Chromatin conformation capture strategies in molecular diagnostics

TY - THES

T1 - Chromatin conformation capture strategies in molecular diagnostics

AU - de Vree, Pauline J.P.

PY - 2015/7/9

Y1 - 2015/7/9

N2 - In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or chromosomal rearrangements as a cause for aberrant expression of copy number neutral genes in a cohort of triple-negative breast cancer. The rationale behind the approach was that detection of recurrent rearrangements in triplenegative breast cancer could provide unique therapeutical targets for treatment of this particular type of aggressive breast cancer. While the chromatin conformation capture technologies only confine to analysis of partial sequences of restriction fragments and thereby cannot be used to identify variants other than large chromosomal rearrangements, TLA provides the possibility to delineate the complete sequence and characterize structural variants as well as other genetic variants of genes or regions of interest. The methodology and exciting applications are described in chapter 3. In chapter 4, I applied TLA to a series of blood samples obtained from Hereditary Hemorrhagic-Telangiectasia (HHT) patients, also known as Rendu-Oslo-Weber (ROW) patients. HHT has a well characterized phenotype and in ~95% of the patients a genetic mutation is found in one of the three HHT-associated genes. The remaining 5% are thought to either carry mutations in a yet to be identified fourth HHT gene or they may have previously unnoticed structural rearrangements in or near one of the three established HHT genes. Since TLA can identify such rearrangements, I applied TLA to blood samples from patients that had been proven negative on genetic mutations, but were positively diagnosed by experts in the field for the HHT phenotype. In the general discussion I will discuss the potential of using chromatin conformation capture technologies in genetical diagnostics and clinical research.

AB - In this thesis I have explored the clinical potential of the 4C-technology and worked on development of a novel chromatin conformation capture based technology, called TLA. In chapter 2 I describe how the 4C-technology can be applied as a targeted strategy to identify putative fusion-genes or chromosomal rearrangements as a cause for aberrant expression of copy number neutral genes in a cohort of triple-negative breast cancer. The rationale behind the approach was that detection of recurrent rearrangements in triplenegative breast cancer could provide unique therapeutical targets for treatment of this particular type of aggressive breast cancer. While the chromatin conformation capture technologies only confine to analysis of partial sequences of restriction fragments and thereby cannot be used to identify variants other than large chromosomal rearrangements, TLA provides the possibility to delineate the complete sequence and characterize structural variants as well as other genetic variants of genes or regions of interest. The methodology and exciting applications are described in chapter 3. In chapter 4, I applied TLA to a series of blood samples obtained from Hereditary Hemorrhagic-Telangiectasia (HHT) patients, also known as Rendu-Oslo-Weber (ROW) patients. HHT has a well characterized phenotype and in ~95% of the patients a genetic mutation is found in one of the three HHT-associated genes. The remaining 5% are thought to either carry mutations in a yet to be identified fourth HHT gene or they may have previously unnoticed structural rearrangements in or near one of the three established HHT genes. Since TLA can identify such rearrangements, I applied TLA to blood samples from patients that had been proven negative on genetic mutations, but were positively diagnosed by experts in the field for the HHT phenotype. In the general discussion I will discuss the potential of using chromatin conformation capture technologies in genetical diagnostics and clinical research.

M3 - PhD thesis

SN - 978-90-393-6367-6

PB - Utrecht University

ER -