Genomic Position Mapping Discrepancies of Commercial SNP Chips
نویسندگان
چکیده
The field of genetics has come to rely heavily on commercial genotyping arrays and accompanying annotations for insights into genotype-phenotype associations. However, in order to avoid errors and false leads, it is imperative that the annotation of SNP chromosomal positions is accurate and unambiguous. We report on genomic positional discrepancies of various SNP chips for human, cattle and mouse species, and discuss their causes and consequences.
منابع مشابه
Technical note: Characteristics and use of the Illumina BovineLD and GeneSeek Genomic Profiler low-density bead chips for genomic evaluation.
The GeneSeek Genomic Profiler (GGP) BeadChip (GeneSeek, Lincoln, NE), which became available commercially in February 2012, is based on the Illumina BovineLD Genotyping BeadChip (Illumina Inc., San Diego, CA), with 1,745 additional single nucleotide polymorphisms (SNP) for genomic evaluation and SNP for proprietary single-gene tests. The BovineLD chip with 6,909 SNP, which replaced the Illumina...
متن کاملThe Pattern of Linkage Disequilibrium in Livestock Genome
Linkage disequilibrium (LD) is bases of genomic selection, genomic marker imputation, marker assisted selection (MAS), quantitative trait loci (QTL) mapping, parentage testing and whole genome association studies. The Particular alleles at closed loci have a tendency to be co-inherited. In linked loci this pattern leads to association between alleles in population which is known as LD. Two metr...
متن کاملProceedings, 10 World Congress of Genetics Applied to Livestock Production SNPchiMp v.2: An Open Access Web Tool for SNP Data Management on Bovine, Porcine and Equine Livestock
Since the beginning of the genomic era, the SNP chip market in livestock species has grown almost exponentially. Today, researchers are asked to deal with many SNP chips on daily basis, and this requires having the (general and specific) information on the SNPs available and at hand. However, the information is often difficult to obtain (e.g. data on chips no longer on the market), integrate an...
متن کاملOptimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications
Low-density (LD) single nucleotide polymorphism (SNP) arrays provide a cost-effective solution for genomic prediction and selection, but algorithms and computational tools are needed for the optimal design of LD SNP chips. A multiple-objective, local optimization (MOLO) algorithm was developed for design of optimal LD SNP chips that can be imputed accurately to medium-density (MD) or high-densi...
متن کاملPhysiology and Endocrinology Symposium: How single nucleotide polymorphism chips will advance our knowledge of factors controlling puberty and aid in selecting replacement beef females.
The promise of genomic selection is accurate prediction of the genetic potential of animals from their genotypes. Simple DNA tests might replace low-accuracy predictions for expensive or lowly heritable measures of puberty and fertility based on performance and pedigree. Knowing with some certainty which DNA variants (e.g., SNP) affect puberty and fertility is the best way to fulfill the promis...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره 7 شماره
صفحات -
تاریخ انتشار 2012