Recognition this month begins with Eric Londin at Coriell Institute for Medical Research for his publication in PLoS ONE: “CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins.” (Abstract below). Also recently published in PLoS ONE is Chiara Magri with Brescia University School of Medicine on her study locating new CNVs in schizophrenia. (Abstract below)
Skipping over to Spain, plaudits to Julio Escribano for his work on “Polymorphic deletions of the GSTT1 and GSTM1 genes and susceptibility to bladder cancer,” an article in the latest BJU International journal. (Abstract below)
And finally, props to Joo-Ho Chung et al. at Kyung Hee University in Korea for their recent inclusion in the European Journal of Pediatrics, “Association between toll-like receptor 10 (TLR10) gene polymorphisms and childhood IgA nephropathy.” (Abstract below)
Congrats to all!
CoAIMs: A Cost-Effective Panel of Ancestry Informative Markers for Determining Continental Origins, PLoS ONE, Londin, E et al.
Background: Genetic ancestry is known to impact outcomes of genotype-phenotype studies that are designed to identify risk for common diseases in human populations. Failure to control for population stratification due to genetic ancestry can significantly confound results of disease association studies. Moreover, ancestry is a critical factor in assessing lifetime risk of disease, and can play an important role in optimizing treatment. As modern medicine moves towards using personal genetic information for clinical applications, it is important to determine genetic ancestry in an accurate, cost-effective and efficient manner. Self-identified race is a common method used to track and control for population stratification; however, social constructs of race are not necessarily informative for genetic applications. The use of ancestry informative markers (AIMs) is a more accurate method for determining genetic ancestry for the purposes of population stratification.
Methodology/Principal Findings:Here we introduce a novel panel of 36 microsatellite (MSAT) AIMs that determines continental admixture proportions. This panel, which we have named Continental Ancestry Informative Markers or CoAIMs, consists of MSAT AIMs that were chosen based upon their measure of genetic variance (Fst), allele frequencies and their suitability for efficient genotyping. Genotype analysis using CoAIMs along with a Bayesian clustering method (STRUCTURE) is able to discern continental origins including Europe/Middle East (Caucasians), East Asia, Africa, Native America, and Oceania. In addition to determining continental ancestry for individuals without significant admixture, we applied CoAIMs to ascertain admixture proportions of individuals of self declared race.
Conclusion/Significance: CoAIMs can be used to efficiently and effectively determine continental admixture proportions in a sample set. The CoAIMs panel is a valuable resource for genetic researchers performing case-control genetic association studies, as it can control for the confounding effects of population stratification. The MSAT-based approach used here has potential for broad applicability as a cost effective tool toward determining admixture proportions. Access the article
Polymorphic deletions of the GSTT1 and GSTM1 genes and susceptibility to bladder cancer, BJU International, Salinas-Sanchez, A et al.
Objectives: To estimate the prevalence and importance of GSTT1 and GSTM1 genotypes (implicated in glutathione S-transferase activity) in bladder cancer, to determine whether smoking and occupational factors influence this relationship, and to identify the value of GSTT1 and GSTM1 genotypes as prognostic factors.
MATERIALS AND METHODS: A cross-sectional study was conducted with a group of patients with bladder carcinoma and a control group with benign conditions and no history of tumours. The controls were selected and paired as subjects were recruited. Sociodemographic variables, smoking, professional occupation, histological features and the presence of GSTT1 and GSTM1 polymorphisms by multiplex PCR techniques were assessed.
Results: GSTM1 genotypes were investigated in 201 patients and 193 controls and GSTT1 genotypes in 190 patients and 163 controls. In the patients group, GSTT1 null genotype was observed in 22.1% (not significant) and GSTM1 null genotype in 54.2% (P= 0.008) (odds ratio, OR, 1.7); when considered together, 15.5% (P < 0.05; OR, 3.5) of patients had both null genotypes. In the multivariate analysis, the presence of GSTM1 null genotype remained in the model (OR, 2.1) in addition to smoking and age. Subjects with bladder tumour and GSTM1 null genotype were younger than patients without gene deletion (P= 0.049). Women with GSTM1 null genotype presented a higher OR than men (P= 0.024). When stratified by smoking habit, smokers with both null genotypes showed an OR of 4.7. The percentage of patients with G3 tumours was higher in patients with GSTT1 null genotype (P= 0.013) and in patients with both null genotypes (P= 0.002). A higher percentage of infiltrating tumours was also observed in patients with both null genotypes (P= 0.035).
Conclusions: The data obtained in the present study suggest a higher risk of bladder cancer in individuals with the GSTM1 null genotype. This risk is twofold higher when GSTM1 and GSTT1 null genotypes are both present and is also higher in smokers. A greater predisposition for more aggressive tumours appears to exist, particularly when both null genotypes are combined. Longer-term longitudinal studies are needed to confirm these results. Access the article
New Copy Number Variations in Schizophrenia, PLoS ONE, Magri, C et al.
Genome-wide screenings for copy number variations (CNVs) in patients with schizophrenia have demonstrated the presence of several CNVs that increase the risk of developing the disease and a growing number of large rare CNVs; the contribution of these rare CNVs to schizophrenia remains unknown. Using Affymetrix 6.0 arrays, we undertook a systematic search for CNVs in 172 patients with schizophrenia and 160 healthy controls, all of Italian origin, with the aim of confirming previously identified loci and identifying novel schizophrenia susceptibility genes. We found five patients with a CNV occurring in one of the regions most convincingly implicated as risk factors for schizophrenia: NRXN1 and the 16p13.1 regions were found to be deleted in single patients and 15q11.2 in 2 patients, whereas the 15q13.3 region was duplicated in one patient. Furthermore, we found three distinct patients with CNVs in 2q12.2, 3q29 and 17p12 loci, respectively. These loci were previously reported to be deleted or duplicated in patients with schizophrenia but were never formally associated with the disease. We found 5 large CNVs (>900 kb) in 4q32, 5q14.3, 8q23.3, 11q25 and 17q12 in five different patients that could include some new candidate schizophrenia susceptibility genes. In conclusion, the identification of previously reported CNVs and of new, rare, large CNVs further supports a model of schizophrenia that includes the effect of multiple, rare, highly penetrant variants. Access the article
Association between toll-like receptor 10 (TLR10) gene polymorphisms and childhood IgA nephropathy, European Journal of Pediatrics, Park, H et al.
Toll-like receptors (TLRs) play an important role in the induction and regulation of the innate immune system and adaptive immune responses. TLR10 gene polymorphisms have been reported to be associated with a range of immune-related diseases. In this study, we investigated the association of TLR10 gene polymorphisms with immunoglobulin A nephropathy (IgAN) in Korean children. To examine the association, we genotyped one promoter single nucleotide polymorphisms (SNP) [rs10004195 (−113T/A)] and three missense SNPs [rs11096957 (Asn241His), rs11096955 (Ile369Leu), and rs4129009 (Ile775Val)] using direct sequencing in 199 IgAN patients and 289 control subjects. Our case–control analysis showed that rs10004195 was associated with IgAN (codominant model, p = 0.016 in TT vs. TA; p = 0.044 in TT vs. AA; dominant model, p = 0.0068). In addition, when comparing the proteinuria level of IgAN patients according to the genotypes of each SNP, we found that in dominant model of rs1004195, the level of proteinuria of patients with TA or AA genotypes (median, 4.01 mg/m2/h) was higher than that of patients with TT genotype (2.00 mg/m2/h, p = 0.033). In conclusion, these results suggest that TLR10 gene may be associated with susceptibility to IgAN in Korean children. Access the article