Bioinformatic and epigenomic characterization of breast cancer
Principal investigator; Ringnér, Markus, , PhD
Research area/areas: Cancer and Oncology
Breast cancer is a heterogeneous disease. At least five different molecular subtypes have been described based on genome-wide gene expression measurements of breast tumors. These subtypes are suggested to originate from different normal precursor cells and follow different progression pathways. Better characterization of the subtypes is required for improved biological understanding of breast cancer and in a longer perspective to benefit clinical management of patients.
Our research is centered on characterizing breast cancer by utilizing genome-wide measurements of expression levels, DNA copy numbers, methylation status, and sequences of genes, and to integrate these different layers of information using computational methods. We are also aiming to begin to functionally validate findings using primarily breast cancer cell lines. Specific projects we are working on include:
- Comprehensive identification of transcriptional programs in breast cancer.
- Characterization of molecular subtypes of breast cancer at the epigenetic level.
- Development of analysis methods to be able to utilize new genomic technologies for measurements of heterogeneous tumor samples.
Our research is carried out in an environment defined by daily interactions with many research groups within the Canceromics Branch (Dept. Oncology, Clinical Sciences) and we are involved in a large number of collaborative projects.
A better characterization of breast cancer subtypes at the molecular level has the potential to influence cancer treatment selection and suggest new therapeutics.
Link to project homepage: http://www.med.lu.se/english/klinvetlund/canceromics/research/computational_oncology
5 recent original publications
Ringnér Markus, Fredlund Erik, Häkkinen PhD Jari, Borg Åke, Staaf Johan
GOBO: Gene Expression-Based Outcome for Breast Cancer Online.
PloS One. 2011; 6: e17911
Holm Karolina, Hegardt PhD Cecilia, Staaf Johan, Vallon-Christersson Johan, Jönsson Göran B, Olsson Håkan, Borg Åke, Ringnér Markus
Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns
Breast Cancer Research. 2010; 12: R36
Staaf Johan, Vallon-Christersson Johan, Lindgren David, Juliusson Gunnar, Rosenquist Richard, Höglund Mattias, Borg Åke, Ringnér Markus
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.
BMC Bioinformatics. 2008; 9: 409
Staaf Johan, Lindgren David, Vallon-Christersson Johan, Isaksson Anders, Goransson Hanna, Juliusson Gunnar, Rosenquist Richard, Höglund Mattias, Borg Åke, Ringnér Markus
Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
Genome Biology. 2008; 9: R136
What is principal component analysis?
Nature Biotechnology. 2008; 26: 303-304
Further publications here (new window)
|Total financing:||MSEK||Gov grant for clinical research ("ALF"):||MSEK|
|Total external financing:||MSEK||Natl and intl prioritized grants:||MSEK|