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A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships.

ABSTRACT: Array-based comparative genomics hybridization (aCGH) has gained prevalence as an effective technique for measuring structural variations in the genome. Copy-number variations (CNVs) form a large source of genomic structural variation, but it is not known whether phenotypic differences between intra-species groups, such as divergent human populations, or breeds of a domestic animal, can be attributed to CNVs. Several computational methods have been proposed to improve the detection of CNVs from array CGH data, but few population studies have used CGH data for identification of intra-species differences. In this paper we propose a novel method of genome-wide comparison and classification using CGH data that condenses whole genome information, aimed at quantification of intra-species variations and discovery of shared ancestry. Our strategy included smoothing CGH data using an appropriate denoising algorithm, extracting features via wavelets, quantifying the information via wavelet power spectrum and hierarchical clustering of the resultant profile. To evaluate the classification efficiency of our method, we used simulated data sets. We applied it to aCGH data from human and bovine individuals and showed that it successfully detects existing intra-specific variations with additional evolutionary implications.

SUBMITTER: Mitra A

PROVIDER: S-EPMC2777320 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature

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A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships.

Mitra Apratim A Liu George G Song Jiuzhou J

PloS one 20091124 11

Array-based comparative genomics hybridization (aCGH) has gained prevalence as an effective technique for measuring structural variations in the genome. Copy-number variations (CNVs) form a large source of genomic structural variation, but it is not known whether phenotypic differences between intra-species groups, such as divergent human populations, or breeds of a domestic animal, can be attributed to CNVs. Several computational methods have been proposed to improve the detection of CNVs from ...[more]

PMID: 19956659

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Project description:BackgroundArray-based Comparative Genomic Hybridization (CGH) data have been used to infer phylogenetic relationships. However, the reliability of array CGH analysis to determine evolutionary relationships has not been well established. In most CGH work, all species and strains are compared to a single reference species, whose genome was used to design the array. In the accompanying work, we critically evaluated CGH-based phylogeny using simulated competitive hybridization data. This work showed that a limited number of conditions, principally the tree topology and placement of the reference taxon in the tree, had a strong effect on the ability to recover the correct tree topology. Here, we add to our simulation study by testing the use of CGH as a phylogenetic tool with experimental CGH data from competitive hybridizations between N. crassa and other Neurospora species. In the discussion, we add to our empirical study of Neurospora by reanalyzing of data from a previous CGH phylogenetic analysis of the yeast sensu stricto complex.ResultsArray ratio data for Neurospora and related species were normalized with loess, robust spline, and linear ratio based methods, and then used to construct Neighbor-Joining and parsimony trees. These trees were compared to published phylogenetic analyses for Neurospora based on multilocus sequence analysis (MLSA). For the Neurospora dataset, the best combination of methods resulted in recovery of the MLSA tree topology less than half the time. Our reanalysis of a yeast dataset found that trees identical to established phylogeny were recovered only by pruning taxa - including the reference taxon - from the analysis.ConclusionOur results indicate that CGH data can be problematic for phylogenetic analysis. Success fluctuates based on the methods utilized to construct the tree and the taxa included. Selective pruning of the taxa improves the results - an impractical approach for normal phylogenetic analysis. From the more successful methods we make suggestions on the normalization and post-normalization methods that work best in estimating genetic distance between taxa.

Dataset Information

A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships.

Publications

A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships.

Similar Datasets

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