DNA Day experts answer your questions about genome sequencing

CurioCity
20 April 2012

Above: Image © RKaulitzki, iStockphoto.com

How much is the Human Genome microchip decoder used by doctors at this point? How accurate is the microchip that can decode an individual's genome?

I am not sure I know what you mean by microchip decoder? But right now we use Next generation DNA sequencing method to determine an individual's genome. This is very accurate through most of the entire genome, although there are repetitive regions and certain types of variation that are harder to determine using these methods. In fact I have had my whole genome sequenced!

- Answer provided by Dr. Dennis McCormac

As the technology becomes more affordable, should all individuals have their genome sequenced? Who should have access to this information?

Genome sequencing as part of routine medical care may happen one day. Already, there is recognition that doing a full sequence once becomes a better use of resources than doing partial sequencing many times over. But, as indicated in a previous reply, currently this represents a lot more information than we actually know how to interpret and how to use in medical care. If this becomes part of medical care, I can only guess that there would be high security measures for this part of a medical record.

- Answer provided by Karine Morin

The Human Genome Project took almost a decade, but these days we're seeing published genomes of new species almost every month . . . how long does it take to decode a genome these days?

This depends upon the size of the genome and the sequencing technology being used to decode it. Mitochondrial genomes are quite small (~16K bp) and can be sequenced using Sanger sequencing in a few days. Similarly microbial genomes are quite small and can be sequenced in a few days using next generation pyrosequencing technology. However, large genomes take longer, often much longer, because of the sheer number of bases to be read and the time required to assemble them.

- Answer provided by Dr. Robert Hanner

When do you think that personalized medicine - based on personal genome sequencing - will become a commercial, widespread reality?

Within a few years, if not sooner. The limiting factor these days is not our ability to sequence DNA, but rather our ability to interpret the results. There will probably be a first tier of services that will report on clear cut genetic risk factors (BRCA) and disease carrier status (e.g,. Cystic Fibrosis). Patient education on what relative risk means will be an important part of the equation. In the case of cancer, there are already commercial companies offering targeted sequencing where it will inform treatment, such as Foundation Medicine. Within the evolution of biotechnology, gene patents have become a topic of debate. What are the advantages and disadvantages of patenting genes, and do you believe genes, especially those naturally occurring in the human genome, should be allowed to be patented? Technically, natural occurring phenomena cannot be patented, and the Supreme Court in the United States has essentially narrowly determined that only specific lab methods for isolating and characterizing genes are covered by patents. In Canada, the law is different, and the BRCA (breast cancer) patents are not honoured.

- Answer provided by Dr. Paul Gordon

The whole-genome shotgun method has proven to be very effective in the past but the drawback is that it is difficult for computerized analysis to detect where the genome has repeating sections. Are there any efforts being made to overcome this drawback?

Repeated DNA sections are indeed hard to decipher properly. What you need ideally are individual sequencing "reads" that span the entire repetitive region and enough unique flanking sequence on both ends to place it unambiguously in the genome. There is a trend towards shotgun (a.k.a. random) sequencing new genomes using a combination of different technologies: very high throughput short read sequencing for coverage (e.g. Illumina tech), plus some very long lower throughput methods to scaffold and span repeats (e.g. PacBioRS tech). Emerging sequencing technologies like nanopores may provide a nice middle ground, but we'll have to wait and see if they live up to their promise.

- Answer provided by Dr. Paul Gordon

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