Challenges in array comparative genomic hybridization for the analysis of cancer samples.
OBJECTIVE
To address some of the challenges facing the incorporation of array comparative genomic hybridization technology as a clinical tool, including archived tumor tissue, tumor heterogeneity, DNA quality and quantity, and array comparative genomic hybridization platform selection and performance.


METHODS
Experiments were designed to assess the impact of DNA source (e.g., archival material), quantity, and amplification on array comparative genomic hybridization results. Two microdissection methods were used to isolate tumor cells to minimize heterogeneity. These data and other data sets were used in a further performance comparison of two commonly used array comparative genomic hybridization platforms: bacterial artificial chromosome (Roswell Park Cancer Institute) and oligonucleotide (Agilent Technologies, Santa Clara, CA).


RESULTS
Array comparative genomic hybridization data from as few as 100 formalin-fixed, paraffin-embedded cells isolated by laser capture microdissection and amplified were remarkably similar to array comparative genomic hybridization copy number alterations detected in the bulk (unamplified) population. Manual microdissection from frozen sections provided a rapid and inexpensive means to isolate tumor from adjacent DNA for amplification and array comparative genomic hybridization. Whole genome amplification introduced no appreciable allele bias on array comparative genomic hybridization. The array comparative genomic hybridization results provided by the bacterial artificial chromosome and Agilent platforms were concordant in general, but bacterial artificial chromosome array comparative genomic hybridization showed far fewer outliers and overall less technical noise, which could adversely affect the statistical interpretation of the data.


CONCLUSIONS
This study demonstrates that copy number alterations can be robustly and reproducibly detected by array comparative genomic hybridization in DNA isolated from challenging tumor types and sources, including archival materials, low DNA yield, and heterogeneous tissues. Furthermore, bacterial artificial chromosome array comparative genomic hybridization offers the advantage over the Agilent oligonucleotide platform of presenting fewer outliers, which could affect data interpretation.
Nowak
Norma J
NJ
New York State Center of Excellence in Bioinformatics and Life Sciences and Department of Biochemistry, University at Buffalo, Buffalo, New York 14203, USA. norma.nowak@roswellpark.org
Miecznikowski
Jeffrey
J
Moore
Stephen R
SR
Gaile
Daniel
D
Bobadilla
Dolores
D
Smith
David D
DD
Kernstine
Kemp
K
Forman
Stephen J
SJ
Mhawech-Fauceglia
Paulette
P
Reid
Mary
M
Stoler
Daniel
D
Loree
Thom
T
Rigual
Nestor
N
Sullivan
Maureen
M
Weiss
Lawrence M
LM
Hicks
David
D
Slovak
Marilyn L
ML
D001399:Azure Stains; D045744:Cell Line, Tumor; D002871:Chromosome Banding; D022202:Chromosomes, Artificial, Bacterial; D002889:Chromosomes, Human, Pair 2; D002897:Chromosomes, Human, Pair 7; D002899:Chromosomes, Human, Pair 9; D015331:Cohort Studies; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics; D005260:Female; D019085:Fluorescent Antibody Technique, Direct; D018628:Gene Dosage; D006689:Hodgkin Disease / Q000235:genetics / Q000473:pathology; D006801:Humans; D007834:Lasers; D042282:Microdissection; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016539:Reed-Sternberg Cells / Q000473:pathology; D015203:Reproducibility of Results; D032681:Spectral Karyotyping
D001399:Azure Stains; D004273:DNA, Neoplasm