bioRxivGenomicsPreprint
Haplotypes associated to gene expression in breast cancer: can they lead us to the susceptibility markers?
Hege Edvardsen, Bettina KulleiD, Anya Tsalenko, Grethe Irene Grenaker Alnæs, Fredrik Ekeberg Johansen, Espen EnerlyiD, Aditya Vailaya, Per Eystein LønningiD, Åslaug HellandiD, Ann‐Christine SyväneniD, Zohar Yakhini BiD, Anne‐Lise Børresen‐DaleiD, Arnoldo FrigessiiD, Vessela Nedelcheva KristenseniD
Abstract
We have undertaken a systematic haplotype analysis of the positional type of biclusters analysing samples collected from 164 breast cancer patients and 86 women with no known history of breast cancer. We present here the haplotypes and LD patterns in more than 80 genes distributed across all chromosomes and how they differ between cases and controls. We aim by this to 1) identify genes with different haplotype distribution or LD patterns between breast cancer patients and controls and 2) to evaluate the intratumoral mRNA expression patterns in breast cancer associated particularly to the cancer susceptibility haplotypes. A significant difference in haplotype distribution between cases and controls was observed for a total of 35 genes including ABCC1, AKT2, NFKB1, TGFBR2 and XRCC4. In addition we see a negative correlation between LD patterns in cases and controls for neighboring markers in 8 genes such as CDKN1A, EPHX1 and XRCC1.
- organism: human
- assay: GWAS summary statistics
- research focus: gene regulatory network inference
- research focus: differential expression
- research focus: eQTL / molecular QTL mapping
- approach: statistical model
- Citations
- 2
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