Abstract
The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic derangement seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alterations present in the tumors, and so define copy number phenotypes as well as to associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use unsupervised Hidden Markov Models approach. The clones are partitioned into the states which represent underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets with known copy number alterations for one of them. The biological conclusions drawn from the analyses are discussed.
| Original language | English (US) |
|---|---|
| Title of host publication | Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 |
| Publisher | Institute of Electrical and Electronics Engineers Inc. |
| Pages | 407-408 |
| Number of pages | 2 |
| ISBN (Print) | 0769520006, 9780769520001 |
| DOIs | |
| State | Published - 2003 |
| Event | 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States Duration: Aug 11 2003 → Aug 14 2003 |
Other
| Other | 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 |
|---|---|
| Country | United States |
| City | Stanford |
| Period | 8/11/03 → 8/14/03 |
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ASJC Scopus subject areas
- Electrical and Electronic Engineering
- Computer Science Applications
Cite this
Statistical issues in the analysis of the array CGH data. / Fridlyand, J.; Snijders, A.; Pinkel, D.; Albertson, D.; Jain, Ajay.
Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 407-408 1227347.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
TY - GEN
T1 - Statistical issues in the analysis of the array CGH data
AU - Fridlyand, J.
AU - Snijders, A.
AU - Pinkel, D.
AU - Albertson, D.
AU - Jain, Ajay
PY - 2003
Y1 - 2003
N2 - The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic derangement seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alterations present in the tumors, and so define copy number phenotypes as well as to associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use unsupervised Hidden Markov Models approach. The clones are partitioned into the states which represent underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets with known copy number alterations for one of them. The biological conclusions drawn from the analyses are discussed.
AB - The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic derangement seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alterations present in the tumors, and so define copy number phenotypes as well as to associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use unsupervised Hidden Markov Models approach. The clones are partitioned into the states which represent underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets with known copy number alterations for one of them. The biological conclusions drawn from the analyses are discussed.
UR - http://www.scopus.com/inward/record.url?scp=34247344275&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34247344275&partnerID=8YFLogxK
U2 - 10.1109/CSB.2003.1227347
DO - 10.1109/CSB.2003.1227347
M3 - Conference contribution
AN - SCOPUS:34247344275
SN - 0769520006
SN - 9780769520001
SP - 407
EP - 408
BT - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PB - Institute of Electrical and Electronics Engineers Inc.
ER -