FTO Polymorphisms Research Articles

Lack of association between genetic polymorphism of FTO, AKT1 and AKTIP in childhood overweight and obesity

ObjectiveObesity is a chronic disease caused by both environmental and genetic factors. Epidemiological studies have documented that increased energy intake and sedentary lifestyle, as well as a genetic contribution, are forces behind the obesity epidemic. Knowledge about the interaction between genetic and environmental components can facilitate the choice of the most effective and specific measures for the prevention of obesity. The aim of this study was to assess the association between the FTO, AKT1, and AKTIP genes and childhood obesity and insulin resistance. MethodsThis was a case–control study in which SNPs in the FTO (rs99396096), AKT1, and AKTIP genes were genotyped in groups of controls and obese/overweight children. The study included 195 obese/overweight children and 153 control subjects. ResultsAs expected, the obese/overweight group subjects had higher body mass index, higher fasting glucose, HOMA‐IR index, total cholesterol, low‐density lipoprotein, and triglycerides. However, no significant differences were observed in genes polymorphisms genotype or allele frequencies. ConclusionThe present results suggest that AKT1, FTO, and AKTIP polymorphisms were not associated with obesity/overweight in Brazilians children. Future studies on the genetics of obesity in Brazilian children and their environment interactions are needed.

Association of KALRN, ADIPOQ, and FTO gene polymorphism in type 2 diabetic patients with coronary artery disease

Recently, several genes have been introduced as potential genetic markers for diabetes mellitus and coronary artery diseases (CAD). In this case-control study, the associations of rs2241766 T/G of ADIPOQ, rs9289231 T/G of KALRN, and rs9939609 A/T of FTO polymorphisms with genetic susceptibility to CAD in type 2 diabetic (T2D) patients were investigated. A total of 224 T2D patients undergoing coronary angiography were randomly recruited into the study. Of the total diabetic patients, 152 were also diagnosed with CAD, whereas the rest were control participants. Genotyping of single-nucleotide polymorphisms was performed by high-resolution melting analysis. Genotype analysis showed that the minor allele (G) frequency of rs2241766 ADIPOQ was statistically significant in the CAD group compared with the control group [odds ratio (OR), 2.779; 95% confidence interval (CI), 1.403-5.504; P=0.003]. Also, it was found that the minor allele (G) frequency of rs9289231 KALRN was significantly associated with the risk of CAD (OR, 2.098; 95% CI, 1.096-4.017; P=0.025). In addition, no significant association was observed between the minor allele (A) of the FTO rs9939609 polymorphism and CAD (OR, 1.088; 95% CI, 0.578-2.015; P=0.788). It is speculated that the GG genotype and the G allele of the rs9289231 polymorphism of KALRN and the rs224766 polymorphism of ADIPOQ genes may be considered genetic risk factors for CAD in T2D patients and genetic variations of these genes may play a major role in the process of these disorders. Our case-control study in the Iranian population suggested a possible association between the mentioned single-nucleotide polymorphisms and CAD in T2D patients. However, further replication studies and comprehensive meta-analyses are required.

Dietary fat intake modifies the influence of the FTO rs9939609 polymorphism on adiposity in adolescents: The HELENA cross-sectional study

Background and aimsThe fat mass and obesity associated gene (FTO) has been associated with obesity and dietary intake. The aims were: (i) To assess whether energy and macronutrient intakes were different across the FTOrs9939609 genotypes in adolescents, and (ii) to explore whether dietary fat intake modified the association of the rs9939609 polymorphism with adiposity. Methods and resultsThe FTOrs9939609 polymorphism was genotyped in 652 adolescents (53% females, 14.8 ± 1.2 years, TT = 246, TA = 296, AA = 110). Energy and macronutrient intake were assessed by two non-consecutive 24 h-recalls. Weight, height, waist circumference and skinfold thicknesses were measured and body fat percent was calculated. Energy and macronutrient intake were similar across the FTOrs9939609 genotypes (P > 0.2). There were significant interactions between the FTO polymorphism and fat intake on adiposity estimates (P < 0.05). In adolescents whose fat intake was below 30% (N = 203), the A allele of rs9939609 was not associated with adiposity indices. In contrast, in adolescents whose fat intake was between 30% and 35% of energy (N = 190), the rs9939609 polymorphism was associated with a 1.9% higher body fat per risk allele (95%CI: 0.39, 3.33; P < 0.05), and in those whose fat intake was higher than 35% (N = 259), it was associated with a 2.8% higher body fat per risk allele (95%CI: 1.27, 4.43; P < 0.001). ConclusionsThese findings support the concept that the deleterious effect of the FTOrs9939609 polymorphism on adiposity is exacerbated in adolescents consuming high fat diets. In contrast, the consumption of low fat diets (<30% of energy) may attenuate the genetic predisposition to obesity in risk allele carriers.

Lack of association between genetic polymorphism of FTO, AKT1 and AKTIP in childhood overweight and obesity

ObjectiveObesity is a chronic disease caused by both environmental and genetic factors. Epidemiological studies have documented that increased energy intake and sedentary lifestyle, as well as a genetic contribution, are forces behind the obesity epidemic. Knowledge about the interaction between genetic and environmental components can facilitate the choice of the most effective and specific measures for the prevention of obesity. The aim of this study was to assess the association between the FTO, AKT1, and AKTIP genes and childhood obesity and insulin resistance. MethodsThis was a case–control study in which SNPs in the FTO (rs99396096), AKT1, and AKTIP genes were genotyped in groups of controls and obese/overweight children. The study included 195 obese/overweight children and 153 control subjects. ResultsAs expected, the obese/overweight group subjects had higher body mass index, higher fasting glucose, HOMA-IR index, total cholesterol, low-density lipoprotein, and triglycerides. However, no significant differences were observed in genes polymorphisms genotype or allele frequencies. ConclusionThe present results suggest that AKT1, FTO, and AKTIP polymorphisms were not associated with obesity/overweight in Brazilians children. Future studies on the genetics of obesity in Brazilian children and their environment interactions are needed.

Lack of Association between NYD-SP18 Variant and Obesity. The Health Alcohol and Psychosocial Factors in Eastern Europe Study

Aim: To replicate the finding that the polymorphism rs6971091 within the NYD-SP18 gene is associated with body mass index (BMI). Method: We analysed data of 29,284 adults (46.2% of males, mean age 58.9 (SD 7.3), mean BMI 28.6 (5.0 kg/m²)) examined within the Health Alcohol and Psychosocial Factors in Eastern Europe study in the Czech Republic, Poland, Lithuania and Russia. Results: BMI did not differ by rs6971091 genotype. In men, the mean BMI (SEs) in GG, GA and AA carriers were 27.8 (0.05), 27.9 (0.06) and 27.9 (0.14) kg/m², respectively, (p = 0.26); in women, the corresponding values were 29.2 (0.06), 29.1 (0.07) and 29.1 (0.16), p = 0.57. In Czech subjects (n = 6,752), for whom the FTO rs17817449 genotype was available, there was no interaction between the NYD-SP18 and FTO polymorphisms in determination of BMI. Adjustment for age, energy and fat intake and physical activity did not materially change the results. There was no association of the NYD-SP18 genotype with waist-hip ratio. Conclusion: This study in a large Slavonic population sample suggests that the rs6971091 variant within the NYD-SP18 gene is not an important determinant of obesity in middle-aged persons.

Selected single-nucleotide polymorphisms in FOXE1, SERPINA5, FTO, EVPL, TICAM1 and SCARB1 are associated with papillary and follicular thyroid cancer risk: replication study in a German population.

Several single-nucleotide polymorphisms (SNPs) have been associated with papillary and follicular thyroid cancer (PTC and FTC, respectively) risk, but few have replicated. After analyzing 17525 tag SNPs in 1129 candidate genes, we found associations with PTC risk in SERPINA5, FTO, HEMGN (near FOXE1) and other genes. Here, we report results from a replication effort in a large independent PTC/FTC case-control study conducted in Germany. We evaluated the best tagging SNPs from our previous PTC study and additionally included SNPs in or near FOXE1 and NKX2-1 genes, known susceptibility loci for thyroid cancer. We genotyped 422 PTC and 130 FTC cases and 752 controls recruited from three German clinical centers. We used polytomous logistic regression to simultaneously estimate PTC and FTC associations for 79 SNPs based on log-additive models. We assessed effect modification by body mass index (BMI), gender and age for all SNPs, and selected SNP by SNP interactions. We confirmed associations with PTC and SNPs in FOXE1/HEMGN, SERPINA5 (rs2069974), FTO (rs8047395), EVPL (rs2071194), TICAM1 (rs8120) and SCARB1 (rs11057820) genes. We found associations with SNPs in FOXE1, SERPINA5, FTO, TICAM1 and HSPA6 and FTC. We found two significant interactions between FTO (rs8047395) and BMI (P = 0.0321) and between TICAM1 (rs8120) and FOXE1 (rs10984377) (P = 0.0006). Besides the known associations with FOXE1 SNPs, we confirmed additional PTC SNP associations reported previously. We also found several new associations with FTC risk and noteworthy interactions. We conclude that multiple variants and host factors might interact in complex ways to increase risk of PTC and FTC.

Association of FTO and near MC4R variants with obesity measures in urban and rural dwelling Sri Lankans

To investigate the association between the fat mass and obesity related (FTO) gene rs9939609 and near melanocortin-4-receptor (MC4R) gene rs17782313 polymorphisms with obesity measures and metabolic parameters in urban and rural dwelling Sri Lankans. 535 subjects (60.9% female) from the general adult population (ages 18-70 years) representative of both urban (28.4%) and rural areas of residence were recruited by multi-stage random sampling. Body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) was obtained by standard methods. DNA extracted from whole blood was genotyped using real-time PCR. The FTO risk genotypes (AA+AT) were associated with higher BMI (p=0.03) and WC (p=0.05) measures as well as categorical obesity (BMI ≥27.5kgm-2 definition) (OR 1.69 95% CI 1.11-2.56, p=0.01). The near MC4R risk genotypes (CC+CT) were associated with greater BMI (p=0.03) as well as categorical obesity (BMI ≥25kgm-2 definition) (OR 1.57 95% CI 1.11-2.22, p=0.01). In addition the MC4R risk genotype carriers (CC+CT) had significantly higher fasting blood sugar (FBS) levels compared to the 'TT' genotype carriers independent of BMI (p=0.05). Urban living was associated with significantly greater BMI values for FTO risk genotypes compared to rural living (p=0.02). FTO and near MC4R variants are associated with obesity measures in Sri Lankan populations whilst urban living accentuates the obesogenic effect of the FTO polymorphism.

Association of FTO and TMEM18 polymorphisms with overweight and obesity in the population of Polish children

The objective of the study was to verify whether or not FTO rs9939609, rs9926289 and TMEM18 rs4854344, rs6548238, rs2867125 variants are important risk factors for overweight and/or obesity in Polish children aged 6-16 (n=283). FTO rs 9939609 and rs9926289 exhibited a strong codominant obesity-predisposing effect of genotypes homozygous for minor alleles (OR=5.42, 95% CI: 2.04-14.39, p=0.0006). The important finding of the study is increased risk of overweight (OR=5.03, 95% CI: 1.15-21.93, p=0.0306) in individuals homozygous for the minor alleles rs4854344, rs6548238 and rs2867125 in the recessive inheritance model, while no other significant associations between TMEM18 variants and risk of obesity were found. Given the identified interaction TMEM18 genotype × BMI category (p=0.0077), it seems that the effect of homozygous for the minor alleles may be compared to a “weight guard”, which significantly increases the risk of overweight, but not of obesity, because it promotes weight gain only up to the threshold of obesity. Conclusion: The proposed hypothetical effect (“weight guard”) of homozygous for the minor alleles in the TMEM18 based on a rather small sample is a possible explanation of the effects of minor alleles, which minimize the risk of obesity.

Contribution of ENPP1, TCF7L2, and FTO polymorphisms to type 2 diabetes in mixed ancestry ethnic population of South Africa.

Transcription factor 7-like 2 gene (TCF7L2), fat mass and obesity-associated gene (FTO), and ectonucleotide pyrophosphatase/phosphodiesterase gene (ENPP1) are known risk loci for type 2 diabetes (T2DM) mostly in European populations. To assess the association of these genes with T2DM risk in a South African mixed-ancestry population. Five hundred and sixty six participants were genotyped for ENPP1-rs997509 and -rs1044498, FTO-9941349 and -rs3751812, TCF7L2-rs12255372 and -rs7903146 polymorphisms using Taqman genotyping assays and validated by automated sequencing to assess the association of the polymorphisms with cardiometabolic traits. In logistic regression models adjusted for age, sex, body mass index (BMI) and insulin resistance, minor allele of rs997509 was associated with a higher risk of prevalent T2DM under a recessive model [odd ratio 4.60 (95% confidence interval: 1.07 to 19.86); p = 0.040].Under additive model, the rs7903146 [1.43 (1.00 to 2.04); p= 0.053] and rs9941349 [1.43 (1.00 to 2.04); p = 0.052] minor alleles showed marginally significant associations with a high risk of T2DM. However, only the rs7903146 alleles (p=0.011) and genotypes (p=0.025) distributions were statistically significantly different between diabetic and non-diabetic individuals. Our findings demonstrate that ENPP1, TCF7L2, and FTO may predispose to T2DM in the mixed-ancestry population.

Gender-Dependent Association of FTO Polymorphisms with Body Mass Index in Mexicans.

To evaluate the associations between six single-nucleotide polymorphisms (SNPs) in intron 1 of FTO and body mass index (BMI), a case-control association study of 2314 unrelated Mexican-Mestizo adult subjects was performed. The association between each SNP and BMI was tested using logistic and linear regression adjusted for age, gender, and ancestry and assuming additive, recessive, and dominant effects of the minor allele. Association analysis after BMI stratification showed that all five FTO SNPs (rs1121980, rs17817449, rs3751812, rs9930506, and rs17817449), were significantly associated with obesity class II/III under an additive model (P<0.05). Interestingly, we also documented a genetic model-dependent influence of gender on the effect of FTO variants on increased BMI. Two SNPs were specifically associated in males under a dominant model, while the remainder were associated with females under additive and recessive models (P<0.05). The SNP rs9930506 showed the highest increased in obesity risk in females (odds ratio = 4.4). Linear regression using BMI as a continuous trait also revealed differential FTO SNP contributions. Homozygous individuals for the risk alleles of rs17817449, rs3751812, and rs9930506 were on average 2.18 kg/m2 heavier than homozygous for the wild-type alleles; rs1121980 and rs8044769 showed significant but less-strong effects on BMI (1.54 kg/m2 and 0.9 kg/m2, respectively). Remarkably, rs9930506 also exhibited positive interactions with age and BMI in a gender-dependent manner. Women carrying the minor allele of this variant have a significant increase in BMI by year (0.42 kg/m2, P = 1.17 x 10−10). Linear regression haplotype analysis under an additive model, confirmed that the TGTGC haplotype harboring all five minor alleles, increased the BMI of carriers by 2.36 kg/m2 (P = 1.15 x 10−5). Our data suggest that FTO SNPs make differential contributions to obesity risk and support the hypothesis that gender differences in the mechanisms involving these variants may contribute to disease development.

FTO polymorphism (RS9939609) and BED in patients with morbid obesity for evaluation towards bariatric surgery

Background Obesity is a major health problem in the twenty-first century. Recent research shows that, among people with severe obesity, there is a sub-population that does not respond to behavioral treatment for weight loss. This group presents a type of eating disorder known as Binge Eating Disorder (BED). Recent studies indicate a link between obesity in adults and the rs9939609 polymorphism of the FTO gene. A frequent association of obesity and BED has also been found. Variations in the gene, including the rs9939609 polymorphism, have been associated with obesity and diabetes.

Effect of six type II diabetes susceptibility loci and an FTO variant on obesity in Pakistani subjects.

The aim of the current study was to analyze the effect of six type II diabetes GWAS loci rs3923113 (GRB14), rs16861329 (ST6GAL1), rs1802295 (VPS26A), rs7178572 (HMG20A), rs2028299 (AP3S2) and rs4812829 (HNF4A), and an FTO polymorphism (rs9939609) on obesity. The probable mechanism of action of these SNPs was analyzed by studying their association with various biochemical and anthropometric parameters. A total of 475 subjects (obese=250, controls=225) were genotyped by TaqMan assay and their lipid profile was determined. Allele/genotype frequencies and an unweighted/weighted gene score were calculated. The effect of the gene score on anthropometric and biochemical parameters was analyzed. The minor allele frequencies of all variants were comparable to that reported in the original studies and were associated with obesity in these Pakistani subjects. Subjects with 9 risk alleles differ from those with <3 and overall there is no significant effect (P-value for trend 0.26). None of the SNPs were associated with any of the serum lipid traits. We are the first to report the association of these T2D SNPs with obesity. In the Pakistani population the reported effect of six SNPs for obesity is similar to that reported for T2D and having a combination of risk alleles on obesity can be considerable. The mechanism of this effect is unclear, but appears not to be mediated by changing serum lipid chemistry.

Sex-Specific Association between Longitudinal Changes in Adiposity, FTO rs9939609 Polymorphism, and Leukocyte Telomere Length

Objective: A longitudinal study was conducted to examine sex-specific associations between changes in adiposity over a 10-year period, the FTO rs9939609 polymorphism, and leukocyte telomere length (LTL).Methods: A population-based cohort including 2128 middle-aged and older Korean men (n = 1087) and women (n = 1041) participated in a prospective study. Anthropometric measurements of weight, height, and waist and hip circumference were taken at baseline (from 2001 to 2003) and at the 10-year follow-up period (from 2011 to 2012). The FTO rs9939609 polymorphism was genotyped using DNA samples collected at baseline and LTL was assessed at the 10-year follow-up period. Multiple linear regression analysis was used with adjustments for age, baseline body mass index, and other potential confounders.Results: Presence of the FTO rs9939609 polymorphism risk allele was inversely associated with LTL (p < 0.01) in all participants, with a significant association seen only in women when the genders were modeled separately. Conversely, a significant inverse association between changes in waist circumference and LTL was found in men (p < 0.001) but not in women. No significant interaction between adiposity measures and the FTO polymorphism in association with LTL was identified for either sex.Conclusions: These data suggest that biological aging in men may be accelerated by increasing waist circumference, whereas in women, aging may be affected by genetic variations in FTO regardless of adiposity changes over time.

FTO Polymorphism rs9939609 Contributes to Weight Changes in Children With Celiac Disease on Gluten-Free Diet.

Studies of adults and children with celiac disease have reported an increased risk of overweight during gluten-free diet (GFD). The fat mass and obesity-associated gene (FTO) variant rs9939609 has been associated with increased risk of developing obesity in children and adults. In our study, we analyzed the effect of this variant on weight gain in a cohort of 280 children with celiac disease on GFD. We found that after a mean follow-up time of 3.0 years on GFD, FTO polymorphism influenced significantly the mean change in body mass index z score (P = 0.01). We conclude that the FTO gene contributes to determine weight changes in children with celiac disease on GFD.

Are obesity risk genes associated with binge eating in adolescence?

ObjectiveCognitions and behaviors characteristic of binge eating are associated with a polymorphism in the FTO gene, robustly related to body mass index (BMI) and obesity risk. We investigated the association between binge eating and the individual and combined effect of 32 SNPs robustly associated with BMI in a population-based sample. We hypothesized that higher BMI and binge eating might share a common genetic etiology.MethodsBinge eating was assessed in adolescents from the Avon Longitudinal Study of Parents and Children at age 14 (n = 5,958) and 16 years (n = 4,948). We tested associations between 32 BMI-related SNPs and binge eating in crude and BMI-, age-, and gender-adjusted regression models.ResultsCrude analyses showed an association between binge eating and rs1558902 (FTO) that persisted after adjustment for BMI (OR = 1.20, P = 8 × 10−3). A weighted allelic score consisting of all 32 BMI-related SNPs was associated with binge eating (P = 8 × 10−4); this association attenuated (P = 0.08) when rs1558902 was removed from the weighted allelic score.ConclusionsBMI-related genes are associated with adolescent binge eating, in particular an FTO polymorphism. Although replication is needed, our findings have biological plausibility and are consistent with a postulated effect of FTO on appetite and food intake. Future studies should aim to understand the mechanisms underlying the relationship between FTO, binge eating, and obesity.

Interaction between common variants of FTO and MC4R is associated with risk of PCOS.

BackgroundPolycystic ovary syndrome (PCOS) is a common and complex endocrine-metabolic disease. One of the well-documented characteristics of PCOS is obesity or overweightness. It is possible to be genetically predisposed to becoming obese or overweight, and several potentially causative single nucleotide polymorphisms (SNPs), such as rs9939609 (A/T) in the fat mass, and obesity-associated gene (FTO) and rs17782313 (T/C) in the melanocortin-4 receptor gene (MC4R), have been investigated. Further investigation of association between obesity-associated SNPs and PCOS susceptibility will contribute to a better understanding of the disease.MethodsIn the present study, we enrolled 733 patients with PCOS and 892 control subjects. The common variants FTO rs9939609 and MC4R rs17782313 were genotyped and their relationship with obesity-related traits was evaluated.ResultsRs9939609 and rs17782313 are associated with PCOS and obesity-related traits and profiles. The association found between PCOS and FTO rs9939609 (p = 0.0302) was attenuated after adjustment for BMI (p = 0.187). MC4R rs17782313 did not confer an increased risk for PCOS (p = 0.368) even after adjustments (p = 0.715). Interestingly, the interaction of FTO and MC4R polymorphisms was more significantly associated with PCOS (p = 0.031, adjusted for age and BMI). The FTO variant rs9939609 is associated with Chinese women with PCOS; however, this association is affected by BMI.ConclusionsThe combined pathogenic effect of FTO and MC4R polymorphisms indicates a direct role of the interaction between FTO and MC4R polymorphisms in the development of PCOS.

Association between FTO polymorphism in exon 3 with carcass and meat quality traits in crossbred ducks

The fat mass and obesity-associated gene (FTO) is an excellent candidate gene that affects energy metabolism. Single nucleotide polymorphisms (SNPs) in FTO are associated with carcass and meat quality traits in pigs, cattle, and rabbits. The aim of this study was to investigate the association between novel SNPs in the FTO coding region and carcass and meat quality traits in 95 crossbred ducks, using DNA sequencing. We found two transitions G/A (SNP 387 and 473) within exon 3. SNP 387 was a synonymous mutation, whereas SNP 473 was a missense mutation. Association analysis suggested that SNP g.387G>A was significantly associated with all of the carcass traits measured, the intramuscular fat content (IMF), cooking yield (CY), pH values 45 min after slaughter (pH45m), drip losses from the breast muscle, and the leg muscle (P < 0.05). For SNP g.473G>A, the genotype AA exhibited greater leg muscle weight than the genotypes GG or AG (P < 0.05). The D value suggested that the two SNPs exhibited strong linkage disequilibrium. Three haplotypes (G1G2, G1A2, and A1A2) were significantly associated with IMF, CY, the a* value, and all of the carcass traits measured (P < 0.05). The results suggest that FTO is a candidate locus that affects carcass and meat quality traits in ducks.

Association between polymorphisms of fat mass and obesity-associated gene and metabolic syndrome in Kazakh adults of Xinjiang, China.

The aim of this study was to assess the association between three FTO polymorphisms (rs9939609, rs8057044, and rs1421085) and metabolic syndrome (MS)-related outcomes in the low-income, rural, nomadic minority Khazakh population in far western China. A total of 489 subjects (245 MS patients, 244 controls) were included in the study and DNA samples were genotyped for the three polymorphisms by matrix-assisted laser desorption/ionization time of flight mass spectrometry. The frequencies of the rs1421085 and rs9939609 genotypes and alleles did not differ significantly between MS patients and control, while the frequencies of rs8057044 G alleles and GG genotypes were higher in MS patients (P < 0.05) than in control subjects (G: 61.16 vs 53.53%, GG: 39.07 vs 29.05%) and the frequencies of rs8057044 A genotypes and alleles were lower (P < 0.05) in MS patients compared with controls (AA: 17.36 vs 21.99%, A: 38.84 vs 46.47%). Risk analysis of the rs8057044 polymorphism revealed individuals with GA and GG genotypes to have 1.112 and 1.731 times higher risks of developing MS than those with the AA genotype, respectively, while the G allele was found to be associated with a 1.367 times higher risk of developing MS compared with the A allele. These apparent correlations, however, did not hold true when adjusted for BMI. Weight, WC, HC, and BMI differed significantly between rs8057044 GG and AA+GA genotypes (P < 0.05).

Nobody Is Perfect: Comparison of the Accuracy of PCR-RFLP and KASP™ Method for Genotyping. ADH1B and FTO Polymorphisms as Examples

DNA genotyping is among the most common analyses currently performed in scientific research. Two high-throughput genotyping techniques are widely used – the “classic” PCR-RFLP and probe-based methods such as TaqMan® PCR assay or KASP™ genotyping. The probe-based techniques are claimed to be more accurate than PCR-RFLP; however, the evidence for this claim is sparse. We have directly compared results of genotyping of two SNPs (rs1229984 and rs17817449) obtained by the PCR-RFLP and KASP™ in 1,502 adult Caucasians. The results were identical in 97.3 % and 95.9 % cases, respectively. Discrepancies (either different results or result obtained with one but not with the other method) were addressed by confirmatory analysis using direct sequencing. The sequencing revealed that both methods can give incorrect results, but the frequency of incorrect genotyping of rs1229984 and rs17817449 was very low for both methods – 0.1 % and 0.5 %, respectively, for PCR-RFLP and 0.1 % and 0.3 %, respectively, for KASP™. These results confirm that the KASP™ technique is slightly more accurate, but it achieves slightly lower call rates than PCR-RFLP. When carefully set up, both PCR-RFLP and KASP™ could have accuracy of 99.5 % or higher.

Association of FTO, KCNJ11, SLC30A8, and CDKN2B polymorphisms with type 2 diabetes mellitus

To test FTO, KCNJ11, SLC30A8, and CDKN2B for association with type 2 diabetes mellitus (DM), the allele and genotype frequency distributions were established for several polymorphisms of the genes. A comparison of allele and genotype frequencies between DM patients and healthy subjects implicated CKNJ11, SLC30A8, and CDKN2B, but not FTO, in the disease. The genes that affect insulin production and secretion in pancreatic β cells proved to play a main role in type 2 DM in the Russian population.