AbstractsBiology & Animal Science

FPGA Hardware acceleration of co-occurring aberrations in aCGH data:

by M.R. Van der Leije

Institution: Delft University of Technology
Year: 2009
Keywords: FPGA; DNA
Record ID: 1250477
Full text PDF: http://resolver.tudelft.nl/uuid:76e3a56a-a8b2-478c-ae04-dba5c6a13a2e


Unbalanced transaction can lead to addition and deletions in genes, which can be an indication of tumor cells. This is measured with array Comparative Genomic Hybridization. To find co-occurring aberrations in DNA, an algorithm was designed. However the execution takes days to find these DNA aberrations. This thesis proposes a partial FPGA based design were the number of parallel computations can be increased. The FPGA communicates with a computer on a gigabit Ethernet, where on the FPGA a hardware based Ethernet controller is build. This design is scalable for FPGA’s, so its performance is linear to the size of the FPGA resources. On a XC4VFX12 device, a minimum speedup of a factor 3 and a maximum speedup of several hundreds is achieved.