eprintid: 105
rev_number: 7
eprint_status: archive
userid: 4
dir: disk0/00/00/01/05
datestamp: 2013-01-03 04:14:14
lastmod: 2013-06-29 04:44:19
status_changed: 2013-01-03 04:14:14
type: conference_item
metadata_visibility: show
creators_name: Nguyen, Son Hoang
creators_name: Le, Sy Vinh
creators_name: Le, Si Quang
creators_id: vinhls@vnu.edu.vn
corp_creators: VNU-UET
title: Detecting Bad SNPs from Illumina BeadChips Using Jeffreys Distance
ispublished: pub
subjects: IT
subjects: IT_CS
divisions: fac_fit
keywords: Accuracy;Approximation methods;Entropy;Gaussian distribution;Genomics;Humans;biology computing;cellular biophysics;genomics;lab-on-a-chip;Gencall;GenoSNP;Illumina BeadChips;Jeffreys distance;Kenyan people;bad SNP detection;chromosome;human genomes;microarray chips;probe intensities data;single nucleotide polymorphisms;software Illuminus;unstable SNP detection;SNP genotype;bad SNPs;quality control;relative entropy;
abstract: Current microarray technologies are able to assay thousands of samples over million of SNPs simultaneously. Computational approaches have been developed to analyse a huge amount of data from microarray chips to understand sophisticated human genomes. The data from microarray chips might contain errors due to bad samples or bad SNPs. In this paper, we propose a method to detect bad SNPs from the probe intensities data of Illumina Beadchips. This approach measures the difference among results determined by three software Illuminus, GenoSNP and Gencall to detect the unstable SNPs. Experiment with SNP data in chromosome 20 of Kenyan people demonstrates the usefulness of our method. This approach reduces the number of SNPs that are needed to check manually. Furthermore, it has the ability in detecting bad SNPs that have not been recognized by other criteria.
date: 2012-08-17
date_type: published
full_text_status: none
pres_type: paper
pagerange: 18 -25
event_title: 2012 Fourth International Conference on Knowledge and Systems Engineering (KSE)
event_location: Danang, Vietnam
event_dates: 17-19 August 2012
event_type: conference
refereed: TRUE
related_url_url: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6299181
related_url_type: pub
citation:   Nguyen, Son Hoang and Le, Sy Vinh and Le, Si Quang  (2012) Detecting Bad SNPs from Illumina BeadChips Using Jeffreys Distance.  In: 2012 Fourth International Conference on Knowledge and Systems Engineering (KSE), 17-19 August 2012, Danang, Vietnam.