Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details concerning how things were actually done. This is really a story that cannot be overemphasized by simply telling it again and again. 

By making inquiries with local surplus brokers, Rienhoff discovered he could buy a secondhand PCR machine for less than a MacBook. He ended up purchasing a full working model for just $750.
Obtaining additional supplies, like the PCR reagents, for his experiment was tougher. Some chemical companies didn’t want to ship to a private address, so Rienhoff pretended his house was the headquarters of the fictional Institute for Future Study.

While Rienhoff could spring for his own PCR machine, a used gene sequencer (assuming he could find one) would cost around $100,000. So he found a university lab (which he declines to identify) that would sequence the genes he had amplified, for $3.50 per 50-microliter sample. In spring 2007, Rienhoff mailed in more than 200 samples.

Rienhoff compared Beatrice’s DNA with the information on Ensembl, looking for any base-pair variants that hadn’t been previously recorded on Ensembl. He was operating on the assumption that Beatrice’s genetic blip was completely unknown, which would explain why she’d been so hard to diagnose. The job was daunting: The printouts contained data for approximately 20,000 base pairs, and there was no feasible way to automate the hunt for variants. After putting in a full day of consulting and then getting the kids to bed, Rienhoff would retire to his attic and spend hours checking Beatrice’s adenines (A), thymines (T), guanines (G), and cytosines (C) against the Ensembl reference genome.

8 thoughts on “Practical DNA: Hugh Rienhoff’s got a story to tell

  1. This is one of the several Wired stories that I have sent to dozens of friends and colleagues. It really does give us a little glimpse of the future, and it brilliantly articulates my frustration with doctors paternalistic attitudes and their unwillingness to consider individualized treatments for rare illnesses.

    This part almost brought me to tears:

    Rienhoff bristled at Milewicz’s dismissive tone. “I remember thinking, ‘Who the fuck is this person?’ I have never been in a situation where it was so obvious that a doctor had contempt for the curiosity of her patients. It was striking how insensitive she was to their dilemma.”

    Such a prickly reaction is out of character for Rienhoff, a soft-spoken man who normally exudes an easy calm. But he has developed a cynical streak about doctors, especially those who are quick to dismiss inquisitive parents as nuisances. “Medicine in general is a slightly paternalistic activity,” he says. “You hear these stories about patients bringing in all sorts of information from the Internet and doctors being exasperated. And part of that is because there is so much they don’t know, and they’re supposed to be omniscient.”

  2. Soft-updates is an alternative to this scheme where the filesystem keeps a list of dependencies that must be satisfied before a change to the filesystem can be visible on disk. For example, you wouldn’t want to write a directory entry pointing at an inode until the inode was initialized on disk and marked allocated. Softdep handles this by rolling back changes to metadata that don’t yet have their dependencies satisfied when we try to write a block. In this way we can commit any completed ‘transactions’ while keeping the disk state consistent. Softdep also allows these dependencies to discover operations which cancel each other out and thus nothing makes it to disk. For example, let’s say you create a temporary file and then remove it after writing some blocks, which compilers often do, if it all happens within the interval of the syncer nothing will make it to disk.

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