Who wrote this?

“Illumina has a SNP chip with 50,000 markers that now costs
about $80 to run.  Public domain software platforms now exist where we
can deposit the markers and training data to increase the accuracy of
our predictions.”

A cattleman that’s who.  Someone I’ve known since he was 6.  His father, also a rancher was and is a friend.  His classmates at Harvard called him a cow farmer.  They were rather surprised when the profs picked him as their assistant, telling him as a Montanan, he was there for the bottom of the curve.  All that was 25 years ago but bicoastal arrogance hasn’t changed about flyover country as far as I can tell.

The full quote is “We are now moving into genomics to assist our population selection
strategies.  Illumina has a SNP chip with 50,000 markers that now costs
about $80 to run.  Public domain software platforms now exist where we
can deposit the markers and training data to increase the accuracy of
our predictions.  This is quite advanced in the dairy industry, but less
so in our beef sector.  ”

He knows what an SNP is.  Do you?  If not see — https://luysii.wordpress.com/2011/07/17/weve-found-the-mutation-causing-your-disease-not-so-fast-says-this-paper/

The family enterprise was always way ahead of the curve, doing in vitro fertilization and embryo transplants in the 70s.  I found it amusing that both of us have spent a significant amount of our lives trying to improve muscle (I founded and ran the local muscular dystrophy clinical for 15 years out there).  So I wrote him, after receiving a catalog about his latest bull sale,  and asked if he know about myostatin — which is mutated in two breeds of cattle (Piedmontese and Belgian Blue) which have lots of muscle.  He knew all about it.

“We raised and marketed a brand of natural, hormone free, Piedmontese
beef from 1999 through 2003.  That is what broke our company in Montana.
The product was good, but managing the supply chain was nearly
impossible.  Two owners later, the company is still going and seems
profitable at this stage.”

Fascinating that he’s using genomics — the problem is that it’s going to be very hard to find out which of the 50,000 SNPs is important to what he’s interested in (ability to gain muscle weight with minimal feed and to gain weight quickly etc. etc.  As most of you know, even when a human trait is known to have a significant hereditary component (e.g. height) and polygenic in nature, genome wide association studies (GWAS to you) explain very little of the heritability.  [ Nature vol. 465 p. 998 ’10 ] The 50 loci found in GWAS studies for height explain only 5% of the heritability of height (which has an estimated heritability of 80%.

Perhaps the cattlemen will do better than the human geneticists have done so far.

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