Journal articles: 'Single nucleotide polymorphisms'

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Shaw, Greg. "Polymorphism and single nucleotide polymorphisms (SNPs)." BJU International 112, no. 5 (August 7, 2013): 664–65. http://dx.doi.org/10.1111/bju.12298.

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Dong, Chunming, Joseph R. Nevins, and Pascal J. Goldschmidt-Clermont. "ABCA1 Single Nucleotide Polymorphisms." Circulation Research 88, no. 9 (May 11, 2001): 855–57. http://dx.doi.org/10.1161/hh0901.091208.

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Meyer, Nuala J. "Beyond Single-Nucleotide Polymorphisms." Clinics in Chest Medicine 35, no. 4 (December 2014): 673–84. http://dx.doi.org/10.1016/j.ccm.2014.08.006.

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Pandav, Surinder Singh, Partha Chakma, Alka Khera, Neera Chugh, Parul Chawla Gupta, Faisal Thattaruthody, Natasha Gautam Seth, et al. "Lack of association between lysyl oxidase-like 1 polymorphism in pseudoexfoliation syndrome and pseudoexfoliation glaucoma in North Indian population." European Journal of Ophthalmology 29, no. 4 (September 6, 2018): 431–36. http://dx.doi.org/10.1177/1120672118795405.

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Introduction:Pseudoexfoliation syndrome is commonly associated with pseudoexfoliation glaucoma. The two nonsynonymous single-nucleotide polymorphisms rs1048661 (R141L) and rs3825942 (G153D) within exon 1 of LOXL1 gene have been found to confer risk of pseudoexfoliation syndrome and pseudoexfoliation glaucoma in different geographical populations. This study aims to find association between two nonsynonymous single-nucleotide polymorphisms with pseudoexfoliation syndrome and pseudoexfoliation glaucoma in North Indian population.Methods:North Indian subjects clinically diagnosed with pseudoexfoliation syndrome/pseudoexfoliation glaucoma and normal age-matched control were enrolled in the study. Genomic DNA was extracted and the two single-nucleotide polymorphisms of LOXL1 gene were genotyped by polymerase chain reaction and sequencing. The association between single-nucleotide polymorphisms with pseudoexfoliation syndrome/pseudoexfoliation glaucoma was evaluated by chi-square test.Results:A total of 30 pseudoexfoliation glaucoma, 27 pseudoexfoliation syndrome and 61 control subjects were enrolled in the study. Patients with pseudoexfoliation syndrome and pseudoexfoliation glaucoma did not show any genetic association with either single-nucleotide polymorphism rs1048661 or rs3825942.Conclusion:The study shows lack of association between LOXL1 single-nucleotide polymorphisms and pseudoexfoliation in North Indian population.

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Zhu, Y. L., Q. J. Song, D. L. Hyten, C. P. Van Tassell, L. K. Matukumalli, D. R. Grimm, S. M. Hyatt, E. W. Fickus, N. D. Young, and P. B. Cregan. "Single-Nucleotide Polymorphisms in Soybean." Genetics 163, no. 3 (March 1, 2003): 1123–34. http://dx.doi.org/10.1093/genetics/163.3.1123.

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Abstract Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

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Wang, Ting, Yuting Liang, Hong Li, Haibo Li, Quanze He, Ying Xue, Cong Shen, et al. "Single Nucleotide Polymorphisms and Osteoarthritis." Medicine 95, no. 7 (February 2016): e2811. http://dx.doi.org/10.1097/md.0000000000002811.

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Karthikeyan, Ramalingam, Manohar Murugan, SyedWali Peeran, MareiHamad Al Mugrabi, Khaled Awidat, and Omar Basheer. "Single nucleotide polymorphisms and periodontitis." Dentistry and Medical Research 2, no. 1 (2014): 3. http://dx.doi.org/10.4103/2348-1471.131556.

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Thomas, Sandy. "Shares in single nucleotide polymorphisms." Expert Opinion on Therapeutic Patents 9, no. 7 (July 1999): 811–12. http://dx.doi.org/10.1517/13543776.9.7.811.

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Phillips, C., M. Lareu, A. Salas, M. Fondevila, G. Berniell Lee, A. Carracedo, N. Morling, P. Schneider, and D. Syndercombe Court. "Population specific single nucleotide polymorphisms." International Congress Series 1261 (April 2004): 233–35. http://dx.doi.org/10.1016/j.ics.2003.12.041.

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Rieder, Mark J., and Deborah A. Nickerson. "Hypertension and single nucleotide polymorphisms." Current Hypertension Reports 2, no. 1 (February 2000): 44–49. http://dx.doi.org/10.1007/s11906-000-0057-4.

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Gaidan, Ayad, Ahmed Abbas, Mohammed Hassan, and Hashim Hashim. "INTERLEUKIN-4 SINGLE NUCLEOTIDE POLYMORPHISM C-590T POLYMORPHISMS IN RELATION TO ASTHMA." Iraqi Journal of Medical Sciences 16, no. 1 (March 31, 2018): 51–56. http://dx.doi.org/10.22578/ijms.16.1.8.

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Background: Single nucleotide polymorphisms in the promoter regions of genes encoding for some interleukins may associate with occurrence of asthma. Objective: To investigate the association of single nucleotide polymorphisms of interleukin-4 (IL-4) (C-590T) and asthma. Methods: Forty-five patients with asthma and 40 apparently healthy subjects (represent the control group) were enrolled in this study. Blood samples were collected from both patients and controls. DNA was extracted from blood samples and gene fragments corresponding to IL-4 C-590T were amplified with specific primers using conventional PCR technique. Results: The heterozygote genotypes of IL-4 C-590T (CT) showed significant association with asthma (OR = 3.922, 95% CI= 1.153-13.339, P = 0.028). Conclusion: These results suggest the significance of IL-4 C-590T polymorphism as a risk factor for asthma. Keywords: Asthma, interleukin-4, polymorphism Citation: Gaidan, Abbas AA, Hassan MA, Hashim HM. Interleukin-4 single nucleotide polymorphism C-590T polymorphisms in relation to asthma. Iraqi JMS. 2018; Vol. 16(1): 51-56. doi: 10.22578/IJMS.16.1.8

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Qatatsheh, Ala A., Rula Amr, Murad A. Al-Holy, Amin N. Olaimat, and R. Ibrahim. "Identification of Single Nucleotide Polymorphisms in Selenium-Glutathione Peroxidase (GPX1) Gene." Current Research in Nutrition and Food Science Journal 7, no. 3 (November 21, 2019): 819–27. http://dx.doi.org/10.12944/crnfsj.7.3.21.

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Human genetic variation is quite common with single nucleotide polymorphisms (SNPs) accounting for the majority of the variants. In the present study, primers for amplification of the appropriate part of the human GPX1 gene by polymerase chain reaction (PCR) were designed. The aim of this study was to develop a restriction fragment length polymorphism (RFLP) assay to detect and characterize GPX1 polymorphism in the coding region and validate the assays by sequencing. This study demonstrated that the RFLP method, which can be rapid, is reliable and valid as a tool for identifying the different polymorphisms with a high degree of specificity and sensitivity.

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Костюк, С. А., О. С. Полуян, and Т. В. Руденкова. "The Use of Real Time PCR for Justificationof Personalized Tactics of Laboratory Diagnosticsand Regimens of Treatment of Multifactorial Diseases on the Base of Identification of the Features of Changes in the Genomes of Diploid Organisms." Лабораторная диагностика. Восточная Европа, no. 2 (June 21, 2021): 146–58. http://dx.doi.org/10.34883/pi.2021.10.2.003.

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Однонуклеотидный полиморфизм – самый распространенный тип полиморфизма. Общее число однонуклеотидных полиморфизмов в геноме человека составляет приблизительно 10 миллионов; распространенность в геноме человека – 3,2×106, встречаются через каждые 1–2 тысячи пар оснований. Они могут быть локализованы как в кодирующих, так и в некодирующих участках генома. Несинонимичные замены в кодирующих участках генов подвергаются действию отбора, тогда как однонуклеотидные полиморфизмы в некодирующих участках влияют на сплайсинг, деградацию мРНК и функцию регуляторных элементов. Однонуклеотидные полиморфизмы могут приводить к нарушениям экспрессии и регуляции генов и появлению белков с измененными функциональными свойствами. Скрининг однонуклеотидных полиморфизмов позволяет определить наследственную предрасположенность к различным мультифакторным заболеваниям, а также прогнозировать индивидуальную чувствительность к фармакологическим препаратам. В данной статье авторами описано несколько технологических подходов, используемых в настоящее время в молекулярно-генетических лабораториях, для определения однонуклеотидных полиморфизмов последовательностей ДНК, основанных на использовании метода ПЦР в режиме реального времени. Single nucleotide polymorphism is the most common type of polymorphism. The total number of single nucleotide polymorphisms in the human genome is approximately 10 million; the prevalence in the human genome is 3.2×106, they occur in every 1–2 thousand base pairs. They can be localized in both coding and non-coding regions of the genome. Non-synonymous substitutions in the coding regions of the genes are the subject to selection, while single nucleotide polymorphisms in non-coding regions affect splicing, mRNA degradation, and the function of regulatory elements. Single nucleotide polymorphisms can lead to violations of gene expression and regulation, and the appearance of proteins with altered functional properties. Screening of single nucleotide polymorphisms allows to determine the hereditary predisposition to various multifactorial diseases, as well as to predict individual sensitivity to pharmacological drugs. In this article, the authors describe several technological approaches currently used in molecular genetic laboratories to determine single nucleotide polymorphisms of DNA sequences based on the use of real-time PCR.

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Ronaghi, Mostafa, and Elahe Elahi. "Discovery of Single Nucleotide Polymorphisms and Mutations by Pyrosequencing." Comparative and Functional Genomics 3, no. 1 (2002): 51–56. http://dx.doi.org/10.1002/cfg.132.

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Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis.

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Chen, Zhongxue, Hon Keung Tony Ng, Jing Li, Qingzhong Liu, and Hanwen Huang. "Detecting associated single-nucleotide polymorphisms on the X chromosome in case control genome-wide association studies." Statistical Methods in Medical Research 26, no. 2 (September 24, 2014): 567–82. http://dx.doi.org/10.1177/0962280214551815.

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In the past decade, hundreds of genome-wide association studies have been conducted to detect the significant single-nucleotide polymorphisms that are associated with certain diseases. However, most of the data from the X chromosome were not analyzed and only a few significant associated single-nucleotide polymorphisms from the X chromosome have been identified from genome-wide association studies. This is mainly due to the lack of powerful statistical tests. In this paper, we propose a novel statistical approach that combines the information of single-nucleotide polymorphisms on the X chromosome from both males and females in an efficient way. The proposed approach avoids the need of making strong assumptions about the underlying genetic models. Our proposed statistical test is a robust method that only makes the assumption that the risk allele is the same for both females and males if the single-nucleotide polymorphism is associated with the disease for both genders. Through simulation study and a real data application, we show that the proposed procedure is robust and have excellent performance compared to existing methods. We expect that many more associated single-nucleotide polymorphisms on the X chromosome will be identified if the proposed approach is applied to current available genome-wide association studies data.

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Ivanova, A. A., V. N. Maksimov, S. K. Malutina, V. P. Novoselov, and M. I. Voevoda. "Association of single nucleotide polymorphisms rs7164665, rs71461059, rs74765750, rs6762529 with sudden cardiac death." Russian Journal of Cardiology, no. 10 (November 3, 2019): 35–41. http://dx.doi.org/10.15829/1560-4071-2019-10-35-41.

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Aim. To confirm the association between sudden cardiac death (SCD) and single nucleotide polymorphisms rs7164665, rs71461059, rs74765750, rs6762529, identified in own genome-wide associative study as new molecular genetic markers of SCD.Material and methods. As design we used case-control study. The SCD group was formed using the SCD criteria of the European Society of Cardiology (n=438, average age 53,2±9,1 years, male — 72,7%, women — 28,3%). The control group (n=435, average age 53,2±8,9 years, men — 70,0%, women — 30,0%) was selected by gender and age for the SCD group from the DNA bank of the international projects MONICA and HAPIEE. DNA was isolated by phenol-chloroform extraction from myocardial tissue in the SCD group and venous blood in the control group. Genotyping was performed by polymerase chain reaction followed by analysis of estriction fragment length polymorphism. The results are statistically processed using the SPSS 16.0 software package.Results. No carriers of the rare allele A of the single nucleotide polymorphism rs74765750 were found in the SCD group and the control group. No statistically significant differences were found between the SCD group and the control group relating to frequencies of genotypes and alleles of single nucleotide polymorphisms rs7164665 and rs71461059. In the age group older than 50 years, the proportion of carriers of the heterozygous CT genotype of the single nucleotide polymorphism rs6762529 in the SCD group is statistically significantly lower compared to the control group (CT vs CC+TT: OR=0,686, 95% CI 0,483-0,967 p=0,035).Conclusion. The CT genotype of the single nucleotide polymorphism rs6762529 is associated with a protective effect on SCD for people over 50 years of age. The association with single nucleotide polymorphisms rs7164665, rs71461059, rs74765750 with SCD has not been confirmed.

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Arcidiacono, Teresa, Marco Simonini, Chiara Lanzani, Lorena Citterio, Erika Salvi, Cristina Barlassina, Donatella Spotti, Daniele Cusi, Paolo Manunta, and Giuseppe Vezzoli. "Claudin-14 Gene Polymorphisms and Urine Calcium Excretion." Clinical Journal of the American Society of Nephrology 13, no. 10 (September 19, 2018): 1542–49. http://dx.doi.org/10.2215/cjn.01770218.

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Background and objectivesClaudin-16 and -19 are proteins forming pores for the paracellular reabsorption of divalent cations in the ascending limb of Henle loop; conversely, claudin-14 decreases ion permeability of these pores. Single-nucleotide polymorphisms in gene coding for claudin-14 were associated with kidney stones and calcium excretion. This study aimed to explore the association of claudin-14, claudin-16, and claudin-19 single-nucleotide polymorphisms with calcium excretion.Design, setting, participants, & measurementsWe performed a retrospective observational study of 393 patients with hypertension who were naïve to antihypertensive drugs, in whom we measured 24-hour urine calcium excretion; history of kidney stones was ascertained by interview; 370 of these patients underwent an intravenous 0.9% sodium chloride infusion (2 L in 2 hours) to evaluate the response of calcium excretion in three different 2-hour urine samples collected before, during, and after saline infusion. Genotypes of claudin-14, claudin-16, and claudin-19 were obtained from data of a previous genome-wide association study in the same patients.ResultsThirty-one single-nucleotide polymorphisms of the 3′ region of the claudin-14 gene were significantly associated with 24-hour calcium excretion and calcium excretion after saline infusion. The most significant associated single-nucleotide polymorphism was rs219755 (24-hour calcium excretion in GG, 225±124 mg/24 hours; 24-hour calcium excretion in GA, 194±100 mg/24 hours; 24-hour calcium excretion in AA, 124±73 mg/24 hours; P<0.001; calcium excretion during saline infusion in GG, 30±21 mg/2 hours; calcium excretion during saline infusion in GA, 29±18 mg/2 hours; calcium excretion during saline infusion in AA, 17±11 mg/2 hours; P=0.03). No significant associations were found among claudin-16 and claudin-19 single-nucleotide polymorphisms and calcium excretion and between claudin-14, claudin-16, and claudin-19 single-nucleotide polymorphisms and stones. Bioinformatic analysis showed that one single-nucleotide polymorphism at claudin-14 among those associated with calcium excretion may potentially influence splicing of transcript.ConclusionsClaudin-14 genotype at the 3′ region is associated with calcium excretion in 24-hour urine and after the calciuretic stimulus of saline infusion.

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Luft, Friedrich C. "Can Single Nucleotide Polymorphisms Beat Schnüffel?" Hypertension 77, no. 4 (April 2021): 1128–32. http://dx.doi.org/10.1161/hypertensionaha.121.16739.

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See, Deven, Vladimir Kanazin, Hope Talbert, and Tom Blake. "Electrophoretic Detection of Single-Nucleotide Polymorphisms." BioTechniques 28, no. 4 (April 2000): 710–16. http://dx.doi.org/10.2144/00284st07.

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Azizzadeh-Roodpish, Shima, Max H. Garzon, and Sambriddhi Mainali. "Classifying single nucleotide polymorphisms in humans." Molecular Genetics and Genomics 296, no. 5 (July 14, 2021): 1161–73. http://dx.doi.org/10.1007/s00438-021-01805-x.

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Huber, Johannes C., and Clemens B. Tempfer. "Single nucleotide polymorphisms in gynecological endocrinology." Expert Review of Endocrinology & Metabolism 1, no. 2 (March 2006): 151–52. http://dx.doi.org/10.1586/17446651.1.2.151.

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Bagheri, Mortaza, Davood Omrani, and Isa Abdi-Rad. "Cytokine Single Nucleotide Polymorphisms in Iran." Journal of Interferon & Cytokine Research 26, no. 6 (June 2006): 414–20. http://dx.doi.org/10.1089/jir.2006.26.414.

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Deng, Na, Heng Zhou, Hua Fan, and Yuan Yuan. "Single nucleotide polymorphisms and cancer susceptibility." Oncotarget 8, no. 66 (November 7, 2017): 110635–49. http://dx.doi.org/10.18632/oncotarget.22372.

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Jairam, Sowmya, and Howard J. Edenberg. "Single-Nucleotide Polymorphisms Interact to AffectADH7Transcription." Alcoholism: Clinical and Experimental Research 38, no. 4 (February 11, 2014): 921–29. http://dx.doi.org/10.1111/acer.12340.

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Van Loon, Elisabet, and Maarten Naesens. "Single Nucleotide Polymorphisms in Renal Transplantation." Transplantation 103, no. 12 (December 2019): 2464–65. http://dx.doi.org/10.1097/tp.0000000000002661.

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Ding, Chunming. "‘Other’ applications of single nucleotide polymorphisms." Trends in Biotechnology 25, no. 7 (July 2007): 279–83. http://dx.doi.org/10.1016/j.tibtech.2007.04.007.

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Kreek, M. J. "Opioids, single nucleotide polymorphisms, and addictions." European Neuropsychopharmacology 9 (September 1999): 170–71. http://dx.doi.org/10.1016/s0924-977x(99)80057-1.

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Hanchard, Neil A. "Genetic susceptibility and single-nucleotide polymorphisms." Seminars in Fetal and Neonatal Medicine 10, no. 3 (June 2005): 283–89. http://dx.doi.org/10.1016/j.siny.2005.01.001.

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Bessenyei, B., M. M�rka, L. Urb�n, M. Zeher, and I. Semsei. "Single nucleotide polymorphisms: aging and diseases." Biogerontology 5, no. 5 (October 2004): 291–304. http://dx.doi.org/10.1007/s10522-004-2567-y.

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Dario, Paulo, Teresa Ribeiro, Deodália Dias, Francisco Corte-Real, and Helena Geada. "Complex casework using single nucleotide polymorphisms." Forensic Science International: Genetics Supplement Series 3, no. 1 (December 2011): e379-e380. http://dx.doi.org/10.1016/j.fsigss.2011.09.051.

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Bunce, Catey, Roger A. Hitchings, Shomi S. Bhattacharya, and Ordan J. Lehmann. "Single-Nucleotide Polymorphisms and Glaucoma Severity." American Journal of Human Genetics 72, no. 6 (June 2003): 1593–94. http://dx.doi.org/10.1086/375627.

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Schwarz, Daniel F., Silke Szymczak, Andreas Ziegler, and Inke R. König. "Picking single-nucleotide polymorphisms in forests." BMC Proceedings 1, Suppl 1 (2007): S59. http://dx.doi.org/10.1186/1753-6561-1-s1-s59.

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Tebbutt, Scott J., Alan James, and Peter D. Paré. "Single-Nucleotide Polymorphisms and Lung Disease." Chest 131, no. 4 (April 2007): 1216–23. http://dx.doi.org/10.1378/chest.06-2252.

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Browning, Brian L., Donna L. Brashear, Andy A. Butler, Devon D. Cyr, Elizabeth C. Harris, Anita J. Nelsen, David P. Yarnall, Margaret G. Ehm, and Michael J. Wagner. "Linkage Analysis Using Single Nucleotide Polymorphisms." Human Heredity 57, no. 4 (2004): 220–27. http://dx.doi.org/10.1159/000081449.

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Musser, James M. "Single Nucleotide Polymorphisms inMycobacterium tuberculosisStructural Genes." Emerging Infectious Diseases 7, no. 3 (June 2001): 486–87. http://dx.doi.org/10.3201/eid0703.017334.

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Collins, A., C. Lonjou, and N. E. Morton. "Genetic epidemiology of single-nucleotide polymorphisms." Proceedings of the National Academy of Sciences 96, no. 26 (December 21, 1999): 15173–77. http://dx.doi.org/10.1073/pnas.96.26.15173.

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Kruglyak, Leonid. "Single-nucleotide polymorphisms in human genetics." Nature Genetics 23, S3 (November 1999): 26. http://dx.doi.org/10.1038/14250.

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Ranade, Koustubh, Mau-Song Chang, Chih-Tai Ting, Dee Pei, Chin-Fu Hsiao, Michael Olivier, Robert Pesich, et al. "High-Throughput Genotyping with Single Nucleotide Polymorphisms." Genome Research 11, no. 7 (June 12, 2001): 1262–68. http://dx.doi.org/10.1101/gr.157801.

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To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5′ nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To demonstrate the utility of these methods, we typed >1600 individuals for a G-to-T transversion that results in a glutamate-to-aspartate substitution at position 298 in the endothelial nitric oxide synthase gene, and a G/C polymorphism (newly identified in our laboratory) in intron 8 of the 11–β hydroxylase gene. The genotyping method is accurate—we estimate an error rate of fewer than 1 in 2000 genotypes, rapid—with five 96-well PCR machines, one fluorescent reader, and no automated pipetting, over one thousand genotypes can be generated by one person in one day, and flexible—a new SNP can be tested for association in less than one week. Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three “pseudo-SNPs” (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication.

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An, X., L. Bao, J. Hou, Y. Bai, X. Zhao, Y. Song, and B. Cao. "Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size." Czech Journal of Animal Science 62, No. 7 (June 17, 2017): 269–75. http://dx.doi.org/10.17221/58/2016-cjas.

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Gonadotropin-inhibitory hormone (GnIH) can decrease luteinizing hormone and/or follicle-stimulating hormone levels in rat, mouse, sheep, and cattle by the direct suppression of gonadotropin-releasing hormone (GnRH). The present study investigated polymorphisms in the GnIH genes of two dairy goat breeds and their association with litter size. Single nucleotide polymorphisms (SNPs) g.1837C>G and g.3195G>A (GenBank Accession Nos. KR778885 and KR819142) were detected in the GnIH genes of Xinong Saanen and Guanzhong dairy goat breeds using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Furthermore, the g.1837C>G and g.3195G>A loci were closely linked in both breeds (r<sup>2</sup> > 0.33). Association analysis showed that these SNPs had significant effects on the litter size of goats (P < 0.05). In both breeds, individuals with the CC/GG (g.1837C>G/g.3195G>A) genotype showed larger litter sizes in the second and average parities than individuals with the GG/AA genotype (P < 0.05). Known biochemical and physiological functions, along with our results, indicate that the CC/GG genotype may be used in marker-assisted selection to choose individuals with a larger litter size from both breeds.

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Hreško, Stanislav, and Ľudmila Tkáčiková. "Variation in the coding region of the prion protein gene in Slovak cattle." Acta Veterinaria Hungarica 60, no. 2 (June 1, 2012): 233–43. http://dx.doi.org/10.1556/avet.2012.020.

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This study was conducted to investigate the presence of single nucleotide polymorphisms (SNPs) in the coding region of the bovine prion protein (PrP) gene among healthy and bovine spongiform encephalopathy (BSE-) affected cattle in Slovakia. Denaturing gradient gel electrophoresis (DGGE) and single-strand conformation polymorphism (SSCP) followed by DNA sequencing were used to identify SNPs and variations in octapeptide repeats. Altogether three single nucleotide polymorphisms (g234a, c339t and c576t) and variations in the number of octapeptide repeat units (5 or 6) were found in the analysed part of the prion protein gene. All single nucleotide polymorphisms were silent, causing no amino acid changes. Significant differences (P < 0.05) in the genotype distribution of g234a polymorphism were observed when the homozygous genotype with a mutated allele (caa/caa) was compared to the heterozygous genotype -/cag among healthy and BSE-affected cattle. The homozygous genotype caa/caa was characteristic of the group of BSE-affected cattle. Additionally, the homozygous genotype caa/caa was significant for the group of Simmental crossbreeds among healthy cattle. The allele and genotype distribution of the other polymorphisms was not significantly different among groups of healthy and BSE-affected cattle. The possible influence of a silent mutation on expression of the gene is not clearly determined and needs further investigations.

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Sombekke, Madeleine H., David Arteta, Mark A. van de Wiel, J. Bart A. Crusius, Diego Tejedor, Joep Killestein, Antonio Martínez, A. Salvador Peña, Chris H. Polman, and Bernard MJ Uitdehaag. "Analysis of multiple candidate genes in association with phenotypes of multiple sclerosis." Multiple Sclerosis Journal 16, no. 6 (April 8, 2010): 652–59. http://dx.doi.org/10.1177/1352458510364633.

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Multiple sclerosis is a heterogeneous neurological disease with varying degrees of severity. The common hypothesis is that susceptibility to multiple sclerosis and its phenotype are caused by a combination of environmental and genetic factors. The genetic part exerts its effect through several genes, each having modest effects. We evaluated whether disease severity could be predicted by a model based on clinical data and data from a DNA chip. The DNA chip was designed containing several single nucleotide polymorphisms in 44 genes, previously described to be associated with multiple sclerosis. A total of 605 patients with multiple sclerosis were included in this analysis, using gender, onset type and age at onset as clinical covariates. We correlated 80 single nucleotide polymorphisms to the degree of disease severity using the following three outcome measures: linear Multiple Sclerosis Severity Score, dichotomous Multiple Sclerosis Severity Score (using a cut-off point of 2.5) and time to reach Expanded Disability Status Scale score 6. Sixty-nine single nucleotide polymorphisms were included in the analysis. No individual single nucleotide polymorphism showed a significant association; however, a combination of single nucleotide polymorphisms significantly improved the prediction of disease severity in addition to the clinical variables. In all three models the Interleukin 2 gene was included, confirming a previously reported modest effect on disease severity. The highest power was obtained using the dichotomized Multiple Sclerosis Severity Score as outcome. Several single nucleotide polymorphisms showed their added predictive value over the clinical data in the predictive models. These results support our hypothesis that disease severity is determined by clinical variables and genetic influences (through several genes with small effects) in concert.

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Peterson, S. W., I. Martin, W. Demczuk, A. Bharat, L. Hoang, J. Wylie, V. Allen, et al. "Molecular Assay for Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae Isolates from Cultures and Clinical Nucleic Acid Amplification Test Specimens." Journal of Clinical Microbiology 53, no. 11 (August 19, 2015): 3606–8. http://dx.doi.org/10.1128/jcm.01632-15.

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We developed a real-time PCR assay to detect single nucleotide polymorphisms associated with ciprofloxacin resistance in specimens submitted for nucleic acid amplification testing (NAAT). All three single nucleotide polymorphism (SNP) targets produced high sensitivity and specificity values. The presence of ≥2 SNPs was sufficient to predict ciprofloxacin resistance in an organism.

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Lu*, Jinglu, Ziping Wu*, Jing Peng, Shuguang Xu, Liheng Zhou, Yanping Lin, Yan Wang, Wenjin Yin, and Jinsong Lu. "Programmed death-ligand 1 single nucleotide polymorphism affects breast cancer chemosensitivity and adverse events in the neoadjuvant setting." International Journal of Biological Markers 35, no. 3 (September 2020): 38–49. http://dx.doi.org/10.1177/1724600820926172.

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Objective We aimed to determine whether single nucleotide polymorphisms in the PD-L1 gene are related to the response and adverse events of patients receiving neoadjuvant therapy and to explore the mechanism. Methods Nine single nucleotide polymorphisms of PD-L1 were selected and tested among patients before neoadjuvant therapy. Four models were used in single nucleotide polymorphism genotype analysis: the addictive model compared TT vs TA vs AA; the dominant model compared TT vs TA+AA; the recessive model compared TT+TA vs AA; and the over-dominant model compared TT+AA vs TA (A as the minor allele). We analyzed the associations between single nucleotide polymorphism genotypes and pathological complete response, disease-free survival, and adverse events. Overexpression of the targeted microRNA was carried out using microRNA mimics. Logistic regression was used to analyze the associations between different single nucleotide polymorphism genotypes and pathological complete response outcome. Kaplan–Meier plots and log-rank tests were used to compare disease-free survival between groups with different single nucleotide polymorphism genotypes. The Cox proportional hazards model was used to calculate the adjusted hazard ratio. The Spearman's correlation test was used to determine the correlations between different genotypes and adverse events. Results rs4143815C>G was associated with better pathological complete response in the addictive and over-dominant models and with poorer disease-free survival in the recessive model. Patients with different genotypes had different adverse events. Overexpression of miR34c resulted in the downregulation of PD-L1 mRNA expression. Conclusion The PD-L1 single nucleotide polymorphism rs4143815 was associated with the pathological complete response rate, disease-free survival, and adverse events in breast cancer patients receiving neoadjuvant therapy. The interaction between miR34c and PD-L1 might be affected by rs4143815.

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Viana, Paula Coelho Silva, Ana Carolina Delgado Malvaccini Mendes, Lucas Farah Delgado, Gustavo Tostes, Lidiane Gonçalves, Homero Gonçalves Júnior, Nádia Rezende Barbosa Raposo, Geraldo Sérgio Farinazzo Vitral, and Pamela Souza Almeida Silva Gerheim. "Association between Single Nucleotide Polymorphisms and Endometriosis in a Brazilian Population." Revista Brasileira de Ginecologia e Obstetrícia / RBGO Gynecology and Obstetrics 42, no. 03 (March 2020): 146–51. http://dx.doi.org/10.1055/s-0040-1708460.

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Abstract Objective To investigate the association between genetic polymorphisms in candidate genes or candidate regions and the development of endometriosis in Brazilian women. Methods A total of 30 women between 25 and 64 years old with a diagnosis of endometriosis participated in the present study, as well as 30 matched control women from the same age group, asymptomatic and without family history of the disease. The patients genotypic and allelic frequencies of polymorphisms in the GREB1 gene (rs13394619) and in the intergenic region at position 7p15.2 (rs12700667) were analyzed and compared. Results There was no significant difference in the frequency of genotypes for the A > G polymorphism (rs13394619) in the GREB1 gene between the two groups. However, the distribution frequencies of the genotypes for the A > G polymorphism (rs12700667) in an intergenic region on chromosome 7 were different for control patients and for patients with endometriosis, with higher frequency of the AG genotype compared to the GG between patients with the disease (odds ratio [OR] = 3.49; confidence interval [CI] = 1.47–8.26). Conclusion The present study suggests that the polymorphism in the intergenic region of chromosome 7 is associated with the risk of developing endometriosis in a population of Brazilian women from Juiz de Fora.

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Shereen, Muhammad Irfan, Mohsin Shah, Sami Siraj, Mohsin Ali, Muhammad Adnan Shereen, and Abeer Kazmi. "Association of Vitamin D and its Receptor (VDR) Gene Single Nucleotide Polymorphism (ApaI and TaqI) with Risk of Psoriasis." ANNALS of JINNAH SINDH MEDICAL UNIVERSITY 6, no. 2 (December 30, 2020): 37–43. http://dx.doi.org/10.46663/ajsmu.v6i2.37-43.

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Introduction: Psoriasis is one of the skin related inflammatory diseases that affects a low percentage of population around the globe. Vitamin D through Vitamin D Receptor (VDR) also regulates the function of white blood cells in psoriasis. Mutations in VDR gene have shown abnormalities in immune responses like psoriatic arthritis. To determine the possible association between Vitamin D Receptor (ApaI and TaqI) gene polymorphism and psoriasis, a case-control study was designed and conducted at the Institute of Basic Medical Sciences (IBMS), Khyber Medical University (KMU) Peshawar and health units of Peshawar. Method: This multi-centre study included 220 samples (110 cases of psoriatic disease and 110 healthy controls). DNA was extracted using modified salting out protocol. VDR gene polymorphisms (TaqI and ApaI) were genotyped using amplification refractory mutation system using polymerase chain reaction (ARMSPCR) method. Results were statistically analyzed. Result: Our study showed significant association between VDR gene (TaqI, ApaI) polymorphisms and psoriasis with p-value of 0.009 (0.0019 and 0.0162) and odds ratios (95% confidence interval) for psoriasis of CC vs CT (TaqI) and AA vs AC (ApaI) were 2.963 (95% CI: 1.508-5.743) and 2.293 (95% CI:1.22-4.246) respectively. Conclusion: Findings indicate that VDR gene polymorphisms (TaqI, ApaI) are significantly associated with onset and progression of psoriasis, and mutations in these loci are risk factors for development of psoriasis. Key words: Psoriasis, VDR polymorphism, TaqI, ApaI, South Asia, Pakistan

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Borowska, A., T. Szwaczkowski, M. Koćwin-Podsiadła, S. Kamiński, A. Ruść, and E. Krzęcio-Nieczyporuk. "Associations of fifty single nucleotide polymorphisms within candidate genes with meatness in pigs." Czech Journal of Animal Science 59, No. 5 (May 19, 2014): 227–37. http://dx.doi.org/10.17221/7403-cjas.

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The objective of the paper was to classify 50 SNPs (from 17 chromosomes) according to their contribution to the meatness of 293 boars of two breeds (Polish Landrace and Polish Large White) using entropy analysis and standard association analysis. The collected data were classified into two groups (according to the official EUROP procedure) and used for entropy analysis. Associations of single genotypes versus their groups (located at single chromosomes) with the trait studied were estimated by the use of the Generalized Linear Model (GLM). Thus meatness was included as a continuous variable. The most important contributions have been estimated by both approaches for the following SNPs: SULT1A1:g.76G>A (SSC3), PKLR:g.384C>T (SSC4), MYOD1:c.566G>C (SSC2), TNNT3:g.153T>C (SSC2), GAA:g.38T>C (SSC12), LDLRR1:c.459A>G (SSC8), MYF6:g.255T>C (SSC5), CAS:g.499A>C (SSC2), PPARGC:c.678T>A (SSC15). Moreover, interactions among some studied loci are suggested, especially for the loci at chromosome 1.  

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Mohsen, Michael G., Debin Ji, and Eric T. Kool. "Polymerase-amplified release of ATP (POLARA) for detecting single nucleotide variants in RNA and DNA." Chemical Science 10, no. 11 (2019): 3264–70. http://dx.doi.org/10.1039/c8sc03901a.

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Jiddou, Renée R., Wan-Li Wei, Kumud S. Sane, and Anthony A. Killeen. "Single-Nucleotide Polymorphisms in Intron 2 of CYP21P: Evidence for a Higher Rate of Mutation at CpG Dinucleotides in the Functional Steroid 21-Hydroxylase Gene and Application to Segregation Analysis in Congenital Adrenal Hyperplasia." Clinical Chemistry 45, no. 5 (May 1, 1999): 625–29. http://dx.doi.org/10.1093/clinchem/45.5.625.

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Abstract Background: Intron 2 of CYP21, the functional steroid 21-hydroxylase gene contains several single-nucleotide polymorphisms (SNPs). We tested the hypothesis that intron 2 of the pseudogene, CYP21P, might also be polymorphic and provide markers for segregation analysis of this region of the genome, including observable markers for segregation analysis of CYP21 gene deletions. A comparison of SNPs in both genes might provide insights into the rates of mutation in these duplicated genes. Methods: After amplification with PCR, we examined restriction site polymorphisms in intron 2 of CYP21P in 24 members of the parental generation of the Centre d’Étude du Polymorphisme Humain families and selected offspring. Results: Intron 2 of CYP21P contains frequent SNPs around nucleotide 398 and nucleotide 509, which can be typed by PCR/restriction enzyme digestion with HaeIII. Of the 48 CYP21P alleles examined, 44 could be characterized unambiguously. Of these 44 alleles, 4 were deleted, and the frequencies of restriction at the polymorphic HaeIII sites were 20 of 40 at nucleotide 398 and 30 of 40 at nucleotide 509. Both polymorphisms result from C→T transitions that occur at CpG dinucleotides. The frequencies of C at these nucleotides in CYP21P are significantly higher than at the corresponding nucleotides in CYP21 of the same individuals (P <0.01). Conclusion: These data suggest that these CpG dinucleotides are more frequently mutated in CYP21 than in CYP21P, and that several mutations at CpG dinucleotides in the coding regions of CYP21 might result from CpG instability rather than the more usually proposed mechanism of gene conversion. These frequent SNPs provide useful markers for studying both allelic segregation of CYP21, particularly for chromosomes with known CYP21 deletions, and for investigating the origin of these polymorphisms.

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Sharma, Neeraj, Priya Tripathi, and Shally Awasthi. "Role of ADAM33 Gene and Associated Single Nucleotide Polymorphisms in Asthma." Allergy & Rhinology 2, no. 2 (January 2011): ar.2011.2.0018. http://dx.doi.org/10.2500/ar.2011.2.0018.

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Asthma is a multifactorial disorder, primarily resulting from interactions between genetic and environmental factors. ADAM33 gene (located on chromosome 20p13) has been reported to play an important role in asthma. This review article is intended to include all of the publications, to date, which have assessed the association of ADAM33 gene polymorphisms as well as have shown the role of ADAM33 gene in airway remodeling and their expression with asthma. A PubMed search was performed for studies published between 1990 and 2010. The terms “ADAM33,” “ADAM33 gene and asthma,” and “ADAM33 gene polymorphisms” were used as search criteria. Based on available literature we can only speculate its role in the morphogenesis and functions of the lung. Fourteen studies conducted in different populations were found showing an association of ADAM33 gene polymorphisms with asthma. However, none of the single nucleotide polymorphisms (SNPs) of ADAM33 gene had found association with asthma across all ethnic groups. Because higher expression of ADAM33 is found in the fibroblast and smooth muscle cells of the lung, over- or underexpression of ADAM33 gene may result in alterations in airway remodeling and repair processes. However, no SNP of ADAM33 gene showed significant associations with asthma across all ethnic groups; the causative polymorphism, if any, still has to be identified.

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Zdanowicz, A., A. Sakowicz, E. Kusidel, and P. Wierzbinski. "Association Between Two Single-nucleotide Polymorphism of TAAR1 Gene and Suicide Attempts." European Psychiatry 41, S1 (April 2017): S103. http://dx.doi.org/10.1016/j.eurpsy.2017.01.318.

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IntroductionTAAR1 is a G protein-coupled receptor expressed broadly throughout the brain. Recently, TAAR1 has been demonstrated to be an important modulator of the dopaminergic, serotonergic and glutamatergic activity.AimsAssessment of the relation between two single-nucleotide polymorphisms of TAAR1 gene, suicide attempts and alcohol abuse.MethodsA total of 150 Polish patients were included, 59 subjects after suicide attempt vs. 91 controls. The chosen SNPs (rs759733834 and rs9402439) were studied using RFLP-PCR methods. The Hardy-Weinberg equilibrium was tested in control group.Statistical testsChi2 or Yeates Chi2 Test were used.ResultsThe mean age of study subjects and controls was: 38 ± 12.3 and 42 ± 12.8 respectively; 49% study males vs. 54% male controls. We did not observe the association between the carriage of the genotypes GG, GA and AA of rs759733834 polymorphisms in either of the groups. The distribution of genotypes in respect to rs9402439 polymorphism (CC, CG, GG) was also insignificant. Among patients with alcohol dependence, the frequency G allele of rs9402439 polymorphism was lower compared to non-addicted ones (27 vs. 47%) P < 0.01.ConclusionsTAAR1 polymorphisms rs759733834 and rs9402439 are not related to suicide attempts. The carriage of allele G of rs9402439 polymorphism is related to lower risk of alcohol addiction OR 0.40 95%Cl 0.20–0.81. To our knowledge, this is the first study on the TAAR1 receptor and the risk of suicide and it might offer a new insight into genetic etiology of TAAR1 receptor.Disclosure of interestThe authors have not supplied their declaration of competing interest.

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Journal articles on the topic 'Single nucleotide polymorphisms'

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