For years, medical researchers have been talking about the day when babies will have their whole genomes sequenced at birth, the day when genomic analysis will allow every patient to be treated not just based on her condition but on which treatment is the best match for her genetic quirks. There will be a day, they say, when we will all carry our genomes around on a thumb drive. But the hurdles, fiscal and otherwise, have proven difficult to overcome.
The DNA of one set of human chromosomes contains 3 billion base pairs—most cells are diploid and have two sets of chromosomes, one from each parent. Sequencing these six billion base pairs, one pair at a time, is unquestionably faster and cheaper than it once was: Since its less-than-humble beginnings almost 15 years ago, human genome sequencing has dropped from $100 million to around $1000. Instead of years, it can now be completed in a day or two.
Yet while that’s incredible progress, it’s not quite enough. Not only is it still too pricey for everyday use, but once that genome has been sequenced it also has to be mapped and analyzed—the process in which the sequenced base pairs are assigned to the correct chromosome and assessed for mutations, something that can take a couple of days or more. What to do with the resulting data is another problem: The genome and its resulting analysis typically occupy about 400GB. (For reference, the 2013 laptop I’m using to write this post has a storage capacity of 250GB—my genome wouldn’t come close to fitting on it.) Securely storing data from 500 or 5000 patients—at about $1 per gigabyte—typically costs hundreds of thousands of dollars per year.
In many areas of life, tall people seem to get all the benefits. On average, they earn more money. They are more successful at work. Taller people are just more, er, highly regarded than their shorter counterparts.
But research is showing that short people might win out in one big way: they might be less prone to cancer, and even have longer lives, than tall people. Although the jury is still out on how much height affects longevity, it shows no signs of stopping our cultural preference for taller people.
The relationship between height and cancer risk is not especially new—scientists had proposed a link between height and breast cancer in women as early as 1975. Many studies, however, have focused specifically on breast cancer. Other studies have looked at how height affects cancer risk at numerous sites, but they have failed to adequately control for variables that could be affected by height, notes epidemiologist Geoffrey Kabat at the Albert Einstein College of Medicine in the Bronx.
Measuring the link between height and health variables, Kabat says, is much more complicated than determining someone’s height and seeing if they develop a particular disease. “You really want to make very sure that you have excluded the possibility that any association you find between height and cancer is not due to the interference of some sort of other factor,” Kabat said.
For one, taller people tend to weigh more than shorter people, even if their BMI isn’t any higher. For another, poor nutrition and stress can stunt height growth, and higher calorie diets have been associated with increased height. And that doesn’t even begin to take into account the psychosocial variables like increased income, education, and socioeconomic status.
By Eliza Strickland
What can you learn from getting your genome sequenced? If you’re a relatively healthy person like me, the answer is, not much… at least not yet.
I embarked on a mission to get myself sequenced for my recent article “The Gene Machine and Me.” The article focused on the sequencing technology that will soon enable a full scan of a human genome for $1000, and to make the story come alive, I decided to go through the process myself. I got my DNA run through the hottest new sequencing machine, the Ion Proton, and had it analyzed by some of the top experts on genome sequencing, a team at Houston’s Baylor College of Medicine.
The Baylor team has been intimately involved in many of the most important advances of genome sequencing over the last decade. And their accomplishments reveal both the astoundingly rapid progress of the technology, and how far we have yet to go. Here’s a synopsis: the story of five genomes.
By now you may have heard about Oxford Nanopore’s new whole-genome sequencing technology, which has the promise of taking the enterprise of sequencing an individual’s genome out of the basic science laboratory, and out to the consumer mass market. From what I gather the hype is not just vaporware; it’s a foretaste of what’s to come. But at the end of the day, this particular device is not the important point in any case. Do you know which firm popularized television? Probably not. When technology goes mainstream, it ceases to be buzzworthy. Rather, it becomes seamlessly integrated into our lives and disappears into the fabric of our daily background humdrum. The banality of what was innovation is a testament to its success. We’re on the cusp of the age when genomics becomes banal, and cutting-edge science becomes everyday utility.
Granted, the short-term impact of mass personal genomics is still going to be exceedingly technical. Scientific genealogy nuts will purchase the latest software, and argue over the esoteric aspects of “coverage,” (the redundancy of the sequence data, which correlates with accuracy) and the necessity of supplementing the genome with the epigenome. Physicians and other health professionals will add genomic information to the arsenal of their diagnostic toolkit, and an alphabet soup of new genome-related terms will wash over you as you visit a doctor’s office. Your genome is not you, but it certainly informs who you are. Your individual genome will become ever more important to your health care.