Showing papers by "Johan Vallon-Christersson published in 2005"

Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization.

Abstract: Mutations in BRCA1 and BRCA2 account for a significant proportion of hereditary breast cancers. Earlier studies have shown that inherited and sporadic tumors progress along different somatic genetic pathways and that global gene expression profiles distinguish between these groups. To determine whether genomic profiles similarly discriminate among BRCA1, BRCA2, and sporadic tumors, we established DNA copy number profiles using comparative genomic hybridization to BAC-clone microarrays providing <1 Mb resolution. Tumor DNA was obtained from BRCA1 (n = 14) and BRCA2 (n = 12) mutation carriers, as well as sporadic cases (n = 26). Overall, BRCA1 tumors had a higher frequency of copy number alterations than sporadic breast cancers (P = 0.00078). In particular, frequent losses on 4p, 4q, and 5q in BRCA1 tumors and frequent gains on 7p and 17q24 in BRCA2 tumors distinguish these from sporadic tumors. Distinct amplicons at 3q27.1-q27.3 were identified in BRCA1 tumors and at 17q23.3-q24.2 in BRCA2 tumors. A homozygous deletion on 5q12.1 was found in a BRCA1 tumor. Using a set of 169 BAC clones that detect significantly (P < 0.001) different frequencies of copy number changes in inherited and sporadic tumors, these could be discriminated into separate groups using hierarchical clustering. By comparing DNA copy number and RNA expression for genes in these regions, several candidate genes affected by up- or down-regulation were identified. Moreover, using support vector machines, we correctly classified BRCA1 and BRCA2 tumors (P < 0.0000004 and 0.00005, respectively). Further validation may prove this tumor classifier to be useful for selecting familial breast cancer cases for further mutation screening, particularly, as these data can be obtained using archival tissue.

Functional and Molecular Characterization of BRCA1 and BRCA2 Associated Breast Cancer

Abstract: This doctoral dissertation is based on five appended papers primarily concerned with three main topics, namely: the functional characterization of specific and clinically relevant perturbations found in BRCA1 ? one of the major breast cancer susceptibility genes; the use of microarray technologies for molecular characterization of hereditary breast tumor samples from a genomic perspective; and finally, the development of software to address some of the logistical problems of data analysis and management that arise when utilizing microarrays. Results obtained from the work presented herein demonstrate the following: that transcription az says can aid in the characterization of C-terminal missense mutations but that it may not be possible to unambiguously characterize variants with a yeast-based assay alone; that a naturally occurring C-terminal germline mutation in BRCA1 encodes a protein with apparent temperature-dependant functional properties; that open-source software can provide comprehensive solutions to meet data management needs of microarray experimenters; that BRCA1 and BRCA2 associated breast tumors exhibit markedly different copy number aberrations when compared to each other as well as to sporadic tumors; and that gene expression profiling in BRCA1 and BRCA2 associated breast tumors reveals specific gene expression patterns. (Less)