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| Status |
Public on Mar 07, 2014 |
| Title |
Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
Chromosomal instability is central to the process of carcinogenesis. The detection of somatic chromosomal alterations in small premalignant lesions genome-wide remains challenging since sample heterogeneity dilutes the aberrant cell information. We introduced an analytic metric termed "delta-θ", and applied this metric to a titrated cancer cell model using a pair of cancer cell line and matched lymphoblastoid cell line. We examined heterogeneous clinical specimens including bronchial biopsies and brushings with this metric. Distinctive genomic variation were successfully detected across the whole genome in invasive cancer cases (6/6), carcinoma in situ (3/3), and high grade dysplasia (severe or moderate) (3/11).
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| Overall design |
We modeled titration series (100%, 25%, 12.5%, 6.3%, 3.1%, 1.6% and 0% tumor content) mixing the genomic DNA of the cell line pair. We also investigated 30 malignant/premalignant samples from 18 patients with heavy smoking histories (6 invasive lung cancer, 3 carcinoma in situ,15 dysplasia, 3 hyperplasia and 3 normal histology) using Illumina HumanOmni2.5 and Human 660w SNP microarrays. All of them were paired with matched reference blood DNA and analyzed.
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| Contributor(s) |
Nakachi I, Rice JL, Coldren CD, Stearman RS, Edwards MG, Gao B, Miller YE, Geraci MW |
| Citation(s) |
24346345 |
| |
| Submission date |
Dec 27, 2012 |
| Last update date |
Mar 07, 2014 |
| Contact name |
Ichiro Nakachi |
| E-mail(s) |
ichiro.nakachi@ucdenver.edu
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| Phone |
303-724-6053
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| Organization name |
University of Colorado Denver
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| Department |
Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine
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| Lab |
Mark Geraci's Lab
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| Street address |
12700 East 19th Avenue, RC2 9th floor
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (2) |
| GPL8888 |
Illumina Human660W-Quad v1.0 BeadChip |
| GPL16110 |
Illumina HumanOmni2.5 BeadChip (hg19) |
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| Samples (57)
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| Relations |
| BioProject |
PRJNA184816 |
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