Comparative genomic analysis of tumors: detection of DNA losses and amplification.
We demonstrate the use of representational difference analysis for cloning probes that detect DNA loss and amplification in tumors. Using DNA isolated from human tumor cell lines to drive hybridization against matched normal DNA, we were able to identify six genomic regions that are homozygously deleted in cultured cancer cells. When this method was applied in the reverse way, using normal DNA to drive hybridization against tumor cell DNA, we readily isolated probes detecting amplification. Representational difference analysis was also performed on DNAs derived from tumor biopsies, and we thereby discovered a probe detecting very frequent homozygous loss in colon cancer cell lines and located on chromosome 3p.
Lisitsyn
N A
NA
Cold Spring Harbor Laboratory, NY 11724.
Lisitsina
N M
NM
Dalbagni
G
G
Barker
P
P
Sanchez
C A
CA
Gnarra
J
J
Linehan
W M
WM
Reid
B J
BJ
Wigler
M H
MH
D000818:Animals; D001254:Astrocytoma / Q000235:genetics; D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics; D002292:Carcinoma, Renal Cell / Q000235:genetics; D002460:Cell Line; D002872:Chromosome Deletion; D002893:Chromosomes, Human, Pair 3; D003110:Colonic Neoplasms / Q000235:genetics; D015179:Colorectal Neoplasms / Q000235:genetics; D004247:DNA / Q000235:genetics*; D017931:DNA Primers; D004273:DNA, Neoplasm / Q000235:genetics*; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D006822:Hybrid Cells; D017404:In Situ Hybridization, Fluorescence; D007680:Kidney Neoplasms / Q000235:genetics; D008545:Melanoma / Q000235:genetics; D008969:Molecular Sequence Data; D009369:Neoplasms / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D012377:Rodentia; D014407:Tumor Cells, Cultured; D001749:Urinary Bladder Neoplasms / Q000235:genetics
D017931:DNA Primers; D004273:DNA, Neoplasm; D004247:DNA