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 0

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

1 Introduction 3 1.1 Biological background 3

1.2 Some common types of mutation 5

1.3 SNP and SNP genotype 6

1.4 Microarray technology and Illumina BeadChips 7

1.5 Genotype callers 8

1.6 Quality control and quality assurance 9

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

2 Genotype callers 14 2.1 Illuminus 14

2.2 GenoSNP 17

2.3 GenCall 18

2.4 Comparing three callers 18

3 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

4.1 Input file format 25

4.2 Experiment 1 27

4.3 Experiment 2 31

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