From amplification to gene in thyroid cancer: A high-resolution mapped bacterial-artificial-chromosome resource for cancer chromosome aberrations guides gene discovery after comparative genome hybridization

Journal Article · Sat Aug 01 04:00:00 EDT 1998 · American Journal of Human Genetics

DOI:https://doi.org/10.1086/301973· OSTI ID:659011

Chen, X N; Gonsky, R; Korenberg, J R ^[1]; Knauf, J A; Fagin, J A ^[2]; Wang, M; Lai, E H ^[3]; Chissoe, S ^[4]

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1. UCLA School of Medicine, Los Angeles, CA (United States). Cedars-Sinai Research Inst.
2. Univ. of Cincinnati, OH (United States). Div. of Endocrinology/Metabolism
3. Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Pharmacology
4. Washington Univ. School of Medicine, St. Louis, MO (United States). Genome Sequencing

Chromosome rearrangements associated with neoplasms provide a rich resource for definition of the pathways of tumorigenesis. The power of comparative genome hybridization (CGH) to identify novel genes depends on the existence of suitable markers, which are lacking throughout most of the genome. The authors now report a general approach that translates CGH data into higher-resolution genomic-clone data that are then used to define the genes located in aneuploid regions. They used CGH to study 33 thyroid-tumor DNAs and two tumor-cell-line DNAs. The results revealed amplifications of chromosome band 2p21, with less-intense amplification on 2p13, 19q13.1, and 1p36 and with least-intense amplification on 1p34, 1q42, 5q31, 5q33-34, 9q32-34, and 14q32. To define the 2p21 region amplified, a dense array of 373 FISH-mapped chromosome 2 bacterial artificial chromosomes (BACs) was constructed, and 87 of these were hybridized to a tumor-cell line. Four BACs carried genomic DNA that was amplified in these cells. The maximum amplified region was narrowed to 3--6 Mb by multicolor FISH with the flanking BACs, and the minimum amplicon size was defined by a contig of 420 kb. Sequence analysis of the amplified BAC 1D9 revealed a fragment of the gene, encoding protein kinase C epsilon (PKC{epsilon}), that was then shown to be amplified and rearranged in tumor cells. In summary, CGH combined with a dense mapped resource of BACs and large-scale sequencing has led directly to the definition of PKC{epsilon} as a previously unmapped candidate gene involved in thyroid tumorigenesis.

• Sponsoring Organization: USDOE, Washington, DC (United States); National Insts. of Health, Bethesda, MD (United States)
• DOE Contract Number: FG03-92ER61402; FC03-96ER62294
• OSTI ID: 659011
• Journal Information: American Journal of Human Genetics, Journal Name: American Journal of Human Genetics Journal Issue: 2 Vol. 63; ISSN AJHGAG; ISSN 0002-9297
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
BIOLOGICAL MARKERS
CHROMOSOMAL ABERRATIONS
DNA
DNA HYBRIDIZATION
GENE AMPLIFICATION
GENES
NEOPLASMS
PATHOGENESIS
THYROID