Flatley's Law: The Company Speeding A Genetic Revolution | Hacker News Reader

Flatley's Law: The Company Speeding A Genetic Revolution

forbes.com

30 pointsNnamdiJr7 comments

Every time I see articles like this, it reminds me how much the FDA's poor treatment of the genetic testing market infuriates me. What the FDA has done to 23andMe is disgusting (an Illumina customer).

Why can't I spend $99 and find out if I have a prominent heart disease marker, that killed both my father and grandfather by 55? Because the healthcare market is regulated by the government for the benefit of various cartels. They want me to spend thousands of dollars and be forced to go through layers of doctors to get the same results instead.

You still can! You just can't ask them to interpret the results for you. 23andMe will still give you access to your raw genetic variant data, they just won't tell you what it "means", simply because what they say might be incorrect. Genetic data interpretation is still quite hard to reproduce, and is very expensive to do well... which is why the FDA has been slow to regulate it.

The datasets used by 23andMe to interpret your genetic variants are the same datasets that you can get access to for free! If you know how to program, then you can use public datasets from the NCBI (http://www.ncbi.nlm.nih.gov/) or SolveBio (my startup, http://solve.bio) to compare your raw data to the clinical reference information you're interested in.

I guess you missed where people were getting different "interpretations" from different companies.

People also get different "interpretations" from different doctors.

I'd make two observations:

1) Illumina/Solexa's breakthrough was to convert sequencing into a problem limited by computing resources (reassembling the jigsaw), so they were able to leverage improvements in semiconductor processing.

2) This quote grabbed me:

"But Flatley is confident that Illumina’s footprint, which includes not just machines but also the software to handle genomic data, will make the company hard to unseat."

A call to arms for the Free Software movement?

As for your first point, shotgun sequencing was not invented by Illumina. Shotgun sequencing, or sequencing many small fragments and then computationally reconstructing a larger contig, was first done in 1979, and later used by many groups (most famously by Celera Genomics in their quest to beat the human genome project). Shotgun sequencing can be done using any short sequencing reads, so this is neither a breakthrough nor even an advantage for Illumina.

Illumina's chemistry was better than the others, and they marketed their advantages better. The Illumina machine produced longer reads than SOLiD (Life Technologies), and produced more reads than 454 (Roche). They produced reliable instruments that were relatively easier to use than the others also, which made them favorites for core facilities.

> A call to arms for the Free Software movement?

No chance, these algorithms are too dependent on very expensive hardware that sole coders can't afford.

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