· · · Repository hosted by TU Delft Library

Hybridization of nucleic acids to microarrays is a crucial step forseveral biological and biomedical applications. However, the poor efficiency and resulting long incubation times are major drawbacks. Inaddition to diffusion limitation, back-hybridization to complementary strands in solution is shown to be an important cause of this lowefficiency. To increase the efficiency of micro-array hybridization, repeated denaturing in an integrated device has been investigated.The sample solution is circulated from the micro-array chamber overa denaturing zone and back in a closed loop. In addition to the improved binding rate due to flow, repeated denaturing increases the total amount of molecules bound significantly. Our approach with cyclic repeated denaturing improves the efficiency of hybridization by upto an order of magnitude over a broad range of concentrations studied (1 pM to100 nM).

The use of a priori knowledge in aligning targeted sequencing data is investigated using computational experiments. With conventional aligners such as Bowtie, BWA or MAQ, alignment is performed against the whole genome. Using an alignment method in which the genomic position information from the target capture is incorporated, alignment can be done to just the target region. Investigating the effect of realistic target size, read length, read redundancy, the amount of off-target reads and sequencing error rate, improvements of up to a factor of 8 +/- 0.3 in alignment speed are found using an implementation of the Needleman-Wunsch algorithm which makes use of direct stringcomparison. This results in a total alignment time in target sequencing of around 1 min.