microsatellite caps and snp genotyping
báo cáo khoa học: " High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species" ppsx
... Species # SNPs with Call rate ≥ 95% % SNPs with Call rate ≥ 95% # SNPs with GC50 ≥ 0.40 % SNPs with GC50 ≥ 0.40 # SNPs with Call rate ≥ 95% % SNPs with Call rate ≥ 95% # SNPs with GC50 ≥ 0.40 % SNPs ... Averages and SNP counts above specific thresholds of SNP reliability parameters (Call Rate, GeneCall50, GeneTrain scores) and polymorphism (MAF) for SNPs in pre-selected candidate genes and for ... within and across species notwithstanding the high nucleotide diversity of the complex Eucalyptus genome and the wide range of species for which SNP genotyping is pursued SNP discovery and selection...
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A population based study of copy number variations and regions of homozygosity in singapore and swedish populations using genome wide SNP genotyping arrays
... or less, and VNTRs are longer 23 tandem repeats (Figure 2b) They are also known as microsatellites and minisatellites respectively The most common types of microsatellites are di-, tri- and tetra-nucleotide ... diseases and traits such as schizophrenia, autism and height Genome-wide mapping of CNVs and ROHs have been previously performed in European, East Asian and African populations using high-density SNP ... microarrays and sequencing-based methods for detecting structural variations Chapter – Materials and methods Table – Summary of samples, genotyping platforms, detection algorithms and data used and generated...
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Báo cáo y học: " Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays" pptx
... RSTA Marker type SNPs and indels Restriction cut site polymorphisms Sequence data: SNPs next to restriction cut sites Restriction cut site polymorphisms: distinguishes SNPs and indels Number ... lineages and natural species of Neurospora : identifying candidate regions by microarray-based genotyping and mapping Evolution 2009, 64:694-709 32 Turner TL, Hahn MW, Nuzhdin SV: Genomic islands ... with targeted SNP genotyping [33-35] For example, for a species without a sequenced genome, the transcriptomes of multiple individuals could be labeled and pooled ('multiplexed') and sequenced...
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Báo cáo y học: "Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping" ppt
... patients' care and data acquisition; FR, GM and AM assisted with laboratory assays; RC, MZ and ADL assisted with manuscript revision and research group leading All authors read and approved the ... 40%, 88.2%, and 96.2% at < = 50 cp/ml, 51-500 cp/ml, and >500 cp/ml respectively The rate of successful sequencing from DNA was 95.1%, 100%, and 100% at < = 50 cp/ml, 50-500 cp/ml, and >500 cp/ml, ... Molecular, Boehringer Ingelheim, Gilead Sciences, and Janssen; and served on speakers' bureaus for Abbott, Bristol-Myers Squibb, Merck, and Pfizer Andrea De Luca received speakers honoraria, served...
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Báo cáo sinh học: "Accuracy of breeding values of ''''unrelated'''' individuals predicted by dense SNP genotyping" pptx
... Evolution 2009, 41:35 of huge SNP panels feasible For example, in human genetics, assays with > 500,000 SNP are routinely used, and in cattle, pigs and sheep ~50,000 SNP chips are commercially available ... structure will be the same for a population with Ne = 100 and 1000 SNPs per Morgan (M), compared to a population with Ne = 1000 and 10,000 SNPs per M, i.e for both populations, the marker density ... on N is linear, and the regression coefficient is a function of h2, which is known, and the effective number of segments, 4NeLν Results and discussion Effect of number of markers and training records...
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Báo cáo y học: " low-cost open-source SNP genotyping platform for association mapping applications" pptx
... the molecular biology steps, and software for designing the SNP assays and for calling genotypes Sensitivity to secondary SNPs Results and discussion We designed SNP genotyping assays for 156 biallelic ... SNP genotyping assays A representative set of SNP genotyping assays Each of the 16 panels represents a single SNP selected using a random number generator from the set of 115 converting OLA genotyping ... locus and 12 SNPs All OLA-based genotyping approaches rely on oligos binding to a small region flanking the query SNP If this flanking region harbors a minor allele at a SNP other than the query SNP, ...
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Genetic diversity of populations of the malesian moss, acanthorrhynchium papillatum, as measured by microsatellite markers and ITS2 sequences
... discussions on ISSRs To Mandar, for our (unfulfilled) vow and for the biscuits To Dileep, for drinking water in the drawer and for (re)teaching me humility Lian-Lian and Jaclyn and Xin Ying, how you ... same and for being so darn calm all the time Reuben for translating and for the maps Norman for showing us what it’s like to be a field pro Matthew for Tioman and the RAM Tommy, for Tioman and ... papillatum Microsatellite Mark- ers 257 Appendix G: Characterizing candidate microsatellite markers 263 Appendix H: Computation of linkage disequilibrium 265 Appendix I: Report on microsatellite...
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Báo cáo y học: "Translational Medicine and Reliability of Single-Nucleotide Polymorphism Studies: Can We Believe in SNP Reports or Not"
... polymorphisms and cancer outcome (mainly colorectal, breast, and lung malignancy) SNPs for GST polymorphisms were used as a substrate for analyses Materials and Methods Search strategy and eligibility ... is increasing rapidly and this trend is expected to accelerate due to the availability of mapped single-nucleotide polymorphisms (SNP) in the human genome and advances in genotyping technologies ... the following criteria: (a) investigate the association between at least of one GST SNP: and cancer outcome; and (b) include only patients with solid tumours We excluded case-control studies that...
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GENOTYPING OF CLOSTRIDIUM PERFRINGENS ISOLATED FROM CATTLE AND PIGS WITH DIARRHEA IN HANOI AND SURROUNDING AREAS, VIETNAM
... Frey, M.R Popoff, and J.F van den Bosch (1999) Detection of the β2 toxin gene of Clostridium perfringens in diarrhoeic piglets in The Netherlands and Switzerland FEMS Immunology and Medical Microbiology ... perfringens from healthy and diseased sheep by multiplex PCR Vet Med - Czech 50, 439-442 631 Genotyping of Clostridium perfringens isolated from cattle and pigs with diarrhea in Hanoi and surrounding ... (41.76) 61 (74.39) No = number 629 Genotyping of Clostridium perfringens isolated from cattle and pigs with diarrhea in Hanoi and surrounding areas, Vietnam 3.2 Genotyping of C perfringens the toxicity...
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Báo cáo sinh học: " Development of a real-time RT-PCR and Reverse Line probe Hybridisation assay for the routine detection and genotyping of Noroviruses in Ireland" pdf
... plasmid DNA for GI NoV and × 107 to × 101 for GII NoV The R2 values for both standard curves were 1.00 with a slope of -3.5 and -3.7 respectively for GI and GII NoV (Fig 1B and Fig 2B) Melting curve ... by large peaks at ~90°C and ~88°C respectively for GI and GII NoV (Fig 1C and Fig 2C) A stool panel containing genotypes of http://www.virologyj.com/content/4/1/86 GI NoV and genotypes of GII NoV ... containing GI/2 and GII/4 PCR products corresponding to Southampton virus and Oxford B2S16 Detection levels of these plasmid molecules were 107 to 101 for GI and × 107 to × 101 for GII (Fig 1A and Fig...
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Báo cáo sinh học: " Typing of human rotaviruses: Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure" pdf
... laboratory tests and wrote the manuscript; RS and GP carried out RT-PCR tests; JM performed the sequencing experiments; AF, KZ, RB and DS supervised the rotavirus surveillance program and critically ... (14.6%), and G4 (13.8%) G1 comprised only 11.6% of the isolates and 36.9% of the rotavirus-positive samples were untypeable VP7 gene sequence analysis We amplified the VP7 genes of five randomly ... of the isolates and became the most prevalent genotype, and the number of untypeable strains was reduced from 36.9 to 2.1 % The other common G types were G9 (21.7%), G2 (15.0%), and G4 (13.8%)...
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Báo cáo sinh học: " Detection, quantification and genotyping of Herpes Simplex Virus in cervicovaginal secretions by real-time PCR: a cross sectional survey" potx
... was designed by MJH and EANA; experimental work was done by EANA, MJH and AN; interpretation and laboratory work was conducted by MJH, EANA, AN, SK and RB; EANA, RLB, SK and MJH were responsible ... ABI sequence detection system included standards of 106 to 10 copies per reaction and negative controls These were used to generate a standard curve and calculate the copy number of the unknown ... diseases in a rural Ugandan population Int J STD AIDS 1994, 5:332-337 Gwanzura L, McFarland W, Alexander D, Burke RL, Katzenstein D: Association between human immunodeficiency virus and herpes simplex...
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Báo cáo hóa học: " Development of a real-time RT-PCR and Reverse Line probe Hybridisation assay for the routine detection and genotyping of Noroviruses in Ireland" ppt
... plasmid DNA for GI NoV and × 107 to × 101 for GII NoV The R2 values for both standard curves were 1.00 with a slope of -3.5 and -3.7 respectively for GI and GII NoV (Fig 1B and Fig 2B) Melting curve ... by large peaks at ~90°C and ~88°C respectively for GI and GII NoV (Fig 1C and Fig 2C) A stool panel containing genotypes of http://www.virologyj.com/content/4/1/86 GI NoV and genotypes of GII NoV ... containing GI/2 and GII/4 PCR products corresponding to Southampton virus and Oxford B2S16 Detection levels of these plasmid molecules were 107 to 101 for GI and × 107 to × 101 for GII (Fig 1A and Fig...
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Báo cáo hóa học: " A novel cloning strategy for isolating, genotyping and phenotyping genetic variants of geminiviruses" pdf
... and was 1.38 × 10-4 mutation per nucleotide sequenced Phenotypic effect of mutations The IR-, AC1- and AC3-mutants, and one of the AV1mutants were tested For each mutant, virus accumulation and ... respectively Each boxplot shows the median (horizontal line), first and third quartiles (lower and upper limits of boxes), and the minimum and maximum values (delimited by the external whiskers) *: Significant ... AC3-mutant accumulating more vDNA than the parental clone at 15 and 25 days (p = 0.08 and p = 0.07, respectively; Figs and 3) and significantly more at 35 days after inoculation (p = × 10-5)...
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Báo cáo hóa học: " Nucleotide mismatches between the VP7 gene and the primer are associated with genotyping failure of a specific lineage from G1 rotavirus strains" potx
... [17,22-24] and one for P-typing [25] In the one developed by Gouvea et al [24], it was reported failures in the correct genotyping of G2, G8, G9 and G10 rotavirus strains [7,12,17,20,21], and In ... lineage III (blue) and lineage IV (red) lected to understand this complex epidemiology [15] However, in recent years it was reported that the accumulation of point mutations in VP4 and VP7 genes was ... corrections of the manuscript, and Juan Stupka and the three anonymous referees for critical corrections 20 References Parashar UD, Gibson CJ, Bresee JS, Glass RI: Rotavirus and severe childhood diarrhea...
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báo cáo hóa học:" Typing of human rotaviruses: Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure" pptx
... laboratory tests and wrote the manuscript; RS and GP carried out RT-PCR tests; JM performed the sequencing experiments; AF, KZ, RB and DS supervised the rotavirus surveillance program and critically ... (14.6%), and G4 (13.8%) G1 comprised only 11.6% of the isolates and 36.9% of the rotavirus-positive samples were untypeable VP7 gene sequence analysis We amplified the VP7 genes of five randomly ... of the isolates and became the most prevalent genotype, and the number of untypeable strains was reduced from 36.9 to 2.1 % The other common G types were G9 (21.7%), G2 (15.0%), and G4 (13.8%)...
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báo cáo hóa học:" Detection, quantification and genotyping of Herpes Simplex Virus in cervicovaginal secretions by real-time PCR: a cross sectional survey" pdf
... was designed by MJH and EANA; experimental work was done by EANA, MJH and AN; interpretation and laboratory work was conducted by MJH, EANA, AN, SK and RB; EANA, RLB, SK and MJH were responsible ... ABI sequence detection system included standards of 106 to 10 copies per reaction and negative controls These were used to generate a standard curve and calculate the copy number of the unknown ... diseases in a rural Ugandan population Int J STD AIDS 1994, 5:332-337 Gwanzura L, McFarland W, Alexander D, Burke RL, Katzenstein D: Association between human immunodeficiency virus and herpes simplex...
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Báo cáo lâm nghiệp: "Development and characteristics of microsatellite markers for sugi (Cryptomeria japonica D. Don) derived from microsatellite-enriched libraries" ppt
... (NA and PIC) on one hand, and two measures of the length of repeat unit (NOR and NNR), total number of nucleotides (TNN) and a measure of the number of nucleotides in flanking regions of microsatellites ... j=1 where, pi and pj refer to the frequency of alleles Ai and Aj, respectively, and summation extends over l alleles The relationships between polymorphic parameters (NA and PIC) and characteristics ... yielding clear single bands and to optimize the annealing temperature and number of PCR cycles for each pair of primers selected 2.3 Plant materials, polymorphism and inheritance of microsatellite markers...
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Báo cáo khoa hoc:" A review on SNP and other types of molecular markers and their use in animal genetics" ppt
... diversity ranging from no SNP to 17 SNPs in fragments of 500 bp each [79] GENOTYPING SNPS For microsatellite markers, there is a standard procedure for genotyping, involving PCR and size determination ... for genotyping are sometimes difficult to overcome and should be taken into account The types of errors and the frequency at which they occur will be different between microsatellites and SNPs ... multifactorial diseases, and the recent progress in polymorphism detection and genotyping techniques SNP DISCOVERY 3.1 Principal strategies Although numerous approaches for SNP discovery have been...
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Báo cáo khoa hoc:"Mapping the Naked Neck (NA) and Polydactyly (PO) mutants of the chicken with microsatellite molecular markers" docx
... extraction and pool preparation Blood was sampled from paternal grand-parents, sire, dams and all progeny Individual extraction of high molecular weight DNA was performed according to standard procedures ... Mapping naked neck and polydactyly in chicken 77 2.3 Typing of microsatellite markers Typings on the sire DNA and the DNA pools (dams + progeny pools) were done with 147 microsatellite markers ... consumables and the use of the ABI sequencer, but does increase the time spent for analysis and requires a good prior knowledge of microsatellite markers, to allow for multiloading on gels, and to...
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