Relevant bibliographies by topics / Single nucleotide polymorphism (SNP)

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Academic literature on the topic 'Single nucleotide polymorphism (SNP)'

Author: Grafiati
Published: 4 June 2021
Last updated: 15 June 2025

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Journal articles on the topic "Single nucleotide polymorphism (SNP)"

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Hommais, Florence, Sabrina Pereira, Cécile Acquaviva, Patricia Escobar-Páramo, and Erick Denamur. "Single-Nucleotide Polymorphism Phylotyping of Escherichia coli." Applied and Environmental Microbiology 71, no. 8 (2005): 4784–92. http://dx.doi.org/10.1128/aem.71.8.4784-4792.2005.

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ABSTRACT We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized in five genes, trpA, trpB, putP, icdA, and polB, and were selected to allow recovery of the main phylogenetic groups (groups A, B1, E, D, and B2) and subgroups of the species. In the first step, we validated the SNP approach in silico by extracting SNP data from the complete sequences of the five genes for a panel of 65 pathogenic strains belonging to different E. coli pathovars, which were previously analyzed by MLST. In the second step, we determined these SNPs by dideoxy single-base extension of unlabeled oligonucleotide primers for a collection of 183 commensal and extraintestinal clinical E. coli isolates and compared the SNP phylotyping method to previous well-established typing methods. This SNP phylotyping method proved to be consistent with the other methods for assigning phylogenetic groups to the different E. coli strains. In contrast to the other typing methods, such as multilocus enzyme electrophoresis, ribotyping, or PCR phylotyping using the presence/absence of three genomic DNA fragments, the SNP typing method described here is derived from a solid phylogenetic analysis, and the results obtained by this method are more meaningful. Our results indicate that similar approaches may be used for a wide variety of bacterial species.
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Peterson, S. W., I. Martin, W. Demczuk, 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 (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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Ravel, Catherine, Sébastien Praud, Alain Murigneux, et al. "Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.)." Genome 49, no. 9 (2006): 1131–39. http://dx.doi.org/10.1139/g06-067.

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Information on single-nucleotide polymorphisms (SNPs) in hexaploid bread wheat is still scarce. The goal of this study was to detect SNPs in wheat and examine their frequency. Twenty-six bread wheat lines from different origins worldwide were used. Specific PCR-products were obtained from 21 genes and directly sequenced. SNPs were discovered from the alignment of these sequences. The overall sequence polymorphism observed in this sample appears to be low; 64 single-base polymorphisms were detected in ~21.5 kb (i.e., 1 SNP every 335 bp). The level of polymorphism is highly variable among the different genes studied. Fifty percent of the genes studied contained no sequence polymorphism, whereas most SNPs detected were located in only 2 genes. As expected, taking into account a synthetic line created with a wild Triticum tauschii parent increases the level of polymorphism (101 SNPs; 1 SNP every 212 bp). The detected SNPs are available at http://urgi.versailles.inra.fr/GnpSNP . Data on linkage disequilibrium (LD) are still preliminary. They showed a significant level of LD in the 2 most polymorphic genes. To conclude, the genome size of hexaploid wheat and its low level of polymorphism complicate SNP discovery in this species.
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Feligini, Maria, Slavica Vlaco, Vlatka Cubric Curik, Pietro Parma, GianFranco Greppi та Giuseppe Enne. "A single nucleotide polymorphism in the sheep κ-casein coding region". Journal of Dairy Research 72, № 3 (2005): 317–21. http://dx.doi.org/10.1017/s0022029905000932.

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Genetic polymorphisms in CSN3 gene in Pag (Croatia), Sarda (Italy) and Pramenka (Serbia) sheep breeds were investigated. A single nucleotide polymorphism (SNP) was localized by sequence analysis (sequence submitted to GenBank under accession AY237637) relying on an original primer pair. Primers for sequencing (κ-casF and κ-casR) were designed on the available CSN3 sequences to amplify the genomic region encoding the major part of the mature protein (exon 4). An SNP was detected at position 237 of the sheep κ-casein mRNA (reference sequence: GenBank X51822), where a thymine was substituted for a cytosine. The SNP was typed by conventional PCR and SYBR Green I-based real-time PCR. C and T alleles were discriminated using a dedicated set of primers that consisted of one common forward primer (SNP-TC) and two reverse primers (SNP-T and SNP-C), the latter two differing in the 3′ end base and in the presence of a 12 bp poly-G tail in SNP-C. The SNP was found in both the heterozygous and the homozygous state in Sarda and Pramenka breeds, and in the heterozygous state only in the Pag breed. The observed allelic frequencies of the SNP were 0·12 in Pag, 0·27 in Sarda and 0·45 in Pramenka.
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Taillon-Miller, Patricia, Ellen E. Piernot, and Pui-Yan Kwok. "Efficient Approach to Unique Single-Nucleotide Polymorphism Discovery." Genome Research 9, no. 5 (1999): 499–505. http://dx.doi.org/10.1101/gr.9.5.499.

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Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence knowledge of the SNPs, any SNP discovery approach must involve both the determination of DNA sequence and allele frequencies. Furthermore, high-throughput genotyping also requires a genomic DNA amplification step, making it necessary to develop sequence-tagged sites (STSs) that amplify only the DNA fragment containing the SNP and nothing else from the rest of the genome. In this report, we demonstrate the utility of a SNP-screening approach that yields the DNA sequence and allele frequency information while screening out duplications with minimal cost and effort. Our approach is based on the use of a homozygous complete hydatidiform mole (CHM) as the reference. With this homozygous reference, one can identify and estimate the allele frequencies of common SNPs with a pooled DNA-sequencing approach (rather than having to sequence numerous individuals as is commonly done). More importantly, the CHM reference is preferable to a single individual reference because it reveals readily any duplicated regions of the genome amplified by the PCR assay before the duplicated sequences are found in GenBank. This approach reduces the cost of SNP discovery by 60% and eliminates the costly development of SNP markers that cannot be amplified uniquely from the genome.[Sequence data for this article were deposited with the NCBI dbSTS and dbSNP data libraries under accession nos. G42862–G42905]
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Abbas, Ahmed Abdul-Hassan, Zainab J. Fadhil, and Shatha Hussein Ali. "Tumor Necrosis Factor Alpha-863 C/A Single Nucleotide Polymorphisms and Nephrotic Syndrome." International Journal of Drug Delivery Technology 10, no. 03 (2020): 319–22. http://dx.doi.org/10.25258/ijddt.10.3.1.

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Introduction: Cytokines act as a mediator of inflammation in childhood nephrotic syndrome. Polymorphisms of cytokines genes may influence susceptibility to nephrotic syndrome (NS), as well as, patients’ steroid responses. Objective: To study the association of tumor necrosis factor-alpha single nucleotide polymorphisms (TNF-α SNP) (-863 C/A) with the development of NS in addition to access to their effects on serum level of TNF and the response to steroid therapy. Patients and Methods: This study included 60 patients (19 female and 41 male) with nephrotic syndrome; their ages ranged from 2 to 18 years. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to assess the TNF-α gene polymorphism. Results: According to the digestion pattern of RFLP-PCR products of TNF-α-863, this polymorphism had three genotypes, which were CC, CA, and AA, in both NS patients and controls. Also, the current result observed that -863 SNP do not affect the serum level of TNF-α and steroid responsiveness in patients with nephrotic syndrome. Conclusion: This polymorphism did not show any significant association with response to steroid therapy and TNF serum level neither at genotype nor at allele level.
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Purwantini, Dattadewi, and Ismoyowati Ismoyowati. "Genetic Characteristic of Indonesian Local Ducks Based on Single Nucleotide Polymorphism (SNP) Analysis in D-loop Region Mitochondria DNA." ANIMAL PRODUCTION 16, no. 3 (2015): 146. http://dx.doi.org/10.20884/1.jap.2014.16.3.460.

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Abstract. The aim of the study was to know the genetic characteristic and polymorphysm of Indonesian local ducks including Magelang, Tegal, Mojosari, Bali and Alabio duck based on Single Nucleotide Polymorphism (SNP) analysis in D-loop region mtDNA. The long term aim was to set the spesific genetic marker based on SNP D-loop region mtDNA which could differentiate local ducks in Indonesia. In the future, it could be used as selection tool for local duck conservation, and refinement strategy as well as the improvement of genetic quality by utilizing the available native duck germplasm. There were 20 ducks for each duck population and were taken 3 ml of its blood as sample. DNA Isolation Kit high pure PCR template preparation (Geneaid) was uded for Genome DNA isolation. Amplification with PCR technique used primer DL-AnasPF (L56) as forward and DL-AnasPR (H773) as reverse. Next, PCR product or amplicon were sequenced. Sequence result were analyzed with SNP technique and observed the similarity and difference of its nucleotide sequence between individual and population. The result of the study showed that genome DNA from local duck in Indonesia was successfully isolated. DNA fragment of 718 bp was amplified with primer pair of DL-AnasPF and DL-AnasPR. Nucleotide sequence was 469 nt and analyzed with SNP technique. It was compared with standard nucleotide sequence of Anas platyrhynchos (HM010684.1) in Gen Bank. The result of nucleotide sequence similarity percentage was 99.68±0.56%. Single Nucleotide Polymorphism D-loop region mtDNA Indonesian local duck was 0.32±0.56%. Some SNP was found in Magelang duck C (Klawu blorok), F (Cemani black), G (Gambiran), H (Jarakan kalung), I (Jowo plain) and K (Plain white) also Tegal duck 8, 1, 2, 5, 2, 8 and 2 SNP respectively. It could be concluded that polymorphic genetic characteristic similarity were existed in Indonesia local duck populations which was shown by its big standard deviation SNP in D-loop region mtDNA. Magelang duck with different feather color relatively more polymorphic to another local duck in Indonesia. Single Nucleotide Polymorphism which was achieved could be used as genetic marker that differentiate genetic characteristic of Indonesian local ducks.Key words: genetic characteristic, local duck, Single Nucleotide Polymorphism (SNP), D-loop mtDNAAbstrak. Penelitian ini bertujuan untuk mengetahui karakteristik genetik dan polimorfisme itik lokal Indonesia yaitu itik Magelang, Tegal, Mojosari, Bali dan Alabio berdasarkan analisis Single Nucleotide Polymorphism (SNP) daerah D-loop mtDNA. Tujuan jangka panjangnya adalah menetapkan marker atau penanda genetik berdasarkan SNP daerah D-loop mtDNA spesifik yang dapat membedakan itik-itik lokal yang ada di Indonesia. Selanjutnya digunakan sebagai alat bantu seleksi untuk konservasi, pembibitan dan pengembangbiakan itik lokal. Populasi masing-masing jenis itik lokal yang digunakan sebanyak 20 ekor untuk diambil 3 ml sampel darahnya. Isolasi DNA genom menggunakan DNA Isolation Kithigh pure PCR template preparation (Geneaid). Amplifikasi dengan teknik PCR menggunakan pasangan primer DL-AnasPF (L56) sebagai forward dan DL-AnasPR (H773) sebagai reverse. Produk PCR atau amplikon yang diperoleh disekuensing. Hasil sekuensing dianalisis dengan teknik SNP dan diamati kesamaan dan perbedaan urutan nukleotida antar individu itik dan antar populasi. Hasil penelitian menunjukkan bahwa DNA genom dari itik lokal di Indonesia berhasil diisolasi. Amplifikasi dengan teknik PCR berhasil memperoleh fragmen berukuran 718 bp. Urutan nukleotida hasil sekuensing sebesar 469 nt dianalisis dengan teknik SNP dan dibandingkan dengan urutan nukleotida standar dari itik Anas platyrhynchos (HM010684.1) yang ada di Gen Bank, diperoleh persentase kesamaan urutan nukleotid sebesar 99,68±0,56%. Single Nucleotide Polymorphism daerah D-loop mtDNA pada itik lokal di Indonesia sebesar 0,32±0,56%. Sejumlah SNP ditemukan pada itik Magelang C (Klawu blorok), F (Hitam cemani), G (Gambiran), H (Jarakan kalung), I (Jowo polos) dan K (Putih polos) serta itik Tegal masing-masing 8, 1, 2, 5, 2, 8 serta 2 SNP. Kesimpulan dari penelitian ini adalah terdapat karakteristik genetik yang polimorfik pada populasi itik lokal di Indonesia, ditunjukkan dengan adanya simpang baku SNP pada daerah D-loop mtDNA yang relatif besar. Itik Magelang dengan warna bulu yang berbeda relatif lebih polimorfik dibandingkan dengan itik lokal lainnya di Indonesia. Single Nucleotide Polymorphism yang diperoleh dapat digunakan sebagai penanda genetik yang dapat membedakan karakteristik genetik yang dimiliki oleh itik lokal di Indonesia.Kata kunci: karakteristik genetik, itik lokal, Single NucleotidePolymorphism (SNP), D-loop mtDNA
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Forche, Anja, P. T. Magee, B. B. Magee, and Georgiana May. "Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicans." Eukaryotic Cell 3, no. 3 (2004): 705–14. http://dx.doi.org/10.1128/ec.3.3.705-714.2004.

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ABSTRACT Single-nucleotide polymorphisms (SNPs) are essential tools for studying a variety of organismal properties and processes, such as recombination, chromosomal dynamics, and genome rearrangement. This paper describes the development of a genome-wide SNP map for Candida albicans to study mitotic recombination and chromosome loss. C. albicans is a diploid yeast which propagates primarily by clonal mitotic division. It is the leading fungal pathogen that causes infections in humans, ranging from mild superficial lesions in healthy individuals to severe, life-threatening diseases in patients with suppressed immune systems. The SNP map contains 150 marker sequences comprising 561 SNPs and 9 insertions-deletions. Of the 561 SNPs, 437 were transition events while 126 were transversion events, yielding a transition-to-transversion ratio of 3:1, as expected for a neutral accumulation of mutations. The average SNP frequency for our data set was 1 SNP per 83 bp. The map has one marker placed every 111 kb, on average, across the 16-Mb genome. For marker sequences located partially or completely within coding regions, most contained one or more nonsynonymous substitutions. Using the SNP markers, we identified a loss of heterozygosity over large chromosomal fragments in strains of C. albicans that are frequently used for gene manipulation experiments. The SNP map will be useful for understanding the role of heterozygosity and genome rearrangement in the response of C. albicans to host environments.
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Somers, Daryl J., Robert Kirkpatrick, Mariko Moniwa, and Andrew Walsh. "Mining single-nucleotide polymorphisms from hexaploid wheat ESTs." Genome 46, no. 3 (2003): 431–37. http://dx.doi.org/10.1139/g03-027.

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Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within a large wheat EST database and to demonstrate the utility of SNPs in genetic mapping and genetic diversity applications. A collection of >90 000 wheat ESTs was assembled into contiguous sequences (contigs), and 45 random contigs were then visually inspected to identify primer pairs capable of amplifying specific alleles. We estimate that homoeologue sequence variants occurred 1 in 24 bp and the frequency of SNPs between wheat genotypes was 1 SNP/540 bp (θ = 0.0069). Furthermore, we estimate that one diagnostic SNP test can be developed from every contig with 10–60 EST members. Thus, EST databases are an abundant source of SNP markers. Polymorphism information content for SNPs ranged from 0.04 to 0.50 and ESTs could be mapped into a framework of microsatellite markers using segregating populations. The results showed that SNPs in wheat can be discovered in ESTs, validated, and be applied to conventional genetic studies.Key words: SNP, bioinformatics, EST, genetic mapping.
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Raha, Oindrila, B. N. Sarkar, P. Veerraju, Lucy Pramanik, and V. R. Rao. "Identification of novel single nucleotide polymorphism (SNP) in DPB1 gene in ethnic population from West Bengal." Genetika 43, no. 1 (2011): 205–8. http://dx.doi.org/10.2298/gensr1101205r.

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HLA-DP antigens present peptides to CD4+ T cells and play an important role in autoimmune diseases and parasitic infections. We have sequenced HLA-DPB1 exon-2 from the ethnic populations in West Bengal, India and report a novel single nucleotide polymorphism (SNP) - rs111221466. The rs111221466 SNP induced silent mutation from CGA (Arg) to TGA (Stop Codon) and showed a frequency of 83.24%. In conventional sense, the frequency of novel SNP is very high. We have sequenced HLA-DPB1 exon-2 from a Bengali Population in West Bengal, India. HLA-DP antigens present peptides to CD4+ T cells and play an important role in autoimmune diseases and parasitic infections. Here, we report a novel single nucleotide polymorphism of HLA-DPB1 gene in the population. rs111221466 showed a frequency of 83.24, which is important to note, in view of common polymorphisms involved in disease susceptibility.
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Dissertations / Theses on the topic "Single nucleotide polymorphism (SNP)"

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Blanchard, Kimberly A. "Analysis of Single Nucleotide Polymorphism Panels for Bovine DNA Identification." DigitalCommons@USU, 2013. https://digitalcommons.usu.edu/etd/1712.

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Single nucleotide polymorphisms (SNPs) are single base-pair variations that exist between individuals. There are approximately a million or more SNPs located throughout the genome of each individual animal. Therefore, by taking advantage of these unique polymorphisms, SNPs can be used to resolve questions of unknown parentage in the livestock industry. Currently a panel of 88 SNPs, obtained from a panel of 121 SNPs originally created by USDA-MARC, is commercially available from Fluidigm®. The objective of this study was to determine whether the number of SNPs from the 88-SNP marker panel could be reduced to form a smaller, more cost-efficient parentage-testing SNP panel. A smaller panel would benefit farmers and researchers alike in reducing the time spent in running and analyzing the test, as well as reducing the overall cost for the procedure. Genotype data from over 3000 cattle samples containing offspring and potential parents were examined using two parentage calling software packages. Parentage assessment was analyzed using nine SNP panels of varying size. It was determined that a panel of 71 SNPs, chosen from the original 88 SNPs, was the minimum number required to maintain statistical accuracy and reliability.
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Pungliya, Manish S. "Single nucleotide polymorphism analysis in application to fine gene mapping." Digital WPI, 2001. https://digitalcommons.wpi.edu/etd-theses/642.

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Single nucleotide polymorphisms (SNPs) are single base variations among groups of individuals. In order to study their properties in fine gene mapping, I considered their occurrence as transitions and transversions. The aim of the study was to classify each polymorphism depending upon whether it was a transition or transversion and to calculate the proportions of transitions and transversions in the SNP data from the public databases. This ratio was found to be 2.35 for data from the Whitehead Institute for Genome Research database, 2.003 from the Genome Database, and 2.086 from the SNP Consortium database. These results indicate that the ratio of the numbers of transitions to transversions was very different than the expected ratio of 0.5. To study the effect of different transition to transversion ratios in fine gene mapping, a simulation study was performed to generate nucleotide sequence data. The study investigated the effect of different transition to transversion ratios on linkage disequilibrium parameter (LD), which is frequently used in association analysis to identify functional mutations. My results showed no considerable effect of different transition to transversion ratios on LD. I also studied the distribution of allele frequencies of biallelic SNPs from the Genome Database. My results showed that the most common SNPs are normally distributed with mean allele frequency of 0.7520 and standard deviation of 0.1272. These results can be useful in future studies for simulating SNP behavior. I also studied the simulated data provided by the Genetic Analysis Workshop 12 to identify functional SNPs in candidate genes by using the genotype-specific linkage disequilibrium method.
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Schwonbeck, Susanne. "Analyse von Single-Nucleotide-Polymorphisms an Glas-Oberflächen." [S.l. : s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=974115568.

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Lin, Kuan-chin. "Candidate Gene Expression and SNP Analyses of Toxin-Induced Dilated Cardiomyopathy in the Turkey(Meleagris gallopavo)." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/42012.

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Dilated cardiomyopathy (DCM), a heart disease, affects many vertebrates including humans and poultry. The disease can be either idiopathic (IDCM) or toxin-induced. Idiopathic DCM often occurs without a consensus cause. Though genetic and other studies of IDCM are extensive, the specific etiology of toxin-induced is still unknown. Here, our objective was to compare the level of mRNA expression of two candidate genes including troponin T (cTnT) and phospholamban (PLN) using quantitative reverse transcription polymerase chain reaction (RT-PCR) in toxin-induced DCM affected and unaffected turkeys. Cardiac TnT and PLN were chosen because their spontaneous expression has been reported to be associated with IDCM. We also scanned these genes for single nucleotide polymorphisms (SNPs) that could be useful in evaluating their functions in the incidence and severity of toxin-induced DCM in turkeys. There were no significant differences between affected and unaffected birds in the expression of both cTnT and PLN. A total of 12 SNPs were detected in cTnT and PLN DNA sequences. One of the seven haplotypes detected in cTnT was the most frequent. Linkage analysis showed that cTnT gene was unlinked on the current turkey genetic map. Resources developed here, including SNPs, haplotypes, cDNA sequences, and the PCR-RFLP genotype procedure will be used for future investigations involving cTnT and PLN and toxin-induced DCM.<br>Master of Science
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Veldsman, Werner Pieter. "SNP based literature and data retrieval." Thesis, University of the Western Cape, 2016. http://hdl.handle.net/11394/5345.

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>Magister Scientiae - MSc<br>Reference single nucleotide polymorphism (refSNP) identifiers are used to earmark SNPs in the human genome. These identifiers are often found in variant call format (VCF) files. RefSNPs can be useful to include as terms submitted to search engines when sourcing biomedical literature. In this thesis, the development of a bioinformatics software package is motivated, planned and implemented as a web application (http://sniphunter.sanbi.ac.za) with an application programming interface (API). The purpose is to allow scientists searching for relevant literature to query a database using refSNP identifiers and potential keywords assigned to scientific literature by the authors. Multiple queries can be simultaneously launched using either the web interface or the API. In addition, a VCF file parser was developed and packaged with the application to allow users to upload, extract and write information from VCF files to a file format that can be interpreted by the novel search engine created during this project. The parsing feature is seamlessly integrated with the web application's user interface, meaning there is no expectation on the user to learn a scripting language. This multi-faceted software system, called SNiPhunter, envisions saving researchers time during life sciences literature procurement, by suggesting articles based on the amount of times a reference SNP identifier has been mentioned in an article. This will allow the user to make a quantitative estimate as to the relevance of an article. A second novel feature is the inclusion of the email address of a correspondence author in the results returned to the user, which promotes communication between scientists. Moreover, links to external functional information are provided to allow researchers to examine annotations associated with their reference SNP identifier of interest. Standard information such as digital object identifiers and publishing dates, that are typically provided by other search engines, are also included in the results returned to the user.<br>National Research Foundation (NRF) /The South African Research Chairs Initiative (SARChI)
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Howell, Walter Mathias. "SNP technology and Alzheimer's disease /." Stockholm, 2003. http://diss.kib.ki.se/2003/91-7349-473-9/.

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Kadioglu, Onat. "Determination Of Performance Parameters For Ahp Based Single Nucleotide Polymorphism (snp) Prioritization Approach On Alzheimers." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613775/index.pdf.

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GWAS mainly aim to identify variations associated with certain phenotypes or diseases. Recently the combined p-value approach is described as the next step after GWAS to map the significant SNPs to genes and pathways to evaluate SNP-gene-disease associations. Major bottleneck of standard GWAS approaches is the prioritization of statistically significant results. The connection between statistical analysis and biological relevance should be established to understand the underlying molecular mechanisms of diseases. There are few tools offered for SNP prioritization but these are mainly based on user-defined subjective parameters, which are hard to standardize. Our group has recently developed a novel AHP based SNP prioritization algorithm. Beside statistical association AHP based SNP prioritization algorithm scores SNPs according to their biological relevance in terms of genomic location, functional consequence, evolutionary conservation, and gene-disease association. This allows researchers to evaluate the significantly associated SNPs quickly and objectively. Here, we have investigated the performance of the AHP based prioritization as the next step in the utilization of the algorithm in comparison to the other available tools for SNP prioritization. The user-defined parameters for AHP based prioritization have been investigated and our suggestion on how to use these parameters are presented. Additionally, the GWAS results from the analysis of two different sets of Alzheimer Disease Genotyping data with the newly proposed AHP based prioritization and the integrated software, METU-SNP, it was implemented, is reported and our new findings on the association of SNPs and genes with AD based on this analysis is discussed.
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Meyer, Jodokus [Verfasser], and Alexander [Akademischer Betreuer] Mellmann. "Single-Nucleotide-Polymorphism-(SNP)-Analyse im Kerngenom der HUSEC-Kollektion / Jodokus Meyer ; Betreuer: Alexander Mellmann." Münster : Universitäts- und Landesbibliothek Münster, 2014. http://d-nb.info/1138284351/34.

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Ramdayal, Kavisha. "Incidence and Regulatory Implications of Single Nucleotide Polymorphisms among Established Ovarian Cancer Genes." Thesis, Online access, 2009. http://etd.uwc.ac.za/usrfiles/modules/etd/docs/etd_gen8Srv25Nme4_5111_1277754725.pdf.

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Hrabik, Sarah A. "The Clinical Utility of a SNP Microarray in Patients with Epilepsy at a Tertiary Medical Center." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1368024881.

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Books on the topic "Single nucleotide polymorphism (SNP)"

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1956-, Kwok Pui-Yan, ed. Single nucleotide polymorphisms: Methods and protocols. Humana Press, 2003.

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Liu, Zhanjiang. Next generation sequencing and whole genome selection in aquaculture. Wiley-Blackwell, 2011.

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1955-, Carracedo Ángel, ed. Forensic DNA typing protocols. Humana Press, 2005.

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Hamilton, Matthew Lloyd. COMT genotypes in pain responses. Edited by Paul Farquhar-Smith, Pierre Beaulieu, and Sian Jagger. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198834359.003.0080.

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The landmark study discussed in this chapter is ‘COMT val158met genotype affects μ‎-opioid neurotransmitter responses to a pain stressor’, published by Zubieta et al. in 2003. Catechol-O-methyl-transferase (COMT) is a key modulator of dopaminergic and noradrenergic neurotransmission. This study focused on a single nucleotide polymorphism of the COMT gene encoding the substitution of valine (val) by methionine (met) at Codon 158 (val158met), resulting in a three- to fourfold reduction in its activity. Individuals with the val/val genotype have the highest activity of COMT, val/met genotypes have intermediate activity, and met/met genotypes have the lowest activity of COMT. Using a mixture of PET imaging of the binding of μ‎-opioid receptors and correlation with clinical outcomes, this groundbreaking study provided evidence that confirmed their hypothesis and established the COMT val158met SNP as one of the first gene modifications with direct ramifications on human pain.
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Komar, Anton A. Single Nucleotide Polymorphisms: Methods and Protocols. Humana Press, 2012.

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Kwok, Pui-Yan. Single Nucleotide Polymorphisms: Methods and Protocols (Methods in Molecular Biology). Humana Press, 2002.

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Osman, Marwa. In Silico Analysis and Modeling of Deleterious Single Nucleotide Polymorphism (Snps) in Human Gata4 Gene. GRIN Verlag GmbH, 2016.

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Carracedo, Angel. Forensic DNA Typing Protocols. Humana Press, 2004.

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Forensic DNA typing protocols. Humana Press, 2004.

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A Primer of Genome Science. Sinauer Associates, 2001.

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Book chapters on the topic "Single nucleotide polymorphism (SNP)"

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Turner, J. Rick. "Single Nucleotide Polymorphism (SNP)." In Encyclopedia of Behavioral Medicine. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-1005-9_720.

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Turner, J. Rick. "Single Nucleotide Polymorphism (SNP)." In Encyclopedia of Behavioral Medicine. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-39903-0_720.

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Mathur, Runjhun, Bhisham Singh Rana, and Abhimanyu Kumar Jha. "Single Nucleotide Polymorphism (SNP)." In Encyclopedia of Animal Cognition and Behavior. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-47829-6_2049-1.

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Mathur, Runjhun, Bhisham Singh Rana, and Abhimanyu Kumar Jha. "Single Nucleotide Polymorphism (SNP)." In Encyclopedia of Animal Cognition and Behavior. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_2049.

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Jensen, Lindsay G., Loren K. Mell, Christin A. Knowlton, et al. "Single-Nucleotide Polymorphisms (SNP)." In Encyclopedia of Radiation Oncology. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-540-85516-3_611.

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Lynch, Gordon S., David G. Harrison, Hanjoong Jo, et al. "Single-Nucleotide Polymorphisms (SNP)." In Encyclopedia of Exercise Medicine in Health and Disease. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-540-29807-6_3034.

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Phan, Lon. "SNPs Classification and Terminology: dbSNP Reference SNP (rs) Gene and Consequence Annotation." In Single Nucleotide Polymorphisms. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-05616-1_1.

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Hettiarachchi, Gaya, and Anton A. Komar. "GWAS to Identify SNPs Associated with Common Diseases and Individual Risk: Genome Wide Association Studies (GWAS) to Identify SNPs Associated with Common Diseases and Individual Risk." In Single Nucleotide Polymorphisms. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-05616-1_4.

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AbstractAssociation studies have enabled the exploration of alternative, more efficient methods for early detection, prevention and treatment of diseases by providing valuable insight into their genetic foundation. Genome wide association studies (GWASs) have been particularly informative with respect to complex diseases whose manifestation depends on a multitude of genetic and environmental factors. In these studies, common Single Nucleotide Polymorphisms (SNPs) are used to locate and identify regions of the genome that may be causative of common complex diseases. These studies have uncovered a number of loci of interest for several diseases and have also allowed for the development of genetic counseling with improved individual disease risk assessment. With the more accurate prediction of the probability of disease development, progression and treatment success, GWASs have also brought about the age of personalized medicine. Despite these promising outcomes, skepticism concerning the power of these studies and their impact on patient care exists. This uncertainty stems from the many inherent limitations of this relatively young technique. This chapter explores the underlying concepts of GWASs, their contributions to research, clinical and commercial development, and their limitations with the hopes of providing a better understanding of the impact of these SNP-based association studies can have on public health.
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Cui, Songkui, Abdelbagi M. A. Ghanim, and Satoko Yoshida. "Identification of Closely Related Polymorphisms with Striga Resistance Using Next Generation Sequencing." In Mutation Breeding and Efficiency Enhancing Technologies for Resistance to Striga in Cereals. Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-68181-7_9.

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AbstractMolecular markers are powerful tools to enhance speed of breeding. Recent advances of sequencing technology allow us to identify most polymorphisms in a genome. Whole genome resequencing of an F2 segregating population can identify those polymorphisms that co-segregate with a mutant phenotype, which theoretically include the gene responsible for Striga resistance gained through mutagenesis. This protocol explains the isolation of high-quality genomic DNA for sequencing and step-by-step procedures for single nucleotide polymorphism (SNP) identification from bulked F2 sequences.
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Earl, Julie, and William Greenhalf. "Single-Nucleotide Polymorphism (SNP) Analysis to Associate Cancer Risk." In Methods in Molecular Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-545-9_10.

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Conference papers on the topic "Single nucleotide polymorphism (SNP)"

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Setiawan, Adi. "Single nucleotide polymorphism (SNP) data analysis by using bootstrap method." In THE 2016 CONFERENCE ON FUNDAMENTAL AND APPLIED SCIENCE FOR ADVANCED TECHNOLOGY (CONFAST 2016): Proceeding of ConFAST 2016 Conference Series: International Conference on Physics and Applied Physics Research (ICPR 2016), International Conference on Industrial Biology (ICIBio 2016), and International Conference on Information System and Applied Mathematics (ICIAMath 2016). Author(s), 2016. http://dx.doi.org/10.1063/1.4953976.

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Erickson, David, Xuezhu Liu, Roberto Venditti, Ulrich Krull, and Dongqing Li. "A DNA Hybridization Chip With Electrokinetically-Based Single Nucleotide Polymorphism (SNP) Discrimination." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-59320.

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Biosensors and more specifically biochips exploit the interactions between a target analyte and an immobilized biological recognition element to produce a measurable signal. Systems based on surface phase nucleic acid hybridization, such as modern microarrays, are particularly attractive due to the high degree of selectivity in the binding interactions. In this work an electrokinetically controlled poly(dimethylsiloxane) based DNA hybridization microfluidic chip is presented. The electrokinetic delivery technique provides the ability to dispense controlled sample sizes to the hybridization array for quantitative analysis while serving to increase the mass transfer rate and therefore reduce the overall analysis time. An automatic, electrokinetically based, single-nucleotide polymorphism (SNP) discrimination technique (that takes advantage of the combined effects of joule heating, applied potential field and the shear gradients within the double layer field on the thermodynamic stability of the target: probe complex) will also be described for the first time. The clinical utility of the technique will be demonstrated through the detection of genetic markers associated with spinal muscular atrophy, specifically the common C←T mutation in the SMN1 gene.
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Pei-Chun Kao, Kan-Chien Li, Shih-Torng Ding, En-Chung Lin, Lon Wang, and Yen-Wen Lu. "Single nucleotide polymorphism (SNP) genotyping methods using bead-based microfluidics with DASH technology." In 2012 IEEE Sensors. IEEE, 2012. http://dx.doi.org/10.1109/icsens.2012.6411210.

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Чемерис, А. В., Ф. Г. Аминев та Р. Р. Гарафутдинов. "ИСПОЛЬЗОВАНИЕ МИКРОДИПЛОТИПОВ С МНОЖЕСТВЕННЫМ ОДНОНУКЛЕОТИДНЫМ ПОЛИМОРФИЗМОМ ДЛЯ ВСЕОБЩЕЙ ДНК-РЕГИСТРАЦИИ НАСЕЛЕНИЯ И ОДНОЗНАЧНОЙ ДНК-ИДЕНТИФИКАЦИИ ЛИЧНОСТИ, ВКЛЮЧАЯ ПРИНЦИП ЦИФРОВИЗАЦИИ ПОЛУЧАЕМЫХ ПЕРВИЧНЫХ ДАННЫХ". У ТЕОРИЯ И ПРАКТИКА ФУНДАМЕНТАЛЬНЫХ И ПРИКЛАДНЫХ ИССЛЕДОВАНИЙ В СФЕРЕ СУДЕБНО-ЭКСПЕРТНОЙ ДЕЯТЕЛЬНОСТИ И ДНК-РЕГИСТРАЦИИ НАСЕЛЕНИЯ РОССИЙСКОЙ ФЕДЕРАЦИИ. Crossref, 2024. http://dx.doi.org/10.56777/lawinn.2023.80.44.042.

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Для ДНК-идентификации личности и ДНК-регистрации населения предлагается использовать однонуклеотидный полиморфизм (Single-Nucleotide Polymorphism - SNP) в виде замен пуринов на пиримидины (‘R’ и ‘Y’ в однобуквенной записи соответственно) и наоборот, легко переводимых в двухразрядные двоичные числа. То есть, ‘R’ (аденин - ‘A’ и гуанин - ‘G’) кодируются как «01», а ‘Y’ (цитозин - ‘C’ и тимин - ‘T’) – как «10». При этом для полиморфных нуклеотидов в составе микродиплотипа в одном SNP будет достаточно для базы данных всего четырех бит, или полбайта информации. При этом микрогаплотипы в составе микродиплотипов должны размещаться в базе данных, начиная с присущего им меньшего двоичного числа.
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Amatya, S., M. Ye, L. Yang, C. Gandhi, R. Wu, and J. Floros. "Single Nucleotide Polymorphism (SNP)-SNP Interactions of the Surfactant Protein Genes Associated with Respiratory Distress Syndrome (RDS) Susceptibility in Preterm Infants." In American Thoracic Society 2021 International Conference, May 14-19, 2021 - San Diego, CA. American Thoracic Society, 2021. http://dx.doi.org/10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a3309.

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Comen, E., L. Balistreri, T. Kirchhoff, et al. "Breast Cancer Risk Single Nucleotide Polymorphism (SNP) Genotypes Do Not Correlate with Risk Estimates from Existing Prediction Models." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-901.

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Hassanien, M., NA Mohamed, and SA Mahran. "AB0804 Single-nucleotide polymorphism (SNP) RS143383 growth and differentiation factor 5 (GDF5) in knee osteoarthritis in egyptian population." In Annual European Congress of Rheumatology, 14–17 June, 2017. BMJ Publishing Group Ltd and European League Against Rheumatism, 2017. http://dx.doi.org/10.1136/annrheumdis-2017-eular.1273.

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LeBron, Cynthia, Prodipto Pal, Mariana Brait, et al. "Abstract 4728: Genome-wide analysis of genetic alterations in seminoma using high resolution single Nucleotide polymorphism (SNP) arrays." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-4728.

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Tada, Motohisa, Fumihiko Kanai, Yoshinari Asaoka, et al. "Abstract 1184: Prognostic significance of genetic alterations detected by high-density single nucleotide polymorphism (SNP) array in gastrointestinal cancer." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-1184.

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Keam, B., H. Kim, S. Im, et al. "Single Nucleotide Polymorphism (SNP) in RASSF1 and Clinical Outcomes of Breast Cancer Patients Treated with Neoadjuvant Docetaxel/Doxorubicin Chemotherapy." In Abstracts: Thirty-Second Annual CTRC‐AACR San Antonio Breast Cancer Symposium‐‐ Dec 10‐13, 2009; San Antonio, TX. American Association for Cancer Research, 2009. http://dx.doi.org/10.1158/0008-5472.sabcs-09-6061.

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Reports on the topic "Single nucleotide polymorphism (SNP)"

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ZHOU, YUHUI, XIAOXIA MA, and JINGLAN SUN. Update on the Relationship Between the SLC4A7 variant rs4973768 and Breast Cancer risk: a systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2023. http://dx.doi.org/10.37766/inplasy2023.2.0013.

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Review question / Objective: The aim of this meta-analysis was to get an updated opinion, which was about the role of the single nucleotide polymorphism (SNP) rs4973768 in the SLC4A7 gene played in the incident of breast cancer. Eligibility criteria: The included criteria were formulated for this meta-analysis as following:(1) studies with both case and control groups;(2) studies assessing the relation between the SLC4A7 rs4973768 polymorphism and sensibility to breast cancer;(3) studies with sufficient information such as genotype frequency for results of odds ratios (ORs) and 95% confidence intervals (95% CIs); and (4) full-text articles of studies with human subjects. Studies meeting any one of the criteria were determined unqualified for this meta-analysis as following:(1) conference abstracts, comments, reviews, case reports, or editorials;(2) inadequate data for OR calculation;(3) no control group; and (4) animal studies.
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Wang, Ying yuan, Zechang Chen, Luxin Zhang, et al. A systematic review and network meta-analysis: Role of SNPs in predicting breast carcinoma risk. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, 2022. http://dx.doi.org/10.37766/inplasy2022.2.0092.

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Review question / Objective: P: Breast cancer patient; I: Single nucleotide polymorphisms associated with breast cancer risk; C: Healthy person; O: By comparing the proportion of SNP mutations in the tumor group and the control group, the effect of BREAST cancer risk-related SNP was investigated; S: Case-control study. Condition being studied: Breast cancer (BC) is one of the most common cancers among women, and its morbidity and mortality have continued to increase worldwide in recent years, reflecting the strong invasiveness and metastasis characteristics of this cancer. BC is a complex disease that involves a sequence of genetic, epigenetic, and phenotypic changes. Polymorphisms of genes involved in multiple biological pathways have been identified as potential risks of BC. These genetic polymorphisms further lead to differences in disease susceptibility and severity among individuals. The development of accurate molecular diagnoses and biological indicators of prognosis are crucial for individualized and precise treatment of BC patients.
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Wongpiyabovorn, Jongkonnee, Nattiya Hirankarn, Yingyos Avihingsanon, Tewin Tencomnao, Yong Poovorawan, and Kriangsak Ruchusatsawat. The association between immunogenetics and genetic susceptibility of psoriasis in Thai population. Chulalongkorn University, 2006. https://doi.org/10.58837/chula.res.2006.27.

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Psoriasis is T-cell-mediated skin autoimmunity, required environmental triggers and genetic susceptibility factors to become manifested. Psoriasis is a chronic skin disease characterized by the abnormal hyperproliferation and differentiation of the epidermis, elongated and prominent blood vessels and a thick perivascular lymphocytic infiltrate. Vascular endothelial growth factor (VEGF) gene play important role in pathogenesis of various diseases with angiogenic basis such as breast cancer and autoimmune disease including psoriasis. Many studies analyzed the association of VEGF gene polymorphism in many positions in Caucasian and non-Caucasian. Most reports in some position that really point to important about single nucleotide polymorphism (SNP) with several autoimmune diseases including psoriasis. Although the precise causes of this auto-immune disease remain elusive. It appears to be influenced by stress. The serotonergic system known to depend primarily on the serotonin transporter (5-HTT) may have a role in psoriasis. The serotonin transporter-linked promoter region (5-HTTLPR) polymorphism occurred by insertion/deletion is evident to result in three different length alleles namely S, L as predominant variant alleles and XL as a rare one. These three alleles have 14, 16 and 18 or 20 repetitive DNA sequences, respectively and have been shown to associate with certain neuropsychiatric diseases. Although roles of serotonin and serotonin receptors in psoriasis were investigated, the impact of 5-HTTLPR on psoriasis has not been studied. Therefore, the 5-HTTLPR polymorphism was analyzed to assess whether these variants are associated with psoriasis. Furthermore, having recognized the relationship between oxidative stress and psoriasis, the association between G82S polymorphism in the gene encoding the receptor for advanced glycation end products (RAGE) and psoriasis was investigated. The aims of study, we determine the distribution of VEGF, RAGE and 5-HTTLPR polymorphism in Thai psoriasis patients. We analyzed SNPs within the VEGF (-1557) (C/A), -460(C/T) and +405(C/G)). G82S RAGE and 5-HTTLPR (S, L and XL) gene polymorphism. In population-based case-control study, allele and genotype frequencies of each marker were compared between 234 unrelated healthy volunteers and 154 chronic plapue psoriasis patients (102 early-onset and 52 late-onset psoriasis) for VEGF gene, one hundred seventy eight healthy donors and 134 psoriasis patients for RAGE gene and one hundred twenty seven healthy controls and 142 psoriasis patients for 5-HTTLPR gene. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and PCR-sequence specific primer (PCR-SSP) methods. The results, The -460 TT or CT compared to CC VEGF genotype were found to be significantly risk associated with early-onset psoriasis patients compared with healthy controls (p=0.0450, odds ratio (OR) =4.67, 95% confidence interval (CI) = 1.03-29.52). Interesthingly, haplotype analysis revealed that the CTG haplotype was found to be significantly associated with susceptibility to psoriasis and early-onset psoriasis compared with healthy controls (p=0.0460, OR=1.37, 95% CI=1.00-1.87, p=0.0163, OR=1.54, 95% CI=1.08-2.18, respectively). Moreover, VEGF plasma concentration was not significantly different between groups of haplotype in psoriasis patients. A significantly greater 82A G82S RAGE allele frequency was observed in psoriatic patients than in control subjects (p=0.001 OR=0.52 95% CI=0.35-0.78). Finally, the 5HTTPR polymorphism was no significant change in the allelic frequencies between psoriatic and control subjects (p=0.531, OR=1.15, 95% CI=0.78-1.70). Thus, the result demonstrated that the CTG haplotype and -460 C/T VEGF polymorphism may be used as a genetic marker for early-onset psoriasis in Thais but the 5-HTTLPR was not associated with psoriasis in Thai population. Furthermore, the G82S RAGE polymorphism was associated with psoriasis, and further investigations should be carried out to gain insights into its molecular mechanism in psoriasis.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Zhelev, Doncho V., Christopher Dupuis, Suelynn Ren, Anna Le, Mia Hunt, and Henry Gibbons. Single Nucleotide Polymorphisms (SNP)-specific Quantitative Real Time Polymerase Chain Reaction (PCR) Assay for Analyzing Competition and Emergence of the Military Hypersporulating Strains of Bacillus Atrophaeous var. Globigii. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada570597.

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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir, and Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.
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นุชประยูร, สุรางค์, จินตนา จิรถาวร, อนุพงค์ สุจริยากุล та อลิสา จันทร์ปี. การศึกษาภูมิคุ้มกันวิทยาเชิงลึกของโรคเท้าช้าง : มุ่งสู่การป้องกันภาวะเท้าช้างและการกำจัดโรคอย่างถาวร : แผนการวิจัย : รายงานการวิจัยฉบับสมบูรณ์. จุฬาลงกรณ์มหาวิทยาลัย, 2009. https://doi.org/10.58837/chula.res.2009.21.

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โรคเท้าช้าง (Lymphatic filariasis) เกิดจากพยาธิ 2 ชนิดหลัก คือ Wuchereria bancrofti และ Brugia malayi ทางองค์การอนามัยโลกได้กำหนดให้โรคเท้าช้างเป็นโรคทางปรสิตที่ควรกำจัดให้หมดไปภายในปี พ.ศ. 2563 โดยมีแนวทางหลักในการควบคุมและป้องกันโรคเท้าช้างคือการจัดให้มีโปรแกรมการรักษาแบบหมู่ โดยให้ยา diethylcarbamazine (DEC) ร่วมกับยา albendazole แก่ประชากรในพื้นที่ที่มีความชุกของโรคสูง และการควบคุมพยาธิภาวะ ปัญหาที่สำคัญของการรักษาโรคเท้าช้าง คือ การใช้ยา DEC ที่ก่อให้เกิดปฏิกิริยาหลังการรักษา กลไกของการเกิดพยาธิสภาพของโรคและการเกิดปฏิกิริยาหลังการรักษายังไม่เป็นที่ทราบแน่ชัดได้ จึงเป็นอุปสรรคที่สำคัญอย่างยิ่งต่อการกำจัดโรค การศึกษาภูมิคุ้มกันวิทยาเชิงลึกของโรคเท้าช้างจะช่วยให้การกำจัดโรคสำเร็จลงได้อย่างยั่งยืน ผลการศึกษาในปีที่ 3 นี้ ได้ศึกษารูปแบบการตอบสนองทางภูมิคุ้มกันหลังการรักษาโรคเท้าช้าง โดยวัดระดับไซโตไคน์ที่เกี่ยวข้องกับการอักเสบ ได้แก่ interleukin (IL)-6 และ tumor necrosis factor (TNF)-α ในผู้ป่วยกลุ่มที่มีปฏิกิริยาหลังการรักษาน้อย (mild) ปฏิกิริยาหลังการรักษาปานกลาง (moderate) และปฏิกิริยาหลังการรักษาชนิดรุนแรง (severe) หลังการรักษาด้วยยา DEC เมื่อเปรียบเทียบกันระดับไซโตไคน์ในกระแสเลือดก่อนการรักษาด้วยยา DEC พบว่าผู้ป่วยโรคเท้าช้างมีระดับ IL-6 และ TNF-α สูงขึ้นอย่างมีนัยสำคัญทางสถิติที่เวลา 24 ชั่วโมงหลังการรักษา (P&lt;0.05) โดยพบว่าระดับของไซโตไคน์ IL-6 สอดคล้องกับระดับความรุนแรงของปฏิกิริยาหลังการรักษา ในขณะที่ระดับไซโตไคน์ TNF- α สูงขึ้นอย่างมีนัยสำคัญทางสถิติเฉพาะในกลุ่มผู้ป่วยโรคเท้าช้างที่เกิดปฏิกิริยาหลังการรักษาชนิดรุนแรงเท่านั้น สำหรับการวัดระดับไซโตไคน์ที่เกี่ยวข้องกับการต้านการอักเสบ IL-10 มีระดับสูงขึ้นอย่างมีนัยสำคัญทางสถิติเฉพาะในกลุ่มผู้ป่วยโรคเท้าช้างที่เกิดปฏิกิริยาหลังการรักษาชนิดปานกลางและชนิดรุนแรงเท่านั้น โดยถูกปล่อยออกมาในระดับสูงสุดที่เวลา 12-24 ชั่วโมงหลักการรักษา ในขณะที่ระดับไซโตไคน์ IL-12 ลดลงอย่างมีนัยสำคัญทางสถิติที่เวลา 24 ชั่วโมงหลังการรักษา และไม่พบความสัมพันธ์ของระดับของไซโตไคน์กับระดับความรุนแรงของปฏิกิริยาหลังการรักษา (โครงการย่อยที่ 1) และจากการทบทวนวรรณกรรมตลอดจนค้นหาจากฐานข้อมูลได้พบยีน peptidoglycan-associated lipoprotein (pal) มีความน่าสนใจที่ใช้ศึกษาทางอิมมูนวิทยาต่อไป จึงได้ทำการโคลนและสร้างโปรตีนบริสุทธิ์ในห้องปฏิบัติการ และวัดระดับแอนติบอดีชนิดต่าง ๆ ที่จำเพาะต่อโปรตีน PAL ในกระแสเลือดของผู้ป่วยโรคเท้าช้างที่มีการติดเชื้อปัจจุบัน (active infections) ทั้งผู้ป่วยที่ตรวจพบไมโครฟิลาเรียในกระแสเลือด (Ag+/Mf+) และตรวจไม่พบไมโครฟิลาเรียในกระแสเลือด (Ag+/Mf-) กลุ่มผู้ป่วยโรคเท้าช้างที่มีพยาธิสภาพเรื้อรัง (chronic pathology; CP) ตลอดจนกลุ่มคนปกติที่อาศัยอยู่ในแหล่งชุกชุมของโรคเท้าช้าง (endemic normals; EN) (Ag-/Mf-) พบว่าแอนติบอดีชนิด IgG3 ที่จำเพาะต่อโปรตีน PAL มีระดับสูงขึ้นอย่างมีนัยสำคัญในกลุ่มการติดเชื้อปัจจุบัน ซึ่งตรวจพบแอนติเจนที่จำเพาะต่อพยาธิโรคเท้าช้าง (Ag+/Mf- และ Ag+/Mf+) เปรียบเทียบกับระดับของแอนติบอดีในกลุ่มคนปกติที่อาศัยอยู่ในแหล่งชุกชุมของโรคเท้าช้าง (P=0.003) โดยพบการสูงขึ้นของระดับแอนติบอดีอย่างมีนัยสำคัญในผู้ป่วยโรคเท้าช้างที่ตรวจพบไมโครฟิลาเรียในกระแสเลือด (Ag+/Mf+) (P=0.04) (โครงการย่อยที่ 2) สำหรับการศึกษาความสัมพันธ์ของความหลากหลายทางพันธุกรรมของยีน toll-like receptor 2 (tlr-2) กับความไวรับและการเกิดพยาธิสภาพของโรคเท้าช้าง ได้ตรวจสอบความหลากหลายทางพันธุกรรมของยีน TLR2 แบบ -197 to -174 ins/del ซึ่งอยู่ในบริเวณ 5’ untranslated region (5’ UTR) โดยใช้เทคนิค allele-specific polymerase chain reaction (AS-PCR) และตรวจสอบความหลากหลายทางพันธุกรรมแบบการเปลี่ยนแปลงลำดับนิวคลีโอไทด์เพียงตำแหน่งเดียว (single nucleotide polymorphisms; SNPs) ของยีน TLR2 แบบ +597 T/C และ +1350 T/C ในบริเวณ exon 3 โดยใช้เทคนิค polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) พบว่าความถี่จีโนไทป์ของความหลากหลายทางพันธุกรรมทั้ง 3 ตำแหน่งที่ทดสอบ -197 to -174 ins/del, +597 T/C, และ +1350 T/C อยู่ในสมดุลฮาร์ดี-ไวน์เบิร์ก (P&gt;0.05) อัลลีล -197 to -174del สัมพันธ์กับความเสี่ยงที่จะเป็นโรคเท้าช้าง ([P=0.005], OR=2.21 [95% CI = 1.25-3.92] อัลลีล +597C และ +1350C เพิ่มความเสี่ยงต่อการติดเชื้อโรคเท้าช้าง ([P = 0.001], OR = 2.58 [95% CI = 1.40-4.75], และ [P =0.0121], OR = 2.37 [95% CI = 1.19-4.77], ตามลำดับ) นอกจากนี้ยังพบว่าความหลากหลายทางพันธุกรรมทั้ง 3 ตำแหน่งถ่ายทอดไปร่วมกัน TLR2 haplotype แบบ -197 to -174del/+597C/+1350C (delCC) สัมพันธ์กับความไวรับโรคเท้าช้างอย่างมีนัยสำคัญ จากการพยากรณ์โดยใช้ซอฟแวร์ Mfold พบว่า RNA ของ -197 to -174 del มีความเสถียรน้อยกว่า RNA ของ -197 to -174 ins อย่างมีนัยสำคัญ การศึกษานี้เป็นการศึกาทางด้านระบาดวิทยาเชิงพันธุศาสตร์เบื้องต้นซึ่งชี้ให้เห็นว่าความหลากหลายทางพันธุกรรมของยีน TLR2 แบบ -197 to -174 ins/del, +597 T/C, และ +1350 T/C มีความสัมพันธ์กับความไวรับโรคเท้าช้าง (โครงการย่อยที่ 3)
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8

Langston, J. W. Large Scale Single Nucleotide Polymorphism Study of PD Susceptibility. Defense Technical Information Center, 2006. http://dx.doi.org/10.21236/ada458414.

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9

Wyatt, Colby A., and Constance E. Brinckerhoff. Effect of a Single Nucleotide Polymorphism (NP) on Breast Cancer Invasion. Defense Technical Information Center, 2001. http://dx.doi.org/10.21236/ada396663.

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10

Hansen, Peter J., Zvi Roth, and Jeremy J. Block. Improving oocyte competence in dairy cows exposed to heat stress. United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7598163.bard.

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Original Objectives. The overall goal is to develop methods to increase pregnancy rate in lactating dairy cows exposed to heat stress through methods that minimize damage to the oocyte and embryo caused by heat stress. Objectives were as follows: (1) examine the protective effects of melatonin on developmental competence of oocytes exposed to elevated temperature in vitro; (2) test whether melatonin feeding can improve developmental competence of oocytes in vivo and, if so, whether effects are limited to the summer or also occur in the absence of heat stress; and (3) evaluate the effectiveness of improving fertility by facilitating follicular turnover in the summer and winter. Revised Objectives. (1) Examine protective effects of melatonin and follicular fluid on developmental competence of oocytes exposed to elevated temperature in vitro; (2) examine the protective effects of melatonin on developmental competence of embryos exposed to elevated temperature in vitro; (3) evaluate effectiveness of improving fertility by administering human chorionicgonadotropin (hCG) to increase circulating concentrations of progesterone and evaluate whether response to hCG depends upon genotype for four mutations reported to be related to cow fertility; and (4) identify genes with allelic variants that increase resistance of embryos to heat shock. Background. The overall hypothesis is that pregnancy success is reduced by heat stress because of damage to the oocyte and cleavage-stage embryo mediated by reactive oxygen species (ROS), and that fertility can be improved by provision of antioxidants or by removing follicles containing oocytes damaged by heat stress. During the study, additional evidence from the literature indicated the potential importance of treatment with chorionicgonadotropin to increase fertility of heat- stressed cows and results from other studies in our laboratories implicated genotype as an important determinant of cow fertility. Thus, the project was expanded to evaluate hCG treatment and to identify whether fertility response to hCG depended upon single nucleotide polymorphisms (SNP) in genes implicated as important for cow fertility. We also evaluated whether a SNP in a gene important for cellular resistance to heat stress (HSPA1L, a member of the heat shock protein 70 family) is important for embryonic resistance to elevated temperature. Major conclusions, solutions &amp; achievements. Results confirmed that elevated temperature increases ROS production by the oocyte and embryo and that melatonin decreases ROS. Melatonin reduced, but did not completely block, damaging effects of heat shock on the oocyte and had no effect on development of the embryo. Melatonin was protective to the oocyte at 0.1-1 μM, a concentration too high to be achieved in cows. It was concluded that melatonin is unlikely to be a useful molecule for increasing fertility of heat-stressed cows. Treatment with hCG at day 5 after breeding increased first-service pregnancy rate for primiparous cows but not for multiparous cows. Thus, hCG could be useful for increasing fertility in first-parity cows. The effectiveness of hCG depended upon genotype for a SNP in COQ9, a gene encoding for a mitochondrial-function protein. This result points the way to future efforts to use genetic information to identify populations of cows for which hormone treatments will be effective or ineffective. The SNP in HSPA1L was related to embryonic survival after heat shock. Perhaps, genetic selection for mutations that increase cellular resistance to heat shock could be employed to reduce effects of heat stress on fertility. Implications, both scientific and agricultural. This project has resulted in abandonment of one possible approach to improve fertility of the heat-stressed cow (melatonin therapy) while also leading to a method for improving fertility of primiparous cows exposed to heat stress (hCG treatment) that can be implemented on farms today. Genetic studies have pointed the way to using genetic information to 1) tailor hormonal treatments to cow populations likely to respond favorably and 2) select animals whose embryos have superior resistance to elevated body temperatures.
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