Clinical characteristics and analysis of HFE gene variants (C282Y and H63D) in Jordanian Arab patients with age-related macular degeneration

Age-related macular degeneration (AMD) is a complex genetic disorder with multiple etiologies. Multiple genes as well as environmental effects are thought to play a role in causing AMD. Recent evidence pointed that elevated iron overload, resulting from hereditary defects of iron homeostasis, is associated with retinal degeneration and consequently plays a role in the pathogenesis of AMD. Hemochromatosis is a genetic disorder in which excess iron is absorbed from the diet and deposited in different tissues, primarily caused by mutations in HFE gene. Two major mutations in HFE are responsible for most hemochromatosis cases, namely, C282Y and H63D. In this work we gathered information relating to 37 AMD patients from Jordan, and investigated the potential association between hemochromatosis, or more specifically, carrier state for a mutation in HFE gene (which may moderately increase dietary iron absorption) and AMD, given the effect of elevated iron levels on AMD occurrence. Questionnaires and blood samples were collected from patients visiting the eye care clinic in the King Abdullah hospital in Jordan. DNA was extracted from patient samples and mutations in HFE were genotyped (using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP), and DNA sequencing) and compared to 106 control samples. We could not detect C282Y (rs1800562) variant in our patient population or in the controls. For carrier status with H63D (rs1799945) we had 30.3% compared to a frequency of 22.7% in the controls (p= 0.37). H63D allele frequency was 15.2% in our patients compared to 11.8% in the controls (p=0.30). H63D variant seems to be more frequent in AMD patients though not reaching a significance of p= 0.05. To date, this is the first attempt to link HFE (particularly, H63D) mutation to AMD.Keywords: AMD; HFE; C282Y; H63D; Association; PolymorphismThe Egyptian Journal of Medical Human Genetics (2013) 14, 177–18

Protein contact map prediction using multi-stage hybrid intelligence inference systems

AbstractProteins are one of the most important molecules in organisms. Protein function can be inferred from its 3D structure. The gap between the number of discovered protein sequences and the number of structures determined by the experimental methods is increasing. Accurate prediction of protein contact map is an important step toward the reconstruction of the protein’s 3D structure. In spite of continuous progress in developing contact map predictors, highly accurate prediction is still unresolved problem. In this paper, we introduce a new predictor, JUSTcon, which consists of multiple parallel stages that are based on adaptive neuro-fuzzy inference System (ANFIS) and K nearest neighbors (KNNs) classifier. A smart filtering operation is performed on the final outputs to ensure normal connectivity behaviors of amino acids pairs. The window size of the filter is selected by a simple expert system. The dataset was divided into testing dataset of 50 proteins and training dataset of 450 proteins. The system produced an average accuracy of 45.2% for the sequence separation of six amino acids. In addition, JUSTcon outperformed SVMcon and PROFcon predictors in the cases of large separation distances. JUSTcon produced an average accuracy of 15% for the sequence separation of 24 amino acids after applying it on CASP9 targets

Frequency of the Hemochromatosis Gene (HFE) Variants in a Jordanian Arab Population and in Diabetics from the Same Region

Hereditary HFE-linked hemochromatosis is a frequent recessive disorder among individuals of northern European ancestry. The clinical characteristic of this disease is the gradual accumulation of iron in internal organs, which ultimately may lead to organ damage and death. Three allelic variants of HFE gene have been correlated with hereditary hemochromatosis: C282Y is significantly associated with hereditary hemochromatosis in populations of Celtic origin, H63D and S65C are associated with milder form of iron overload. In this study we performed mutation analysis to identify allele frequency of the three variants of HFE gene in Jordanian Arab population, to assess deviations of these frequencies from those detected elsewhere, and to determine if there is an increased frequency of these variants in a diabetic population (Type 2 diabetes) from the same area. DNA was extracted from blood samples of 440 individuals attending King Abdullah University Hospital for ambulatory services. We used polymerase chain reaction (PCR) to amplify exons 2 and 4 of the HFE gene then restriction fragment length polymorphism (RFLP) method to detect the variants. There were neither homozygous nor heterozygous for C282Y variant. For the H63D variant, 0.68% were homozygous and 21.1% were heterozygous. For the S65C variant, there were no homozygous and 0.23% were heterozygous. Allelic frequencies were, 0%, 11.25%, and 0.11% for C282Y, H63D, and S65C, respectively. Our samples were subdivided into two categories of type 2 diabetic (89 cases) and controls (blood donors, 204 cases) and compared with regard to the H63D variant. Both groups did not have homozygous H63D variant. H63D heterozygous in diabetics were 23.60% and in blood donor controls 22.55%. Allelic frequency of the mutant H63D allele was 11.80% in diabetics and 11.27% for the blood donor controls. This is the first study to show the frequency of the three hemochromatosis gene variants in Jordan with the interesting finding of no C282Y allele detected in 440 samples. Additionally, no significant difference was observed in H63D variant frequency in type 2 diabetics as compared to controls

Immunohistochemical expression of substance P in breast cancer and its association with prognostic parameters and Ki-67 index.

BackgroundThe neuropeptide substance P is a potential biomarker and therapeutic target in cancer. The main objectives of this study were to investigate the expression level of substance P in different breast cancer molecular subtypes and identify its association with clinicopathological parameters of patients and with Ki-67 index.MethodsA retrospective analysis was performed for a total of 164 paraffin-embedded breast cancer tissue samples [42 Her2/neu-enriched, 40 luminal A, 42 luminal B (triple-positive) and 40 triple negative subtypes]. The tissue microarray slides containing specimens were used to determine the expression of substance p and Ki-67 by immunohistochemical staining.ResultsThe mean age of the cohort was 51.35 years. Twenty two percent of cases had low substance P expression levels (TS ≤ 5), while 78% had high expression levels (TS > 5). A significant association was found between SP expression level and breast cancer molecular subtype (p = 0.002), TNM stage (p = 0.034), pN stage (p = 0.013), axillary lymph node metastasis (p = 0.004), ER and PR statuses (pConclusionSP is overexpressed in most of the analyzed tissues and has a negative prognostic value in the breast cancer patients. Besides substance P is a potential therapeutic target in breast cancer

A Genomewide Screen for Generalized Vitiligo: Confirmation of AIS1 on Chromosome 1p31 and Evidence for Additional Susceptibility Loci

Generalized vitiligo is a common autoimmune disorder characterized by the development of white patches of skin and overlying hair due to loss of pigment-forming melanocytes from the involved areas. Family clustering of cases is not uncommon, in a pattern suggestive of multifactorial, polygenic inheritance, and there is strong association between vitiligo and other autoimmune diseases. To map genetic loci that confer susceptibility to generalized vitiligo and perhaps other autoimmune diseases, we performed a genomewide linkage scan in 71 white multiplex families with vitiligo from North America and the United Kingdom. Linkage was assessed by multipoint nonparametric linkage analyses. One linkage signal, AIS1, located at 1p31, met genomewide criteria for highly significant linkage (nonparametric LOD 5.56; P=.000000282), establishing its importance as a major vitiligo susceptibility locus. An additional seven signals, on chromosomes 1, 7, 8, 11, 19, and 22, met genomewide criteria for “suggestive linkage,” and will thus be of particular importance for follow-up studies