Three of the GABAA receptor subunit genes (GABRB3, GABRA5 and GABRG3) form a cluster on chromosome 15q11-q13, in a region that has been genetically associated with autistic disorder (AutD). Based on these data, we examined 16 single nucleotide polymorphisms (SNPs) located within GABRB3, GABRA5 and GABRG3 for linkage disequilibrium (LD) in 226 AutD families (AutD patients and parents). Genotyping was performed using either OLA (oligonucleotide ligation assay), or SSCP (single strand conformation polymorphism) followed by DNA sequencing. We tested for LD using the Pedigree Disequilibrium Test (PDT). PDT results gave significant evidence that AutD is associated with two SNPs located within the GABRG3 gene (exon5_539T/C, p=0.02 and intron5_687T/C, p=0.03), suggesting that the GABRG3 gene or a gene nearby contributes to genetic risk in AutD.

Genetic studies in autistic disorder and chromosome 15.

Autistic disorder (AD) is a developmental disorder affecting social interactions, communication, and behavior. AD is a disease of complex genetic architecture. It is postulated that several genes contribute to the underlying etiology of AD. Chromosome 15 is of particular interest due to numerous reports of AD in the presence of chromosomal abnormalities, located mainly in the 15q11-q13 region. There are also a number of plausible candidate genes in this area, including the gamma-aminobutyric acidA (GABA(A)) receptor gene complex. We have undertaken a study of this region of chromosome 15 in a data set of 63 multiplex families (with 2 or more AD affected individuals per family). We found evidence in support of linkage to the 15q11-q13 region, as well as evidence of increased recombination in this region. These findings provide further support for the involvement of chromosome 15q11-q13 in the genetic etiology of AD.

Three children with a syndrome of obesity and overgrowth, atypical psychosis, and seizures: a problem in neuropsychopharmacology.

Three children presented with a complex syndrome of atypical psychotic and extremely immature behavior, obesity and overgrowth, borderline retardation, and seizures (prominent in two). Weight overgrowth exceeded height overgrowth and was stratospheric (up to 8 SD above mean). Obesity seemed related to lack of satiety. The cases fit no known condition: hypothalamic damage, Sotos' syndrome, and Prader-Willi syndrome were excluded. Empirical treatment with anticonvulsants (carbamazepine and acetazolamide) together with psychotropic agents (selective serotonin reuptake inhibitors and risperidone) controlled seizures, improved behavior, and stopped weight gain in each patient. We have not found this syndrome previously described. The etiology is unknown: perinatal encephalopathy could be a factor in the two patients with prominent seizures; in the third, familial major affective disorder is implicated. Medication responses suggest a low-serotonin state underlying the lack of satiety, an imbalance of serotonin and noradrenergic modulation in the hypothalamus, and epileptogenic disorders (or affective disorder responsive to anticonvulsants in one case) involving these same systems.

Female with autistic disorder and monosomy X (Turner syndrome): parent-of-origin effect of the X chromosome.

We have ascertained and examined a patient with autistic disorder (AD) and monosomy X (Turner syndrome). The patient met Diagnostic and Statistical Manual of Mental Disorders (DSM-IV)/International Classification of Diseases (ICD-10) criteria for AD verified by the Autism Diagnostic Interview-Revised. The patient exhibited both social and verbal deficits and manifested the classical physical features associated with monosomy X. Skuse et al. [1997: Nature 387:705-708] reported three such cases of AD and monosomy X in their study of Turner syndrome and social cognition. They observed that monosomy X females with a maternally inherited X chromosome had reduced social cognition when compared with monosomy X females with a paternally inherited X chromosome. All three cases of AD and monosomy X were maternally inherited. Based on their data, they suggested that there was a gene for social cognition on the X chromosome that is imprinted and not expressed when the X chromosome is of maternal origin. Thus, we conducted parent-of-origin studies in our AD/monosomy X patient by genotyping X chromosome markers in the patient and her family. We found that the patient's X chromosome was of maternal origin. These findings represent the fourth documented case of maternal inheritance of AD and monosomy X and provide further support for the hypothesis that parent-of-origin of the X chromosome influences social cognition.

Analysis of linkage disequilibrium in gamma-aminobutyric acid receptor subunit genes in autistic disorder.

Autistic disorder (AD) is a neurodevelopmental disorder characterized by abnormalities in behavior, communication, and social interactions and functioning. Recently, Cook et al. reported significant linkage disequilibrium with an AD susceptibility locus and a marker, GABRB3 155CA-2, in the gamma-aminobutyric acid(A) (GABA(A)) receptor beta3-subunit gene on chromosome 15q11-q13. This linkage disequilibrium was detected using a multiallelic version of the transmission/disequilibrium test (TDT) in a sample of nuclear families having at least one child with autistic disorder. In an attempt to replicate this finding we tested for linkage disequilibrium with this marker, as well as with three additional markers in and around the GABA(A) receptor beta3-subunit gene, in an independent, clinically comparable set of AD families. Unlike Cook et al., we failed to detect significant linkage disequilibrium between GABRB3 155CA-2 and AD in our sample. We did, however, find suggestive evidence for linkage disequilibrium with a marker, GABRB3, approximately 60 kb beyond the 3' end of beta3-subunit gene. This finding lends support for previous reports implicating the involvement of genes in this region with AD. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:43-48, 2000

Genetic studies of autistic disorder and chromosome 7.

Genome-wide scans have suggested that a locus on 7q is involved in the etiology of autistic disorder (AD). We have identified an AD family in which three sibs inherited from their mother a paracentric inversion in the chromosome 7 candidate region (inv(7)(q22-q31.2)). Clinically, the two male sibs have AD, while the female sib has expressive language disorder. The mother carries the inversion, but does not express AD. Haplotype data on the family suggest that the chromosomal origin of the inversion was from the children's maternal grandfather. Based on these data, we have genotyped 76 multiplex (>/=2 AD affecteds/family) families for markers in this region of 7q. Two-point linkage analysis yielded a maximum heterogeneity lod score of 1.47 and maximum lod score (MLS) of 1.03 at D7S495. Multipoint MLS and NPL analyses resulted in peak scores of 1.77 at D7S2527 and 2.01 at D7S640. Examination of affected sibpairs revealed significant paternal (P = 0.007), but not maternal (P = 0. 75), identity-by-descent sharing at D7S640. Significant linkage disequilibrium was detected with paternal (P = 0.02), but not maternal (P = 0.15), transmissions at D7S1824 in multiplex and singleton families. There was also evidence for an increase in recombination in the region (D7S1817 to D7S1824) in the AD families versus non-AD families (P = 0.03, sex-averaged; and P = 0.01, sex-specific). These results provide further evidence for the presence of an AD locus on chromosome 7q, as well as provide evidence suggesting that this locus may be paternally expressed.

Effects of fluoxetine treatment in young children with idiopathic autism.

Thirty-seven children, aged between 2 and 7 years, with idiopathic autism underwent an open-label trial of fluoxetine treatment. All had assessment of diagnosis, developmental status, and family psychiatric history. Independent developmental testing before and after starting fluoxetine permitted quantification of language acquisition in a subgroup. Twenty-two of the 37 children had a beneficial treatment response sustained during continuing treatment for 13 to 33 months (mean 21 months). Eleven had an excellent response and were able to attend mainstream classrooms. Eleven had a good response though they remained identifiably autistic. Fifteen children had no benefit. Responders showed behavioral, language, cognitive, affective, and social improvements. Responders with adequate testing showed marked increases in language acquisition at every stage of development as compared with (1) pretreatment status, (2) responses to other treatments, (3) ability in non-language (matching) tasks, and (4) historical controls from the literature. The response to fluoxetine strongly correlated with a family history of major affective disorder. These preliminary findings implicate serotonergic mechanisms in autistic symptomatology and warrant further study with controlled trials.

Effect on infant mortality of iodination of irrigation water in a severely iodine-deficient area of China.

BACKGROUND: Hotien county in Xinjiang province, China, is an area of severe iodine deficiency and has a high infantmortality rate. We investigated whether iodine replacement through iodination of the irrigation water would decrease infant mortality. METHODS: We added potassium iodate to irrigation water over a 2 to 4 week period beginning in 1992 in certain areas of three townships (Tusala, Long Ru, and Bakechi). Logistic regression analysis was used to compare the odds ratios for infant and neonatal mortality in treated and intreated areas. FINDINGS: The median urinary iodine concentration significantly increased in women of child-bearing age from < 10 micrograms/L to 55 micrograms/L. Infant-mortality rates decreased in the treated areas of Long Ru (mean [SD] 58.2 [4.4] per 1000 births to 28.7 [7.1] per 1000 births), Tusala (47.4 [12.4] per 1000 births to 19.1 [1.5] per 1000 births), and Bakechi (106.2 [9.5] per 1000 births to 57.3 [7.3] per 1000 births). Similar results were also seen for neonatal mortality. On regression analysis iodine treatment and time were significant independent predictors of infant mortality. INTERPRETATION: Iodine supplementation of irrigation water in areas of severe iodine deficiency decreases neonatal and infant mortality. Iodine replacement has probably been an important factor in the national decrease in infant mortality in China.

PIP: Hotien county in Xinjiang province is an area of severe iodine deficiency which also has a high infant mortality rate (IMR). The authors investigated whether iodine replacement through iodination of irrigation water would decrease the level of infant mortality. Potassium iodine was added to irrigation water over a 2-4 week period beginning in 1992 in certain areas of Long Ru, Tusala, and Bakechi. The median urinary iodine concentration significantly increased in women of child-bearing age from less than 10 mg/l to 55 mg/l, while IMR decreased in Long Ru from a mean of 58.2/1000 births to 28.7/1000, in Tusala from 47.4/1000 to 19.1/1000, and in Bakechi from 106.2/1000 to 57.3/1000. Similar results were also observed for neonatal mortality. Iodine treatment and time were significant independent predictors of infant mortality.

The clinical syndrome of early-life bilateral hippocampal sclerosis.

Four infants had bilateral hippocampal sclerosis by magnetic resonance scans, including oblique coronal fast spin echo images of the temporal lobes; [18F]fluorodeoxyglucose-positron emission tomographic scans, done in 2 infants, showed isolated bilateral anterior temporal lobe hypometabolism. All had epilepsy with episodes of status epilepticus. Despite adequate motor and sensory functions, all failed to develop language (or lost attained language), social skills, and complex purposive or adaptive activity, even after epilepsy was controlled. Bilateral hippocampal dysfunction in early life appears to be associated with a profound failure of cognitive capacities, including language learning and learning of complex social and adaptive skills in general. The deficits correspond to the cognitive deficits of severe infantile autism. Hippocampal function, or more generally medial temporal lobe function, appears necessary for language learning in the infant, as well as for complex social and adaptive learning.

Dynamics of environmental supplementation of iodine: four years' experience of iodination of irrigation water in Hotien, Xinjiang, China.

Hotien prefecture, Xinjiang Province, China, in the Taklamakan Desert, is an area of severe iodine deficiency. Because usual methods of iodine supplementation failed here, we began supplementation in 1992 with potassium iodate, which was added to irrigation water (Lancet 1994; 334:107-110). We report 4 y experience with this method in 3 townships that contained a total treated population of 37,000. Potassium iodate was dripped into irrigation water (to a concentration 10-80 microg/l) during a 2- to 4-wk period. During the 3 y that followed, no further supplementation was made, and iodine concentrations increased several fold in crops and plants, sheep and chicken thyroid glands, and meat and in urine of children 2-6 y of age and of women who were of childbearing age. Infant mortality decreased 50%, and sheep production increased 43%. Iodine repletion of soil through irrigation water is an effective and cost-efficient way of providing iodine in appropriate situations.

Intracranial fibromuscular dysplasia in a 5-year-old child.

A 5-year-old girl presenting with acute middle cerebral artery stroke was diagnosed as having intracranial fibromuscular dysplasia by angiographic findings of focal changes in the proximal right middle cerebral artery and pathological dilatation of the right internal carotid artery at the base of the skull, as well as dissection of at least one of the middle cerebral artery branches and nonfilling of two or perhaps three remaining middle cerebral artery segmental branches. Her clinical condition improved after management of the increased intracranial pressure. She did not receive any medication after discharge and had virtually no residual sequelae. Our case documents an unusual location and age of onset of a patient with fibromuscular dysplasia.