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DNA sequencing for the masses
How far are we from Gattaca?
Etech New fathers always think their newborn baby daughters are beautiful, and Hugh Reinhoff was no exception. Sure, she had giant feet, a cleft uvula, and contractures in some of her fingers. But those thoughts, along with a suspicion that her eyes were oddly widely spaced and her chin was a bit recessive, were easily forgotten in the excitement.
To a geneticist those apparently minor physical characteristics are extremely significant. Over the next year and a half, Reinhoff's bright, happy daughter, now four, stayed very small, and her muscles were weak.
What can a doting father who happens to be a doctor trained as a clinical geneticist do? Even a few years ago not much, after specialists confessed ignorance and lumped her in with a small group of others with some of the same unexplained conditions. These days... Reinhoff spent a year forming a theory he wanted to test by getting a piece of her DNA sequenced.
"I couldn't get anybody to do it," he said at etech on Tuesday, a problem he attributes to liability concerns. He bought software and DNA bits known as primers and eventually, by sending out small pieces of his daughter's DNA serially, he got academic labs to decode the base sequences. Those he compared against the base reference sequences from the human genome database in Heidelberg, and eventually found a mutation. Through Pubmed, he found all the known experts on that particular mutation and phoned most of them.
"Half of them were extremely helpful," he said. His daughter now takes a common drug that will at worst protect against the vascular disease that seems to be associated with her particular mutation and at best help her gain weight and muscle mass. She has, he says, put on weight. "I'm not sure if that's why. We will have to see."
As Pauline Ng, who assembled the first genome sequence of a human at the Craig Venter Institute, said Wednesday, Moore's law is at work on DNA sequencing. When the genomes of Venter and DNA discoverer James Watson were sequenced, it cost $1m each. This year, she said, it would cost $100,000, and the size of the computers has shrunk from room to desk.
Personalised genomics companies aimed at researchers are beginning to offer $1,000 to $3,000 services for less than a quarter per cent of the genome.
How far are we from Gattaca?
The question is particularly apt because law enforcement in both the US and the UK has been assembling huge databases of DNA samples. But, says Ng, despite all the superfast, super-accurate technology on TV shows, real-life DNA analysis can be fuzzy, smudged, and inaccurate. There may be laboratory failures, introduced bias, and errors.
In one recent case, she said, Burlington Northern Santa Fe railroad, in trying to limit its liability for a cluster of cases of carpal tunnel syndrome, asked for an employee's DNA to test for a rare disease that might be an alternative cause. (The company, taken to court, eventually withdrew the request.)
For the moment, however, DIY personal DNA sequencing remains, in Reinhoff's words, "something only a parent would do". ®