Clinical practitioners can now interactively produce and query a patient report for genetic tests spanning over 2000 inherited diseases from a single whole-genome sequence, using www.genetests.org (www.ncbi.nlm.nih.gov/sites/GeneTests/?db=GeneTests) as a valid guide. GenomeQuest (www.genomequest.com) , a company based near Boston, MA, which serves as the data management provider for most of the U.S. pharmaceutical industry, has a sequence database engine that is purpose-built for storing, managing, and analyzing next generation sequence data at whole- and multi-genome scale.
The company claims that it can span from sequencing and analysis of a patient’s entire genome to clinical diagnostic test results that can be stored in the Electronic Health Record. The entire genome, or whole exome arrays, can be stored and subsequently analyzed as new genome-disease associations are discovered over time.
The amount of human genomic data is accumulating at an unprecedented rate (see Figure #1 below). For example, the BGI at Shenzhen, China has recently installed over one exabyte (one billion gigabytes) of storage to house DNA sequencing data. The institute will use the storage infrastructure to unify its 250 next generation sequencers onto a single shared pool of storage with a single file system. The BGI’s computing platform is greater than 1000 Teraflops, or one quadrillion floating point operations per second. BGI, as it is now known, is the world’s largest genome sequencing center. Its sequencing output is more than 15,000 human genomes per year. Its key accomplishments have included the first de novo sequencing and assembly of various mammalian species including the human genome with short-read sequencing (so-called “next generation sequencing”) and the first sequencing of an ancient human genome. It has received over $1.5 B in collaborative U.S. funds from the China Bank.
So what does this mean for the hospital CIO? I would suggest that we be prepared for data management and storage adequate for whole genome analysis of patients. Even if the administrators and clinicians don’t recognize the value of these data, you know that patients will be pounding on the door for implementation of this capability.
Also see my previous post: https://healthsystemcio.com/2010/03/20/future-of-the-ehr-exponential-increase-in-storage-expected/