Polymorphic Dinucleotide Research Articles

THU0014 A Regulatory Variant in CCR6 is Associated with Anti-Topoisomerase Positive Systemic Sclerosis Susceptibility

BackgroundSystemic sclerosis (SSc) is a rare autoimmune disease (AID) with a complex genetic etiology. Evidence for a shared pathogenesis across AIDs is supported by the well-known pleiotropism of autoimmune genes....

SAT0013 Candidate gene study in systemic sclerosis identifies a rare and functional variant of TNFAIP3 locus as a risk factor for individual polyautoimmunity

BackgroundSystemic lupus erythematosus (SLE) and systemic sclerosis (SSc) share some physiopathologic bases as supported by individual and familial polyautoimmunity and common susceptibility genetic factors. For the latter, there is a...

Evaluation of a new panel of six mononucleotide repeat markers for the detection of DNA mismatch repair-deficient tumours

Background:Microsatellite instability (MSI) is a molecular phenotype due to defective DNA mismatch repair (MMR) system. It is used to predict outcome of colorectal tumours and to screen tumours for Lynch syndrome (LS). A pentaplex panel composed of five mononucleotide markers has been largely recommended for determination of the MSI status. However, its sensitivity may be taken in default in occasional situations. The aim of the study was to optimise this panel for the detection of MSI.Methods:We developed an assay allowing co-amplification of six mononucleotide repeat markers (BAT25, BAT26, BAT40, NR21, NR22, NR27) and one polymorphic dinucleotide marker (D3S1260) in a single reaction. Performances of the new panel were evaluated on a cohort of patients suspected of LS.Results:We demonstrate that our assay is technically as easy to use as the pentaplex assay. The hexaplex panel shows similar performances for the identification of colorectal and non-MSH6-deficient tumours. On the other hand, the hexaplex panel has higher sensitivity for the identification of MSH6-deficient tumours (94.7% vs 84.2%) and MMR-deficient tumours other than colorectal cancer (92.9% vs 85.7%).Conclusion:The hexaplex panel could thus be an attractive alternative to the pentaplex panel for the identification of patients with LS.

Abstract 2394: Impact of epidermal growth factor receptor (EGFR) gene intron 1 dinucleotide CA repeat polymorphism on protein expression and clinical outcome in oral cavity squamous cell carcinoma.

Abstract Epidermal growth factor receptor (EGFR) is one of the four members of the ErbB receptor family and has been shown to play a key role in tumorigenesis of many human cancers including oral cavity squamous cell carcinoma (OSCC). Previous studies have observed a significant relationship between EGFR overexpression and poor outcomes in head and neck squamous cell carcinoma (HNSCC) including OSCC. Elevated EGFR levels have primarily been attributed to enhanced transcriptional activity, rather than amplification of the gene. Since the EGFR intron 1 polymorphic CA dinucleotide repeats has been suggested to affect EGFR transcription efficiency, the present study was designed to explore the relationship between this CA repeats polymorphism, gene copy number and protein levels in Taiwanese OSCC. A total of 194 OSCCs were examined for EGFR protein overexpression using immunohistochemistry and for copy number using a fluorescence in situ hybridization (FISH) assay. DNAs from peripheral blood of 164 OSCC patients were also available for EGFR intron 1 CA dinucleotide repeats analysis. Overexpression and increased gene copy numbers of EGFR were found in 101 (52.06%) and 59 (30.41%) cases, respectively. The length of EGFR CA repeats were not associated with EGFR protein expression (p = 0.261) while the copy number was strongly related to protein overexpression (p < 0.001). EGFR protein overexpression was associated with young age (p = 0.036), tumor differentiation (p < 0.001) and lymph node metastasis (p = 0.028). EGFR gene copy number was also associated with young age (p = 0.009), tumor cell differentiation (p = 0.002), tumor depth (p = 0.001), lymph node metastasis (p = 0.051) and bone invasion (p = 0.003). However, the length of EGFR CA repeats was not associated with clinicopathologic factors. Patients with EGFR overexpression in their tumors were found to have significant poorer disease-free survival (DFS) (p = 0.026, log-rank test) and overall survival (OS) (p = 0.019, log-rank test) than those without overexpression. Patients with CA repeats SS form (both alleles < 19 repeats) had significantly shorter DFS and OS than those with SL and LL forms (both alleles ≥ 19 repeats) (p = 0.039 and 0.018 for DFS and OS, respectively). On the other hand, the association between an increase in EGFR gene copies and DFS or OS was insignificant. In summary, our current findings confirm that EGFR protein overexpression is closely related to EGFR copy number; but, do not support the role of CA repeats as an EGFR expression regulator. On the other hand, the length of CA repeats was significantly associated with both DFS and OS. Citation Format: Shiang-Fu Huang, I-How Chen, Chun-Ta Liao, Hung-Ming Wang, Ling-Ling Hsieh. Impact of epidermal growth factor receptor (EGFR) gene intron 1 dinucleotide CA repeat polymorphism on protein expression and clinical outcome in oral cavity squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2394. doi:10.1158/1538-7445.AM2013-2394

Polymorphic CT dinucleotide repeat in the GATA3 gene and risk of breast cancer in Iranian women

GATA3 is an enriched transcription factor in mammary epithelium. To date, there has been no study on the relationship between microsatellites in the GATA3 gene and breast cancer risk. In this study, we investigated the existence of polymorphisms in the cytosine-thymine (CT) dinucleotide repeat in intron 3 of the GATA3 gene and its association with breast cancer risk. A case-control study of 206 breast cancer patients and 262 controls was conducted in Iranian women. Several different CT repeat alleles of GATA3 were detected in both the patients and controls. The frequencies of 17 and 18 alleles in patients were significantly lower than controls. Our findings demonstrate that women who carry 17-CT (OR = 0.5; p = 0.003) or 18-CT (OR = 0.41, p = 0.02) alleles of GATA3 gene are at lower risk of developing breast cancer. The highest protection against breast cancer was observed with heterozygotes of 16/17 repeats (OR = 0.12, p = 0.02). Also, the presence of the 17-CT allele has a positive relation with estrogen receptor expression. However, we found that the allelic length of GATA3 polymorphisms had no significant effect on the age onset or grade of the disease, as well as the expression of progesterone receptors and HER2.

Gαq gene promoter polymorphisms and rheumatoid arthritis in the Han Chinese population are not associated

Mice that lose Gαq from their immune system can spontaneously develop inflammatory arthritis. Gαq expression in the peripheral blood lymphocytes of rheumatoid arthritis (RA) patients is significantly decreased in comparison to that in healthy individuals, and reduced Gαq expression is closely correlated with RA disease activity. These indicate that Gαq plays critical roles in the pathogenesis of RA. To address whether single nucleotide polymorphism in the promoter region of the Gαq gene (GNAQ) influenced Gαq expression in RA patients and was a genetic risk factor for RA, we sequenced the promoter region of GNAQ in a Han Chinese population. A common dinucleotide polymorphism at position -695/-694, an exchange of 2 adjacent nucleotides (GC>TT), was revealed in 118 RA patients and 101 healthy adults. The proportions of genotypes observed for -695/-694 in the RA group were GC/GC (65.25%), GC/TT (33.05%), and TT/TT (1.70%), and those in the control group were GC/GC (62.38%), GC/TT (33.66%), and TT/TT (3.96%). No significant difference in the allele and genotype frequencies between RA patients and healthy controls for dinucleotide polymorphism was found in the Han Chinese population, neither in the whole data set nor in stratified subsets, i.e., rheumatoid factors, anti-cyclic citrullinated peptide antibody, and Gαq expression status (P > 0.05). We conclude that the GNAQ promoter polymorphism is not a genetic risk factor for RA in the Han Chinese population, and that decreased Gαq expression in peripheral blood lymphocytes of RA might potentially be due to other causes.

Polymorphism at P21 codon 31 and dinucleotide polymorphism of P73 gene and susceptibility to bladder cancer in individuals from North India

BACKGROUND AND AIM:p73, a novel P53 homolog and plays an important role in modulating cell cycle control, apoptosis and cell growth while P21, functions to negatively control the cell cycle. P53 up regulates p21 expression in response to deoxyribonucleic acid damage leading to cell cycle arrest at G1 checkpoint. In the present study, we are targeting p21 codon 31 and p73 gene variants of G4C14-to-A4T14 (Exon 2) polymorphism for bladder cancer (BC) risk in North Indians.MATERIALS AND METHODS:The above gene variants of P21 and P73 were assessed in the case-control study comprising of 200 BC cases and 200 healthy controls of the same age, gender and similar ethnicity. Genotyping was performed by polymerase chain reaction (PCR) restriction fragment length polymorphism method and PCR-based confronting two-pair primers (PCR with CTPP).RESULTS:The variant genotype of p73Exon 2 polymorphism showed significant risk for BC (p = 0.014). While combining with heterozygous genotype, variant genotype of p73Exon2 showed a significant association with BC risk (p = 0.010). While in case of p21 codon31 showed no significant association for BC risk at genotypic level. Significant association between p73Exon2 polymorphism and smoking was observed for BC risk. Furthermore, gene combination analysis revealed that AT/AT-Ser/Ser is associated with risk for BC. Variant genotype of P73Exon2 was associated with reduced risk of recurrence (p = 0.039) in superficial BC patients receiving Bacillus Calmette-Guerin treatment thus showing least survival (log rank = 0.029).CONCLUSION:Our study provided evidence that the p73 G4C14 > A4T14 (Exon2) polymorphisms were associated with higher risk of BC in North Indian population.

Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome

A tandem repeat’s (TR) propensity to mutate increases with repeat number, and can become very pronounced beyond a critical boundary, transforming it into a microsatellite (MS). However, a clear understanding of the mutational behavior of different TR classes and motifs and related mechanisms is lacking, as is a consensus on the existence of a boundary separating short TRs (STRs) from MSs. This hinders our understanding of MSs’ mutational properties and their effective use as genetic markers. Using indel calls for 179 individuals from 1000 Genomes Pilot-1 Project, we determined polymorphism incidence for four major TR classes, and formalized its varying relationship with repeat number using segmented regression. We observed a biphasic regime with a transition from a faster to a slower exponential growth at 9, 5, 4, and 4 repeats for mono-, di-, tri-, and tetranucleotide TRs, respectively. We used an in vitro mutagenesis assay to evaluate the contribution of strand slippage errors to mutability. STRs and MSs differ in their absolute polymorphism levels, but more importantly in their rates of mutability growth. Although strand slippage is a major factor driving mononucleotide polymorphism incidence, dinucleotide polymorphism incidence is greater than that expected due to strand slippage alone, indicating that additional cellular factors might be driving dinucleotide mutability in the human genome. Leveraging on hundreds of human genomes, we present the first comprehensive, genome-wide analysis of TR mutational behavior, encompassing several motif sizes and compositions.

Association of a p73 exon 2 G4C14-to-A4T14 polymorphism with risk of hepatocellular carcinoma in a Chinese population

P73, a p53 homolog, has some p53-like activities and plays an important role in modulating cell cycle, apoptosis, and DNA repair. A potentially functional dinucleotide polymorphism, G4C14-to-A4T14, has been identified in the 5' untranslated region of exon 2 of the p73 gene, which may theoretically form a stem-loop structure and affect gene expression. We hypothesized that genetic variants in p73 may modify individual susceptibility to hepatocellular carcinoma (HCC). To test this hypothesis that these two common variants play a role in HCC susceptibility, we conducted a hospital-based case-control study of 476 HCC patients and 526 cancer-free controls in a Chinese population. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry method was performed to detect these polymorphisms. The results showed that the genotype and allele frequencies of the p73 G4C14-A4T14 did not differ significantly between the HCC patients and the control group (all P values are above 0.05). However, with stratification analysis by age, sex, smoking status, drinking status, HBV carrier state, and family history of cancer, we found that the variant genotypes (GC/AT + AT/AT) of the p73 G4C14-A4T14 was associated with a significant increased risk of HCC among HbsAg-positive individuals (adjusted OR = 2.19, 95% CI = 1.25-3.83) and among women (adjusted OR = 2.62, 95% CI = 1.47, 4.66). These results suggest that the p73 G4C14-to-A4T14 dinucleotide polymorphism may play a role in the development of chronic HBV-infected HCC in the Chinese population, especially among women.

Abstract B11: EGFR polymorphism as a predictor of clinical outcome in advanced lung cancer patients treated with EGFR-TKI

Abstract Background: Mutations in the epidermal growth factor receptor (EGFR) have been confirmed as predictors of efficacy for EGFR-tyrosine kinase inhibitors (TKIs). We investigated whether polymorphisms of the EGFR gene were associated with clinical outcome in NSCLC patients treated with EGFR-TKI. Methods: A polymorphic dinucleotide repeat (CA simple sequence repeat 1 [CA-SSR1]) in intron one and single nucleotide polymorphisms in the promoter region (SNP -216 GG or GT) were evaluated in 71 NSCLC patients by PCR-RFLP and DNA sequencing. Genetic polymorphisms were correlated with clinical outcomes of EGFR-TKIs. Results: SNP-216G/T polymorphisms were associated with the efficacy of EGFR-TKI. The response rate for the SNP-216G/T was significantly higher than that for the GG (62.5% vs. 27.4%, P=0.044). SNP-216G/T genotype was also associated with longer progression-free survival compared with GG genotype (16.7 months vs. 5.1 months, P=0.005). However, Genotypes for the CA-SSR1 was not associated with the efficacy of EGFR-TKI. Conclusions: SNP-216G/T polymorphism is potential predictor for clinical outcome in NSCLC patients treated with EGFR-TKI.

Head injury, alpha‐synuclein Rep1, and Parkinson's disease

To test the hypothesis that variability in SNCA Rep1, a polymorphic dinucleotide microsatellite in the promoter region of the gene encoding α-synuclein, modifies the association between head injury and Parkinson's disease (PD) risk. Participants in the Farming and Movement Evaluation (FAME) and the Study of Environmental Association and Risk of Parkinsonism using Case-Control Historical Interviews (SEARCH), 2 independent case-control studies, were genotyped for Rep1 and interviewed regarding head injuries with loss of consciousness or concussion prior to Parkinson's disease (PD) diagnosis. Logistic regression modeling adjusted for potential confounding variables and tested interaction between Rep1 genotype and head injury. Consistent with prior reports, relative to medium-length Rep1, short Rep1 genotype was associated with reduced PD risk (pooled odds ratio [OR], 0.7; 95% confidence interval [CI], 0.5-0.9), and long Rep1 with increased risk (pooled OR, 1.4; 95% CI, 0.95-2.2). Overall, head injury was not significantly associated with PD (pooled OR, 1.3; 95% CI, 0.9-1.8). However, head injury was strongly associated with PD in those with long Rep1 (FAME OR, 5.4; 95% CI, 1.5-19; SEARCH OR, 2.3; 95% CI, 0.6-9.2; pooled OR, 3.5; 95% CI 1.4-9.2, p-interaction = 0.02). Individuals with both head injury and long Rep1 were diagnosed 4.9 years earlier than those with neither risk factor (p = 0.03). While head injury alone was not associated with PD risk, our data suggest head injury may initiate and/or accelerate neurodegeneration when levels of synuclein are high, as in those with Rep1 expansion. Given the high population frequency of head injury, independent verification of these results is essential.

EGFRPolymorphism as a Predictor of Clinical Outcome in Advanced Lung Cancer Patients Treated withEGFR-TKI

PurposeMutations in the epidermal growth factor receptor (EGFR) have been confirmed as predictors of the efficacy of treatment with EGFR-tyrosine kinase inhibitors (TKIs). We investigated whether polymorphisms of the EGFR gene were associated with clinical outcomes in non-small cell lung cancer (NSCLC) patients treated with EGFR-TKI.Materials and MethodsA polymorphic dinucleotide repeat in intron 1 [CA simple sequence repeat in intron 1(CA-SSR1)] in intron 1 and single nucleotide polymorphisms (SNP-216) in the promoter region of the EGFR gene were evaluated in 71 NSCLC patients by restriction fragment length polymorphism and DNA sequencing. The relationship between genetic polymorphisms and clinical outcomes of treatment with EGFR-TKIs was evaluated.ResultsSNP-216G/T polymorphisms were associated with the efficacy of EGFR-TKI. The response rate for the SNP-216G/T tended to be higher than that for G/G (62.5% vs. 27.4%, p=0.057). The SNP-216G/T genotype was also associated with longer progression-free survival compared with the GG genotype (16.7 months vs. 5.1 months, p=0.005). However, the length of CA-SSR1 was not associated with the efficacy of EGFR-TKI.ConclusionSNP-216G/T polymorphism was a potential predictor of clinical outcomes in NSCLC patients treated with EGFR-TKI.

P73 G4C14-to-A4T14 gene polymorphism and interaction with p53 exon 4 Arg72Pro on cancer susceptibility: a meta-analysis of the literature

The p73 gene (1p36-33) is involved in cancer development through cell growth inhibition by inducing apoptosis in a p53-like manner. The p73 G4C14-to-A4T14 dinucleotide polymorphism, consisting of two single-nucleotide polymorphisms in the non-coding region of exon 2 that are in complete linkage disequilibrium, has been extensively studied in association with cancer risk. We performed a meta-analysis of published studies that examined the association between this p73 G4C14-to-A4T14 polymorphism and cancer by searching for relevant studies on Medline and Embase up to February 28, 2010. Pooling data from 19 case-control studies that included 6510 cancer cases and 5711 controls, we found that carriers of the p73 G4C14-to-A4T14 homozygous variant genotype (AT/AT) had an increased global risk of cancer [odds ratio (OR) = 1.30, 95% confidence interval (CI), 1.03-1.65]. There was no evidence of an effect modification of p73 AT/AT by age, gender, ethnicity or smoking status in subgroup analyses; however, a 1.35-fold statistically significant increased risk was found among individuals <55 years old. In case-only analysis, the homozygous p73 G4C14-to-A4T14 variant of p73 genotype was associated with the presence of the p53 exon 4 Arg72Pro allele (OR = 1.30, 95% CI, 1.02-1.64), which is suggestive of a biological interaction between the two genes in carcinogenesis. In conclusion, the p73 G4C14-to-A4T14 homozygous variant genotype might be a risk factor for cancer, especially in combination with the p53 exon 4 Arg72Pro polymorphism. Further studies looking at p73 G4C14-to-A4T14 and p53 exon 4 Arg72Pro interaction are required to support our findings.

Impact of MICA-TM, MICB-C1_2_A and C1_4_1 microsatellite polymorphisms on the susceptibility to chronic periodontitis in Germany

The major histocompatibility complex class I chain-related gene A (MICA)-TM exon 5 trinucleotide polymorphism, the MICB-C1_2_A intron 1 dinucleotide polymorphism and the tetranucleotide polymorphism C1_4_1 located in the major histocompatibility complex class I region on chromosome 6 were shown to influence various chronic inflammatory conditions. We investigated the association of these microsatellite polymorphisms with chronic periodontitis, a highly prevalent oral inflammatory disease in 389 periodontitis patients and 771 healthy controls with South German genetic background. Genotyping of the MICA-TM, MICB-C1_2_A and C1_4_1 microsatellite polymorphisms was performed by PCR amplification and fragment analysis. Global frequency distribution of MICB-C1_2_A (P = 0.006) and C1_4_1 (P = 0.028) alleles was significantly different between both study groups. Allele-specific analysis revealed that the MICA-TM allele A5 was more prevalent among male periodontitis patients [P = 0.0001; odds ratio (OR) 2.17, 95% confidence interval (CI) 1.55-3.03]. In C1_4_1 allele, three was significantly higher in healthy controls (P = 0.006; OR 0.74, 95% CI 0.60-0.91). Two haplotypes (MICA:A5-C1_4_1:5; P = 0.002; OR 2.63, 95% CI 1.46-4.74 and MICB:CA16-C1_4_1:3; P = 0.014; OR 0.68, 95% CI 0.50-0.92) showed significant differences between periodontitis patients and controls. The MICA-TM, MICB-C1_2_A and C1_4_1 microsatellite polymorphism seem to influence the individual susceptibility to chronic periodontitis in patients with German genetic background.

Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus

Systemic lupus erythematosus (SLE, MIM152700) is an autoimmune disease characterized by self-reactive antibodies resulting in systemic inflammation and organ failure. TNFAIP3, encoding the ubiquitin-modifying enzyme A20, is an established susceptibility locus for SLE. By fine mapping and genomic re-sequencing in ethnically diverse populations, we fully characterized the TNFAIP3 risk haplotype and identified a TT>A polymorphic dinucleotide (deletion T followed by a T to A transversion) associated with SLE in subjects of European (P = 1.58 × 10(-8), odds ratio = 1.70) and Korean (P = 8.33 × 10(-10), odds ratio = 2.54) ancestry. This variant, located in a region of high conservation and regulatory potential, bound a nuclear protein complex composed of NF-κB subunits with reduced avidity. Further, compared with the non-risk haplotype, the haplotype carrying this variant resulted in reduced TNFAIP3 mRNA and A20 protein expression. These results establish this TT>A variant as the most likely functional polymorphism responsible for the association between TNFAIP3 and SLE.

Risk for antipsychotic-induced extrapyramidal symptoms: influence of family history and genetic susceptibility

This study aims to further evaluate the impact of family history of primary movement disorders (FHpMD) and a candidate genetic variant on risk of antipsychotic-induced extrapyramidal symptoms (EPS). We examined 156 (76 men) inpatients receiving antipsychotics for EPS and FHpMD stratified by patient characteristics. The genetic analysis included genotyping of a multiallelic dinucleotide polymorphism in the ATP1A3 gene. EPS lifetime prevalence was 69% and more frequent in the presence of FHpMD (p = 0.052), particularly in patients younger than 60years (p = 0.012) and with acute dystonic reactions. The ATP1A3 polymorphism showed an allele length-dependent association with parkinsonism (p=0.019 uncorrected, p=0.057 corrected) exclusively. Carriers of the shortest allele had a 7.7-fold increased risk for parkinsonism. The association of FHpMD and EPS may be linked to the EPS subtype and age of the patient. A common ATP1A3 genomic variation may represent a susceptibility factor for the risk for antipsychotic-induced parkinsonism in an allele-dependent manner.

Multibiomarker analysis homing in on EGFR-TKIs therapy in non-small cell lung cancer.

e18025 Background: EGFR mutation has been identified to be a strong predictive biomarker to EGFR-TKIs in non-small cell lung cancer (NSCLC), but it isn't exclusive molecular mechanism to TKI therapy. So developing platforms of serial of biomarkers detection is important for personalized TKI therapy. This study investigated the relationships between genetic factors and clinical outcome in Chinese NSCLC patients treated by gefitinib. Methods: A total of 156 NSCLC were enrolled for genetic screening and 101 of which were treated by gefitinib. EGFR AKRAS mutation (mEGFR, mKRAS) were identified by denaturing high performance liquid chromatography (DHPLC) and EGFR copy number AEML4-ALK rearrangement were detected using fluorescent in situ hybridization (FISH). A polymorphic dinucleotide repeat (CA simple sequence repeat1 [CA-SSR1]) was determined by DNA sequencing. Results: mEGFR, mKRAS, EGFR FISH positive and EML4-ALK rearrangement were detected in 62 (39.7%),13 (8.3%), 49 (20.2%), 6 (3.8%) pts, respectively. Pts with shorter (CA)n repeat genotype (< 18) account for 45.5%. The mKRAS was found to be significantly higher in the shorter (CA)n than in the longer group (≥ 18) (p = 0.018), but EGFR FISH positive was higher in longer (CA)n group (p = 0.004) and the associations between (CA)n length and EGFR mutations and EML4-ALK rearrangement were observed. Among 102 pts with gefitinib therapy, EGFR mutant had significantly higher ORR than wild-type group (28/47, 60% versus 9/54, 17% p = 0.000). Further analyzing 54 patients with EGFR wild-type, 32 was in longer (CA)n and 22 in shorter (CA)n. Of 9 pts carrying wild-type EGFR who had response to gefitinib, 8 showed longer (CA)n polymorphism, and only 1 was in shorter (CA)n (p = 0.048). All of 6 mKRAS pts were present in the 22 shorter (CA)n group. The survival analysis showed the pts with mEGFR (9.4months ver 6.8months, p = 0.055), KRAS wild-type (8.4 months ver 3.1months, p = 0.019) and longer (CA)n (9.4months ver 6.2months, p = 0.073) had longer PFS. Conclusions: Multibiomarkers analysis may be more accurate for predicting response to TKI than single biomarker. The valid combination of molecular testing should be validated by large- samples study. No significant financial relationships to disclose.

A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility

Rheumatoid arthritis is a common autoimmune disease with a complex genetic etiology. Here, through a genome-wide association study of rheumatoid arthritis, we identified a polymorphism in CCR6, the gene encoding chemokine (C-C motif) receptor 6 (a surface marker for Th17 cells) at 6q27, that was associated with rheumatoid arthritis susceptibility and was validated in two independent replication cohorts from Japan (rs3093024, a total of 7,069 individuals with rheumatoid arthritis (cases) and 20,727 controls, overall odds ratio = 1.19, P = 7.7 x 10(-19)). We identified a triallelic dinucleotide polymorphism of CCR6 (CCR6DNP) in strong linkage disequilibrium with rs3093024 that showed effects on gene transcription. The CCR6DNP genotype was correlated with the expression level of CCR6 and was associated with the presence of interleukin-17 (IL-17) in the sera of subjects with rheumatoid arthritis. Moreover, CCR6DNP was associated with susceptibility to Graves' and Crohn's diseases. These results suggest that CCR6 is critically involved in IL-17-driven autoimmunity in human diseases.

Development of Novel Microsatellite DNA Markers by Cross-Amplification and Analysis of Genetic Variation in Gerbils

The objectives of this study are to establish microsatellite loci for the Mongolian gerbil based on mouse microsatellite DNA sequences and to investigate genetic variation in the laboratory gerbil (Capital Medical University, CMU) and 2 wild gerbil populations (from Yin Chuan city [YIN] and the Hohehot Municipality [HOH]). In total, 536 mouse microsatellite markers were chosen to identify polymorphic dinucleotide repeat loci in the gerbil by cross-amplification. Of these markers, 313 (58.39%) have been discretely amplified from the CMU laboratory gerbil and been sequenced. Of the 313 sequenced markers, 130 were confirmed as simple sequence repeat (SSR) loci in the gerbil. In total, 6 of those newly identified loci plus 6 identified in previous reports were used to estimate the genetic polymorphism for 30 laboratory gerbils and 54 wild gerbils (27 each of the HOH and YIN groups). A total of 29 alleles were observed in the 3 populations, and 11 of 12 loci (91.67%) are polymorphic markers. Nei's standard genetic distances of 0.0592 (CMU vs. HOH) and 0.1033 (CMU vs. YIN) were observed. The averages of observed versus expected heterozygosity are 0.5231/0.4008, 0.5051/0.3882, and 0.4825/0.3665 for the YIN, HOH, and CMU populations, respectively. These results show that cross-amplification using mouse microsatellite primers is an efficient way to identify gerbil SSR loci. By using these 12 selected markers, we have demonstrated that genetic variation level within the CMU population is higher than that has been reported previously and are comparable with the levels found in 2 wild populations.

Association study between P53 and P73 gene polymorphisms and the sporadic late-onset form of Alzheimer’s disease

An important pathological aspect of Alzheimer's disease (AD) is the apoptosis of neuronal and glial cells. Two members of the same protein family that regulates many genes involved in apoptosis are P53 and the heterologue P73. One single nucleotide polymorphism (SNP) in the gene encoding P53 (Arg72Pro, RS1042522), one dinucleotide polymorphism (G4C14-to-A4T14, RS 2273953, RS1801173) in the gene encoding P73, and two further SNPs in the same gene (-386 G/A, RS3765728; exon 5 T/C, RS1801174) were studied to determine whether DNA variations could influence the occurrence of the disease in a sample of Italian subjects with the sporadic late-onset form of AD. We observed that carrying the Pro/Pro genotype of P53 Arg72Pro was a risk factor with respect to the Pro/Arg + Arg/Arg genotypes [Odds Ratio (OR) = 2.02; 95% Confidence Interval (CI) 1.02-4.00; p = 0.047]. Furthermore, carrying the G/G genotype of the P73 -386 G/A was a risk factor with respect to the G/A + A/A genotypes (OR = 4.27; 95% CI 1.00-18.65; p = 0.047). A significant result was also obtained for P73 G4C14-to-A4T14. Among the patients, the homozygotes for the AT allele of this SNP had developed AD symptoms 5 years earlier than other genotypes (ANOVA p = 0.017). Though the results of particular polymorphisms analyses were not highly significant after correction for multiple comparisons, present data suggest that variation at the two genes may have a role in AD occurrence.