Search

Your search keyword '"Chamberlain, Amanda J"' showing total 21 results
Start Over Author "Chamberlain, Amanda J" Publication Year Range Last 3 years
21 results on '"Chamberlain, Amanda J"'

13. A multi-tissue atlas of regulatory variants in cattle

Author

Liu, Shuli, Gao, Yahui, Canela-Xandri, Oriol, Wang, Sheng, Yu, Ying, Cai, Wentao, Li, Bingjie, Xiang, Ruidong, Chamberlain, Amanda J., Pairo-Castineira, Erola, D’Mellow, Kenton, Rawlik, Konrad, Xia, Charley, Yao, Yuelin, Navarro, Pau, Rocha, Dominique, Li, Xiujin, Yan, Ze, Li, Congjun, Rosen, Benjamin D., Van Tassell, Curtis P., Vanraden, Paul M., Zhang, Shengli, Ma, Li, Cole, John B., Liu, George E., Tenesa, Albert, and Fang, Lingzhao

Published
2022
Full Text
View/download PDF

17. Mitochondrial sequence variants: testing imputation accuracy and their association with dairy cattle milk traits.

Author

Dorji, Jigme, Chamberlain, Amanda J., Reich, Coralie M., VanderJagt, Christy J., Nguyen, Tuan V., Daetwyler, Hans D., and MacLeod, Iona M.

Subjects
MITOCHONDRIAL DNA, PEARSON correlation (Statistics), SINGLE nucleotide polymorphisms, GENOME-wide association studies, DAIRY cattle
Abstract

Background: Mitochondrial genomes differ from the nuclear genome and in humans it is known that mitochondrial variants contribute to genetic disorders. Prior to genomics, some livestock studies assessed the role of the mitochondrial genome but these were limited and inconclusive. Modern genome sequencing provides an opportunity to re-evaluate the potential impact of mitochondrial variation on livestock traits. This study first evaluated the empirical accuracy of mitochondrial sequence imputation and then used real and imputed mitochondrial sequence genotypes to study the role of mitochondrial variants on milk production traits of dairy cattle. Results: The empirical accuracy of imputation from Single Nucleotide Polymorphism (SNP) panels to mitochondrial sequence genotypes was assessed in 516 test animals of Holstein, Jersey and Red breeds using Beagle software and a sequence reference of 1883 animals. The overall accuracy estimated as the Pearson's correlation squared (R2) between all imputed and real genotypes across all animals was 0.454. The low accuracy was attributed partly to the majority of variants having low minor allele frequency (MAF < 0.005) but also due to variants in the hypervariable D-loop region showing poor imputation accuracy. Beagle software provides an internal estimate of imputation accuracy (DR2), and 10 percent of the total 1927 imputed positions showed DR2 greater than 0.9 (N = 201). There were 151 sites with empirical R2 > 0.9 (of 954 variants segregating in the test animals) and 138 of these overlapped the sites with DR2 > 0.9. This suggests that the DR2 statistic is a reasonable proxy to select sites that are imputed with higher accuracy for downstream analyses. Accordingly, in the second part of the study mitochondrial sequence variants were imputed from real mitochondrial SNP panel genotypes of 9515 Australian Holstein, Jersey and Red dairy cattle. Then, using only sites with DR2 > 0.900 and real genotypes, we undertook a genome-wide association study (GWAS) for milk, fat and protein yields. The GWAS mitochondrial SNP effects were not significant. Conclusion: The accuracy of imputation of mitochondrial genotypes from the SNP panel to sequence was generally low. The Beagle DR2 statistic enabled selection of sites imputed with higher empirical accuracy. We recommend building larger reference populations with mitochondrial sequence to improve the accuracy of imputing less common variants and ensuring that SNP panels include common variants in the D-loop region. [ABSTRACT FROM AUTHOR]

Published
2024
Full Text
View/download PDF

19. Additional file 4 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Author

Prowse-Wilkins, Claire P., Lopdell, Thomas J., Xiang, Ruidong, Vander Jagt, Christy J., Littlejohn, Mathew D., Chamberlain, Amanda J., and Goddard, Michael E.

Abstract

Additional file 4: Supplementary Table 6. The frequencies of the top 10 predicted transcription factor (TF) classes from the JASPAR 2018 CORE database. Supplementary Table 7. The frequencies of the top six predicted promotor element classes from the JASPAR 2018 POLII database.

Published
2023
Full Text
View/download PDF

20. Additional file 2 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Author

Prowse-Wilkins, Claire P., Lopdell, Thomas J., Xiang, Ruidong, Vander Jagt, Christy J., Littlejohn, Mathew D., Chamberlain, Amanda J., and Goddard, Michael E.

Abstract

Additional file 2: Supplementary Table 2. The number of genes or exons with a heterozygous SNP (tSNP), the number of genes or exons with multiple tSNP and the number of genes or exons where the tSNP phenotypes within were significantly different (p

Published
2023
Full Text
View/download PDF

21. Additional file 3 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle

Author

Prowse-Wilkins, Claire P., Lopdell, Thomas J., Xiang, Ruidong, Vander Jagt, Christy J., Littlejohn, Mathew D., Chamberlain, Amanda J., and Goddard, Michael E.

Abstract

Additional file 3: Supplementary Table 4. The number of peak-exon pairs with shared allele-specific QTL variants as well as the distance between peak-exon pairs and the average number of times a peak was associated with an exon and vice versa. Supplementary Table 5. The number of peak-exon pairs with shared traditional QTL as well as the distance between peak-exon pairs and the average number of times a peak was associated with an exon and vice versa.

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results