Single nucleotide polymorphisms (SNPs) are inherited from parents and they measure heritable events

Genes polymorphism as risk factor of recurrent urolithiasis: a systematic review and meta-analysis

INTRODUCTION

Urolithiasis is one of the most prevalent diseases worldwide. Its prevalence is rising, both in developing and developed countries. It is known that genetic factors play big roles in the development of urolithiasis. One of the suspected factors is gene polymorphism. This study aims to find an accurate estimate of the association between genetic polymorphism and the risk of recurrent urolithiasis.

METHODS

A systematic review and meta-analysis were performed on 12 studies from 3 databases that investigated gene polymorphism as an risk factor of urolithiasis. The review was done using Review Manager® version 5.3.

RESULTS

Insignificant heterogenicity was found in this study. Populations from Asia and the Middle East are more likely to experience recurrent urolithiasis. Additionally, variation in the VDR and urokinase genes, particularly in the Asian population, increases the risk of developing recurrent urolithiasis.

CONCLUSIONS

Gene polymorphisms have significant roles in the development of urolithiasis, especially in the Middle Eastern region.

Genetic variants of the nuclear factor erythroid 2-related factor 2/antioxidant reaction element pathway on the risk of antituberculosis drug-induced liver injury: a systematic review

Aim: To evaluate the effects of genetic variants in the nuclear factor erythroid 2-related factor 2/antioxidant reaction element signaling pathway on antituberculosis drug-induced liver injury (AT-DILI) susceptibility. Methods: The PubMed, Embase, Cochrane, Web of Science, China National Knowledge Infrastructure and Wanfang databases were searched from inception to April 2022. Results: Seven case-control studies with 4676 patients were included. Six genes with 35 SNPs in the pathway have been reported. Among 17 SNPs reported in two or more studies, the meta-analysis indicated that only one SNP (rs3735656 in MAFK) was significantly associated with a decreased risk for AT-DILI under the dominant model (odds ratio: 0.636; 95% CI: 0.519-0.780; p < 0.001). Conclusion: SNP rs3735656 in the MAFK gene was significantly associated with the risk of AT-DILI.

The correlation of salivary telomere length and single nucleotide polymorphisms of the ADIPOQ, SIRT1 and FOXO3A genes with lifestyle-related diseases in a Japanese population

Background

It has been reported that genetic factors are associated with risk factors and onset of lifestyle-related diseases, but this finding is still the subject of much debate.

Objective

The aim of the present study was to investigate the correlation of genetic factors, including salivary telomere length and three single nucleotide polymorphisms (SNPs) that may influence lifestyle-related diseases, with lifestyle-related diseases themselves.

Methods

In one year at a single facility, relative telomere length and SNPs were determined by using monochrome multiplex quantitative polymerase chain reaction and TaqMan SNP Genotyping Assays, respectively, and were compared with lifestyle-related diseases in 120 Japanese individuals near our university.

Results

In men and all participants, age was inversely correlated with relative telomere length with respective p values of 0.049 and 0.034. In men, the frequency of hypertension was significantly higher in the short relative telomere length group than in the long group with unadjusted p value of 0.039, and the difference in the frequency of hypertension between the two groups was of borderline statistical significance after adjustment for age (p = 0.057). Furthermore, in men and all participants, the sum of the number of affected lifestyle-related diseases, including hypertension, was significantly higher in the short relative telomere length group than in the long group, with p values of 0.004 and 0.029, respectively. For ADIPOQ rs1501299, men’s ankle brachial index was higher in the T/T genotype than in the G/G and G/T genotypes, with p values of 0.001 and 0.000, respectively. For SIRT1 rs7895833, men’s body mass index and waist circumference and all participants’ brachial-ankle pulse wave velocity were higher in the A/G genotype than in the G/G genotype, with respective p values of 0.048, 0.032 and 0.035. For FOXO3A rs2802292, women’s body temperature and all participants’ saturation of peripheral oxygen were lower in the G/T genotype than in the T/T genotype, with respective p values of 0.039 and 0.032. However, relative telomere length was not associated with physiological or anthropometric measurements except for height in men (p = 0.016). ADIPOQ rs1501299 in men, but not the other two SNPs, was significantly associated with the sum of the number of affected lifestyle-related diseases (p = 0.013), by genotype. For each SNPs, there was no significant difference in the frequency of hypertension or relative telomere length by genotype.

Conclusion

Relative telomere length and the three types of SNPs determined using saliva have been shown to be differentially associated with onset of and measured risk factors for lifestyle-related diseases consisting mainly of cardiovascular diseases and cancer.

Association analyses of a genetic variant in long non-coding RNA MEG3 with breast cancer susceptibility and serum MEG3 expression level in the Egyptian population

BACKGROUND

LncRNA MEG3 rs7158663 has been shown to confer cancer susceptibility, maybe through altering its gene expression level.

OBJECTIVE

We aimed to weigh the effect of rs7158663 on MEG3 serum level and breast cancer susceptibility.

METHODS

We genotyped rs7158663 G > A and measured serum MEG3 in 150 breast cancer, 95 fibroadenoma , and 154 controls by the TaqMan method.

RESULTS

The presence of rs7158663 G > A is a risk factor for breast cancer among fibroadenoma patients and controls, AA vs. GG genotypes (OR = 6.320, 95% CI = 2.587-15.439, P< 0.0001 when compared to controls and OR = 10.825, 95% CI = 1.929-60.742, P= 0.007 when compared to fibroadenoma). Decreased serum MEG3 was observed in breast cancer group when compared with fibroadenoma and/or controls [median (IQR) = 0.43 (0.27-0.55)] (P< 0.0001). However, increased serum MEG3 was noted in fibroadenoma group when compared with controls (P< 0.0001). A significance decreased serum MEG3 was found to be associated with mutant A allele than with wild G allele (P< 0.0001). The results showed that rs7158663 and lower MEG3 were significantly associated with patients with higher TNM staging and larger tumor size > 5 cm.

CONCLUSION

The presence of both rs7158663 and low MEG3 are diagnostic and unfavorable prognostic factors for BC patients.

Polymorphism of DNA Repair Genes via Homologous Recombination (HR) in Ovarian Cancer

Ovarian cancer is one of the most common types of cancer in women. The repair system via homologous recombination repairs double-strand breaks (DSB) of DNA, which are the most mortal for cell, out of all DNA damages. The genes, which encode the double-strand break repairing proteins, are highly polymorphic and, taking into account the significance of the repaired defects for cancer development, it seems important to learn the role of the polymorphisms in ovarian cancer development. The aim of the study was to determine the relationship between DNA repair genes via homologous recombination (HR) and modulation of the risk of ovarian cancer. The following polymorphisms were analysed: XRCC3-Thr241Met (rs861539), XRCC2--41657C/T (rs718282), XRCC2-Arg188His (rs3218536), BRCA1-Q356R (rs1799950) and RAD51-135 G/C (rs1801320). The study group included 600 patients with ovarian cancer and 600 healthy controls. The PCR-RFLP (PCR-based restriction fragment length polymorphism) technique was applied for polymorphism analysis. Allele XRCC3-241Met (OR 0.85, 95%CI 0.72-0.99, p < 0.045), XRCC2-41657 T (OR 1.67, 95% CI 1.42-1.96, p < .0001), BRCA1-356R (OR 1.61; % CI 1.37-1.90, p < .0001) and RAD51-135C (OR 5.16; 95% CI 4.29-6.20, p < .0001) strongly correlated with the neoplastic disease. No relationship was observed between the studied polymorphisms and the cancer progression stage according to FIGO classification. The results indicate that polymorphisms of DNA repair genes via homologous recombination may be associated with the incidence of ovarian cancer. Further research on larger groups is warranted to determine the influence of above-mentioned genetic variants on ovarian cancer risk.

Beliefs and attitudes towards participating in genetic research - a population based cross-sectional study

Background

Biobanks have the potential to offer a venue for chronic disease biomarker discovery, which would allow for disease early detection and for identification of carriers of a certain predictor biomarker. To assess the general attitudes towards genetic research and participation in biobanks in the Long Island/Queens area of New York, and what factors would predict a positive view of such research, participants from the NSLIJ hospital system were surveyed.

Methods

Participants were recruited at six hospital centers in the NSLIJ system during the summers of 2009 and again in 2011 (n = 1,041). Those who opted to participate were given a questionnaire containing 22 questions assessing demographics, lifestyle and attitudes towards genetic research. These questions addressed individual participant’s beliefs about the importance of genetic research, willingness to participate in genetic research themselves, and their views on informed consent issues.

Results

Respondents took a generally positive view of genetic research in general, as well as their own participation in such research. Those with reservations were most likely to cite concerns over the privacy of their medical and genetic information. Those who were married tended to view genetic research as important, while those in the younger age group viewed it as less important. Prior blood donation of respondents was found to be a predictor of their approval for genetic research. Demographic factors were not found to be predictive of personal willingness to participate in genetic research, or of approval for the opt-out approach to consent.

Conclusions

While respondents were generally inclined to approve of genetic research, and those who disapproved did not do so based on an underlying moral objection to such research, there is a disconnect between the belief in the importance of genetic research and the willingness of individuals to participate themselves. This indicates a continued concern for the ways in which genetic materials are safeguarded once they are collected. Also indicated was a general lack of understanding about the various consent processes that go along with genetic research, which should be addressed further to ensure the successful continuation of biobanks.

Regulatory approval of cancer risk-reducing (chemopreventive) drugs: moving what we have learned into the clinic

This article endeavors to clarify the current requirements and status of regulatory approval for chemoprevention (risk reduction) drugs and discusses possible improvements to the regulatory pathway for chemoprevention. Covering a wide range of topics in as much depth as space allows, this report is written in a style to facilitate the understanding of nonscientists and to serve as a framework for informing the directions of experts engaged more deeply with this issue. Key topics we cover here are as follows: a history of definitive cancer chemoprevention trials and their influence on the evolution of regulatory assessments; a brief review of the long-standing success of pharmacologic risk reduction of cardiovascular diseases and its relevance to approval for cancer risk reduction drugs; the use and limitations of biomarkers for developing and the approval of cancer risk reduction drugs; the identification of individuals at a high(er) risk for cancer and who are appropriate candidates for risk reduction drugs; business models that should incentivize pharmaceutical industry investment in cancer risk reduction; a summary of scientific and institutional barriers to development of cancer risk reduction drugs; and a summary of major recommendations that should help facilitate the pathway to regulatory approval for pharmacologic cancer risk reduction drugs.

The heritability of G2 chromosomal radiosensitivity and its association with cancer in Danish cancer survivors and their offspring

PURPOSE

To investigate the relationship between chromosomal radiosensitivity and early-onset cancer under the age of 35 years and to examine the heritability of chromosomal radiosensitivity.

MATERIALS AND METHODS

Peripheral blood lymphocytes were cultured for 72 hours prior to being irradiated with 0.5 Gy, 300 kV X-rays. Colcemid was added to cultures 30 min post-irradiation. Cultures were harvested 90 min post-irradiation and analysed for chromatid gaps and breaks. Heritability was estimated using Sequential Oligogenic Linkage Analysis Routines (SOLAR) software and by segregation analysis.

RESULTS

Elevated radiosensitivity was seen for seven out of 29 (24.1%) cancer survivors, three out of 29 (10.3%) partners and 10 out of 53 (20.8%) offspring. Although the proportion of individuals displaying enhanced radiosensitivity was twice as high in both the cancer survivor and offspring groups than the partner controls, neither reached statistical significance. Heritability analysis of the radiosensitive phenotype suggested 57.9-78.0% of the variance could be attributed to genetic factors.

CONCLUSION

An association between G(2) chromosomal radiosensitivity and childhood and young adult cancer is suggested but was not statistically significant. In contrast, there is strong evidence for heritability of the radiosensitive phenotype. The cancer survivors included a broad range of malignancies and future studies should focus on specific cancers with known or likely faults in deoxyribonucleic acid (DNA) damage recognition and repair mechanisms.

Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping

Many sequence-alignment tools were developed to discover single nucleotide polymorphisms (SNPs) derived from resequencing in genomic regions. Whether an identified SNP is indeed a novel SNP or is already contained in dbSNP is often difficult to answer. Here, we describe a freely available software, Seq-SNPing, which is a Java-based software for SNP discovery, and ID identification and editing and visualizating of sequence alignments. It is easy to use, fast, and provides an accurate method for searching and organizing SNP IDs from multiple sequence inputs, thereby greatly facilitating genetic studies. Seq-SNPing provides SNP identification by selecting any range of unaligned or aligned sequences in sequences that are similar. SNP IDs in the National Center for Biotechnology Information (NCBI) or user-defined SNPs within a selected sequence can be identified by Seq-SNPing. Information needed for SNP-RFLP (restriction fragment length polymorphism) genotyping is provided, such as SNP-REs (restriction enzymes), the sequence trimmer, sequence finder, BLAST (Basic Local Alignment Search Tool), SNP-BLAST, UCSC BLAT (BLAST-like alignment tool), RE mining, antisequencer (Anti-seq), and T(m) (melting temperature)/GC% of selected sequence. The thresholds for SNP calling are adjustable by selecting the height of the peak for each nucleotide representative curve in the chromatogram. Therefore, Seq-SNPing can discover SNPs and identify SNP IDs in both sequence text and chromatogram files in a fast and reliable way. The software is fully compatible with Microsoft Windows. The program and user manual are available at http://bio.kuas.edu.tw/Seq-SNPing for download.

SNP ID-info: SNP ID searching and visualization platform

Many association studies provide the relationship between single nucleotide polymorphisms (SNPs), diseases and cancers, without giving a SNP ID, however. Here, we developed the SNP ID-info freeware to provide the SNP IDs within inputting genetic and physical information of genomes. The program provides an "SNP-ePCR" function to generate the full-sequence using primers and template inputs. In "SNPosition," sequence from SNP-ePCR or direct input is fed to match the SNP IDs from SNP fasta-sequence. In "SNP search" and "SNP fasta" function, information of SNPs within the cytogenetic band, contig position, and keyword input are acceptable. Finally, the SNP ID neighboring environment for inputs is completely visualized in the order of contig position and marked with SNP and flanking hits. The SNP identification problems inherent in NCBI SNP BLAST are also avoided. In conclusion, the SNP ID-info provides a visualized SNP ID environment for multiple inputs and assists systematic SNP association studies. The server and user manual are available at http://bio.kuas.edu.tw/snpid-info.

Familial risks for common diseases: etiologic clues and guidance to gene identification

Familial clustering of a disease is a direct indicator of a possible heritable cause, provided that environmental sharing can be excluded. If the familial clustering is lacking, the likelihood of a heritable influence is also small. In the era of genome scans, the consideration of data on heritability should be important in the assessment of the likely success of the genome scan. The availability of a Multigeneration Register in Sweden provides a reliable access to families throughout the last century. This Register has been extensively used to study a number of different diseases through linkage to the Hospital Discharge Register. In the present article we review the obtained and some unpublished results for nine main disease classes. For each of these, familial risks are given for four disease subtypes. As measures of familial clustering we use risks between siblings, twins and spouses. Disease correlation between spouses suggests environmental sharing and a higher correlation between siblings and particularly twins shows heritable effects. We will also comment on the established susceptibility genes and the risks conferred by them. The data suggest high heritabilities for chronic obstructive pulmonary disease, asthma, noninfective enteritis and colitis, cerebral palsy and endocrine and metabolic diseases. Among the performed first-generation genome scans on various diseases, the success appears to be related to the a priori heritability estimates. To our knowledge this is a first attempt to summarize familial risks for a large number of diseases using data from a single population on which reasonable uniform diagnostic criteria have been applied.

The balance between heritable and environmental aetiology of human disease

The Human Genome Project and the ensuing International HapMap Project were largely motivated by human health issues. But the distance from a DNA sequence variation to a novel disease gene is considerable; for complex diseases, closing this gap hinges on the premise that they arise mainly from heritable causes. Using cancer as an example of complex disease, we examine the scientific evidence for the hypothesis that human diseases result from interactions between genetic variants and the environment.

Gene-Environment Interactions in Cancer: Do They Exist?

Single nucleotide polymorphisms (SNPs) are extensively used in case-control studies of practically all cancer types. In addition to the pure genetic studies, gene-environment studies, which simultaneously consider environmental factors, have been increasingly conducted. All SNP studies aim at the identification of the role of inherited cancer susceptibility genes. However, being genetic markers, they are applicable only on heritable conditions, which is often a neglected fact. Based on the data on the heritability of cancer and the importance of environmental factors in cancer etiology, we discuss the likelihood of successful gene-environment studies. The available evidence is not conclusive, but it consistently points to a minor heritable etiology in cancer, which will hamper the success of SNP-based association studies. We use simulation techniques to examine which situations would favor the application of a gene-environment approach instead of the traditional environmental approach in case-control studies. The results show that well-chosen candidate gene with a relatively low allele frequency may improve the power to detect environmental determinants of a disease. However, this advantage is lost when the number of underlying genes increases. We are concerned about an indiscriminate use of genetic tools for cancers, which are mainly environmental in origin. The likelihood of success for SNP-based gene-environment studies increases if established environmental risk factors are tested on proven candidate genes. Enhancing the likelihood that the disease causation is genetic, for example, by selecting familial cases, may increase the power of the studies, and the rareness of those cases calls for collaborative networks.

Cytochrome P2A13 and P1A1 gene polymorphisms are associated with the occurrence of uterine leiomyoma

PROBLEM

To investigate the association between the occurrence of uterine leiomyoma and two SNPs of the CYP 2A13 and CYP 1A1 genes.

METHOD OF STUDY

Prospective case control study with 132 women with clinically and surgically diagnosed uterine leiomyoma and 260 controls. Genotyping was performed by polymerase chain reaction (PCR) based amplification of CYP 2A13 and CYP 1A1 genes, and restriction fragment length polymorphism (RFLP) analysis.

RESULTS

Comparing women with uterine leiomyoma and controls, we demonstrate statistical significant differences of allele frequency and genotype distribution for the CYP 1A1 polymorphism (P = 0.025 and P = 0.046, respectively). Furthermore, for the CYP 2A13 polymorphism we found a significant difference concerning allele frequency (P = 0.033). However, for the genotype distribution, only borderline significance was observed (P = 0.064).

CONCLUSIONS

The CYP 2A13 and CYP 1A1 SNPs are associated with uterine leiomyoma in a Caucasian population and may contribute to the understanding of the pathogenic mechanisms of uterine leiomyoma.

Polymorphisms in the IGF-1 and IGFBP3 promoter and the risk of breast cancer

Binding of IGF-1 to the type I IGF receptor starts a signalling cascade that plays an important role in regulating cell proliferation, differentiation and apoptosis. The interaction between the IGF-1 and its receptor is mainly regulated by a binding protein, IGFBP 3. We studied a CA repeat polymorphism 969 bp upstream of the transcription start site in the IGF-1 gene and an A-202 C polymorphism in the IGFBP 3 gene and tested their association with breast cancer risk using four case-control series with a total of 787 cases and 900 controls. We did not find any association between the breast cancer risk and the IGF-1 repeat length (19 versus non-19) or the IGFBP 3 A-202 C polymorphism in the postmenopausal breast cancer series or in women diagnosed for breast cancer under the age of 50. In the familial breast cancer series we observed a non-significantly increased odds-ratio (OR) in homozygotes for the non-19 alleles of the IGF-1 gene (OR 1.51, 95% CI 0.96-2.39, p=0.07). Similarly, in the familial breast cancer series we detected an increased frequency of the IGFBP 3 -202 C allele carriers (OR 1.50, 95% CI 1.05--2.14, p=0.03). The association was stronger in individuals homozygous for these alleles (OR 3.76, 95% CI 1.44-v-9.81, p=0.006). Thus, the polymorphisms in the IGF-1 and IGFBP 3 genes associated with an increased risk of breast cancer in familial cases carrying the variant alleles.

Familial Lung Cancer and Aggregation of Smoking Habits: A Simulation of the Effect of Shared Environmental Factors on the Familial Risk of Cancer

BACKGROUND

Tobacco smoking is the principal cause of lung cancer. The risk of lung cancer in the offspring of lung cancer patients is about twice higher than the risk in the general population. The present study investigated the contribution of shared smoking habits to the familial clustering of lung cancer.

METHODS

We estimated the relative risk of lung cancer attributable to smoking according to the extent to which smokers transmit their smoking habits to the offspring (heritability of smoking), the prevalence of smoking in the general population, and the risk of lung cancer for smokers compared with nonsmokers.

FINDINGS

The relative risk of lung cancer for the offspring of lung cancer patients attributable to smoking was 1.19 when published data on smoking practice were modeled (i.e., assuming that the heritability of smoking was 0.5, the smoking prevalence 40%, and the odds ratio of lung cancer for smokers versus nonsmokers was 20).

INTERPRETATION

Most familial cases of lung cancer cannot be attributed to shared smoking habits. The example of smoking can be used for other familial cancers, for which no strong environmental risk factors are usually known, to infer the primary role for heritable genes.