Infobox Software name PrimerPlex screenshot caption developer PREMIER Biosoft latest release version 2.50 latest preview version latest preview date operating system Windows, Macintosh platform genre Bioinformatics license commercial website http www.premierbiosoft.com www.premierbiosoft.com PrimerPlex designs oligos for standard Multiplex PCR multiplex PCR assays and for bead based suspension array systems such as BioPlex 200 and Luminex 100 200 based on xMAP technology. The assays are used for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. It is supported on both Windows and Mac. The following oligo design options are supported Multiplex PCR Primer Design Can design highly specific multiplex primers for standard PCR assays for up to 30 sequences. Direct Hybridization Assay DHA Oligo Design Can design probes for 100 individual targets in a multiplex reaction. The SNPs are located at the center to maximize discrimination. ASPE Assay Oligo Design Can design primers for 40 individual targets in a multiplex reaction. The mutation is located at the 3 end. The author company, Premier Biosoft PREMIER Biosoft , has supported strain differentiation multiplex xMAP assays in one of their other products, AlleleID . References http www.luminexcorp.com Luminex Corporation http www.labhoo.com PressImage 2009 PR 5503.htm PREMIER Biosoft International Releases version 2.00 of PrimerPlex with Support for Using Proven Pre designed oligos and Analyzing SNPs of Medium sized Genomes http jac.oxfordjournals.org content early 2010 05 28 jac.dkq175.full A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A External links http www.premierbiosoft.com primerplex index.html PrimerPlex Home Page http www.premierbiosoft.com tech notes multiplex pcr.html Multiplex PCR An Overview Category Bioinformatics so ... more details
Essay like date February 2008 A dark quencher is a substance that absorbs excitation energy from a fluorophore and dissipates the energy as heat while a typical fluorescent Quenching fluorescence quencher re emits much of this energy as light ref Osterman, H., The Next Step in Near Infrared Fluorescence IRDye QC 1 Dark Quencher, 2009 Review Article. http biosupport.licor.com docs QC 1DarkQuencher v5.pdf Download PDF ref . Dark quenchers are used in molecular biology in conjunction with fluorophores. When the two are close together, such as in a molecule or protein, the fluorophore s emission is suppressed. This effect can be used to study molecular geometry and motion. An example of its use is in Taqman or invader assay, SNP genotyping methods. For instance, a hairpin loop with a fluorophore and quencher at the base of the stem is used. An unlabeled SNP specific PCR primer one of many with a specific 5 tail binds to the sequence to be probed, and the taq polymerase extends the sequence that will have a specific 5 end dependent on the SNP insensitive to polymorphisms upstream of the SNP in question . In the next run a primer molecular biology primer , complementary to that tail, with a hairpin loop is extended. In the next run the elongation of the complementary strand will linearise the hairpin separating the fluorophore and quencher . An alternative to using quenchers is to use F rster resonance energy transfer FRET where the combination of two dyes gives a signal ref Peng, X., Chen, H., Draney, D.R., Volcheck, W.M., A Non fluorescent, Broad Range Quencher Dye for FRET Assays, Analytical Biochemistry, 2009 Vol. 388 , pp. 220 228. http biosupport.licor.com docs NonfluorQuencherDyePaper09.pdf Download PDF ref . Mode of function Dark quenchers are dyes with no native fluorescence . Until the last few years, quenchers have typically been a second fluorescent dye, for example, fluorescein as the reporter and rhodamine as the quencher FAM TAM probes . However, quencher f ... more details
. For each SNP, the combination of alleles a person has is called a genotype . Genotyping refers to uncovering ... as a single nucleotide polymorphism SNP , and each of the two possibilities is called an allele ... that if the allele of one SNP for a given individual is known, the alleles of nearby SNPs can often be predicted. This is because each SNP arose in evolutionary history as a single point mutation .... In this region one locates a set of tag SNP s from the HapMap data these are SNPs that are very ... For the Phase I, one common SNP was genotyped every 5,000 bases. Overall, more than one million SNPs were genotyped. The genotyping was carried out by 10 centres using five different genotyping technologies. Genotyping quality was assessed by using duplicate or related samples and by having periodic ... Institute and focused on chromosomes 1, 6, 10, 13 and 20. There were four United States genotyping ..., including SNP frequencies, genotypes and haplotypes , were placed in the public domain and are available ... more details
format ASN.1 , Fasta , XML url http www.ncbi.nlm.nih.gov projects SNP download ftp ftp.ncbi.nih.gov snp webservice http eutils.ncbi.nlm.nih.gov EUtils br http eutils.ncbi.nlm.nih.gov soap v2.0 eutils.wsdl ... SNPsnp summary.cgi File DbSNP diagram no caption.jpg 600px thumb a Various sources submit data, and each variation is assigned a unique submitted SNP number ID ss . b dbSNP compiles identical ss records into one reference SNP cluster rs containing data from each ss . c Users can retrieve ... sequencing centers, other SNP databases e.g. the SNP consortium, HapMap , etc. , and private businesses ... 2. Types of records Every submitted variation receives a submitted SNP ID number ss . ref name Sherry This accession number is a stable and unique identifier for that submission. Unique submitted SNP records also receive a reference SNP ID number rs refSNP cluster . However, more than one record ... this, dbSNP routinely assembles identical submitted SNP records into a single reference SNP record, which is also a unique and stable identifier see below . ref name Kitts 3. How to submit ... Kitts A sample submission sheet can be found at http www.ncbi.nlm.nih.gov SNP get html.cgi?whichHtml ... into one refSNP cluster and are assigned a reference SNP ID number. However, if two refSNP cluster ... site e.g. a SNP and a DIP , then the two refSNP number IDs are not merged. Secondly, clinically important ... SNP search tool found at http www.ncbi.nlm.nih.gov projects SNP . A variety of queries can be used ... Phillips, C title Online resources for SNP analysis A review and route map journal Molecular Biotechnology ... Single Nucleotide Differences SNDs in the dbSNP Database May Lead to Errors in Genotyping and Haplotyping ... frequency distributions from varying genotyping error rates and patterns journal Bioinformatics ... A, et al. title High Throughput Variation Detection and Genotyping Using Microarrays journal Genome ..., et al. title Quality and completeness of SNP databases journal Nature Genetics volume 33 pages 457 ... more details
Infobox company name Illumina, Inc. logo File Illumina company logo.jpg 250px type Public company Public nasdaq ILMN genre foundation 1998 founder location city San Diego, California location country United States U.S. location locations area served key people industry Biotechnology products services revenue 212.00 million Q2 2010 operating income net income owner num employees parent divisions subsid slogan homepage http www.illumina.com footnotes intl Illumina, Inc. nasdaq ILMN is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing , genotyping and gene expression markets. Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies. Its tools provide researchers with the capability to perform genetic tests needed to extract medical information from advances in genomics and proteomics . Its headquarters are located in San Diego , California . History Illumina was founded in April 1998 by David Walt, Ph.D., Larry Bock ,John Stuelpnagel, D.V.M., Anthony Czarnik, Ph.D., and Mark Chee, Ph.D. While working with CW Group, a venture capital firm, Larry and John uncovered what would become Illumina s BeadArray technology at Tufts University and negotiated an exclusive license to that technology. Illumina completed its initial public offering in July 2000. Illumina began offering single nucleotide polymorphism SNP genotyping services in 2001 and launched its first system, the Illumina BeadLab, in 2002, using GoldenGate Genotyping technology. Illumina currently offers microarray based products and services for an expanding range of genetic analysis sequencing, including SNP genotyping, gene expression , and protein analysis . Illumina s technologies are used by a broad range ... more details
applications such as real time pcr real time , quantitative PCR and SNPgenotyping . Stellaris ... that allows the software to model and propose quantitative PCR and SNPgenotyping assays. RealTimeDesign ... www.qpcrdesign.com RealTimeDesign Online Design Service for qPCR and SNPGenotyping Assays http patft.uspto.gov ... more details
enough to detect single nucleotide polymorphisms SNP and can distinguish between homozygous wildtype ... research and clinical examples ref Lay MJ, Wittwer CT. 1997 Real time fluorescence genotyping of factor ... sensitivity for SNP detection within an entire dye stained amplicon. It is less expensive and simpler in design to develop probeless melting curve systems. However, for genotyping applications, where ... the total throughput and ease of interpretation, thus favoring probe based genotyping methods. See also ... more details
CL, Sekeres MA, Theil KS, Maciejewski JP. Chromosomal lesions and uniparental disomy detected by SNP ... using high density oligonucleotide SNP arrays. PLoS Comput Biol. 2006 May 2 5 e41. ref ref Ishikawa S, Komura D, Tsuji S, Nishimura K, Yamamoto S, Panda B, et al. Allelic dosage analysis with genotyping ... in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined .... ref Determination of Virtual Karyotype virtual karyotypes using SNP based arrays can provide genome ... be detected by arrayCGH, FISH, or conventional cytogenetics. SNP based arrays are preferred for virtual ... LOH.jpg thumb Copy neutral LOH uniparental disomy Image CRCforwiki.jpg thumb SNP array Virtual ... be assessed by Virtual Karyotype virtual karyotyping using SNP arrays. See also Microsatellite instability ... more details
ref http www.med.unc.edu anclinic Tm.htm full ref and the Invader single nucleotide polymorphism SNP assay. ref cite journal doi 10.1016 j.mrfmmm.2004.08.016 title The Invader assay for SNPgenotyping ... more details
Wiktionary opa Opa OPA OPA may refer to TOC right Government Office of the Pardon Attorney , an agency of the United States Department of Justice Office of Price Administration , a United States government office set up by President Roosevelt to stabilize prices and rents after the outbreak of World War II Ontario Power Authority , a government agency in Canada International agreements Ouagadougou Peace Agreement, that put an end to the Ivorian Civil War Outward Processing Arrangement , a trade agreement between Hong Kong and mainland China Laws Obscene Publications Act 1959 , an Act of Parliament in the United Kingdom Oil Pollution Act of 1990 , a United States law Medicine Oropharyngeal airway , a device used to keep the upper respiratory airway open Out patient appointments Ovine Pulmonary Adenocarcinoma, a disease of the lungs in sheep and goats, also known as Jaagsiekte Music OPA song OPA song , a song by Giorgos Alkaios & Friends competing in the Eurovision Song Contest 2010 for Greece Opa Opa , a song by Notis Sfakianakis, later covered by both Antique and Despina Vandi Opa band , Uruguayan jazz group Opa Opa , an alternative name to the album Mera Me Ti Mera album Mera Me Ti Mera by Antique Sports FC OPA , association football club from Oulu, Finland Other Oligo Pool Assay , a SNP genotyping platform from Illumina Online Privacy Alliance , a coalition of Internet companies Opa programming language , a web development platform Open Platform Architecture , a software interface from Ericsson Mobile Platforms for use internally in cellular phones Optical parametric amplifier , a method to amplify laser light Oracle Policy Automation , an enterprise applications suite Ordre des Palmes Academiques , an Order of Chivalry of France for academics and cultural and educational figures Oregon Potters Association , not for profit group of clay artists Opa, the nickname of Dorus Rijkers , Dutch lifeboat captain who rescued over 500 people in the course of his career OPA, ... more details
a novel strategy called SNP Microarrays and Pooling SNP MaP , which is a cost effective and powerful way of genotyping DNA as it allows researchers to use one DNA microarrays microarray instead of hundreds to genotype a group s pooled DNA. ref cite journal author Butcher, L. M. et al. title Genotyping ... year 2004 pmid 15319578 issue 5 ref ref cite journal author Meaburn, E. et al. title Genotyping ... ref ref cite journal author Meaburn, E., Butcher, L. M., Schalkwyk, L. C. & Plomin, R. title Genotyping pooled DNA using 100K SNP microarrays a step towards genomewide association scans journal Nucleic ... more details
between all three of these scenarios. Image STD HRM plot.JPG 500px Applications of HRM SNP typing Point mutation detection Conventional Single nucleotide polymorphism SNP typing methods are typically ... probes to detect the variants of the genes SNP typing is the simplest case . In cases where longer ... author Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ title High resolution genotyping by amplicon ... more details
AlleleID Assay Design for Bacterial Identification ref assays DNA quantification SNPgenotyping Verification ... Leukocyte Antigen HLA genotyping Determine the viral load in clinical specimens HIV , tuberculosis ... more details
ZA, Selker EU, Cresko WA, Johnson EA. 2008 Rapid SNP discovery and genetic mapping using sequenced ... and genotyping of RAD markers Once RAD tags have been isolated, they can be analyzed to identify ... more details
significantly more expensive than SNP chip based genotyping , this approach yields significantly ... kits for SNPgenotyping . ref https www.23andme.com ourservice process 23andMe Our Service How the Process ... Decodeme.com date 15 October 2011 accessdate 19 October 2011 ref charges 1100 to carry out genotyping ... 19 October 2011 ref began offering SNP based genomic risk assessments as of April 2008. Navigenics .... Affymetrix Genome Wide Human SNP Array 6.0, which genotypes 900,000 SNPs. ref cite web author Aaron ... genotyping and full genome sequencing launched by Theragen in Korea. HelloGenome is the first commercial ... Affymetrix SNP chips while HelloGenome uses Solexa machines. Illumina company Illumina , Oxford Nanopore ... and genotyping are opening for personal genomics author Robertson, G. volume 449 issue 4 pages 627 630 ... more details
. A genome wide scalable SNPgenotyping assay using microarray technology. Nature Genetics 37, 549 ... with 2,4 dinitrophenol DNP ref name Stee Steemers, FJ. et al. Whole genome genotyping with the single ... of Illumina Infinium whole genome SNP data improves copy number estimates and allelic intensity ratios ... more details
. Depending on the nature of the experiment, the GMS can provide SNP detection and genotyping, copy ... conservation, regulatory SNP effects and much more are all processes carried out on the GGA ... more details
Association mapping , also known as linkage disequilibrium mapping , is a method of mapping quantitative trait locus quantitative trait loci QTLs that takes advantage of historic linkage disequilibrium to link phenotype s observable characteristics to genotype s the genetic constitution of organisms . Theory Association mapping is based on the idea that traits that have entered a population only recently will still be linked to the surrounding genetic sequence of the original evolutionary ancestor, or in other words, will more often be found within a given haplotype , than outside of it. It is most often performed by scanning the entire genome for significant associations between a panel of SNPs which, in many cases are spotted onto glass slides to create SNP genotyping SNP chips and a particular phenotype. These associations must then be independently verified in order to show that they either a. contribute to the trait of interest directly, or b. are linked to in linkage disequilibrium with a quantitative trait locus QTL that contributes to the trait of interest. ref name Gibson cite book title A Primer of Genome Science last Gibson first G. coauthors Muse S.V. year 2009 publisher Sinauer Associates location MA ref File Linkage association.jpg full linkage vs association Use The advantage of association mapping is that it can map quantitative traits with high resolution in a way that is statistically very powerful. Association mapping, however, also requires extensive knowledge of SNPs within the genome of the organism of interest, and is therefore difficult to perform in species that have not been well studied or do not have well annotated genome s. ref name Yu et al. cite journal author Yu, J., Holland, J.B., McMullen, M.D., Buckler, E.S. year 2008 title Genetic design and statistical power of nested association mapping in maize journal Genetics volume 178 pages 539&ndash 551 url http www.genetics.org cgi content abstract 178 1 539 doi 10.1534 genetics.107.07424 ... more details
Glasgow Govan by election or Govan by election may refer to Govan by election, 1889 , won by John Wilson of the Liberal Party Glasgow Govan by election, 1973 , won by Margo MacDonald of the Scottish National Party SNP Glasgow Govan by election, 1988 , won by Jim Sillars of the Scottish National Party SNP Disambig ... more details
of 10 sup 1 sup to 10 sup 4 sup See also PCR Genotyping Single nucleotide polymorphism SNPgenotyping ... group that developed COLD PCR and used it to compare the sensitivity of regular PCR for genotyping ... more details
Multiple issues cleanup August 2009 orphan August 2009 Restriction Fragment Mass Polymorphism RFMP is a technology which Restriction digest digests DNA into oligonucleotide fragments, and detects variation of DNA sequence s by molecular weight of the fragments. RFMP is a Property proprietary technology of GeneMatrix and can be utilized for genotyping viruses and microorganisms , and for human genome research. References Kim, Y 2005 . Population Genotyping of Hepatitis C Virus by Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry Analysis of Short DNA Fragments , Clinical Chemistry , 51 1123 1131 External links http www.genematrix.net eng sic 01.htm RFMP platform technology Category DNA sequencing biotech stub ... more details
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