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High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

ABSTRACT: High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

PROVIDER: PRJNA508360 | ENA |

REPOSITORIES: ENA

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High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

2016-07-05 | GSE83910 | GEO

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs. To compare SNPs identified by genotyping arrays and de novo assembly method, we genotyped 10 pig breeds by porcine 60K BeadChip genotyping array (Illumina), including 1 berkshire pig, 1 hampshire pig, 1 landrace pig, 1 large white pig,1 piÃ©train pig, 1 bamei pig,1 jinhua pig, 1 meishan pig, 1 rongchang pig and 1 Tibetan wild boar.

2016-07-05 | E-GEOD-83910 | biostudies-arrayexpress

High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the whole-genome sequencing

Project description:Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.

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Genotyping of Infinium OmniZhongHua BeadChip from Illumina for haplotype construction

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Genotyping analysis employing Illumina Infinium ImmunoArray-24 v2.0 BeadChip

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Project description:High concordance between SNPs identified by the porcine 60K BeadChip genotyping array (Illumina) and the assembly-versus-assembly method

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Genome-wide association studies for sheep growth and meat production traits using Illumina OvineSNP50 BeadChip

Project description:Mear prodution is the most important trait for sheep. In this study, we performed a Genome-wide association study (GWAS) by using Illumina Ovine SNP50 BeadChip in 329 purebred sheep phenotyped for 11 growth and meat production traits (birth weight, weaning weight, 6-month weight, eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height at withers , chest girth and shin circumference). A total of 319 sheep and 48,198 SNPs were fitted using TASSEL 3.0 software as random effects in a mixed linear model. 36 chromosome-wise significant SNPs were identified for 7 traits and 10 of them reached genome-wide significance level consistently for post-weaning gain. Gene annotation was implemented based on the latest version3.1 ovine genome sequence (released October 2012), and meanwhile we referenced genomic information of human, bovine, mouse and rat. More than one-third SNPs (14 out of 36) were located within ovine genes , some other were located close to ovine genes (878bp-398165bp apart).

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Genome-wide association studies for sheep growth and meat production traits using Illumina OvineSNP50 BeadChip

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Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies.

Project description:Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding impact of the genomic variation on the results of methylation studies performed using Illumina's Infinium methylation probes. However, the complexity of SNPs impact on the methylation level measurements (? values) has not been comprehensively described.In our comparative study of European and Asian populations performed using Illumina HM450K, we found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. Characteristic tri-modal or bi-modal patterns of ? values distribution among individual samples were observed for CpGs with SNPs in the first and second position, respectively. To better understand how SNPs affect methylation readouts, we investigated their impact in the context of SNP position and type, and of the Illumina probe type (Infinium I or II).Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. In addition, it provides important practical clues for discriminating between differences due to the methylation status and to the genomic polymorphisms, based on the inspection of methylation readouts in individual samples. This approach is of special importance when Illumina Infinium assay is used for any comparative population studies, whether related to cancer, disease, ethnicity where SNP frequencies differentiate the studied groups.

| S-EPMC4659175 | biostudies-literature

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