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Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.
Naj AC, Lin H, Vardarajan BN, White S, Lancour D, Ma Y, Schmidt M, Sun F, Butkiewicz M, Bush WS, Kunkle BW, Malamon J, Amin N, Choi SH, Hamilton-Nelson KL, van der Lee SJ, Gupta N, Koboldt DC, Saad M, Wang B, Nato AQ Jr, Sohi HK, Kuzma A; Alzheimer's Disease Sequencing Project (ADSP); Wang LS, Cupples LA, van Duijn C, Seshadri S, Schellenberg GD, Boerwinkle E, Bis JC, Dupuis J, Salerno WJ, Wijsman EM, Martin ER, DeStefano AL. Naj AC, et al. Genomics. 2019 Jul;111(4):808-818. doi: 10.1016/j.ygeno.2018.05.004. Epub 2018 May 29. Genomics. 2019. PMID: 29857119 Free PMC article.
The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls f …
The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each …
A New Cloud-Native Tool for Pharmacogenetic Analysis.
Yuan DY, Park JH, Li Z, Thomas R, Hwang DM, Fu L. Yuan DY, et al. Genes (Basel). 2024 Mar 11;15(3):352. doi: 10.3390/genes15030352. Genes (Basel). 2024. PMID: 38540411 Free PMC article.
METHODS: Bioinformatics utilities specialized for human genomics and the latest cloud-based technologies were used to develop a bioinformatics pipeline for analyzing the genomic sequence data and reporting PGx genotypes. A database was created and integrated …
METHODS: Bioinformatics utilities specialized for human genomics and the latest cloud-based technologies were used to develop a bioinformati …
Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity.
Shrine N, Tobin MD, Schurmann C, Soler Artigas M, Hui J, Lehtimäki T, Raitakari OT, Pennell CE, Ang QW, Strachan DP, Homuth G, Gläser S, Felix SB, Evans DM, Henderson J, Granell R, Palmer LJ, Huffman J, Hayward C, Scotland G, Malarstig A, Musk B, James AL; UK BiLEVE; Wain LV. Shrine N, et al. BMC Genet. 2016 Aug 11;17(1):116. doi: 10.1186/s12863-016-0423-0. BMC Genet. 2016. PMID: 27514831 Free PMC article.
To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pi …
To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy num …