Category: Biotech

PGD:2010s::IVF:1980s

By Razib Khan | January 7, 2012 10:59 pm

Get ready for PGD, the acronym for preimplantation genetic diagnosis. We don’t really talk about “test tube babies” anymore. It’s “IVF,” and as American as apple pie (OK, perhaps as Israeli as falafel). Here’s the Ngrams result:

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Genzyme Oncology question

By Razib Khan | July 14, 2011 11:32 pm

If anyone works at, or knows someone who works at, Genzyme Oncology in San Antonio, can you contact me? I have a few questions. Any of these methods will work:

CATEGORIZED UNDER: Biotech
MORE ABOUT: Genzyme Oncology

Ban them! (including ancestry analysis)

By Razib Khan | May 31, 2011 10:05 am

Direct-to-Consumer Genetic Tests Neither Accurate in Their Predictions nor Beneficial to Individuals, Study Suggests:

Direct-to-consumer (DTC) genetic tests give inaccurate predictions of disease risks and many European geneticists believe that some of them should be banned, the annual conference of the European Society of Human Genetics heard May 31….

Here’s the abstract for the talk which argued that DTC companies don’t give the best disease risk estimates:

Objective: Direct-to-consumer (DTC) companies predict risks of common complex diseases on the basis of genetic markers. Given the low number of markers involved and their small effect sizes, it is unclear whether high-risk groups can be identified. We investigated the risk distributions generated by two DTC companies for 8 diseases.

Methods: We simulated genotype data for 100,000 individuals based on published genotype frequencies. Predicted risks were obtained using the formulas and risk data provided by the companies.

Results: The table presents observed and trimmed ranges of predicted risks. The two companies used different formulas to calculate risks. One company predicted risks higher than 100% for 5 out of 8 diseases, which for AMD concerned 1 in 200 individuals. Observed ranges were smaller for the second company, except for Type 1 Diabetes. Predicted risks higher than 50% were frequently observed for company 1, but were exceptions for company 2. When predicted risks of company 1 were calculated using the formulas of company 2, observed ranges were substantially smaller.

Since I don’t put much stock in the small effect disease risk predictions currently, I am not surprised. But I’d be curious to look at the guts of their results. This was presented at conference, so some caution has to enter into the picture. The main issue I’d always want to emphasize with critiques of the lack of efficacy of DTC is that they need to be evaluated against the baseline of the limits to the efficacy of medical professionals and medicine in general. Genomics and DNA doesn’t make something magical, whether for good or ill.

The second presentation covered in the ScienceDaily release is kind of more disturbing to me. Here’s the abstract:

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Biology to the masses

By Razib Khan | May 25, 2011 9:17 am

Josh Roseneau, when he’s taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice:

On DNA Day, 23 and Me had a sale on their personal genomics service. They’d do their standard scan of your genome for free, as long as you paid for a year’s worth of their online subscription service.

For the price (nearly free up front, and a modest cost for the online community provided), my wife and I jumped on the deal. Since I got the results back two weeks ago, I’ve been exploring not only the services and information provided by 23 and Me, but the various other tools that individuals have started producing to help analyze and investigate this insight into my ubiquitous but invisible DNA.

My genome, for instance, revealed a genetic predisposition towards late-onset Alzheimers. The odds of getting Alzheimers are still quite small, but elevated because of this particular mutation to the APOE4 gene. This wasn’t a total surprise, given my family history, and as a healthy, young guy with a background in biology and biostatistics, it wasn’t hard for me to put that information into a context and move on. Down the road, I’ll probably keep an eye out for new research on Alzheimers medicines and look into tools for early detection, but I’m not going to kill myself if I forget my keys. (Thanks to the federal Genetic Information Nondiscrimination Act and the Affordable Care Act’s prohibition on “pre-existing conditions” – not to mention the inherent uncertainties in translating this genetic result to a specific outcome – I’m not especially worried about discussing that result in public)

We need to demystify DNA. It’s pretty obvious to me that people perceive genetics to be in the domain of magic, when in reality it manifests itself in the banal realities of correlations within the family, which we’re intuitively aware of. But Josh’s post is more than just personal, he reviews the book Biopunk: DIY Scientists Hack the Software of Life:

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CATEGORIZED UNDER: Biology, Biotech, Personal Genomics
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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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