Crunching the numbers to boost odds against cancer

Frankfurt: Software engineers are moving to the fore in the war on cancer, designing programs that sift genetic sequencing data at lightning speed and minimal cost to identify patterns in s that could lead to the next medical breakthrough.


A dispensing chemist prepares drugs for a chemotherapy treatment in a sterile room at Antoine-Lacassagne Cancer Centre ...
A dispensing chemist prepares drugs for a chemotherapy treatment in a sterile room at Antoine-Lacassagne Cancer Centre in Nice. 




Oncology is the largest area of therapy in the global drugs market with market researcher IMS predicting it will increase to $US83-$US88 billion by 2016 from $US62 billion in 2011. Computational genomics - using computers to decipher a person's genetic instructions and the mutations in cancerous cells - is emerging as the driver of this growth.


Life Technologies and Illumina are among firms developing equipment that can extract a person's entire genetic code - their genome - from a cell sample.

The newest machines are about the size of an office printer and can sequence a genome in a day, compared with six to eight weeks a few years ago. They can read the 3.2 billion chemical "bases" that make up the human genetic code for $US1000, compared with $US100,000 dollars in 2008.


"Many labs can now generate the data but fewer people or labs have the expertise and infrastructure to analyse it - this is becoming the bottleneck," said Gad Getz, who heads the Cancer Genome Analysis group at the Broad Institute in Boston, jointly run by MIT and Harvard.


He and his team of 30 are trying to establish recurring patterns in the mutations and how they are linked to tumour growth. They are using some 1200 processing units, each with 4-8 gigabytes of random access memory - about the computing power that comes with most desktop PCs.

Harvesting knowledge

Eli Lilly CEO John Lechleiter sees potential for progress.


Approved drugs that take genetic information into account include Amgen's Vectibix and AstraZeneca's Iressa. But both these drugs derive from a single mutation. Sequencing has laid bare many more mutant genes — often hundreds in any given tumour — nd highlighted the need for a subtler approach to cancer treatment.



Roberts said the project, which uses processing power equivalent to hundreds of high-end desktop PCs, was self contained but there were plans to draw in external data. This would require advances in cloud computing — using software and computing power from remote data centres — but Roberts said the technology would soon be available.


Opportunities in clouds


Amazon, with its cloud computing unit AWS, said it is benefiting as life science researchers rethink how data is stored, analysed and shared. "We are happy with the growth we are seeing," a spokesman said, declining to provide figures.



The world's largest business software company SAP has teamed up with German genetic testing specialist Qiagen. They are modifying SAP database software so that certain cancer diagnostic tests, which now keep a network of supercomputers busy for days, can be run on a desktop PC within hours.


Hans Lehrach at the Max Planck Institute for Molecular Genetics in Berlin says every single tumour should be seen as an "orphan disease", using a term for rare illnesses that typically prompt drug regulators to make drug approval easier.

He has designed software he describes as a virtual patient. It suggests a drug or a mix of drugs based on each tumour's genetic fingerprint. A single case can take several days to be processed.



