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Y Chromosome Single Nucleotide Polymorphisms Typing by SNaPshot MINISEQUENCING

Y Chromosome Single Nucleotide Polymorphisms Typing by SNaPshot MINISEQUENCING

Analysis of Y chromosome haplogroups, defined by single nucleotide polymorphisms (SNPs), is now a standard approach for study of the origin of human populations and measurement of the variability among them. It is also a new forensic tool, because it may allow determination of the origin of any male sample of interest. We have used a strategy for rapid, simple and inexpensive Y chromosome SNP typing of 343 male DNA samples, of which 211 were Macedonians, 111 Albanians and 21 Roma, Serbs or Turks. Using multiplex polymerase chain reaction (mPCR) and a SNaPshot multiplex kit for single nucleotide extension reaction, 28 markers were grouped into five multiplexes. Twenty different Y haplogroups were found in these samples. The most common Y haplogroups in Macedonians were I2a-P37b (27.5%), E1b1b1a-M78 (15.6%), R1a1-SRY1532 (14.2%) and R1b1-P25 (11.4%). In the Albanians E1b1b1a-M78 accounted for 28.8%, R1b1-P25 for 18.0%, J2b2-M241 for 13.5% and R1a1-SRY1532 for 12.6%. We conclude that five haplogroups (E1b1b1a-M78, I2a-P37b, J2b2-M241, R1a1-SRY1532 and R1b1-P25) comprised 72.6% of the Y chromosomes, this being characteristic of the typical European Y chromosome gene pool.

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DICENTRIC CHROMOSOME 14;18 PLUS TWO ADDITIONAL CNVs IN A GIRL WITH MICROFORM HOLOPROSENCEPHALY AND TURNER STIGMATA

ABSTRACT

We report a 20-year-old female with features evocative of Turner syndrome (short stature, broad trunk, mild webbed neck), dysmorphic face, minor features of holo-prosencephaly (HPE), small hands and feet, excessive hair growth on anterior trunk and intellectual disability. Cytogenetic analysis identified a pseudodicentric 14;18 chromosome. Genome wide single nucleotide polymorphism (SNP) array showed a terminal deletion of approximately 10.24 Mb, from 18p11.32 to 18p11.22, flanked by a duplication of approximately 1.15 Mb, from 18p11.22 to 18p11.21. In addition, the SNP array revealed a duplication of 516 kb in 16p11.2. We correlated the patient’s clinical findings with the features mentioned in the literature for these copy number variations. This case study shows the importance of microarray analysis in the detection of cryptic chromosomal rearrangements in patients with intellectual disability and multiple congenital anomalies

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Polymorphism of the IL13 gene may be associated with Uterine leiomyomas in Slovenian women

Abstract

Uterine leiomyomas (ULM) are a common cause of solid pelvic tumors in women. Their etiopathogenesis remains unclear. Interleukins (ILs) and their receptors can influence tumor biology of ULM. The aim of this study was to evaluate single nucleotide polymorphisms (SNPs) exhibited in the genes IL4 (rs2070874), IL4R (rs1801275), IL12RB1 (rs11575934), IL12B (rs6887695), IL13 (rs20541) and IL23R (rs7517847) as risk factors for ULM in Slovenian women and to identify associations between corresponding clinical parameters and the analyzed SNPs. In addition, solitary and multiple ULM were compared to identify clinical and/or genetic parameters influencing their occurrence. We conducted a case-control study that included 181 women with leiomyomas and 133 control subjects. Genotyping of selected SNPs was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and high resolution melting (HRM) techniques. The TT genotype of rs20541 (IL13) was significantly associated with decreased risk of ULM compared to both the CC and CT genotypes [p = 0.018; odds ratio (OR) = 0.184; 95% confidence interval (95% CI) = 0.048-0.7121. Using genetic and clinical data to develop a predictive model with logistic regression, we found that adenomyosis, higher age at diagnosis, family history of ULM occurrence, earlier menarche, lower number of pregnancies and lower age at first sexual intercourse, the G allele and genotypes AG and GG of rs1801275 (IL4R) were associated with an increased risk of multiple ULM occurrence. We also found an association between rs20541 (IL13) and 17ß-estradiol serum levels in patients with multiple ULM (p 0.003). Our study showed, for the first time, that rs20541 (IL13) may contribute to susceptibility of ULM development and that rs1801275 (IL4R) can predispose patients to develop multiple ULM.

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Rare case of a heterozygous microdeletion 9q21.11-q21.2: Clinical and genetic characteristics

Abstract

Intellectual disability is affecting 3.0-4.0% of the general population. Copy number variants (CNVs) are a significant cause leading to neurodevelopmental disorders such as intellectual disability, epilepsy, autism spectrum disorders and developmental delay. The use of single nucleotide polymorphism (SNP)-array and array comparative genomic hybridization (aCGH) as diagnostic tools has led to the recognition of new microdeletion/microduplication syndromes associated with neurodevelopmental disorders. It is also useful for further characterization of marker chromosomes. Here, we report a girl with mild intellectual disability and mild facial dysmorphisms. Cytogenetic analysis showed a marker chromosome in some percent of the cells and was followed by SNP-array karyotyping that detected, in addition, a 9655 Mb de novo interstitial deletion at 9q21.1-9q21.2.

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Single nucleotide polymorphisms in genes MACC1, RAD18, MMP7 and SDF-1a as prognostic factors in resectable colorectal cancer

Abstract

Background

Colorectal cancer (CRC) represents one of the most common malignancies worldwide. Research has indicated that functional gene changes such as single nucleotide polymorphism (SNP) influence carcinogenesis and metastasis and might have an influence on disease relapse. The aim of our study was to evaluate the role of SNPs in selected genes as prognostic markers in resectable CRC.

Patients and methods

In total, 163 consecutive patients treated surgically for CRC of stages I, II and III at the University Medical Centre in Maribor in 2007 and 2008 were investigated. DNA was isolated from formalin-fixed paraffin-embedded CRC tissue from the Department of Pathology and SNPs in genes SDF-1a, MMP7, RAD18 and MACC1 were genotyped using polymerase chain reaction followed by high resolution melting curve analysis or restriction fragment length polymorphism.

Results

We found worse disease-free survival (DFS) for patients with TT genotype of SNP rs1990172 in gene MACC1 (p = 0.029). Next, we found worse DFS for patients with GG genotype for SNP rs373572 in gene RAD18 (p = 0.020). Higher frequency of genotype GG of MMP7 SNP rs11568818 was found in patients with T3/T4 stage (p = 0.014), N1/N2 stage (p = 0.041) and with lymphovascular invasion (p = 0.018). For MACC1 rs1990172 SNP we found higher frequency of genotype TT in patients with T3/T4 staging (p = 0.024). Higher frequency of genotype GG of RAD18 rs373572 was also found in patients with T1/T2 stage with disease relapse (p = 0.041).

Conclusions

Our results indicate the role of SNPs as prognostic factors in resectable CRC.

Open access
Analysis in silico of the single nucleotide polymorphism G–152A in the promoter of the angiotensinogen gene of Indonesian patients with essential hypertension

Abstract

Background

Single nucleotide polymorphism (SNP) G–152A (rs11568020) in the promoter of the angiotensinogen gene (AGT) may modulate its transcription. Translation of mRNA to angiotensinogen induces hypertension during hypoxia. The G allele at position –152 is located within the hypoxia-response element (HRE) transcription factor-binding site for the hypoxia-inducible factor 1 (HIF-1) heterodimer. However, the function of the –152 site in HIF-1 binding is not fully elucidated.

Objectives

To determine the frequency of SNP G–152A in Indonesian patients with hypertension and the function of this SNP.

Methods

We determined the frequency of the SNP in 100 patients by direct sequencing, and the influence of SNP G–152A on predicted binding of HIF-1 to the HRE using a docking approach in silico.

Results

The AGT promoter in our patients had genetic variants –152G and –152A (19:1). Predicted binding indicated that HIF-1 directly contacts the major groove of the G allele, but not the A allele. Scoring according to weighted sum High Ambiguity Driven biomolecular DOCKing showed that the score for the A allele–HIF-1 complex (–47.1 ± 6.9 kcal/mol) was higher than that for the G allele–HIF-1 complex (–94.6 ± 14.1 kcal/mol), indicating more favorable binding of HIF-1 to the G allele.

Conclusions

SNP G–152A reduces the favorability of binding of HIF-1 to the HRE. The occurrence of this SNP in the AGT promoter of Indonesian patients with essential hypertension suggests that the G allele is a genetic susceptibility factor in hypertension regulated by HIF-1.

Open access
TLR4 polymorphisms seem not to be associated with prediabetes and type 2 diabetes but predispose to diabetic retinopathy; TLR4 polymorphisms in glucose continuum

Abstract

Objectives. Compared to type 1 diabetes, the role of the immune and autoimmune pathogenetic mechanisms is much less studied in the type 2 diabetes. Toll-like receptors 4 (TLR4) have a leading role in inflammation, insulin resistance, and vascular damage. This study aimed to analyze the relationship between the polymorphisms in TLR4 gene and different stages in the glucose continuum from prediabetes to the type 2 diabetes and chronic microvascular complications.

Materials and Methods. The study included 113 patients with the type 2 diabetes, 29 participants with prediabetes, and 28 controls. Polymerase chain reaction (PCR) was used for genotyping Asp299Gly and Thr399Ile polymorphism, followed by restriction analysis.

Results. The difference in the genotype frequency for both polymorphisms in patients with the type 2 diabetes or prediabetes compared to that in controls was not significant. Patients with heterozygous genotype of Asp299Gly polymorphism had a higher prevalence of diabetic retinopathy (42.9%) than participants with homozygous genotype (9.0%) (OR [95%CI]=7.61 [1.41–41.08]; p=0.018). No association was established for diabetic polyneuropathy and nephropathy. Prevalence of chronic diabetes complications was not related to Thr399Ile polymorphism.

Conclusion. Our study demonstrates that Asp299Gly and Thr399Ile polymorphisms seem not to be associated with the type 2 diabetes and prediabetes but Asp299Gly may contribute to diabetic retinopathy predisposition.

Open access
Polymorphisms of AZIN1 rs2679757 and TRPM5 rs886277 are Associated with Cirrhosis Risk in Chinese Patients with Chronic Hepatitis B

Abstract

Objective Genome-wide association studies (GWAS) have linked many single nucleotide polymorphisms (SNPs) to the outcomes of a variety of liver diseases. The aim of the present study was to evaluate the association of several candidate SNPs with the risk and severity of cirrhosis due to chronic hepatitis B in a Chinese population.

Methods A total of 714 Chinese participants with persistent HBV infection were studied. Patients were divided into cirrhotic (n = 429) and non-cirrhotic (n = 285) groups based on clinical and pathological evidence. The progression rate and severity of liver cirrhosis were evaluated with an arbitrary t-score system. Genotypes of six SNPs in five candidate genes were detected with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The genotypic distributions of the SNPs were compared between the age-matched cirrhotic and non-cirrhotic subjects. The association between the risk of SNPs and the severity and progression rate of cirrhosis was further analyzed.

Results Rs2679757 polymorphism of the antizyme inhibitor 1 (AZIN1) gene and Rs886277 in the transient receptor potential cation channel subfamily M, member 5 gene (TRPM5) were found to be associated with cirrhosis risk in CHB. They were also correlated with the overall severity and progression rate of cirrhosis. Genotype frequencies of other SNPs were not different between the cirrhosis and non-cirrhosis groups.

Conclusions AZIN1 rs2679757 and TRPM5 rs886277 are associated with the risk and the progression rate of HBV-related liver fibrosis in Chinese patients. The emerging SNPs associated with cirrhosis prognosis warrant further clinical validation in other CHB cohorts or ethnic groups, and merit mechanistic studies to reveal their roles in fibrosis progression.

Open access
Matrix Matalloproteinase-8 Gene Polymorphism in Chronic Periapical Lesions

Abstract

Background/Aim: Increased levels of matrix metalloproteinase-8 (MMP-8) have been associated with risk of developing chronic periapical lesion (CPL). Gene polymorphisms are contributing factors in the pathogenesis of the inflammation. The aim of this study was to analyze polymorphism in the gene MMP-8 and its association and influence on clinical manifestation of CPL.

Methods: A total of 240 unrelated Macedonian subjects were included in the present study. Polymorphism -799 C/T in the gene MMP-8 detected with restriction enzyme BgIII was studied in 120 patients with CPL and 120 controls without any signs of chronic or acute inflammatory process in the jaw. The amplification of the region of selected gene was made with polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP).

Results: Our results showed that there were differences in the allele and genotype frequencies of the MMP8 -799 C/T polymorphisms between patients with CPL and controls (p < 0.05). Also this study suggests that MMP-8 polymorphism -799 C/T was a risk for expression of CPL (OR=8.27<3.44<OR<20.26).

Conclusion: The detection of this genetic polymorphism is relevant for obtaining providential treatment of patients who are at high risk of chronic periapical inflammation.

Open access
in PRILOZI
Lack of Association Between Variants within the AHSG, HCRT and NPY2R Genes and Anthropometrical Parameters in Czech Post-Monica Study

Abstract

The aim of this study was to examine single nucleotide polymorphisms (SNPs) of candidate genes α2-Heremans-Schmid glycoprotein (AHSG, rs4917), Hypocretin (HCRT, rs760282) and Neuropetide Y2 receptor (NPY2R, rs 1047214), which are known to have a potential effect on body mass index (BMI) and other indicators of obesity. A population study was performed in 2007/2008 on 2559 adults (1191 males and 1368 females) from the Czech post-MONICA project. The SNPs were examined using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We did not find any significant association between the examined SNPs and BMI across the whole population. A significantly lower triglyceride level was found in the AHSG gene CC homozygotes compared to T allele carriers in the entire population (p = 0.009). In conclusion, we are not able to confirm the hypothesis that polymorphisms within the AHSG, HCRT and NPY2R genes are major genetic determinants of BMI and plasma lipids in the Czech-Slavonic population.

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