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Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB.

Lee JH, Lee T, Lee HK, Cho BW, Shin DH, Do KT, Sung S, Kwak W, Kim HJ, Kim H, Cho S, Park KD - Asian-australas. J. Anim. Sci. (2014)

Bottom Line: In order to better understand horses, more variants and other integrated information are needed.Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants.The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

No MeSH data available.


Related in: MedlinePlus

Genotype concordance. Genotype concordance rate which is the proportion of concordant calls having a consistent same genotype between the SNP chip and re-sequencing datasets of 11 samples. Loci of SNP chip were filtered with Hardy-Weinberg equilibrium p-value <0.001, SNP call rate <99%. Type of genotypes are showed as 0/0, 0/1, 1/1 and “./.”. 0 and 1 represents reference allele, alternative allele and “.” means missing allele. SNP, single nucleotide polymorphism.
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f2-ajas-27-9-1236: Genotype concordance. Genotype concordance rate which is the proportion of concordant calls having a consistent same genotype between the SNP chip and re-sequencing datasets of 11 samples. Loci of SNP chip were filtered with Hardy-Weinberg equilibrium p-value <0.001, SNP call rate <99%. Type of genotypes are showed as 0/0, 0/1, 1/1 and “./.”. 0 and 1 represents reference allele, alternative allele and “.” means missing allele. SNP, single nucleotide polymorphism.

Mentions: We checked the level of concordance and validated the SNPs by comparing the results. We used commercial horse chips to confirm allele type and used RNA-seq data to reduce the false positive rate. The SNPs were validated on 11 horse SNP Chip data by showing that 16,795 (99.96%) of the 16,802 identified loci had same alleles. We also calculated concordance as the fraction of identical genotypes between the SNP chip and re-sequencing data (Figure 2). Eleven samples had 99.02% genotype concordance with ranges from 98.3% to 99.57%. Four out of 18 re-sequenced samples were used as RNA-seq samples, so we calculated the loci and genotype concordance of the two datasets per-individual. Each sample had a similar number of SNPs, at about 2,128K. About 214K out of the total loci (10%) was shared between samples when the loci of SNPs from RNA-seq and re-sequencing were compared. Average genotype concordance rate, which is the proportion of concordant calls with the same allele between the two datasets, is 96.6% out of over ~217K loci. The high genotype concordance rate and percentage of known SNPs indicate that the concordant SNPs were of high quality and accuracy.


Thoroughbred Horse Single Nucleotide Polymorphism and Expression Database: HSDB.

Lee JH, Lee T, Lee HK, Cho BW, Shin DH, Do KT, Sung S, Kwak W, Kim HJ, Kim H, Cho S, Park KD - Asian-australas. J. Anim. Sci. (2014)

Genotype concordance. Genotype concordance rate which is the proportion of concordant calls having a consistent same genotype between the SNP chip and re-sequencing datasets of 11 samples. Loci of SNP chip were filtered with Hardy-Weinberg equilibrium p-value <0.001, SNP call rate <99%. Type of genotypes are showed as 0/0, 0/1, 1/1 and “./.”. 0 and 1 represents reference allele, alternative allele and “.” means missing allele. SNP, single nucleotide polymorphism.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150188&req=5

f2-ajas-27-9-1236: Genotype concordance. Genotype concordance rate which is the proportion of concordant calls having a consistent same genotype between the SNP chip and re-sequencing datasets of 11 samples. Loci of SNP chip were filtered with Hardy-Weinberg equilibrium p-value <0.001, SNP call rate <99%. Type of genotypes are showed as 0/0, 0/1, 1/1 and “./.”. 0 and 1 represents reference allele, alternative allele and “.” means missing allele. SNP, single nucleotide polymorphism.
Mentions: We checked the level of concordance and validated the SNPs by comparing the results. We used commercial horse chips to confirm allele type and used RNA-seq data to reduce the false positive rate. The SNPs were validated on 11 horse SNP Chip data by showing that 16,795 (99.96%) of the 16,802 identified loci had same alleles. We also calculated concordance as the fraction of identical genotypes between the SNP chip and re-sequencing data (Figure 2). Eleven samples had 99.02% genotype concordance with ranges from 98.3% to 99.57%. Four out of 18 re-sequenced samples were used as RNA-seq samples, so we calculated the loci and genotype concordance of the two datasets per-individual. Each sample had a similar number of SNPs, at about 2,128K. About 214K out of the total loci (10%) was shared between samples when the loci of SNPs from RNA-seq and re-sequencing were compared. Average genotype concordance rate, which is the proportion of concordant calls with the same allele between the two datasets, is 96.6% out of over ~217K loci. The high genotype concordance rate and percentage of known SNPs indicate that the concordant SNPs were of high quality and accuracy.

Bottom Line: In order to better understand horses, more variants and other integrated information are needed.Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants.The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

No MeSH data available.


Related in: MedlinePlus