A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH

BackgroundCurrently, two main technologies are used for screening of DNA copy number; the BAC (Bacterial Artificial Chromosome) and the recently developed oligonucleotide-based CGH (Chromosomal Comparative Genomic Hybridization) arrays which are capable of detecting small genomic regions with amplification or deletion. The correlation as well as the discriminative power of these platforms has never been compared statistically on a significant set of human patient samples.ResultsIn this paper, we present an exhaustive comparison between the two CGH platforms, undertaken at two independent sites using the same batch of DNA from 19 advanced prostate cancers. The comparison was performed directly on the raw data and a significant correlation was found between the two platforms. The correlation was greatly improved when the data were averaged over large chromosomic regions using a segmentation algorithm. In addition, this analysis has enabled the development of a statistical model to discriminate BAC outliers that might indicate microevents. These microevents were validated by the oligo platform results.ConclusionThis article presents a genome-wide statistical validation of the oligo array platform on a large set of patient samples and demonstrates statistically its superiority over the BAC platform for the Identification of chromosomic events. Taking advantage of a large set of human samples treated by the two technologies, a statistical model has been developed to show that the BAC platform could also detect microevents.

[1]  Yutaka Miura,et al.  Frequent somatic mutations of the transcription factor ATBF1 in human prostate cancer , 2005, Nature Genetics.

[2]  D. Pinkel,et al.  Genomic Alterations in Primary Gastric Adenocarcinomas Correlate with Clinicopathological Characteristics and Survival , 2004, Cellular oncology : the official journal of the International Society for Cellular Oncology.

[3]  Ash A. Alizadeh,et al.  Genome-wide analysis of DNA copy-number changes using cDNA microarrays , 1999, Nature Genetics.

[4]  D. Pinkel,et al.  Comparative Genomic Hybridization for Molecular Cytogenetic Analysis of Solid Tumors , 2022 .

[5]  Jane Fridlyand,et al.  Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors , 2004 .

[6]  Ash A. Alizadeh,et al.  Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. , 2003, Blood.

[7]  N. Carter,et al.  DNA microarrays for comparative genomic hybridization based on DOP‐PCR amplification of BAC and PAC clones , 2003, Genes, chromosomes & cancer.

[8]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[9]  Peter J. Park,et al.  Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data , 2005, Bioinform..

[10]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[11]  Ash A. Alizadeh,et al.  Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays , 1999, Nature Genetics.

[12]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[13]  K Autio,et al.  DNA copy number losses in human neoplasms. , 1999, The American journal of pathology.

[14]  D. Pinkel,et al.  Mantle-cell lymphoma genotypes identified with CGH to BAC microarrays define a leukemic subgroup of disease and predict patient outcome. , 2005, Blood.

[15]  W. Kuo,et al.  High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays , 1998, Nature Genetics.

[16]  S. Chin,et al.  Human and mouse oligonucleotide-based array CGH , 2005, Nucleic acids research.

[17]  Carlos Caldas,et al.  Identification and validation of prognostic markers in breast cancer with the complementary use of array‐CGH and tissue microarrays , 2005, The Journal of pathology.

[18]  S. Knuutila,et al.  DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. , 1998, The American journal of pathology.

[19]  B. Ylstra,et al.  BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH) , 2006, Nucleic acids research.

[20]  L. Chin,et al.  High-Resolution Global Profiling of Genomic Alterations with Long Oligonucleotide Microarray , 2004, Cancer Research.

[21]  Jane Fridlyand,et al.  Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. , 2005, Human molecular genetics.