High Performance Computing can help understand the secrets of the DNA

Description: Understanding the secrets of DNA is the key to the next generation of medical care involving extremely personalized treatment

The Use of High-Performance Computing in Understanding the Secrets of DNA

Introduction

High-performance computing (HPC) is the use of advanced teraflop computer systems, such as supercomputers or cluster of computers, to solve complicated and time consuming scientific research problems. Integrated circuits (ICs) such as field programmable gate arrays (FPGA) and high-speed microprocessors are the foundation of such hybrid computing platforms. Hybrid systems are not only faster than supercomputers or clustered computers but also flexible and cheaper.

Deoxyribonucleic acid (DNA) is a nucleic acid that contains genetic instructions for functioning, growth and reproduction of living organisms.DNA is composed of Adenine, Guanine, Cytosine and Thymine. These four nucleotide bases are commonly abbreviated as A, G, C and T. Understanding the secrets of DNA is very important as it is the key to the next generation of medical care involving extremely personalized treatment.

Technology and Applications

The use of HPC in the field of genetic engineering, forensics, bio-informatics and DNA nanotechnology is advancing drug discovery and personalized healthcare. Some of the technologies used are as follows:

  • Bio-IT equipment: Determine entire genome or genetic makeup of an individual by sequencing millions of DNA bases
  • Dye-terminator sequencing:Use of fluorescent dyes, each of which emits light at a different wavelength, to label the nucleotide bases and the sequence is read by using a laser beam.
  • FPGAs:Speed up parallel processing of algorithms exponentially for gene sequence search, detection and comparison and help pinpoint the origins of Alzheimer’s disease and cancer

Evolutionary, functional and structural relationships are explored by looking for similarities or mismatches in regions between two DNA sequences. Genomic analysis and sequencing in large clinical trials are more efficient than traditional drug discovery approaches. These studies help in drug discovery and subjects who will respond to the discovered drugs.

Consumer Genomics

HPC has strengthened consumer genomics in predictive medicine and made non-invasive and easy administration of genetic testing possible. Just send in a saliva sample and get back comprehensive web-based report on the subject’s predisposition to diseases like diabetes, cancer, heart diseases and more.

Pharmagenomics

Pharmagenomics deals with treatment of the patient based on his or her specific genetic makeup. It helps physicians to select optimal medicine for their patients especially for diseases such as asthma, cancer, diabetes, HIV and tuberculosis. HPC has reduced the cost of personal genomic sequencing and the costs are only going to drop further as more people starting sequencing.

 

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