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

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

Experimental result
25
4.1 Input file format ........................................................................................... 25
4.2

Experiment 1 ................................................................................................. 27

4.3

Experiment 2 ................................................................................................ 31

Conclusion

34

Publications

35

References
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