A New Normalizing Algorithm for BAC CGH Arrays with Quality Control Metrics

Overview

Journal J Biomed Biotechnol

Specialty Biology

Date 2011 Mar 16

PMID 21403910

Citations 2

Authors

Jeffrey C Miecznikowski

Daniel P Gaile

Song Liu

Lori Shepherd

Norma Nowak

Affiliations

Soon will be listed here.

Abstract

The main focus in pin-tip (or print-tip) microarray analysis is determining which probes, genes, or oligonucleotides are differentially expressed. Specifically in array comparative genomic hybridization (aCGH) experiments, researchers search for chromosomal imbalances in the genome. To model this data, scientists apply statistical methods to the structure of the experiment and assume that the data consist of the signal plus random noise. In this paper we propose "SmoothArray", a new method to preprocess comparative genomic hybridization (CGH) bacterial artificial chromosome (BAC) arrays and we show the effects on a cancer dataset. As part of our R software package "aCGHplus," this freely available algorithm removes the variation due to the intensity effects, pin/print-tip, the spatial location on the microarray chip, and the relative location from the well plate. removal of this variation improves the downstream analysis and subsequent inferences made on the data. Further, we present measures to evaluate the quality of the dataset according to the arrayer pins, 384-well plates, plate rows, and plate columns. We compare our method against competing methods using several metrics to measure the biological signal. With this novel normalization algorithm and quality control measures, the user can improve their inferences on datasets and pinpoint problems that may arise in their BAC aCGH technology.

Citing Articles

Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?.

Alsolami R, Knight S, Schuh A Per Med. 2014; 10(4):361-376.

PMID: 24611071 PMC: 3943176. DOI: 10.2217/pme.13.33.

Differential copy number aberrations in novel candidate genes associated with progression from in situ to invasive ductal carcinoma of the breast.

Liao S, Desouki M, Gaile D, Shepherd L, Nowak N, Conroy J Genes Chromosomes Cancer. 2012; 51(12):1067-78.

PMID: 22887771 PMC: 3465468. DOI: 10.1002/gcc.21991.

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