Association of PIP5K2A with schizophrenia A study in an indonesian family sample.код для вставкиСкачать
American Journal of Medical Genetics Part B (Neuropsychiatric Genetics) 147B:1310 –1313 (2008) Brief Research Communication Association of PIP5K2A With Schizophrenia: A Study in an Indonesian Family Sample L. Saggers-Gray,1,2 H. Heriani,3 H.Y. Handoko,4 I. Irmansyah,3 A.A.A.A. Kusumawardhani,3 I. Widyawati,3 N. Amir,3 M.W.S. Nasrun,3 S.G. Schwab,1,2,5* and D.B. Wildenauer2,6 1 Western Australian Institute for Medical Research, Centre for Medical Research, University of Western Australia, Perth, Western Australia, Australia 2 School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, Western Australia, Australia 3 Department of Psychiatry, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia 4 Queensland Institute for Medical Research, Brisbane, Australia 5 School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia 6 Centre for Clinical Research in Neuropsychiatry, Graylands Hospital, Mt Claremont, Western Australia, Australia PIP5K2A variants have been shown to be associated with schizophrenia in Caucasian populations. This study tested 12 PIP5K2A SNPs for association with schizophrenia in a sample of 152 sib-pair families of Indonesian descent. All SNPs had previously been tested for association with schizophrenia in a German family sample by Schwab et al. [2006; Mol Psychiatry] and seven SNPs were nominally associated with schizophrenia in this previous study. The purpose of the study was to examine whether previously implicated PIP5K2A variants influence susceptibility to schizophrenia in populations of non-European descent. No single markers showed nominal association with schizophrenia in this Indonesian family sample, however multi-marker haplotypes including a previously associated exonic SNP marker revealed nominally significant association (P ¼ 0.03). Power to detect association was greater than 80% for all previously implicated variants except for rs11013052, where power was greatly reduced due to the low minor allele frequency of this marker in the Indonesian sample. An explorative study combining the results of this study with those of our previous study indicated that rs11013052 was significantly associated with schizophrenia in the combined sample (P ¼ 0.002). The results of this study suggest that any contribution of previously implicated DNA variants within the PIP5K2A gene to schizophrenia susceptibility in the Indonesian population is only minor. ß 2008 Wiley-Liss, Inc. KEY WORDS: schizophrenia; PIP5K2A; association; Indonesia; genetic heterogeneity Please cite this article as follows: Saggers-Gray L, Heriani H, Handoko HY, Irmansyah I, Kusumaward- Grant sponsor: NHMRC; Grant number: 404012. *Correspondence to: Dr. S.G. Schwab, SCGH QEII, B-Block Ground Floor, Hospital Avenue, 6009, Western Australia, WA 6009, Australia. E-mail: email@example.com Received 28 October 2007; Accepted 23 January 2008 DOI 10.1002/ajmg.b.30736 Published online 3 March 2008 in Wiley InterScience (www.interscience.wiley.com) ß 2008 Wiley-Liss, Inc. hani AAAA, Widyawati I, Amir N, Nasrun MWS, Schwab SG, Wildenauer DB. 2008. Association of PIP5K2A With Schizophrenia: A Study in an Indonesian Family Sample. Am J Med Genet Part B 147B:1310–1313. The phosphatidylinositol-4-phosphate-5-kinase type IIa (PIP5K2A) gene has been proposed as a putative susceptibility gene for schizophrenia and bipolar disorder on both positional and functional grounds. The gene maps to chromosome 10p (10p12), a replicated linkage region for both disorders [Rice et al., 1997; Faraone et al., 1998; Schwab et al., 1998; Straub et al., 1998; Foroud et al., 2000; Levinson et al., 2000; DeLisi et al., 2002; Holliday et al., 2005]. The PIP5K2A enzyme catalyses the phosphorylation of phosphatidylinositol-5-phosphate on the D-4 position of the inositol ring to form phosphatidylinositol-4,5-bisphosphate, an important phosphoinositide signaling molecule [Rameh et al., 1997]. Attenuation of phosphoinositide signaling has been proposed as a mode of action for the mood stabilizing drugs lithium, valproic acid, and carbamazepine, therefore the PIP5K2A gene has been implicated as a functional candidate for both disorders [Hallcher and Sherman, 1980; Wolfson et al., 2000; Shaltiel et al., 2004]. DNA sequence variants within the PIP5K2A gene have previously been shown to be associated with schizophrenia in two samples of Caucasian origin. Schwab et al. examined 54 variants in the vicinity of the PIP5K2A gene in a sample of 65 families. Four variants were significantly associated with schizophrenia at an experiment wide level including a coding SNP (rs10828317), located in exon 7 of the gene. This SNP causes a non-synonymous amino-acid exchange (N ! S) in the PIP5K2A protein [Schwab et al., 2006]. This association between rs10828317 and schizophrenia has been replicated by Bakker et al.  in a Dutch sample [Bakker et al., 2006]. While association of the SNP rs10828317 with schizophrenia has been replicated in independent samples, the evidence for association is not as strong for other SNPs within the PIP5K2A gene [Bakker et al., 2006; Schwab et al., 2006]. Studies by Abou Jamra et al.  and Stopkova et al. [2003, 2005] were unable to detect a significant association between PIP5K2A polymorphisms and schizophrenia or bipolar disorder [Stopkova et al., 2003, 2005; Abou Jamra et al., 2006]. All of the studies investigating the association of PIP5K2A variants with schizophrenia have been conducted in populations of European descent. Genetic heterogeneity may play a role in the non-replication of linkage and association findings in psychiatric disorders. As such, it is unclear whether the association between PIP5K2A variants and schizophrenia in European populations will also be detected in populations of Association of PIP5K2A With Schizophrenia different ethnicity. This report describes a family based association study that was conducted in a sample of 152 Indonesian sib-pair families. The purpose of this study was to investigate whether variation at the PIP5K2A locus is associated with schizophrenia in a population of non-European descent. The Indonesian sib-pair family sample comprised 687 individuals from 152 families. The sample size was reduced to 612 individuals from 126 families following the exclusion of 75 individuals. These DNA samples were excluded primarily on the basis of preliminary results from a genome-wide scan using the same family sample, which indicated Mendelian errors in some families, or DNA of insufficient quantity or quality for the genotyping procedure. All individuals were interviewed using Psychosis Screen (PS), Diagnostic Interview for Psychosis (DIP) [Jablensky et al., 2000], Psychiatric and Personal History Schedule (PPHS) [WHO, 1996], and Family Interview for Genetic Studies (FIGS) [Maxwell, 1992]. Consensus diagnosis of schizophrenia was established by independent psychiatrists based on DSM-IV and ICD-10 criteria. Written informed consent was obtained from all participants. This research was approved by the local Human Research Ethics Committees. Twelve SNPs from within the PIP5K2A gene and the surrounding regions were selected for examination of association with schizophrenia. All SNPs had previously been studied for association with schizophrenia in a sample of 65 families by Schwab et al. . Seven of these SNPs were associated with schizophrenia in our previous study (rs1417374, rs11013052, rs943190, rs10828317, rs10430590, rs746203, and rs8341). Individuals were genotyped for the 12 markers using either the Amplifluor1 SNPs Genotyping System or a TaqMan1 Validated SNP Genotyping Assay (Applied Biosystems, Foster City, CA), as described by us previously [Morar et al., 2007]. Departure from Hardy–Weinberg equilibrium in the parental generation was assessed using a w2 test (1 d.f.). P-values for association of single markers and two- and three-marker haplotypes with schizophrenia were calculated using FAMHAP 15 with the ‘‘zhao’’ option. Under this option the program performs a haplotypes TDT-like test for association which is valid for families containing multiple offspring, even in the presence of linkage. Monte Carlo simulations are used to produce an overall corrected P-value for the global null 1311 hypothesis of no association in the presence of linkage [Zhao et al., 2000; Knapp and Becker, 2003; Becker and Knapp, 2004a,b]. Genotyping completeness was >98% for all markers except rs943194 (97.4%) and rs8341 (95.1%). Genotyping completeness was lowest for the one marker genotyped using the TaqMan1 method. No deviation from Hardy–Weinberg equilibrium was detected for any of the markers in the parental generation. Single markers were not associated with schizophrenia (P < 0.05). Transmitted/non-transmitted ratios and P-values for association with schizophrenia for all markers are shown in Table I. rs1171506 and rs11013052 had high transmitted/non-transmitted ratios (13/6 and 10/3, respectively), but low minor allele frequencies (<4.5%), which resulted in reduced power to detect association. All possible two- and three-marker haplotype combinations were calculated and tested for association with schizophrenia. Seven haplotypes produced nominally significant P-values (0.047–0.022), however under the global null hypothesis of no association in the presence of linkage, none of these P-values remained significant. The three haplotypes with the lowest nominal P-values contained either rs1171506 or rs11013052. Transmitted/non-transmitted ratios and P-values for association with schizophrenia for all nominally associated multimarker haplotypes are shown in Table II. Power to detect association was calculated using the Genetic Power Calculator [Purcell et al., 2003] and genotypic relative risks as reported by Schwab et al. , assuming a multiplicative model. Power to detect association at the a ¼ 0.05 level was greater than 80% for all previously associated markers except rs11013052, for which power was only 19%. Allele frequencies had a major impact on power, as power was less than 30% for the two markers where the over-transmitted allele had a frequency greater than 0.96 (rs11013052 and rs1171506). In order to increase power for rs11013052 and rs1171506, we combined the data from the current study with the data previously reported by Schwab et al. . rs11013052 was significantly associated with schizophrenia (P ¼ 0.002) in this exploratory study. The P-value of 0.002 for association of rs11013052 with schizophrenia in the combined sample was slightly lower than the P-value of 0.005 in the German sample alone, indicating that the Indonesian sample contributed to the observed association. TABLE I. Characteristics and P-Values for All SNPs Tested for Association With Schizophrenia in the Present Study Variant dbSNP IDa Distance to next locus (kb)b M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 M11 M12 rs1417374 rs946961 rs1891898 rs1132816 rs1171506 rs943194 rs11013052 rs943190 rs10828317 rs10430590 rs746203 rs8341 33.6 77.3 14.4 51.4 42.0 47.4 20.1 2.7 6.6 2.5 5.4 — a Frequencyd Location Polymorphismc Intergenic Intergenic Intergenic PIP5K2A, exon 1 PIP5K2A, intron 1 PIP5K2A, intron 1 PIP5K2A, intron 4 PIP5K2A, intron 6 PIP5K2A, exon 7 PIP5K2A, intron 7 PIP5K2A, intron 8 Intergenic C/T G/C T/C T/C G/A T/G C/A A/G A/G T/A A/G C/T Affected 0.820459 0.47247 0.860174 0.886159 0.963629 0.905369 0.973025 0.609114 0.579898 0.563777 0.557479 0.622669 Unaffected T/NTe PTDT 0.80897 0.483088 0.851056 0.879718 0.960636 0.877327 0.953869 0.558567 0.556701 0.563509 0.537547 0.588886 46/45 76/73 36/25 34/26 13/6 31/22 10/3 71/72 69/75 67/78 74/85 67/71 1.000 0.885 0.1453 0.300 0.215 0.224 0.125 1.000 0.685 0.399 0.423 0.816 Variant ID as listed on the NCBI dbSNP database. Calculated from the locations given in the UCSC Human Genome Browser Gateway March 2006 Assembly. Major/minor allele. Note that alleles are described in relation to the þ strand. d Frequency estimates for ‘‘affected’’ are based on the frequency in a single affected offspring per family, frequency for ‘‘unaffected’’ is calculated from the nontransmitted alleles to a single affected offspring per family. Frequencies are given for the major allele as determined by Schwab et al. . These alleles correspond to the major alleles in the Indonesian population for all markers except rs946961. e Transmitted/non-transmitted alleles, corresponding to major alleles. b c 1312 Saggers-Gray et al. TABLE II. Transmission of Two and Three-Locus Haplotypes to Affected Offspring a Loci M3-M5 M3-M5-M7 M5-M7 M4-M10 M4-M9-M10 M4-M7-M10 M3-M4-M10 Risk haplotypeb T/NTc PTDT 1-1 1-1-1 1-1 1-2 1-2-2 1-1-2 1-1-2 38/21 38/21 14/3 66.04/42.04 61.04/41.04 66.04/42.04 66.04/42.04 0.02198 0.0274 0.03128 0.03288 0.03288 0.0415 0.04716 P(Global) >0.05. a Loci are labeled as per Table I. b 1; major allele, 2; minor allele. c Transmitted/non-transmitted from heterozygous parents. From our data it appears that any role that the PIP5K2A gene plays in the etiology of schizophrenia in the Indonesian population may be minor. While rs11013052 showed a statistically significant association with schizophrenia in the combined Indonesian and German sample and was more strongly associated than in the German sample alone, this ad hoc analysis was of an exploratory nature and does not provide sufficient evidence to conclude that the variant influences susceptibility to schizophrenia in the Indonesian population. The three haplotypes that showed the strongest nominal evidence for association all contained one or both of rs1171506 and 11013052, the two markers that displayed high T/NT ratios and very low minor allele frequencies. As such, we cannot exclude the possibility that the low minor allele frequencies of these markers are driving the observed nominal association. The study had over 80% power to detect association for all previously implicated PIP5K2A variants except rs11013052, using the genotypic relative risks calculated by Schwab et al. . While these estimates for relative risk are the best available, it is known that estimates of relative risk arising from the first positive association report for a given gene are frequently overestimates [Lohmueller et al., 2003]. If these estimates of relative risk are substantially higher than the true values, the power calculations may have overestimated the power of this study to detect association between these variants and schizophrenia. The power of this study was further undermined by the differences in allele frequencies observed between the Indonesian and Caucasian populations. As such, it is possible that this study failed to detect a true association due to insufficient power. Genetic heterogeneity has been proposed as a major factor in the non-replication of linkage studies in schizophrenia [Risch, 1990]. Linkage and association studies of schizophrenia have not only implicated different genes (inter-locus heterogeneity), but also different variants within the same gene (intra-locus heterogeneity). The Neuregulin 1 (NRG1) gene provides an example of this phenomenon. Different NRG1 haplotypes have been shown to be associated with schizophrenia in European and East Asian populations, as summarized by Munafo et al. . Differences in allele and haplotype frequencies between populations are likely to play a major role in this intra-locus heterogeneity. Allele frequencies are known to vary substantially between populations of East Asian and Caucasian descent and this phenomenon has also been demonstrated for NRG1 [Risch et al., 2002; Gardner et al., 2006]. The LD patterns seen in the Indonesian sample were very similar to those seen in the HapMap Data for both the JPTCHB and CEPH populations, with haplotype blocks formed between markers rs1891878 and rs1132816, and between rs943190 and rs8341 (data not shown). A notable difference between the JPTCHB and CEPH samples is that the size of these two haplotypes blocks is larger in the CEPH sample (53 and 47 kb in the CEPH sample, as opposed to 28 and 44 kb in the JPTCHB sample) [Barrett et al., 2005]. One possible explanation for the differences in association seen between the Indonesian and Caucasian samples is that associated markers within these blocks are tagging additional markers in the Caucasian samples. 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