Getting personal with genomics

DNA chips

Most people are familiar with Moore’s law, which holds that the number of transistors that can be placed on a 1-inch diameter silicon square doubles approximately every 24 months. This is usually interpreted to mean that processor speed will double every 24 months.

People who work in genomics would likely consider that rate of change to be tortoise-like.

Kenneth Beckman, director of the University of Minnesota’s Biomedical Genomics Center, talks about how genomics research across a wide range of disciplines will impact each one of us in a very personal way.

Background and basics

DNA (deoxyribonucleic acid) is the chemical compound that contains the genetic instructions needed to develop and direct the activities of every organism. A genome is an organism’s complete set of DNA. Genomics research uses the genetic information in DNA to create a better understanding of virtually all organisms on the planet.

“The speed and scale of sequencing resembles what goes on in any factory.”

The technologies used for characterizing genomes have advanced at a very rapid pace. Just a decade ago, the first sequencing of a human genome cost some $3 billion dollars to complete. Today the cost is about $4,000.

Within the next year or two, new technologies will reduce the cost to less than $1,000, and it’s possible that within five years, the cost will be on the order of $100 – $200, about the same as a standard cholesterol or urine test.

Genomics instrumentation, however, has become very expensive: sequencers can cost up to $700,000 per machine and require a high level of expertise to calibrate and operate properly. But because the performance of each new generation of sequencer is increasing exponentially, the cost per unit of data is dropping dramatically.

“Increasing industrialization has been a trend since the time the genome project started,” says Beckman. “The speed and scale of sequencing, and the resulting reduction in its cost, resembles what goes on in any factory when it increases production capacity and scale.”

Genomics at the U

Some 500 U of M researchers rely on the instrumentation and expertise provided by the Biomedical Genomics Center, along with an additional 200-plus researchers from other institutions.

“Planning a genomics project typically involves a lot of different steps: making sure the sample material is OK, understanding what technology to use, having the expertise to carry out the work,” says Beckman. “We provide a workflow that extends all the way up to bioinformatics.”

The university recently made a substantial investment in the center that will enable it to continue offering the high-level equipment and expertise that researchers require, and to develop new projects.

Genomics research at the U of M covers a wide range of disciplines. A few examples:

The genome of the domesticated turkey was sequenced by an international consortium of researchers that included veterinary bioscientist Kent Reed.

Microbiologist Michael Sadowsky leads the development of the Minnesota Mississippi Genome Project (M3P), which aims to create a DNA database of microorganisms at the headwaters of the Mississippi and to evaluate human impact, notably from agriculture, at points downstream.

A large number of researchers at the Masonic Cancer Center and in departments across the university are investigating how genomics can inform the treatment of various forms of cancer, including breast, prostate and brain tumors.

“The most near-to-market application of genomics is not sequencing an individual and tailoring medications to their germline genome, but assays where you sequence someone’s tumor, for example, and identify the drug that works for that specific tumor,” says Beckman.

“In the future, oncologists may no longer use a label such as ‘bladder tumor,’ for example, as the main way to characterize and treat such a cancer. Instead, they may focus on the specific genomic characteristics of the tumor itself, and base treatment options on those specifics. So genomics may provide more complete, unbiased data than the current approaches do.”

Yes, there’s an app for that

Applications, not speed, are what’s next for genomics.

“Whoever can take the massive amounts of data that are generated in a typical genomics research project, and quickly put together an informatic workflow for analysis, will drive the next wave of discoveries,” says Beckman. “It’s also critical for scientists to make sure that they are early adopters of new techniques.”

According to Beckman, the biggest benefits will come to researchers who develop and use next-generation sequencing applications before they’re widely commercialized.

“That’s where a university like the U wants to be: on the front end of the development of new applications.”

For that reason there will be an ever-increasing need for high-level informatics expertise. Beckman encourages students who have an aptitude for math and science to explore informatics as a potential career.

“The generation of data is becoming commoditized. The important area now is dealing with the data. While the terms ‘big data’ and ‘big science’ may be clichés, they accurately describe the future of genomics research.”

Over the next decade, patients will increasingly have access to their own medical information, says Beckman, and genomic data — from sequencing and other tools — will be part of that.

In fact, a company called Illumina has already developed an iPad app called MyGenome. While the app is currently educational in nature, future versions will allow users to explore their own genome. The company intends to deliver genetic data first to the ordering physician via the app, then provide direct access to the consumer after the doctor has discussed the result with the consumer.

“The potential for social media applications will be phenomenal,” says Beckman. “People who share genetic diagnoses, for example, will be able to connect via social media and share information about their experience, current treatments, and so forth. Genomics is quickly becoming a consumer product.”

Watch and learn more about the center

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