Author Correction: Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta.

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Hybrid de novo whole-genome assembly and annotation of the model tapeworm Hymenolepis diminuta.

Despite the use of Hymenolepis diminuta as a model organism in experimental parasitology, a full genome description has not yet been published. Here we present a hybrid de novo genome assembly based on complementary sequencing technologies and methods. The combination of Illumina paired-end, Illumina mate-pair and Oxford Nanopore Technology reads greatly improved the assembly of the H. diminuta genome. Our results indicate that the hybrid sequencing approach is the method of choice for obtaining high-quality data. The final genome assembly is 177 Mbp with contig N50 size of 75 kbp and a scaffold N50 size of 2.3 Mbp. We obtained one of the most complete cestode genome assemblies and annotated 15,169 potential protein-coding genes. The obtained data may help explain cestode gene function and better clarify the evolution of its gene families, and thus the adaptive features evolved during millennia of co-evolution with their hosts.

Selected RANKL/RANK/OPG system genetic variants in diabetic foot patients.

PURPOSE: Diabetic foot is a complication of long-lasting diabetes mellitus affecting up to 15% of patients, both in type 1 and type 2 diabetes. Osteoprotegerin is involved in osteogenesis and calcification. The aim of the study was to assess the role of selected osteoprotegerin gene variants in diabetes patients with diabetic foot. METHODS: The study involved 300 patients with diabetes and diabetic foot and 968 healthy controls. The study group was formed by 243 patients with diabetic foot of neuropathic origin, 102 with diabetic foot of neuroischemic origin and 77 with Charcot neuroarthropathy. RESULTS: Compared to controls, rs1872426 and rs1485286 showed correlation with diabetic foot in diabetes subjects. Significant associations between rs2073618, rs1872426, rs7464496 and rs1485286 in men were reported. The aforementioned correlations were also present in type 2 diabetes patient subgroup. Variant rs1485286 was associated to diabetic foot of neuropathic origin. Sex-specificity for females was present for rs6993813 in patients with diabetic foot of neuropathic origin and type 1 diabetes. Variants rs1872426, rs2073617 and rs1485286 were correlated with CN. We found that age, body weight, body mass index, waist circumference, hip circumference and waist-hip ratio were among the basic risk factors of diabetic foot. CONCLUSIONS: The following variants TNFRSF11B (rs2073618, rs2073617, rs1872426, rs1032128, rs7464496, rs11573829 and rs1485286), COLEC10 (rs6993813, rs3134069) and TNFSF11 (rs9533156) present differences in allele frequencies in diabetic foot patients and show correlation with gender, diabetes type and diabetic foot etiology.

New mtDNA Association Model, MutPred Variant Load, Suggests Individuals With Multiple Mildly Deleterious mtDNA Variants Are More Likely to Suffer From Atherosclerosis.

The etiology of common complex diseases is multifactorial, involving both genetic, and environmental factors. A role for mitochondrial dysfunction and mitochondrial DNA (mtDNA) variation has been suggested in the pathogenesis of common complex traits. The aim of this study was to investigate a potential role of mtDNA variants in the development of obesity, diabetes, and atherosclerosis in the Polish population. Whole mtDNA sequences from 415 Polish individuals representing three disease cohorts and a control group were obtained using high-throughput sequencing. Two approaches for the assessment of mtDNA variation were applied, traditional mitochondrial haplogroup association analysis and the mutational or variant load model using the MutPred pathogenicity prediction algorithm for amino acid substitutions in humans. We present a possible association between mildly deleterious mtDNA variant load and atherosclerosis that might be due to having more than one likely mildly deleterious non-synonymous substitution. Moreover, it seems largely dependent upon a few common haplogroup associated variants with MutPred score above 0.5.

Genetic predictors associated with diabetic retinopathy in patients with diabetic foot.

INTRODUCTION    Early detection of diabetic retinopathy (DR) is crucial for preventing irreversible blindness. Recent studies identified some of the genetic factors involved in the pathology of DR, although their precise underlying mechanisms remain unclear. OBJECTIVES    This pilot study aimed to determine genetic predictors of DR among patients with type 2 diabetes (T2D) and diabetic foot (DF) based on pathogenetic pathways. PATIENTS AND METHODS    The study included 114 patients with T2D and DF (64 with DR, 50 without DR). Genetic analysis was performed for each patient and the following alterations were analyzed: rs759853 (AKR1B1), rs1800469 (TGFB1), rs2073618 and rs3134069 (TNFRSF11B), rs6330 and rs11466112 (NGF), rs1801133 (MTHFR), rs8192678 (PPARGC1A), rs1799983 (NOS3), rs1553005 (CALCA), and rs121917832 (CDKN1B). RESULTS    Correlations with DR were identified for the following single nucleotide variants (SNVs): rs759853, rs2073618, and rs3134069. Carriers of the G allele of the rs759853 variant had a higher risk of DR in the dominant model (odds ratio [OR], 3.0; 95% confidence interval [CI], 1.15-7.81; P = 0.02). We analyzed 2 SNVs of the osteoprotegerin gene (rs3134069 and rs2073618), and found that the A allele of the rs3134069 variant decreased the risk of DR in both the recessive and additive models (OR, 3.33; 95% CI, 1.07-10.3; P = 0.04). Conversely, there were fewer carriers of the C allele of the rs2073618 variant in patients with DR in the dominant model (OR, 0.28; 95% CI, 0.09-0.92; P = 0.04). CONCLUSIONS    The results of our study suggest that the SNVs rs759853, rs3134069, and rs2073618 may be involved in the development of DR in patients with T2D and DF.

Role of the rs2274907 allelic variant of the ITLN1 gene in patients with diabetic foot.

INTRODUCTION Diabetic foot (DF) is a serious complication of diabetes mellitus (DM) that occurs due to neuropathy or atherosclerosis of the lower limbs. Omentin (encoded by the ITLN1 gene) has been implicated as a protective factor in vascular complications of diabetes, likely due to its endothelial vasodilator activity and its anti­inflammatory actions. However, susceptibility to DF with respect to the allelic variants of the ITLN1 gene has not been studied so far. OBJECTIVES This study aimed to evaluate the association between the rs2274907 allelic variant of the ITLN1 gene and the occurrence of DF in patients with type 2 diabetes mellitus (T2DM).  PATIENTS AND METHODS The study included 670 individuals: 204 with T2DM and DF (DF group), 299 with T2DM without DF (T2DM group), and 167 healthy controls.  RESULTS Ischemic heart disease, retinopathy, nephropathy, neuropathy, obesity, hyperlipidemia, and active smoking were more frequent in the DF group than in the T2DM group. Allele A of the rs2274907 variant was observed more frequently in the DF group compared with healthy controls in an additive model (odds ratio [OR] = 0.7, P = 0.034). This effect was also sex­specific for males in both the additive and recessive models (OR = 0.6, P = 0.015 and OR = 0.52, P = 0.0017, respectively). However, no differences in the distribution of alleles was observed between the DF and T2DM groups. CONCLUSIONS The rs2274907 variant of the ITLN1 gene is associated with increased prevalence of DF.

OXTR polymorphism in depression and completed suicide-A study on a large population sample.

In the light of contradictory results concerning OXTR polymorphism rs53576 and depression, we decided to verify the potential association between the two on 1) a large, ethnically homogenous sample of 1185 individuals who completed the Beck Depression Inventory (BDI), as well as on 2) a sample of 763 suicide victims. In the population sample, AA males showed significantly lower BDI scores (p=0.005, pcor=0.030). Exploratory analyses suggested that this effect was limited to a subgroup within 0-9 BDI score range (p=0.0007, U-Mann Whitney test), whereas no main effect on depressive symptoms (BDI>9) was found. In the suicide sample no association with rs53576 genotype was present. Exploratory analyses in suicides revealed higher blood alcohol concentration (BAC) among AA than GG/GA males (p=0.014, U-Mann Whitney test). Our results show that the OXTR rs53576 variant modulates the mood in male individuals and may positively correlate with alcohol intake among male suicides, but is not associated with suicide or depression. The study adds to the growing knowledge on rs53576 genotype characteristics.

Risk factors of diabetic foot of neuropathic origin in patients with type 2 diabetes.

INTRODUCTION: Diabetic foot is a diabetes mellitus complication leading to recurrent ulcerations, risk of osteomyelitis and tissue necrosis which may finally result in amputation. Diabetic foot of neuropathic origin manifesting as autonomic and sensory motor neuropathy is the most common type of this complication. The aim of this study was to identify risk factors of diabetic foot of neuropathic origin occurrence in patients with type 2 diabetes. MATERIAL AND METHODS: The study included 240 patients, 74 with diabetic foot of neuropathic origin and 166 with diabetes. Cases and controls were matched in terms of age structure. Patients with peripheral arterial disease were excluded from the study. The study was conducted in the Gastroenterology and Metabolic Diseases Department, Medical University of Warsaw, Poland. We used logistic regression models, χ2, U Mann-Whitney's and t-Student tests. RESULTS: Logistic regression analysis showed that diabetic foot of neuropathic origin risk factors were: male gender (OR = 6.63; 95% CI: 3.31-13.27; p = 0.00001), duration of diabetes (OR = 1.10; 95% CI: 1.06-1.14; p = 0.00001), height (OR = 1.09; 95% CI: 1.06-1.13; p = 0.00001), weight (OR = 1.04; 95% CI: 1.04-1.06; p = 0.00001) and waist circumference (OR = 1.05; 95% CI: 1.02-1.08; p = 0.001). Although there was a correlation between diabetic foot of neuropathic origin and BMI value, it had no impact on DF occurrence risk. CONCLUSION: It is possible to identify patients at risk of diabetic foot development by evaluating anthropometric features. The existence of specific factors increasing the odds of diabetic foot of neuropathic origin occurring may lead to the identification of patients at risk of its development.

A note of caution on the diagnosis of Martin-Probst syndrome by the detection of the p.D59G mutation in the RAB40AL gene.

UNLABELLED: Martin-Probst syndrome (MPS) is an X-linked multisystem neurodevelopmental disorder, reported to be caused by the p.D59G mutation in RAB40AL. Whereas evidence against the pathogenic role of p.D59G has been published, the presence of RAB40AL p.D59G continues to be used as a support for MPS diagnosis. Our purpose was to provide further arguments for excluding pathogenicity of RAB40AL p.D59G. We detected p.D59G in two healthy males ascertained as family members of p.D59G carriers who underwent whole exome sequencing for diagnostic reasons. Furthermore, we found that p.D59G was present in 2.86% (4/140) of randomly selected Polish males with higher education. CONCLUSION: Our findings are inconsistent with a causative effect of RAB40AL p.D59G on cognitive impairment combined with severe to profound bilateral hearing loss but indicate that p.D59G is a common genetic variation. Our data emphasize the need for genotyping large sample sizes of diverse populations as a basic tool in determining variant pathogenicity.

Diabetic foot risk factors in type 2 diabetes patients: a cross-sectional case control study.

BACKGROUND: Diabetic foot is a serious condition in patients with a long lasting diabetes mellitus. Diabetic foot treated improperly may lead not only to delayed ulceration healing, generalized inflammation, unnecessary surgical intervention, but also to the lower limb amputation. The aim of this study was to compare diabetic foot risk factors in population with type 2 diabetes and risk factors for diabetes in healthy subjects. METHODS: The study included 900 subjects: 145 with diabetic foot, 293 with type 2 diabetes without diabetic foot and 462 healthy controls matched in terms of mean age, gender structure and cardiovascular diseases absence. Study was conducted in Gastroenterology and Metabolic Diseases Department, Medical University of Warsaw, Poland. In statistical analysis a logistic regression model, U Mann-Whitney's and t-Student test were used. RESULTS: The binomial logit models analysis showed that the risk of diabetic foot in patients with type 2 diabetes was decreased by patient's age (odds ratio [OR] = 0.94; 95% confidence interval [CI]: 0.92-0.96; p = 0.00001) and hyperlipidaemia (OR = 0.54; 95% CI: 0.36-0.81; p = 0.01). In contrast, male gender (OR = 2.83; 95% CI: 1.86-4.28; p = 0.00001) diabetes duration (OR = 1.04; 95% CI: 1.03-1.06; p = 0.0003), weight (OR = 1.04; 95% CI: 1.03-1.06; p = 0.00001), height (OR = 1.08; 95% CI: 1.05-1.11; p = 0.00001) and waist circumference (OR = 1.028; 95% CI: 1.007-1.050; p = 0.006) increase the risk of diabetic foot. The onset of type 2 diabetes in healthy subjects was increased by weight (OR = 1.035; 95% CI: 1.024-1.046; p = 0.00001), WC (OR = 1.075; 95% CI: 1.055-1.096; p = 00001), hip circumference (OR = 1.03; 95% CI: 1.01-1.05; p = 0.005), overweight defined with body mass index (BMI) above 24,9 kg/m(2) (OR = 2.49; 95% CI: 1.77-3.51; p = 0.00001) and hyperlipidaemia (OR = 3.53; 95% CI: 2.57-4.84; p = 0.00001). CONCLUSIONS: Risk factors for Type 2 diabetes and diabetic foot are only partially common. Study proved that patients who are prone to developing diabetic foot experience different risk factors than patients who are at risk of diabetes. Identification of relationship between diabetic foot and diabetes risk factors in appropriate groups may help clinicians to focus on certain factors in diabetic foot prevention.

Osteoprotegerin gene rs2073617 and rs3134069 polymorphisms in type 2 diabetes patients and sex­specific rs2073618 polymorphism as a risk factor for diabetic foot.

INTRODUCTION:  Diabetic foot is a severe diabetic complication, which may result in ulcerations that are unresponsive to treatment and in lower limb amputation. Osteoprotegerin is a protein that is involved in the pathogenesis of diabetic foot. OBJECTIVES:  The aim of the study was to evaluate the frequency of alleles in the TNFRSF11B gene rs2073617, rs2073618, and rs3134069 polymorphisms in patients with diabetic foot, diabetes, and healthy controls. PATIENTS AND METHODS: The study comprised 877 patients, including 122 with diabetic foot, 293 with type 2 diabetes without diabetic foot, and 462 healthy controls. RESULTS: In the rs2073618 polymorphism, the C allele was a risk factor for diabetic foot in patients with diabetes in the allelic variants [CC] vs. [CG + GG] (odds ratio [OR], 1.72; 95% confidence interval [CI], 1.03-2.86; P = 0.035), and in men in the following allelic variants: CC vs. GG (OR, 3.16; 95% CI, 1.27-7.87; P = 0.011), CC vs. CG (OR, 3.33; 95% CI, 1.47-7.54; P = 0.002), and [CC] vs. [CG + GG] (OR, 3.28; 95% CI, 1.48-7.24; P = 0.002). A similar association was observed between men with diabetic foot and those only with diabetes in the following allelic variants: CC vs. GG (OR, 2.30; 95% CI, 0.91-5.85; P = 0.076), CC vs. CG (OR, 2.69; 95% CI, 1.16-6.22; P = 0.018) and [CC] vs. [CG + GG] (OR, 2.56; 95% CI, 1.13-5.77; P = 0.02). For patients with neuropathic diabetic foot, the association was demonstrated in variant CC vs. CG (OR, 2.5; 95% CI, 1.00-6.23; P = 0.044) and only for men in the following allelic variants: [CC] vs. [CG + GG] (OR, 3.17; 95% CI, 1.07-9.38; P = 0.029) and CC vs. CG (OR, 3.49; 95% CI, 1.15-10.58; P = 0.02). The A allele of the rs2073617 polymorphism protected women in variant AA vs. AG against diabetic foot compared with controls (OR, 0.45; 95% CI, 1.00-4.92; P = 0.045). The rs3134069 polymorphism was not observed to be a risk factor for diabetic foot. CONCLUSIONS:  The analysis of the TNFRSF11B gene may be used to assess the risk of diabetic foot and neuropathic diabetic foot in patients with type 2 diabetes.

No association between MTHFR C677T polymorphism and completed suicide.

MTHFR C677T polymorphism (rs1801133) was associated with numerous psychiatric conditions but no prior study investigated whether it predisposes to completed suicide. We typed rs1801133 in 692 suicide victims and 3257 controls representative of a Polish adult population (the WOBASZ cohort). Although we had a power of 0.8 to detect (at alpha 0.05) an allelic OR=1.19, we did not find significant difference among suicides vs. controls in the prevalence of the MTHFR 677T allele (OR=1.02, p=0.759) or the TT genotype (OR=1.01, p=0.926). Since among controls we found an association between TT and depression defined by Beck Depression Inventory (BDI, OR=1.61, p=0.049) we also compared suicides with controls without signs of depression (BDI ≤ 11) but found no association (OR=1.0, p=0.976). Analyses within suicides showed trends (not significant after Bonferroni correction) for correlations between the dose of the T allele and age at death among males and blood ethanol concentration among females, who committed suicide under the influence of alcohol. We conclude that MTHFR C677T polymorphism is not a risk factor for completed suicide. The sex-specific trends for correlations between rs1801133 and age at death, and blood ethanol concentration should be studied further.

MTHFR 677T is a strong determinant of the degree of hearing loss among Polish males with postlingual sensorineural hearing impairment.

Hearing impairment (HI) is the most common sensory handicap. Congenital HI often has a genetic basis, whereas the etiology of nonsyndromic postlingual HI (npHI) usually remains unidentified. Our purpose was to test whether the MTHFR C677T (rs1801133) polymorphism affecting folate metabolism is associated with the occurrence or severity of npHI. We studied rs1801133 genotypes in 647 npHI patients (age <40, sudden sensorineural loss excluded, HI characterized as mean of better ear hearing thresholds for 0.5-8 kHz) and 3273 adult controls from the background population. Genotype distribution among patients and controls was similar, but among male cases (n = 302) we found a dose-dependent correlation of MTHFR 677T with the degree of HI (mean thresholds in dB: 38.8, 44.9, and 53.3, for CC, CT, and TT genotypes, respectively; p = 0.0013, p(cor.) = 0.017). Among male patients rs1801133 TT significantly increased the risk of severe/profound HI (odds ratio = 4.88, p = 0.001). Among controls the known effect of MTHFR 677T on plasma total homocysteine was more pronounced in men than in women (p<0.00004 for genotype-sex interaction) suggesting that in Poland folate deficiency is more prevalent in males. In conclusion, we report a novel strong effect of MTHFR 677T among males with npHI. The functional significance of rs1801133 suggests that these patients may benefit from folate supplementation-an intervention which is simple, cheap, and devoid of side effects.

Inverse association of the obesity predisposing FTO rs9939609 genotype with alcohol consumption and risk for alcohol dependence.

AIMS: To investigate whether the FTO rs9939609 A allele (a risk factor for obesity) is associated with measures of alcohol consumption. DESIGN: Population-based cross-sectional study and two case-control studies. SETTING: Poland and the Warsaw area. PARTICIPANTS: A total of 6584 subjects from the WOBASZ survey and two cohorts of alcohol-dependent patients (n = 145 and n = 148). MEASUREMENTS: Questionnaire data analysis, rs9939609 typing. FINDINGS: Among individuals drinking alcohol, the obesity-associated AA genotype was also associated with lower total ethanol consumption [sex-, age- and body mass index (BMI)-adjusted difference: 0.21 g/day, P = 0.012] and distinct drinking habits with relatively low frequency of drinks but larger volume consumed at a time as evidenced by (i) association between AA and frequency/amount of typical drinks (P = 0.023, multiple logistic regression analysis); (ii) inverse correlation between AA and drink frequency adjusted for drink size (P = 0.007 for distilled spirits, P = 0.018 for beer); (iii) decreased frequency of AA [odds ratio (OR) = 0.46, P = 0.0004] among those who drank small amounts of distilled spirits (≤ 100 ml at a time) but frequently (≥ 1-2 times/week). A decrease of AA was also found in both cohorts of alcohol-dependent patients versus geographically matched subjects from WOBASZ yielding a pooled estimate of OR = 0.59, confidence interval (CI): 0.40-0.88, P = 0.008. Exploratory analysis showed that those with rs9939609 AA reported lower (by 1.22) mean number of cigarettes/day during a year of most intense smoking (P = 0.003) and were older at start of smoking by 0.44 years (P = 0.016). CONCLUSIONS: The FTO AA genotype, independently from its effect on BMI, is associated with measures of ethanol consumption and possibly tobacco smoking.

Impact of MTHFR C677T gene polymorphism and vitamins intake on homocysteine concentration in the Polish adult population.

BACKGROUND: Homocysteine (Hcy) levels are modulated by nutritional and genetic factors, among which is the enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR). AIM: To determine the effects of the MTHTR C677T polymorphism, as well as the intake of folate, vitamins B(6) and B(12) on serum Hcy concentration in the Polish population. METHODS: Within the framework of the National Multicentre Health Survey (WOBASZ), a representative sample of the whole Polish population aged 20-74 was screened in 2003-2005. Vitamins intake, Hcy level and known MTHTR C677T genotype were available for 1,561 men and 1,712 women. RESULTS: In the Polish population, T/T, C/T and C/C genotype frequencies were 10%, 43% and 47%, respectively in men, and 9%, 42% and 49%, respectively in women. The T/T genotype was associated with increased levels of Hcy (13.14 µmol/L in men, and 9.77 mmol/L in women) compared to the C/C and C/T genotypes (10.18 and 8.77, respectively), after adjustment for age, methionine, coffee and alcohol intake, smoking and drugs used. In a multivariable linear regression model, among subjects with the T/T genotype, the only factor influencing Hcy was age in women. In the case of the other groups (C/C and C/T), there was a relationship between Hcy and age, alcohol consumption, drugs used, folate and vitamin B(6) in men, and age, smoking, coffee consumption, drugs used, folate and vitamin B(12) in women. CONCLUSIONS: The T/T genotype is associated with higher levels of Hcy (29% in men, and 11% in women) compared to other genotypes. Nutritional factors affect Hcy levels only in the C/C and C/T MTHFR genotypes.