Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization.
BACKGROUND
Array-based comparative genomic hybridization (aCGH) enables genome-wide quantitative delineation of genomic imbalances. A high-resolution contig array was developed specifically for chromosome 8q because this chromosome arm is frequently altered in many human cancers.


METHODS
A minimal tiling path contig of 702 8q-specific bacterial artificial chromosome (BAC) clones was generated with a novel computational tool (BAC Contig Assembler). BAC clones were amplified by degenerative oligonucleotide primer (DOP) polymerase chain reaction and subsequently printed onto glass slides. For validation of the array DNA samples of gastroesophageal and prostate cancer cell lines, and chronic myeloid leukemia specimens were used, which were previously characterized by multicolor fluorescence in situ hybridization and conventional CGH.


RESULTS
Single and double copy gains were confidently demonstrated with the 8q array. Single copy loss and high-level amplifications were accurately detected and confirmed by bicolor fluorescence in situ hybridization experiments. The 8q array was further tested with paraffin-embedded prostate cancer specimens. In these archival specimens, the copy number changes were confirmed. In fresh and archival samples, additional alterations were disclosed. In comparison with conventional CGH, the resolution of the detected changes was much improved, which was demonstrated by an amplicon of 0.7 Mb and a deletion of 0.6 Mb, both spanned by only six BAC clones.


CONCLUSIONS
A comprehensive array is presented, which provides a high-resolution method for mapping copy number alterations on chromosome 8q.
van Duin
Mark
M
Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands.
van Marion
Ronald
R
Watson
J E Vivienne
JE
Paris
Pamela L
PL
Lapuk
Anna
A
Brown
Nils
N
Oseroff
Vanessa V
VV
Albertson
Donna G
DG
Pinkel
Daniel
D
de Jong
Pieter
P
Nacheva
Elizabeth P
EP
Dinjens
Winand
W
van Dekken
Herman
H
Collins
Colin
C
D000230:Adenocarcinoma / Q000235:genetics; D002299:Cardia; D002869:Chromosome Aberrations; D002898:Chromosomes, Human, Pair 8; D005404:Fixatives; D005557:Formaldehyde; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011471:Prostatic Neoplasms / Q000235:genetics; D013274:Stomach Neoplasms / Q000235:genetics; D014407:Tumor Cells, Cultured
D005404:Fixatives; D005557:Formaldehyde