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Association of Single Nucleotide Polymorphism In PROCEEDINGS OF THE LATVIAN ACADEMY OF SCIENCES. Section B, Vol. 67 (2013), No. 6 (687), pp. 453–456. DOI: 10.2478/prolas-2013-0079 ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISM IN CHROMOSOME 11 WITH AUTISM SPECTRUM DISORDER Daiga Bauze*, **, Linda Piekuse***, Laura Kevere*, Zane Kronberga*, Arnis Riþevs*, Iveta Vaivade****, Kristîne Vîksne****, Raisa Andrçziòa*, ***, and Baiba Lâce**** * Children’s University Hospital, Child Psychiatry Clinic, Juglas iela 20, Rîga, LV–1079, LATVIA; [email protected] ** Children’s University Hospital, Medical Genetics Clinic, Juglas iela 20, Rîga, LV–1079, LATVIA *** Rîga Stradiòð University, Dzirciema 16, Rîga, LV-1007, LATVIA **** Latvian Biomedical Research and Study Centre, Râtsupîtes iela 1, Rîga, LV-1067, LATVIA Communicated by Isaak Rashal Several genetic loci in chromosomes 11 and 15 have recently been associated with non-syndromic autism spectrum disorder (ASD) in populations from North America and Europe. The aim of the present study was to investigate whether such an association exists in a Latvian population. Ninety-five patients with ASD in the age range 3–20 years (mean age 8 years, SD 3.18) participated in the study. The control group consisted of 161 healthy, non-related individuals without ASD randomly selected from the Latvian Genome Database. Four single nucleotide poly- morphisms (SNPs) — rs11212733, SNP rs1394119, rs2421826, rs1454985 — were genotyped by the TaqMan method. Allele frequency differences between ASD patients and control subjects were compared for each SNP using a standard chi-square test with Bonferroni correction. The level of statistical significance was set at 0.05 for nominal association. Only the genetic marker rs11212733, localised on the long arm of chromosome 11 in locus 22.3, was found to be strongly 2 associated with the ASD patient group (c 6.982, Padjusted 0.033, odds ratio 1.625). Our data demonstrating a significant relationship between the SNP rs11212733 and the development of ASD in a Latvian population suggest that it is not a population-specific relationship. Thus, future studies focusing on the DDX10 gene and related genetic loci are needed. Key words: autism spectrum disorder (ASD), single nucleotide polymorphisms (SNPs), rs11212733, DDX10. INTRODUCTION gression, and mental retardation. This collection of symp- toms should be classified as ASD (Gillberg et al., 2006). Autism spectrum disorders (ASD) are serious early child- The International Classification of Diseases (ICD-10) dis- hood neurodevelopmental disorders with unknown etiology tinguishes between autism and ASD, which are subdivided and a rapid annual increase in prevalence. ASD are a broad into syndromic autism and non-syndromic or idiopathic phenotype including less severe disorders (Anonymous, autism (Anonymous, 1992; Lintas and Persico, 2009). 1994; Bailly et al., 1996; Johnson et al., 2007). ASD are clinically characterised by impaired social and communica- tion skills, hyperactivity and attention deficit, stereotypic Linkage and association studies have identified potential movements and interests, stereotypic rituals, emotional dis- ASD candidate genes in different chromosomes — the most turbances, and varying degrees of expressive and receptive significant ones being 2q, 7q, 15q and the X chromosome language development disorders (Bailly et al., 1996; Risch (Muhle et al., 2004; Lintas and Persico, 2009). As several et al., 1999). genetic loci have been implicated in ASD development, ex- tensive studies have been conducted worldwide to detect ASD is not a disease but rather a syndrome that is character- potential candidate genes for ASD (Liu et al., 2008; Cho et ised by a multifactorial type of inheritance. In some cases, it al., 2011). Genome-wide linkage analyses of quantitative is one of the symptoms of monogenic or chromosomal pa- and categorical autism subphenotypes, carried out in North thology, and can also be a symptom of inherited metabolic America and Europe, revealed association between ASD disorders. In early childhood, the latter can manifest primar- and locus 15.4-p15.3 in the short arm of chromosome 11 ily with autistic behaviour, speech development delay or re- (Liu et al., 2008). Furthermore, cytogenetic abnormalities at Proc. Latvian Acad. Sci., Section B, Vol. 67 (2013), No. 6. 453 locus 11-13 in the long arm of chromosome 15 have been Methods. DNA was extracted from each patient’s venous reported to cause ASD. Population studies and case reports blood sample (collected at the Children’s Psychiatry and describe the duplication, deletions and inversions of this lo- Medical Genetics Clinics of the Children’s University Hos- cus, as well as the phenotype of chromosome 15 in ASD pa- pital) using a standard phenol/chloroform extraction proto- tients (Muhle et al., 2004; Johnson et al., 2011). col (Sambrook et al., 1989). The aim of this study was to investigate whether the associ- Single Nucleotide Polymorphism (SNP) Selection. On the ation between reported ASD informative genetic markers in basis of the data of recent reports on the most significant chromosomes 11q, 11p, and 15q and non-sindromic autism SNPs involved in the development of ASD, four SNPs were spectrum disorders exists in a Latvian population. selected for the genotyping assay: rs11212733 at the long arm of chromosome 11 in locus 22.3, SNP rs1394119 at the short arm of chromosome 11 in locus 15.4–15.3, rs2421826 MATERIALS AND METHODS at the short arm of chromosome 11 in locus 13 and rs1454985 at the long arm of chromosome 15 in locus Subjects. The Children’s Psychiatry Clinic of the 13.3–14 (Liu et al., 2008; Cho et al., 2011). Children’s University Hospital is one of four specialised centres in Latvia. Since 2006, 195 patients with possible TaqMan Genotyping. SNPs were genotyped using ASD have attended for a consultation. The given patient TaqMan® probe-based chemistries (Applied Biosystems, group was primarily examined by a psychiatrist using Carlsbad, CA, USA) on an automatic sequence-detection in- ICD-10 diagnostic criteria, as well as standardised scales strument (Real-Time PCR System, Applied Biosystems). corresponding to each patient’s age: The CHecklist for Au- All reactions were carried out using standard conditions as tism in Toddlers (the CHAT) (assessment in the first 18 recommended by the manufacturer. months); Autism Spectrum Quotient (autism spectrum ques- tions for children aged 4–11 years); Cambridge University Statistical analysis. Allele frequency differences between Behaviour and Personality questions for children up to the ASD patients and control subjects were compared for each age of four years; Cambridge University social and commu- SNP using a standard chi-square test with Bonferroni cor- nicative development questions; and Childhood Asperger rection. Allelic odds ratios and 95% confidence intervals Syndrome Test (CAST) (Anonymous, 1992; Baron-Cohen were estimated using a standard chi-square test, assuming a et al., 1992; Scott et al., 2002; Baron-Cohen et al., 2006; multiplicative model. The level of statistical significance Williams et al., 2006). In order to specify the diagnosis of was set at 0.05 for nominal association. Statistical analyses ASD in cases with positive test results, they were referred to were conducted using PLINK 1.06 software (Purcell et al., a psychologist for the Autism Diagnostic Observation 2007). Schedule (ADOS) test, using the most appropriate model of the given test for each patient (Lord et al., 2002). Thus, on RESULTS the basis of the test results, of the 195 patients, diagnoses of ASD were confirmed in 169 and were selected. Four SNPs in the analysed genetic loci related to ASD were genotyped in 95 patients with ASD and 161 healthy, non- A clinical geneticist performed the genetic assessment of all related controls. The average genotype call rate for these patients. Seventy-four patients were excluded from the SNPs was 99.8%. group as monogenic, chromosomal and metabolic patholo- gies, diagnosed using standard karyotype, long arm of chro- The genotype distributions in the study groups were in mosome 15 locus 11.13 (15q11.13) deletion/duplication and Hardy-Weinberg equilibrium, except for rs1394119, which long arm of chromosome 22 locus 11.2 (22q11.2) deletion was excluded from further studies. The genomic control in- analyses. flation factor (kGC) was 1.008 for the entire data set. The results are shown in Table I. Ninety-five patients with ASD in the age range 3–20 years (mean age 8 years, SD 3.18) agreed to participate in the Our results showed that the genetic marker rs11212733, study. The male to female ratio was 3.5:1. The patients, le- localised on the long arm of chromosome 11 in locus 22.3, gal guardians or parents signed informed consent forms in 2 was found to be associated with ASD (χ – 6.982, Padjusted accordance with the instructions issued by the Medical Eth- – 0.033, odds ratio – 1.625). The genetic markers ics Committee of Rîga Stradiòð University. rs2421826, localised on the short arm of chromosome 11 in locus 3 and rs1454985, localised on the long arm of chro- The control group comprised 161 healthy, non-related indi- mosome 15 in locus 13.3–14 did not have an association viduals randomly selected from the Latvian Genome Data- 2 2 with ASD (χ – 0.554, Padjusted –1.0, odds ratio –1.154; χ base. A subject was excluded from the control group if there – 1.118, P – 1.0, odds ratio – 1.217, accordingly). was information concerning possible mental illness. The adjusted male to female ratio was 1.7 : 1. DISCUSSION
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