Journal articles on the topic 'SNPs genotyping'
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Xu, Han, Sihuan Zhang, Xiaoyan Zhang, Ruihua Dang, Chuzhao Lei, Hong Chen, and Xianyong Lan. "Evaluation of novel SNPs and haplotypes within the <i>ATBF1</i> gene and their effects on economically important production traits in cattle." Archives Animal Breeding 60, no. 3 (August 29, 2017): 285–96. http://dx.doi.org/10.5194/aab-60-285-2017.
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Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C>G (SNP1), g.146573T>C (SNP2), g.205468C>T (SNP3), g.205575A>G (SNP4) and g.297690C<T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.
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Claassen, Daniel O., Jody Corey-Bloom, E. Ray Dorsey, Mary Edmondson, Sandra K. Kostyk, Mark S. LeDoux, Ralf Reilmann, et al. "Genotyping single nucleotide polymorphisms for allele-selective therapy in Huntington disease." Neurology Genetics 6, no. 3 (May 14, 2020): e430. http://dx.doi.org/10.1212/nxg.0000000000000430.
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BackgroundThe huntingtin gene (HTT) pathogenic cytosine-adenine-guanine (CAG) repeat expansion responsible for Huntington disease (HD) is phased with single nucleotide polymorphisms (SNPs), providing targets for allele-selective treatments.ObjectiveThis prospective observational study defined the frequency at which rs362307 (SNP1) or rs362331 (SNP2) was found on the same allele with pathogenic CAG expansions.MethodsAcross 7 US sites, 202 individuals with HD provided blood samples that were processed centrally to determine the number and size of CAG repeats, presence and heterozygosity of SNPs, and whether SNPs were present on the mutant HTT allele using long-read sequencing and phasing.ResultsHeterozygosity of SNP1 and/or SNP2 was identified in 146 (72%) individuals. The 2 polymorphisms were associated only with the mHTT allele in 61% (95% high density interval: 55%, 67%) of individuals.ConclusionsThese results are consistent with previous reports and demonstrate the feasibility of genotyping, phasing, and targeting of HTT SNPs for personalized treatment of HD.
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Min, Josine L., Nico Lakenberg, Margreet Bakker-Verweij, Eka Suchiman, Dorret I. Boomsma, P. Eline Slagboom, and Ingrid Meulenbelt. "High Microsatellite and SNP Genotyping Success Rates Established in a Large Number of Genomic DNA Samples Extracted From Mouth Swabs and Genotypes." Twin Research and Human Genetics 9, no. 4 (August 1, 2006): 501–6. http://dx.doi.org/10.1375/twin.9.4.501.
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AbstractIn this article, we present the genomic DNA yield and the microsatellite and single nucleotide polymorphism (SNP) genotyping success rates of genomic DNA extracted from a large number of mouth swab samples. In total, the median yield and quality was determined in 714 individuals and the success rates in 378,480 genotypings of 915 individuals. The median yield of genomic DNA per mouth swab was 4.1 μg (range 0.1–42.2 μg) and was not reduced when mouth swabs were stored for at least 21 months prior to extraction. A maximum of 20 mouth swabs is collected per participant. Mouth swab samples showed in, respectively, 89% for 390 microsatellites and 99% for 24 SNPs a genotyping success rate higher than 75%. A very low success rate of genotyping (0%–10%) was obtained for 3.2% of the 915 mouth swab samples using microsatellite markers. Only 0.005% of the mouth swab samples showed a geno-typing success rate lower than 75% (range 58%–71%) using SNPs. Our results show that mouth swabs can be easily collected, stored by our conditions for months prior to DNA extraction and result in high yield and high-quality DNA appropriate for genotyping with high success rate including whole genome searches using microsatellites or SNPs.
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Rustgi, S., R. Bandopadhyay, H. S. Balyan, and P. K. Gupta. "EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure." Czech Journal of Genetics and Plant Breeding 45, No. 3 (October 6, 2009): 106–16. http://dx.doi.org/10.17221/16/2009-cjgpb.
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The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1–18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.
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Li, Peng-Le, Mo-Hua Yang, Xiao-Long Jiang, Huan Xiong, Hui-Liang Duan, Feng-Lan Zou, Qian-Yu Xu, Wei Wang, Yong-Hui Hong, and Neng-Qing Lin. "De Novo SNP Discovery and Genotyping of Masson Pine (Pinus massoniana Lamb.) via Genotyping-by-Sequencing." Forests 14, no. 2 (February 14, 2023): 387. http://dx.doi.org/10.3390/f14020387.
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Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic research by facilitating the discovery of thousands of single nucleotide polymorphisms (SNPs) and genotyping in non-model organisms, at relatively low cost. Here, we performed de novo SNP discovery and genotyping in 299 trees via the genotyping-by-sequencing (GBS) approach. The effort produced 9.33 × 109 sequence reads, 265,525 SNP-associated contigs, and 6,739,240 raw SNPs. Further filtering and validation of the SNP-associated contigs for reliable SNPs were performed using blasting against the Pinus tabuliformis reference genome, functional annotation, technical replicates, and custom parameter settings for the optimization. The 159,372 SNP-associated contigs were aligned and validated for SNP prediction, in which 60,038 contigs were searched with hits in the NCBI nr database. We further improved the SNP discovery and genotyping with multiple technical replicates and custom parameter settings filtering. It was found that the use of blasting, annotation, technical replicates, and specific parameter settings removed many unreliable SNPs and identified 20,055 more precise and reliable SNPs from the 10,712 filtered contigs. We further demonstrated the informativeness of the identified SNPs in the inference of some genetic diversity and structure. These findings should be useful to stimulate genomic research and genomics-assisted breeding of Masson pine.
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Calvo, Jorge H., Magdalena Serrano, Flavie Tortereau, Pilar Sarto, Laura P. Iguacel, María A. Jiménez, José Folch, José L. Alabart, Stéphane Fabre, and Belén Lahoz. "Development of a SNP parentage assignment panel in some North-Eastern Spanish meat sheep breeds." Spanish Journal of Agricultural Research 18, no. 4 (October 27, 2020): e0406. http://dx.doi.org/10.5424/sjar/2020184-16805.
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Aim of study: To validate two existing single nucleotide polymorphism (SNP) panels for parentage assignment in sheep, and develop a cost effective genotyping system to use in some North-Eastern Spanish meat sheep populations for accurate pedigree assignment.Area of study: SpainMaterial and methods: Nine sheep breeds were sampled: Rasa Aragonesa (n=38), Navarra (n=39), Ansotana (n=41), Xisqueta (n=41), Churra Tensina (n=38), Maellana (39), Roya Bilbilitana (n=24), Ojinegra (n=36) and Cartera (n=39), and these animals were genotyped with the Illumina OvineSNP50 BeadChip array. Genotypes were extracted from the sets of 249 SNPs and 163 SNPs for parentage assignment designed in France and North America, respectively. Validation of a selected cost-effective genotyping panel of 158 SNPs from the French panel were performed by Kompetitive allele specific PCR (KASP). Additionally, some functional SNPs (n=15) were also genotyped.Main results: The set of 249 SNPs for parentage assignment showed better diversity, probability of identity, and exclusion probabilities than the set of 163 SNPs. The average minor allele frequency for the set of 249, 163 and 158 SNPs were 0.41 + 0.01, 0.39 + 0.01 and 0.42 + 0.01, respectively. The parentage assignment rate was highly dependent to the percentage of putative sires genotyped.Research highlights: The described method is a cost-effective genotyping system combining the genotyping of SNPs for the parentage assignment with some functional SNPs, which was successfully used in some Spanish meat sheep breeds.
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Graham, Natalie, Emily Telfer, Tancred Frickey, Gancho Slavov, Ahmed Ismael, Jaroslav Klápště, and Heidi Dungey. "Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)." Forests 13, no. 2 (January 24, 2022): 176. http://dx.doi.org/10.3390/f13020176.
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Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.
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Chiapparino, E., D. Lee, and P. Donini. "Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS–PCR." Genome 47, no. 2 (April 1, 2004): 414–20. http://dx.doi.org/10.1139/g03-130.
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Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS–PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.Key words: single nucleotide polymorphisms (SNPs), genotyping, barley, tetra-primers ARMS–PCR.
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Germer, Søren, and Russell Higuchi. "Single-Tube Genotyping without Oligonucleotide Probes." Genome Research 9, no. 1 (January 1, 1999): 72–78. http://dx.doi.org/10.1101/gr.9.1.72.
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We report the development of a self-contained (homogeneous), single-tube assay for the genotyping of single-nucleotide polymorphisms (SNPs), which does not rely on fluorescent oligonucleotide probes. The method, which we call Tm-shift genotyping, combines allele-specific PCR with the discrimination between amplification products by their melting temperatures (Tm). Two distinct forward primers, each of which contains a 3′-terminal base that corresponds to one of the two SNP allelic variants, are combined with a common reverse primer in a single-tube reaction. A GC-tail is attached to one of the forward allele-specific primers to increase theTm of the amplification product from the corresponding allele. PCR amplification, Tmanalysis, and allele determination of genomic template DNA are carried out on a fluorescence-detecting thermocycler with a dye that fluoresces when bound to dsDNA. We demonstrate the accuracy and reliability ofTm-shift genotyping on 100 samples typed for two SNPs, and recommend it both as a simple and inexpensive diagnostic tool for genotyping medically relevant SNPs and as a high-throughput SNP genotyping method for gene mapping.
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Ahmed, Mahbubl, Chee Goh, Edward Saunders, Clara Cieza-Borrella, Zsofia Kote-Jarai, Fredrick R. Schumacher, and Ros Eeles. "Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT." Prostate Cancer and Prostatic Diseases 23, no. 2 (November 27, 2019): 333–42. http://dx.doi.org/10.1038/s41391-019-0181-y.
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Abstract Background The development of prostate cancer can be influenced by genetic and environmental factors. Numerous germline SNPs influence prostate cancer susceptibility. The functional pathways in which these SNPs increase prostate cancer susceptibility are unknown. Finasteride is currently not being used routinely as a chemoprevention agent but the long term outcomes of the PCPT trial are awaited. The outcomes of the SELECT trial have not recommended the use of chemoprevention in preventing prostate cancer. This study investigated whether germline risk SNPs could be used to predict outcomes in the PCPT and SELECT trial. Methods Genotyping was performed in European men entered into the PCPT trial (n = 2434) and SELECT (n = 4885). Next generation genotyping was performed using Affymetrix® Eureka™ Genotyping protocols. Logistic regression models were used to test the association of risk scores and the outcomes in the PCPT and SELECT trials. Results Of the 100 SNPs, 98 designed successfully and genotyping was validated for samples genotyped on other platforms. A number of SNPs predicted for aggressive disease in both trials. Men with a higher polygenic score are more likely to develop prostate cancer in both trials, but the score did not predict for other outcomes in the trial. Conclusion Men with a higher polygenic risk score are more likely to develop prostate cancer. There were no interactions of these germline risk SNPs and the chemoprevention agents in the SELECT and PCPT trials.
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Fabbri, Elena, R. Caniglia, Nadia Mucci, H. P. Thomsen, K. Krag, C. Pertoldi, V. Loeschcke, and E. Randi. "Comparison of single nucleotide polymorphisms and microsatellites in non-invasive genetic monitoring of a wolf population." Archives of Biological Sciences 64, no. 1 (2012): 321–35. http://dx.doi.org/10.2298/abs1201321f.
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Single nucleotide polymorphisms (SNPs) which represent the most widespread source of sequence variation in genomes, are becoming a routine application in several fields such as forensics, ecology and conservation genetics. Their use, requiring short amplifications, may allow a more efficient genotyping of degraded DNA. We provide the first application of SNP genotyping in an Italian non-invasive genetic monitoring project of the wolf. We compared three different techniques for genotyping SNPs: pyrosequencing, SNaPshot? and TaqMan? Probe Assay in Real-Time PCR. We successively genotyped nine SNPs using the TaqMan Probe Assay in 51 Italian wolves, 57 domestic dogs, 15 wolf x dog hybrids and 313 wolf scats collected in the northern Apennines. The obtained results were used to estimate genetic variability and PCR error rates in SNP genotyping protocols compared to standard microsatellite analysis. We evaluated the cost, laboratory effort and reliability of these different markers and discuss the possible future use of VeraCode, SNPlex and Fluidigm EP1 system in wild population monitoring.
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Morita, Akihiko, Tomohiro Nakayama, Nobutaka Doba, Shigeaki Hinohara, Tomohiko Mizutani, and Masayoshi Soma. "Genotyping of triallelic SNPs using TaqMan® PCR." Molecular and Cellular Probes 21, no. 3 (June 2007): 171–76. http://dx.doi.org/10.1016/j.mcp.2006.10.005.
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Pavey, Scott A. "High-throughput SNPs for all: genotyping-in-thousands." Molecular Ecology Resources 15, no. 4 (June 15, 2015): 685–87. http://dx.doi.org/10.1111/1755-0998.12405.
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Foster, Jeffrey T., Lance B. Price, Stephen M. Beckstrom-Sternberg, Talima Pearson, William D. Brown, Danika M. Kiesling, Christina A. Allen, et al. "Genotyping of Brucella species using clade specific SNPs." BMC Microbiology 12, no. 1 (2012): 110. http://dx.doi.org/10.1186/1471-2180-12-110.
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King, Garry C., Daniel A. Di Giusto, Wjatschesslaw A. Wlassoff, Susanne Giesebrecht, Eleanor Flening, and Gregory D. Tyrelle. "Proofreading genotyping assays and electrochemical detection of SNPs." Human Mutation 23, no. 5 (2004): 420–25. http://dx.doi.org/10.1002/humu.20034.
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Sayadi Maazou, Abdoul-Raouf, Melaku Gedil, Victor O. Adetimirin, Silvestro Meseka, Wende Mengesha, Deborah Babalola, Queen Nkem Offornedo, and Abebe Menkir. "Comparative Assessment of Effectiveness of Alternative Genotyping Assays for Characterizing Carotenoids Accumulation in Tropical Maize Inbred Lines." Agronomy 11, no. 10 (October 9, 2021): 2022. http://dx.doi.org/10.3390/agronomy11102022.
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The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content.
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Yang, Shangbin, Lihui Xu, and Haifeng Wu. "Rapid Genotyping of SNPs Influencing Warfarin Drug Response by SELDI-TOF Mass Spectrometry." Blood 112, no. 11 (November 16, 2008): 4053. http://dx.doi.org/10.1182/blood.v112.11.4053.4053.
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Abstract The anticoagulant drug Warfarin exhibits significant inter-individual variability in dosing requirements. Different responses to Warfarin therapy are partly attributed to the single nucleotide polymorphisms (SNPs) that influence either Warfarin drug action (VKORC1) or drug metabolism (CYP2C9). Rapid genotyping of these SNPs is essential for clinicians to choose appropriate initial doses in order to quickly achieve anticoagulation effects and to prevent the complications associated with Warfarin overdoses. In this study, we explore the utility of surface-enhanced laser desorption and ionization time-of- flight (SELDI-TOF) mass spectrometry in the rapid genotyping of SNPs that control Warfarin drug sensitivity. The DNA containing the targeted SNPs is first amplified by polymerase chain reactions and then underwent the single base extension to generate specific SNP product. Afterwards, genetic variants displaying different masses are bound to Q10 anionic proteinChips and genotyped using a SELDI-TOF mass spectrometer in a multiplexed fashion. SELDI-TOF mass spectrometer offers a unique property of on-chip sample enrichment and clean-ups. Therefore, this genotype method eliminated many tedious experimental steps, such as sample desalting and concentrating, that are required prior to detection by standard mass spectrometers. The turnaround time for genotyping three known Warfarin sensitivity SNPs, CYP2C9*2, CYP2C9*3, VKORC1, is less than five hours. The analytical accuracy of genotyping detected by SELDI mass spectrometer has been confirmed by DNA sequencing. In summary, we have devised a novel multiplex genotyping method using a SELDI-TOF mass spectrometer. This test is fast, accurate, and therefore provides a superb clinical laboratory platform to promote the personalized health care in Warfarin therapy.
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Moqa, Rashad, Irfan Younas, and Maryam Bashir. "Assessing effectiveness of many-objective evolutionary algorithms for selection of tag SNPs." PLOS ONE 17, no. 12 (December 8, 2022): e0278560. http://dx.doi.org/10.1371/journal.pone.0278560.
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Background Studies on genome-wide associations help to determine the cause of many genetic diseases. Genome-wide associations typically focus on associations between single-nucleotide polymorphisms (SNPs). Genotyping every SNP in a chromosomal region for identifying genetic variation is computationally very expensive. A representative subset of SNPs, called tag SNPs, can be used to identify genetic variation. Small tag SNPs save the computation time of genotyping platform, however, there could be missing data or genotyping errors in small tag SNPs. This study aims to solve Tag SNPs selection problem using many-objective evolutionary algorithms. Methods Tag SNPs selection can be viewed as an optimization problem with some trade-offs between objectives, e.g. minimizing the number of tag SNPs and maximizing tolerance for missing data. In this study, the tag SNPs selection problem is formulated as a many-objective problem. Nondominated Sorting based Genetic Algorithm (NSGA-III), and Multi-Objective Evolutionary Algorithm based on Decomposition (MOEA/D), which are Many-Objective evolutionary algorithms, have been applied and investigated for optimal tag SNPs selection. This study also investigates different initialization methods like greedy and random initialization. optimization. Results The evaluation measures used for comparing results for different algorithms are Hypervolume, Range, SumMin, MinSum, Tolerance rate, and Average Hamming distance. Overall MOEA/D algorithm gives superior results as compared to other algorithms in most cases. NSGA-III outperforms NSGA-II and other compared algorithms on maximum tolerance rate, and SPEA2 outperforms all algorithms on average hamming distance. Conclusion Experimental results show that the performance of our proposed many-objective algorithms is much superior as compared to the results of existing methods. The outcomes show the advantages of greedy initialization over random initialization using NSGA-III, SPEA2, and MOEA/D to solve the tag SNPs selection as many-objective optimization problem.
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Misra, Ashish, Jun-Yan Hong, and Sobin Kim. "Multiplex Genotyping of Cytochrome P450 Single-Nucleotide Polymorphisms by Use of MALDI-TOF Mass Spectrometry." Clinical Chemistry 53, no. 5 (May 1, 2007): 933–39. http://dx.doi.org/10.1373/clinchem.2006.080739.
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Abstract Background: Polymorphisms in cytochrome P450 (CYP450) genes contribute to interindividual differences in the metabolism of xenobiotic chemicals, including the vast majority of drugs, and may lead to toxicity and adverse drug reactions. Studies on these polymorphisms in research and diagnostic settings typically involve large-scale genotyping and hence require high-throughput assays. Methods: We used the previously developed solid-phase capture–single-base extension (SPC-SBE) approach for concurrent analysis of 40 single-nucleotide polymorphisms (SNPs) of CYP2C9 and 50 SNPs of CYP2A13, both genes belonging to the CYP450 family. Desired SNP-containing regions for each gene were amplified in a single-step multiplex PCR. We designed a library of primers to anneal immediately upstream of the selected SNPs and extended it with biotinylated terminators using PCR products as templates. Biotinylated extension products were isolated by affinity purification and analyzed with MALDI-TOF mass spectrometry to determine SNP genotypes. Results: We analyzed 11 samples for CYP2C9 and 14 samples for CYP2A13 with unambiguous detection of SNPs in all samples. Many samples showed a high occurrence of heterozygotes for both genes, with as many as 10 of 50 SNPs appearing as heterozygotes in 1 sample genotyped for CYP2A13. Conclusions: The SPC-SBE method provides an efficient means for genotyping SNPs from the CYP450 family. This approach is suitable for automation and can be extended to other genotyping applications.
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Lipkin, S. M., J. Yeakley, E. Chao, J. Velasquez, M. Lopez, J. Rhee, T. McDaniel, I. Lewis, and H. Chen. "Multiplexed genotyping using a novel digitally inscribed bead-based system." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 21089. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.21089.
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21089 Background: Genotyping of clinical samples has been limited to low levels of multiplexing, ranging from one to a few dozen single nucleotide polymorphisms (SNPs) per sample. By increasing multiplexing levels, a clinical lab can increase information content per sample, decreasing costs and sample material requirements. Methods: We have adapted the GoldenGate® Assay for simultaneously genotyping 96 to 1,536 SNPs to the BeadXpress™ System, a new high-throughput platform that utilizes digitally inscribed VeraCode™ beads in a compact fluidic instrument. Genotyping on this platform ranges from 96 to 384 multiplexing, using the same GoldenGate Assay that has proven highly robust for millions of genotypes. In preliminary tests, we have observed greater than 99% call rates, and greater than 99.5% rates for reproducibility and heritability. In a test of 96 SNP genotypes chosen for a study of colorectal cancer, a point mutation in the MSH2 gene, previously implicated in predisposition to several cancers, was correctly genotyped when compared to qPCR analysis of the same samples. Conclusion: Together with genotyping data from reference samples, the GoldenGate Assay on the BeadXpress System has yielded highly reproducible and accurate genotypes, suggesting that this approach will prove useful for rapid refinement of SNPs for development of clinical genotyping tests. No significant financial relationships to disclose.
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Hyun, Do Yoon, Raveendar Sebastin, Gi-An Lee, Kyung Jun Lee, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, et al. "Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing." International Journal of Molecular Sciences 22, no. 13 (June 23, 2021): 6722. http://dx.doi.org/10.3390/ijms22136722.
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Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.
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Falzoi, Matteo, Luigi Pira, Paolo Lazzari, and Luca Pani. "Genotyping of CYP2D6 Polymorphisms by MALDI-TOF Mass Spectrometry in Sardinian People." ISRN Genetics 2013 (May 12, 2013): 1–10. http://dx.doi.org/10.5402/2013/609797.
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The CYP2D6 enzyme is involved in the metabolism of many commonly prescribed drugs. The presence of CYP2D6 gene SNPs can alter CYP2D6 enzymatic activity with effects ranging considerably within a population. Objectives. In this study, we have developed a genotyping platform able to determine the alleles related to interindividual variability in the CYP2D6 gene. Design and Methods. We used a long PCR strategy coupled to MALDI-TOF mass spectrometry (Sequenom) to develop a SNPs genotyping method. Furthermore, an amplification allele specific was carried out to infer the correct allelic phase. Results. We tested the multiplex platform in 250 DNA Sardinian samples and found it to be 100% concordant with the sequencing results of our previous work. Conclusions. The MALDI-TOF-based multiplexing system allowed simultaneous and efficient genotyping of a set of CYP2D6 SNPs, evidencing its potential use in diagnostic test development to predict drug responses and clinical outcomes.
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Wang, Weili, Kerby A. Shedden, and Feng-Ming (Spring) Kong. "Association between genetic variations in transforming growth factor beta pathway and overall survival in patients with non-small cell lung cancer treated with definitive radiotherapy." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e17530-e17530. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e17530.
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e17530 Background: The transforming growth factor beta (TGFβ) pathway, an important regulator in cellular metabolic process, has been reported for significant association with cancer prognosis. This study was to exam the association between single nucleotide polymorphisms (SNPs) of TGFβ pathway and overall survival (OS) in subjects with non-small cell lung cancer (NSCLC). Methods: Patients with stage I-III NSCLC received definitive radiotherapy with/without chemotherapy were eligible to this prospective study. The primary endpoint was OS which was calculated from radiation treatment start to death or censored. DNA samples for genotyping were extracted from buffy-coat which was collected before commencement of treatment. 19 SNPs in 10 genes (BMP1, BMP2, INHBC, SMAD1, SMAD3, SMAD4, SMAD6, SMAD7, SMAD8, TGFβ1), which was reported to have significant correlation with OS of lung cancer, were selected. MassArray System (Sequenom Company) was used for genotyping. Cox regression was performed for multivariate analysis to examine the effects of genotypes on OS using dominant and recessive genetic model. Results: 126 consecutive patients, 91% of them were Caucasian, were recruited in this study. All SNPs call rates were over 90%. Assay reproducibility was over 99% by random double-blinding duplicate or triplicate genotyping. Among clinical factors analyzed, radiation dose was only significant independent factor predicting OS (P=0.001). Genotypic association study showed that 7 SNPs (rs235756, rs11939979, rs12102171, rs6494633, rs12456284, rs12906898 and rs4803455) were significantly associated with OS, adjusted for age, gender, smoking, histology, clinical stage, tumor volume, Karnofsky Performance Status, radiotherapy dose, and chemotherapy. The strongest association was in SMAD3: rs12102171 (P=0.004, HR=2.28, 95%CI, 1.26-4.15). Conclusions: This study partly validated findings from previous studies that genetic variations in the TGFβ pathway are significant predictors of overall survival in NSCLC patients treated with definitive radiotherapy with/without chemotherapy.
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Semlali, Abdelhabib, Mikhlid H. Almutairi, Abdullah Alamri, Narasimha Reddy Parine, Maha Arafah, Majid A. Almadi, Abdulrahman M. Aljebreen, et al. "Expression and Polymorphism of TSLP/TSLP Receptors as Potential Diagnostic Markers of Colorectal Cancer Progression." Genes 12, no. 9 (September 6, 2021): 1386. http://dx.doi.org/10.3390/genes12091386.
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Colorectal cancer (CRC) is the third most common malignancy and the fourth leading cause of cancer-related mortality worldwide. Inflammation is considered as a critical driver for CRC development and growth. We investigated the association between polymorphisms/expression levels of thymic stromal lymphopoietin (TSLP) /TSLP receptors and CRC risk in Saudi population. DNA samples were isolated from blood samples from 220 participants. Case subjects were 112 patients diagnosed with CRC, while control subjects were 108 healthy individuals, who were not diagnosed with any type of malignancy. We selected two single nucleotide polymorphisms (SNPs) located in the thymic stromal lymphopoietin gene (rs10043985 and rs2289276), three SNPs in TSLP receptor gene (TSLPR; rs36139698, rs36177645, and rs36133495), and two other SNPs in interleukin-7 receptor gene (IL-7R; rs12516866 and rs1053496), and designated these SNPs for a case-control genotyping study. The gene expression was analyzed using quantitative RT-PCR and immunohistochemistry assays array on 20 matching colorectal cancer/normal tissues. mRNA expressions and protein levels of TSLP, TSLPR-α subunit, and IL-7R-α subunit showed a 4-fold increase in colon cancer tissues when compared to normal colon tissues. Furthermore, two SNPs (rs10043985 of TSLP and rs1053496 of IL-7R) showed statistically significant correlations with CRC susceptibility. Interestingly, only rs10043985 showed a statistically significant association (p < 0.0001) in the genotypic and phenotypic levels with CRC for all clinical parameters (age, gender, and tumor location) tested. However, IL-7R rs1053496 genotyping results presented a significant correlation (p < 0.05) in male CRC patients and in individuals under 57 years of age. TSLP rs2289276, IL-7R rs12516866, and all TSLPR variants did not display any significant genotypic or phenotypic correlations in all tested clinical parameters. This study identified that TSLP rs10043985 and IL-7R rs1053496 SNPs, and the expression levels of TSLP and TSLPR-α subunit, can be used as markers for CRC development and treatment. However, additional investigations are required on larger group of patients from diverse ethnicities to confirm the genetic association of these variants to CRC.
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Lu, Yi, Xiaoqing Chen, Jonathan Beesley, Sharon E. Johnatty, Anna deFazio, Sandrina Lambrechts, Diether Lambrechts, et al. "Genome-Wide Association Study for Ovarian Cancer Susceptibility Using Pooled DNA." Twin Research and Human Genetics 15, no. 5 (July 13, 2012): 615–23. http://dx.doi.org/10.1017/thg.2012.38.
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Recent Genome-Wide Association Studies (GWAS) have identified four low-penetrance ovarian cancer susceptibility loci. We hypothesized that further moderate- or low-penetrance variants exist among the subset of single-nucleotide polymorphisms (SNPs) not well tagged by the genotyping arrays used in the previous studies, which would account for some of the remaining risk. We therefore conducted a time- and cost-effective stage 1 GWAS on 342 invasive serous cases and 643 controls genotyped on pooled DNA using the high-density Illumina 1M-Duo array. We followed up 20 of the most significantly associated SNPs, which are not well tagged by the lower density arrays used by the published GWAS, and genotyping them on individual DNA. Most of the top 20 SNPs were clearly validated by individually genotyping the samples used in the pools. However, none of the 20 SNPs replicated when tested for association in a much larger stage 2 set of 4,651 cases and 6,966 controls from the Ovarian Cancer Association Consortium. Given that most of the top 20 SNPs from pooling were validated in the same samples by individual genotyping, the lack of replication is likely to be due to the relatively small sample size in our stage 1 GWAS rather than due to problems with the pooling approach. We conclude that there are unlikely to be any moderate or large effects on ovarian cancer risk untagged by less dense arrays. However, our study lacked power to make clear statements on the existence of hitherto untagged small-effect variants.
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Do, Duy Ngoc, Nathalie Bissonnette, Pierre Lacasse, Filippo Miglior, Xin Zhao, and Eveline M. Ibeagha-Awemu. "A targeted genotyping approach to enhance the identification of variants for lactation persistency in dairy cows." Journal of Animal Science 97, no. 10 (October 2019): 4066–75. http://dx.doi.org/10.1093/jas/skz279.
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Abstract Lactation persistency (LP), defined as the ability of a cow to maintain milk production at a high level after milk peak, is an important phenotype for the dairy industry. In this study, we used a targeted genotyping approach to scan for potentially functional single nucleotide polymorphisms (SNPs) within 57 potential candidate genes derived from our previous genome wide association study on LP and from the literature. A total of 175,490 SNPs were annotated within 10-kb flanking regions of the selected candidate genes. After applying several filtering steps, a total of 105 SNPs were retained for genotyping using target genotyping arrays. SNP association analyses were performed in 1,231 Holstein cows with 69 polymorphic SNPs using the univariate liner mixed model with polygenic effects using DMU package. Six SNPs including rs43770847, rs208794152, and rs208332214 in ADRM1; rs209443540 in C5orf34; rs378943586 in DDX11; and rs385640152 in GHR were suggestively significantly associated with LP based on additive effects and associations with 4 of them (rs43770847, rs208794152, rs208332214, and rs209443540) were based on dominance effects at P < 0.05. However, none of the associations remained significant at false discovery rate adjusted P (FDR) < 0.05. The additive variances explained by each suggestively significantly associated SNP ranged from 0.15% (rs43770847 in ADRM1) to 5.69% (rs209443540 in C5orf34), suggesting that these SNPs might be used in genetic selection for enhanced LP. The percentage of phenotypic variance explained by dominance effect ranged from 0.24% to 1.35% which suggests that genetic selection for enhanced LP might be more efficient by inclusion of dominance effects. Overall, this study identified several potentially functional variants that might be useful for selection programs for higher LP. Finally, a combination of identification of potentially functional variants followed by targeted genotyping and association analysis is a cost-effective approach for increasing the power of genetic association studies.
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Díaz-Peña, Roberto, Ana M. Aransay, Beatriz Suárez-Álvarez, Jacome Bruges-Armas, Naiara Rodríguez-Ezpeleta, María Regueiro, Fernando M. Pimentel-Santos, et al. "A high density SNP genotyping approach within the 19q13 chromosome region identifies an association of a CNOT3 polymorphism with ankylosing spondylitis." Annals of the Rheumatic Diseases 71, no. 5 (January 31, 2012): 714–17. http://dx.doi.org/10.1136/annrheumdis-2011-200661.
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ObjectiveTo identify genomic variants in the 19q13 chromosome region associated with ankylosing spondylitis (AS) in human leucocyte antigen (HLA)-B27-positive populations.MethodsHigh-throughput genotyping of 1536 haplotype-tag single nucleotide polymorphisms (SNPs) was performed in 249 patients with AS and 302 healthy controls. Some of the identified associations were validated by genotyping four SNPs in two additional cohorts consisting of 412 cases/301 controls and 144 cases/203 controls. All individuals selected (both cases and controls) were HLA-B27-positive.ResultsTwo markers in two different genes (CNOT3 and LAIR2) showed significant association (p<10−3) with AS. In addition, sliding windows analysis showed association of groups of adjacent SNPs in regions located around CNOT3 (Chr19: 59347459-59356564, p=2.43×10−4 to 6.54×10−4). The associations were validated by genotyping four SNPs from regions located near LAIR2 and CNOT3 genes (rs1055234, rs8111398, rs2287828 and rs4591276) in two additional cohorts. The CNOT3 polymorphism (rs1055234) remained associated with AS (combined p=9.73×10−6). One SNP, located downstream of KIR3DL1, was detected which, tested in combination with HLA-Bw4I80, was associated with AS.ConclusionA novel significant association was detected between SNP rs1055234 and AS susceptibility.
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Houghton, Katelyn A., Alexandre Lomsadze, Subin Park, Fernanda S. Nascimento, Joel Barratt, Michael J. Arrowood, Erik VanRoey, Eldin Talundzic, Mark Borodovsky, and Yvonne Qvarnstrom. "Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis." Parasite 27 (2020): 24. http://dx.doi.org/10.1051/parasite/2020022.
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Cyclospora cayetanensis is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in C. cayetanensis genomes. Four whole C. cayetanensis genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating C. cayetanensis into 19 new unique genotypes.
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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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Yang, Shangbin, Lihui Xu, and Haifeng Wu. "A Rapid Multiplexed Genotyping of Hereditary Thrombophilia by SELDI-TOF Mass Spectrometer." Blood 112, no. 11 (November 16, 2008): 5347. http://dx.doi.org/10.1182/blood.v112.11.5347.5347.
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Abstract It is known that approximately 50% of patients presenting with venous thromboembolism are associated with polymorphic SNPs in the genes for coagulation factor V (factor V Leiden), prothrombin (prothrombin G20210A), and MTHFR (C677T). Genotyping these thrombophiliac SNPs helps clinicians to properly manage patients with thrombotic disorders. In this study, we reported a novel method to rapidly genotype all three thrombophiliac SNPs in a multiplexed fashion. First, patient DNA samples were subjected to PCR reactions to amplify and extend the DNA products with masses corresponding to genotypes for each of the three targeted thrombophiliac SNPs. PCR products were then applied to Q10 anionic Protein Chips, undergoing on-chip sample enrichment and clean-up. Finally, genetic variants were genotyped by Surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) mass spectrometry based on their masses. This method offers a rapid turnaround time of less than five hours. The analytical accuracy of each SNP genotyping result has been confirmed by DNA sequencing. Additionally, the genotype results produced by this method were validated by comparing them to the results obtained by the approved method in the clinical reference laboratory. In summary, we have developed a novel approach of multiplex genotyping for known thrombophilic SNPs by SELDI-TOF mass spectrometer. This method is fast, accurate, reproducible, and is ready for immediate application in the clinical laboratory.
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De Leeneer, Kim, Ilse Coene, Bruce Poppe, Anne De Paepe, and Kathleen Claes. "Genotyping of Frequent BRCA1/2 SNPs with Unlabeled Probes." Journal of Molecular Diagnostics 11, no. 5 (September 2009): 415–19. http://dx.doi.org/10.2353/jmoldx.2009.090032.
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Sheikhi, Ali, and David Ramsey. "A Bayesian approach for genotyping single nucleotide polymorphisms (SNPs)." International Journal of Data Mining and Bioinformatics 20, no. 4 (2018): 341. http://dx.doi.org/10.1504/ijdmb.2018.094890.
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Sheikhi, Ali, and David Ramsey. "A Bayesian approach for genotyping single nucleotide polymorphisms (SNPs)." International Journal of Data Mining and Bioinformatics 20, no. 4 (2018): 341. http://dx.doi.org/10.1504/ijdmb.2018.10016323.
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Saito, Y., S. S. Bag, S. Kodate, and I. Suzuka. "Design of dual-labeled oligonucleotide probes for SNPs genotyping." Nucleic Acids Symposium Series 51, no. 1 (November 1, 2007): 23–24. http://dx.doi.org/10.1093/nass/nrm012.
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Shajii, Ariya, Deniz Yorukoglu, Yun William Yu, and Bonnie Berger. "Fast genotyping of known SNPs through approximatek-mer matching." Bioinformatics 32, no. 17 (September 1, 2016): i538—i544. http://dx.doi.org/10.1093/bioinformatics/btw460.
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Sasayama, Takuro, Mayu Kato, Hiroyuki Aburatani, Akinori Kuzuya, and Makoto Komiyama. "Simultaneous genotyping of indels and SNPs by mass spectroscopy." Journal of the American Society for Mass Spectrometry 17, no. 1 (January 2006): 3–8. http://dx.doi.org/10.1016/j.jasms.2005.08.016.
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Labate, Joanne A., Jeffrey C. Glaubitz, and Michael J. Havey. "Genotyping by sequencing for SNP marker development in onion." Genome 63, no. 12 (December 2020): 607–13. http://dx.doi.org/10.1139/gen-2020-0011.
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Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F2 and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean He = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.
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LIU, TIE-FEI, WING-KIN SUNG, YI LI, JIAN-JUN LIU, ANKUSH MITTAL, and PEI-LIN MAO. "EFFECTIVE ALGORITHMS FOR TAG SNP SELECTION." Journal of Bioinformatics and Computational Biology 03, no. 05 (October 2005): 1089–106. http://dx.doi.org/10.1142/s0219720005001521.
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Single nucleotide polymorphisms (SNPs), due to their abundance and low mutation rate, are very useful genetic markers for genetic association studies. However, the current genotyping technology cannot afford to genotype all common SNPs in all the genes. By making use of linkage disequilibrium, we can reduce the experiment cost by genotyping a subset of SNPs, called Tag SNPs, which have a strong association with the ungenotyped SNPs, while are as independent from each other as possible. The problem of selecting Tag SNPs is NP-complete; when there are large number of SNPs, in order to avoid extremely long computational time, most of the existing Tag SNP selection methods first partition the SNPs into blocks based on certain block definitions, then Tag SNPs are selected in each block by brute-force search. The size of the Tag SNP set obtained in this way may usually be reduced further due to the inter-dependency among blocks. This paper proposes two algorithms, TSSA and TSSD, to tackle the block-independent Tag SNP selection problem. TSSA is based on A* search algorithm, and TSSD is a heuristic algorithm. Experiments show that TSSA can find the optimal solutions for medium-sized problems in reasonable time, while TSSD can handle very large problems and report approximate solutions very close to the optimal ones.
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Love, R. Rebecca, Marco Pombi, Moussa W. Guelbeogo, Nathan R. Campbell, Melissa T. Stephens, Roch K. Dabire, Carlo Costantini, Alessandra della Torre, and Nora J. Besansky. "Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms." G3 Genes|Genomes|Genetics 10, no. 9 (September 1, 2020): 3299–307. http://dx.doi.org/10.1534/g3.120.401418.
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Abstract Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches vs. traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.
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Martino, Alessandro, Tommaso Mancuso, and Anna Maria Rossi. "Application of High-Resolution Melting to Large-Scale, High-Throughput SNP Genotyping." Journal of Biomolecular Screening 15, no. 6 (April 6, 2010): 623–29. http://dx.doi.org/10.1177/1087057110365900.
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Because of the wide use of single-nucleotide polymorphisms (SNPs) as markers of genetic variation, several high-throughput genotyping methods have been developed and applied during the past decades. High-resolution melting (HRM) is a very attractive, advanced, fast, and cost-effective SNP genotyping technology based on the analysis of the melting profile of PCR products, using intercalating fluorescent dyes to monitor the transition from unmelted to melted DNA. The authors used HRM for genotyping 215 human DNA samples for SNPs in the ABCB1, NQO1, and SLC19A1 genes and 96 samples for SNPs in the IL1A and IL12B genes with the aim of assessing HRM sensitivity and accuracy in comparisons with the TaqMan® assay in view of large-scale, high-throughput SNP-typing applications. The potential effect of PCR product size, TM, GC content, and SNP position on HRM performances was explored with amplicons that were heterogeneous for these factors. Discrimination power ranged from 91.4% to 98.4%, being significantly lower only when the number of rare homozygotes dropped to 1 or few units. The availability of specific and validated assays, in addition to a better standardization of HRM experimental conditions, can considerably reduce time and costs of large-scale genotyping studies with a negligible risk of failure or misclassification.
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Selga, Catja, Alexander Koc, Aakash Chawade, and Rodomiro Ortiz. "A Bioinformatics Pipeline to Identify a Subset of SNPs for Genomics-Assisted Potato Breeding." Plants 10, no. 1 (December 24, 2020): 30. http://dx.doi.org/10.3390/plants10010030.
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Modern potato breeding methods following a genomic-led approach provide means for shortening breeding cycles and increasing breeding efficiency across selection cycles. Acquiring genetic data for large breeding populations remains expensive. We present a pipeline to reduce the number of single nucleotide polymorphisms (SNPs) to lower the cost of genotyping. First, we reduced the number of individuals to be genotyped with a high-throughput method according to the multi-trait variation as defined by principal component analysis of phenotypic characteristics. Next, we reduced the number of SNPs by pruning for linkage disequilibrium. By adjusting the square of the correlation coefficient between two adjacent loci, we obtained reduced subsets of SNPs. We subsequently tested these SNP subsets by two methods; (1) a genome-wide association study (GWAS) for marker identification, and (2) genomic selection (GS) to predict genomic estimated breeding values. The results indicate that both GWAS and GS can be done without loss of information after SNP reduction. The pipeline allows for creating custom SNP subsets to cover all variation found in any particular breeding population. Low-throughput genotyping will reduce the genotyping cost associated with large populations, thereby making genomic breeding methods applicable to large potato breeding populations by reducing genotyping costs.
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Zappe, Katja, Christine Pirker, Heidi Miedl, Martin Schreiber, Petra Heffeter, Georg Pfeiler, Stefan Hacker, Werner Haslik, Sabine Spiegl-Kreinecker, and Margit Cichna-Markl. "Discrimination between 34 of 36 Possible Combinations of Three C>T SNP Genotypes in the MGMT Promoter by High Resolution Melting Analysis Coupled with Pyrosequencing Using A Single Primer Set." International Journal of Molecular Sciences 22, no. 22 (November 20, 2021): 12527. http://dx.doi.org/10.3390/ijms222212527.
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Due to its cost-efficiency, high resolution melting (HRM) analysis plays an important role in genotyping of candidate single nucleotide polymorphisms (SNPs). Studies indicate that HRM analysis is not only suitable for genotyping individual SNPs, but also allows genotyping of multiple SNPs in one and the same amplicon, although with limited discrimination power. By targeting the three C>T SNPs rs527559815, rs547832288, and rs16906252, located in the promoter of the O6-methylguanine-DNA methyltransferase (MGMT) gene within a distance of 45 bp, we investigated whether the discrimination power can be increased by coupling HRM analysis with pyrosequencing (PSQ). After optimizing polymerase chain reaction (PCR) conditions, PCR products subjected to HRM analysis could directly be used for PSQ. By analyzing oligodeoxynucleotide controls, representing the 36 theoretically possible variant combinations for diploid human cells (8 triple-homozygous, 12 double-homozygous, 12 double-heterozygous and 4 triple-heterozygous combinations), 34 out of the 36 variant combinations could be genotyped unambiguously by combined analysis of HRM and PSQ data, compared to 22 variant combinations by HRM analysis and 16 variant combinations by PSQ. Our approach was successfully applied to genotype stable cell lines of different origin, primary human tumor cell lines from glioma patients, and breast tissue samples.
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Lee, Il-Kwon, Hee Nam Kim, Yeo-Kyeoung Kim, Kyeong-Soo Park, Deok-Hwan Yang, Je-Jung Lee, Myung Geun Shin, et al. "Identification of Genes Associated with Risk to Aplastic Anemia (AA) Using Array-Based Genotyping." Blood 110, no. 11 (November 16, 2007): 4153. http://dx.doi.org/10.1182/blood.v110.11.4153.4153.
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Abstract In this study we tested whether 3104 SNPs in 200 candidate genes were associated with risk to aplastic anemia (AA). Genes were considered potential candidates for their known or suspected roles in DNA repair system, pharmacogenomics and transcriptional regulation in hematopoiesis or putative pathways related to development of AA. Selection of SNPs was performed using dbSNP and HapMap project databases, with emphasis on non-synonymous SNPs or haplotype tagging SNPs. To discover potential SNPs responsible for AA susceptibility, a case-control study using Affymetrix targeted genotyping 3K array was designed. We applied 3K array to analyze the samples from 132 AA patients and 382 healthy controls. Genotyping were processed using GeneChip scanner 3000 TG(Affymetrix) and analyzed with GCOS software(Affymetrix). In total more than 160,000 SNPs were genotyped for this study. Samples with suboptimal call rates were excluded. Statistical testing were carried out using χ2, Cochran-Armitage trend, Fisher’s exact, odds ratio, haplotype estimation, LD block definition. Here we report that 19 SNPs in 14 genes are associated with elevated or reduced risk to AA. Three associated genes map to chromosome 11 and 16 respectively. Some of associated genes were transcription factors such as RARB and ZNF233. Among those associated SNPs, one was located in coding region while the rest of SNPs were located in introns of associated genes. In conclusion, we identified SNPs responsible for AA susceptibility by candidate gene-based SNP array approach. These promising data when supported by further molecular validation would greatly enhance the current understanding of AA predisposition and diseases progression. Implication of polymorphic variants in AA etiopathogenesis will be presented and discussed.
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Deng, Jing, Handan Tan, Jiayue Hu, Guannan Su, Qingfeng Cao, Xinyue Huang, Chunjiang Zhou, Yao Wang, Aize Kijlstra, and Peizeng Yang. "Genetic aspects of idiopathic paediatric uveitis and juvenile idiopathic arthritis associated uveitis in Chinese Han." British Journal of Ophthalmology 104, no. 3 (April 2, 2019): 443–47. http://dx.doi.org/10.1136/bjophthalmol-2018-313200.
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BackgroundIdiopathic paediatric uveitis (IPU) and juvenile idiopathic arthritis associated uveitis (JIA-U) are the two most common entities in paediatric uveitis. This study addressed the possible association of IPU and JIA-U with genes that had been shown earlier to be associated with juvenile idiopathic arthritis.MethodsWe carried out a case-control association study involving 286 IPU, 134 JIA-U patients and 743 healthy individuals. A total of 84 candidate single nucleotide polymorphisms (SNPs) in 60 genes were selected for this study. The MassARRAY platform and iPLEX Gold Genotyping Assay was used to genotype 83 candidate SNPs and the remaining SNP (rs27293) was analysed using the TaqMan SNP Genotyping Assay.ResultsNo evidence was found for an association of the candidate polymorphisms tested with IPU. Six SNPs (PRM1/rs11074967, JAZF1/rs73300638, IRF5/rs2004640, MEFV/rs224217, PSMA3/rs2348071 and PTPN2/rs7234029) showed an association with JIA-U (p<1.0×10−2).ConclusionOur findings showed associations of six SNPs (PRM1/rs11074967, JAZF1/rs73300638, IRF5/rs2004640, MEFV/rs224217, PSMA3/rs2348071 and PTPN2/rs7234029) with JIA-U. No association was detected between the 84 tested SNPs and IPU.
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Yang, Mei-juan, Yan-long Hou, Xiao-lan Yang, Chun-xia Wang, Li-xia Zhi, and Chong-ge You. "Development and application of a PCR-HRM molecular diagnostic method of SNPs linked with TNF inhibitor efficacy." Diagnosis 6, no. 3 (August 27, 2019): 277–86. http://dx.doi.org/10.1515/dx-2018-0062.
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Abstract Background Clinical evidence indicates that genetic variations may interfere with the mechanism of drug action. Recently, it has been reported that the single nucleotide polymorphisms (SNPs) of STAT4, PTPN2, PSORS1C1 and TRAF3IP2RA genes are associated with the clinical efficacy of tumor necrosis factor (TNF) inhibitors in the treatment of rheumatoid arthritis (RA) patients. Therefore, the detection of the SNPs linked with TNF inhibitor efficacy may provide an important basis for the treatment of RA. This study intended to establish molecular diagnostic methods for genotyping the linked SNPs based on high resolution melting (HRM) curve analysis. Methods The polymerase chain reaction-HRM (PCR-HRM) curve analysis detecting systems were established by designing the primers of the four SNPs, rs7574865G>T, rs7234029A>G, rs2233945C>A and rs33980500C>T, and the performance and clinical applicability of which were evaluated by using the Sanger sequencing method and genotyping test for 208 clinical samples. Results The self-developed molecular diagnostic methods of PCR-HRM were confirmed to be able to correctly genotype the four SNPs, the sensitivity and specificity of which were 100% in this study. The repeatability and reproducibility tests showed that there is little variable in intra-assay and inter-assay (the coefficient of variation ranged from 0.01% to 0.07%). The slight changes of DNA template and primer concentrations, PCR cycle number and reaction system volume had no significant effect on the genotyping performance of the method. The PCR-HRM assays were also applied to other PCR thermocyclers with HRM function and use different saturation fluorescent dyes. Conclusions The PCR-HRM genotyping method established in this study can be applied to the routine molecular diagnosis of rs7574865, rs7234029, rs2233945 and rs33980500.
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Straub, Timothy M., Don S. Daly, Sharon Wunshel, Paul A. Rochelle, Ricardo DeLeon, and Darrell P. Chandler. "Genotyping Cryptosporidium parvum with an hsp70 Single-Nucleotide Polymorphism Microarray." Applied and Environmental Microbiology 68, no. 4 (April 2002): 1817–26. http://dx.doi.org/10.1128/aem.68.4.1817-1826.2002.
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ABSTRACT We investigated the application of an oligonucleotide microarray to (i) specifically detect Cryptosporidium spp., (ii) differentiate between closely related C. parvum isolates and Cryptosporidium species, and (iii) differentiate between principle genotypes known to infect humans. A microarray of 68 capture probes targeting seven single-nucleotide polymorphisms (SNPs) within a 190-bp region of the hsp70 gene of Cryptosporidium parvum was constructed. Labeled hsp70 targets were generated by PCR with biotin- or Cy3-labeled primers. Hybridization conditions were optimized for hybridization time, temperature, and salt concentration. Two genotype I C. parvum isolates (TU502 and UG502), two C. parvum genotype II isolates (Iowa and GCH1), and DNAs from 22 non-Cryptosporidium sp. organisms were used to test method specificity. Only DNAs from C. parvum isolates produced labeled amplicons that could be hybridized to and detected on the array. Hybridization patterns between genotypes were visually distinct, but identification of SNPs required statistical analysis of the signal intensity data. The results indicated that correct mismatch discrimination could be achieved for all seven SNPs for the UG502 isolate, five of seven SNPs for the TU502 isolate, and six of seven SNPs for both the Iowa and GCH1 isolates. Even without perfect mismatch discrimination, the microarray method unambiguously distinguished between genotype I and genotype II isolates and demonstrated the potential to differentiate between other isolates and species on a single microarray. This method may provide a powerful new tool for water utilities and public health officials for assessing point and nonpoint source contamination of water supplies.
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Abed, Amina, Ana Badea, Aaron Beattie, Raja Khanal, James Tucker, and François Belzile. "A high-resolution consensus linkage map for barley based on GBS-derived genotypes." Genome 65, no. 2 (February 2022): 83–94. http://dx.doi.org/10.1139/gen-2021-0055.
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As genotyping-by-sequencing (GBS) is widely used in barley genetic studies, the translation of the physical position of GBS-derived SNPs into accurate genetic positions has become relevant. The main aim of this study was to develop a high-resolution consensus linkage map based on GBS-derived SNPs. The construction of this integrated map involved 11 bi-parental populations composed of 3743 segregating progenies. We adopted a uniform set of SNP-calling and filtering conditions to identify 50 875 distinct SNPs segregating in at least one population. These SNPs were grouped into 18 580 non-redundant SNPs (bins). The resulting consensus linkage map spanned 1050.1 cM, providing an average density of 17.7 bins and 48.4 SNPs per cM. The consensus map is characterized by the absence of large intervals devoid of marker coverage (significant gaps), the largest interval between bins was only 3.7 cM and the mean distance between adjacent bins was 0.06 cM. This high-resolution linkage map will contribute to several applications in genomic research, such as providing useful information on the recombination landscape for QTLs/genes identified via GWAS or ensuring a uniform distribution of SNPs when developing low-cost genotyping tools offering a limited number of markers.
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Lalouschek, Wolfgang, Georg Endler, Martin Schillinger, Kety Hsieh, Wilfried Lang, Suzanne Cheng, Peter Bauer, Oswald Wagner, and Christine Mannhalter. "Candidate Genetic Risk Factors of Stroke: Results of a Multilocus Genotyping Assay." Clinical Chemistry 53, no. 4 (April 1, 2007): 600–605. http://dx.doi.org/10.1373/clinchem.2006.073494.
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Abstract Background: Epidemiological studies indicate that genetic factors play a role in the risk of stroke, particularly in younger individuals, but the role of single-nucleotide polymorphisms (SNPs) is controversial. We tested the possible association of a number of previously described SNPs with stroke risk. Methods: We investigated the prevalence of 60 polymorphisms located in 35 genes in 450 white patients who suffered an acute stroke or transient ischemic attack before the age of 60 years and in 817 healthy control individuals by a multilocus PCR-based assay. The controls were randomly selected from attendees of a health service program. Genetic variations were detected by hybridization to nylon strips (Roche Molecular Systems) containing detection oligonucleotides for the SNPs. We used P values of <0.05 for confirmatory analysis of the SNPs in the genes for APOE (allele 4), angiotensin converting enzyme, factor V, prothrombin, and methylenetetrahydrofolate reductase. To account for multiple testing we defined a P value of <0.001 as statistically significant for all exploratory tests. The genes represented in the test panel by more than 1 SNP were also evaluated by haplotype analysis. Results: Frequencies of all 60 tested SNPs among patients and controls were very similar. No SNP reached an odds ratio of 2, and no association with stroke risk was statistically significant. Conclusions: Our results do not indicate a clinically relevant role of any of the investigated SNPs for stroke risk in individuals hospitalized for ischemic stroke/transient ischemic attack before or at 60 years of age. These results are in accordance with previous metaanalyses showing at most a very modest or no significant effect of these SNPs on stroke risk.
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Touati, A., Y. Blouin, P. Sirand-Pugnet, H. Renaudin, T. Oishi, G. Vergnaud, C. Bébéar, and S. Pereyre. "Molecular Epidemiology of Mycoplasma pneumoniae: Genotyping Using Single Nucleotide Polymorphisms and SNaPshot Technology." Journal of Clinical Microbiology 53, no. 10 (July 22, 2015): 3182–94. http://dx.doi.org/10.1128/jcm.01156-15.
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Molecular typing ofMycoplasma pneumoniaeis an important tool for identifying grouped cases and investigating outbreaks. In the present study, we developed a new genotyping method based on single nucleotide polymorphisms (SNPs) selected from the whole-genome sequencing of eightM. pneumoniaestrains, using the SNaPshot minisequencing assay. Eight SNPs, localized in housekeeping genes, predicted lipoproteins, and adhesin P1 genes were selected for genotyping. These SNPs were evaluated on 140M. pneumoniaeclinical isolates previously genotyped by multilocus variable-number tandem-repeat analysis (MLVA-5) and adhesin P1 typing. This method was also adapted for direct use with clinical samples and evaluated on 51 clinical specimens. The analysis of the clinical isolates using the SNP typing method showed nine distinct SNP types with a Hunter and Gaston diversity index (HGDI) of 0.836, which is higher than the HGDI of 0.583 retrieved for the MLVA-4 typing method, where the nonstable Mpn1 marker was removed. A strong correlation with the P1 adhesin gene typing results was observed. The congruence was poor between MLVA-5 and SNP typing, indicating distinct genotyping schemes. Combining the results increased the discriminatory power. This new typing method based on SNPs and the SNaPshot technology is a method for rapidM. pneumoniaetyping directly from clinical specimens, which does not require any sequencing step. This method is based on stable markers and provides information distinct from but complementary to MLVA typing. The combined use of SNPs and MLVA typing provides powerful discrimination of strains.
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Konan, Jacky Amenan, Romain Guyot, Kouamé Kevin Koffi, Irié Vroh-Bi, and Arsène Irié Bi Zoro. "Molecular confirmation of varietal status in bottle gourd (Lagenaria siceraria) using genotyping-by-sequencing." Genome 63, no. 11 (November 2020): 535–45. http://dx.doi.org/10.1139/gen-2020-0050.
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Bottle gourd (Lagenaria siceraria) is an important food, medicinal, and utilitarian crop with a large pan-tropical distribution. Two morphologically different types in the siceraria subspecies are sufficiently different to be considered as varieties, but they are assigned into different taxonomic ranks. Genotyping-by-sequencing (GBS) of 95 different accessions from the Nangui Abrogoua University collection was used to confirm the varietal status in bottle gourd. This analysis produced 22 575 single-nucleotide polymorphisms (SNPs). Cluster analyses conducted with 2250 (9.96%) SNPs distinctly separated hard-shelled from soft-shelled types. Analysis of 23 SNPs located in 11 genes coding for traits that differentiate the two types of gourds revealed that genes in the soft-shelled types had about 21% fewer SNPs than genes within hard-shelled gourds, but the latter had more non-synonymous SNPs. Cluster analyses conducted with the 23 SNPs fitted well with the structure defined by the 2250 SNPs, suggesting the implication of these SNPs in the varietal differentiation of bottle gourd. These nucleotide changes along with the genetic relationships between the accessions provide molecular proof supporting the status of two varieties. To prevent the confusion inherent in the use of synonyms and homonyms in bottle gourd, we suggest the terms hard-shelled and soft-shelled to designate, respectively, the varieties used as utensils and those grown for their edible seeds.