Reference based SNP identification from Genotyping-by-
Simple SNP based minimal marker genotyping for Humulus lupulus L identification and variety validation
... for genotyping are based upon 25 microsatellites that provides relatively accurate genotyping but cannot always differentiate ...A genotyping protocol based upon SNPs would enable rapid ...
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Comparison of three PCR-based assays for SNP genotyping in plants
... A set of pre-validated SNPs ([12]; Additional file 2: Table S2) was used to design TaqMan, KASP and rhAmp assays. Supplementary material contains the flanking sequences with evaluated SNPs indicated by brackets. All ...
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SNP genotyping [16]. However, the incorporated
... target SNP must be discriminated by digestion with available restriction enzymes at the same ...of SNP-RFLPing [22, ...principle from natural ...solutions based on a fitness rule are refined ...
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Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip
... the identification of polymorphic alpaca SNPs, based on the use of the BovineHD Genotyping Beadchip (Illumina), was ...successful identification of polymorphic SNPs in cross hybridization ...
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Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples.
... Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction STR profiling is a powerful, multiplex PCR-based assay that uses up to 16 ...
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Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates.
... sive genotyping or strain identification was implemented prior to this ...lineage identification and phylogenetic analysis need to be performed outside of the ...lineage identification and ...
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Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum (Prunus salicina Lindl.)
... quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference ...derived ...
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Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success
... variety of outstanding questions in evolutionary biology, conservation genetics and wildlife management [6–8]. In non-model species, SNPs are often mined from transcriptome assemblies, as these are smaller and ...
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Forensic SNP genotyping using nanopore MinION sequencing
... SNP amplicon subreads (see Data analysis for an explanation on subreads) were extracted from the high qual- ity 2D reads, resulting in 1542739 ...per SNP locus (grey) as well as the number of ...
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GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
... reduced genotyping error rate. Remarkably, the reference- independent version of GBS-SNP-CROP was also shown to outperform the reference-based TASSEL-GBS pipe- line in terms of these ...
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Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays
... custom-designed SNP panels based on molecular inversion probe technology (7,8) allow for such an ...output from this assay is that there is only one chip feature per SNP rather than multiple ...
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Automated SNP genotype clustering algorithm to improve data completeness in high throughput SNP genotyping datasets from custom arrays
... custom-designed SNP panels based on molecular inversion probe technology (7,8) allow for such an ...output from this assay is that there is only one chip feature per SNP rather than multiple ...
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SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data
... are based on sequencing post- ...methodology based on classical population genetic theory, ...data from MethylCap-seq with associated SNP profiles to identify monoallelically methylated ...the ...
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Medium-throughput SNP genotyping and linkage mapping in Haliotis midae
... handle from 48- to 384-plex levels, allowing thousands of genotypes to be achieved simultaneously in a short period of time (Illumina ...GoldenGate genotyping assay permits a high degree of loci ...
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Robust SNP genotyping by multiplex PCR and arrayed primer extension
... per SNP, as well as multiple buffer-only spots and positive control normalization ...probe based on a plant-specific gene sequence that will extend by a single N base due to the presence of an exogenous ...
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Forensic tri-allelic SNP genotyping using nanopore sequencing
... the SNP position using respec- tively the 1D and 1D 2 reads resulting from the 1D 2 sequencing ex- periment for all five ...samples. From this figure it is clear that the more accurate 1D 2 reads ...
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Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)
... 2.2. SNP location and analysis of synonymous and non-synonymous SNPs in oil palm coding regions The majority of SNPs uncovered through the GBS approach were distributed in non-coding portions of the ...fied ...
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Arrayed Primer Extension in the Array of Arrays Format: A Rational Approach for Microarray-Based SNP Genotyping ABSTRACT
... sample from HapMap are compara- ble (Weiss and Clark, ...our SNP replace- ment procedure (block 9, r 2 LD , Table 1) because, occasion- ally, genotyped markers were substituted by nearby validated HapMap ...
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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
... a reference genome or a reference ...data from two ex- treme modalities of the phenotype, we were able to estab- lish a catalog of SNPs, stratify them by their impact on the protein sequence, and ...
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Comparison of msp genotyping and a 24 SNP molecular assay for differentiating Plasmodium falciparum recrudescence from reinfection
... the SNP based ...samples from geographically separated regions for design and validation of the truncated bar code may have resulted in less than ideal performance of the truncated ...
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