DSpace at VNU: A maximum likelihood method for detecting bad samples from Illumina BeadChips data

A maximum likelihood method for detecting bad samples from Illumina BeadChips data Nguyễn Hà Anh Tuấn Trường Đại học Công nghệ Luận văn Thạc sĩ ngành: Khoa học máy tính; Mã số: 60 48 01 Người hướng dẫn: TS Lê Sỹ Vinh Năm bảo vệ: 2012 Keywords Công nghệ thông tin; Dữ liệu Content Table of Contents Overview 1 Introduction 1.1 Biological background 1.2 Some common types of mutation 1.3 SNP and SNP genotype 1.4 Microarray technology and Illumina BeadChips 1.5 Genotype callers 1.6 Quality control and quality assurance 1.6.1 Identify samples with discordant sex information 10 1.6.2 Identify samples that have high missing and heterozygosity rate 11 1.6.3 Identify duplicated or related samples 11 1.6.4 Identify samples that have different ancestries 12 Genotype callers 14 2.1 Illuminus 14 2.2 GenoSNP 17 2.3 GenCall 18 2.4 Comparing three callers 18 Maximum likelihood method for detecting bad samples 20 3.1 Create potential bad sample list 21 3.2 Estimate the fitness of data 22 3.3 Remove bad samples 24 Experimental result 25 4.1 Input file format 25 4.2 Experiment 27 4.3 Experiment 31 Conclusion 34 Publications 35 References [APC+10] C.A Anderson, F.H Pettersson, G.M Clarke, L.R Cardon, A.P Morris, and K.T Zondervan Data quality control in genetic case-control association studies Nat Protoc, 5(9):1564-73, 2010 [CBSI07] Benilton Carvalho, Henrik Bengtsson, Terence P Speed, and Rafael A Irizarry Exploration, normalization, and genotype calls of high-density oligonucleotide snp array data Biostatistics, 8(2):485-499, 2007 [CM01] Francis S Collins and Victor A McKusick Implications of the human genome project for medical science JAMA: The Journal of the American Medical Association, 285(5):540-544, 2001 [GYC+08a] Eleni Giannoulatou, Christopher Yau, Stefano Colella, Jiannis Ragous- sis, and Christopher C Holmes Genosnp: a variational bayes within- sample snp genotyping algorithm that does not require a reference population Bioinformatics, 24(19):2209-2214, 2008 [GYC+08b] Eleni Giannoulatou, Christopher Yau, Stefano Colella, Jiannis Ragous- sis, and Christopher C Holmes A genotype calling algorithm for the illumina beadarray platform Bioinformatics, 24(19):2209-2214, 2008 [Inc05] Illumina Inc Illumina gencall data analysis software //www.illumina.com/documents/products/technotes/technote_ gencall_data_analysis_software.pdf, 2005 http: [Inc06] Illumina Inc Infinium ii assay workflow http://www.illumina.com/ documents/products/workflows/workflow_infinium_ii.pdf, 2006 [KF01] Larry J Kricka and Paolo Fortina Microarray technology and appli- ... illumina beadarray platform Bioinformatics, 24(19):2209-2214, 2008 [Inc05] Illumina Inc Illumina gencall data analysis software //www .illumina. com/documents/products/technotes/technote_ gencall _data_ analysis_software.pdf,...2.4 Comparing three callers 18 Maximum likelihood method for detecting bad samples 20 3.1 Create potential bad sample list 21 3.2 Estimate the fitness of data ... [CBSI07] Benilton Carvalho, Henrik Bengtsson, Terence P Speed, and Rafael A Irizarry Exploration, normalization, and genotype calls of high-density oligonucleotide snp array data Biostatistics, 8(2):485-499,