A Steak in Genomics™

Larry Kuehn USDA-MARC When we go from less than a thousand animals to several thousands of animals, genomic predictions can explain about 50% of the genetic variance for important traits. Genomic prediction is working and providing tremendous benefits to seedstock and commercial producers. But, we still struggle with genomic predictions with very little data recording and genomic predictions that work well across breeds. Two methods are used to use genomics in national cattle evaluation. With the genomic pedigree method you track genetic effects more accurately than with pedigree data. With the second method you are relying on linkage on chromosomes between the DNA markers and the variants responsible for the differences (causal mutations). The linkage signal between DNA markers and causal variants breaks down over generations due to recombination (switching) between paternal and maternal chromosomes. Because this linkage breaks down over time is part of the reason genomic pr...

Angus Convention 2015 Richard Resnick CEO of GenomeQuest One can not impede scientific progress. - Mahmoud Ahmadinejad   Resnick gave a series of examples of how genomics is changing society. Resnick put a nice spin on the typical sequencing cost figure . He overlays Illumina's ( $ILMN ) stock price on top of the figure. He went on to explain that the only real differences between humans, cattle, corn, and other species is the proteins they make. The amino acids, the building block of proteins, are actually the same between species. Resnick used cystic fibrosis as an example of a disease in which genetics has been very important. One DNA variant that causes the disease is called ΔF508. When a person has this variant, the gene produces the protein, but a check and balance in the cell recognizes the protein as not correct and destroys it. A different variant, G551D, is not so severe that the protein is destroyed, but the protein does not function properly. A drug call...

And where are we going next? Data via  http://www.genome.gov/sequencingcosts/ . Code for generating the plot at  https://missouri.box.com/SequencingCost . This graph never ceases to amaze me. On the horizontal axis we have dates from September 2001 to July 2015. On the vertical axis we have the cost to sequence a million base pairs of DNA, with the axis having a logarithmic scale  (each tick mark is multiplied by 10, e.g. change from 10 to 100 to 1000). The blue line describes what is called Moore's Law  which describes the increase in purchasing power as computer costs come down. The rate of improvement in DNA sequencing easily outpaces the improvement in computing. Since September 2001, the price of DNA sequencing has dropped 6 orders of magnitude  from $5,292.39 to $0.015. From more than $5,000 to less than 2 cents!!! Same data as above by with the vertical cost axis  on a normal scale, not logarithmic. What caused the drop in sequencing f...

The American Angus Association® and Angus Genetics Inc. (AGI) will host the first-ever International Genomics Symposium as part of the 2015 Angus Means Business National Convention and Trade Show. The event takes place Nov. 3 in Overland Park, Kan., and will provide cattle producers with cutting-edge information about advancements in genomics technology – and how these advances impact their businesses. The symposium is sponsored by GeneSeek, a leading provider of comprehensive genomics solutions to the cattle industry, including the GeneSeek Genomic Profiler (GGP-HD). “We are excited about the symposium and what it will mean for the cattle business,” says Dan Moser, AGI president. “Genomics is rapidly reshaping the way we produce livestock, and providing producers with the best information available will not only help us improve quality and consistency, but also make our industry more competitive.” Genomics researcher and entrepreneur Richard Resnick (previously featured on this blog) ...

I talked about use of high-throughput DNA sequencing to improve fertility by removing DNA variants from a breed that cause embryonic losses during pregnancy. Here is a  link  (Managing Broken Genes in the Age of Genomics) to the PowerPoint presentation I gave. I discussed the development of a genomic EPD based on the number of embryonic lethal variants (broken genes) that an animal carries that causes losses of embryos during pregnancy. DNA Sequencing Costs, Data from the NHGRI Genome Sequencing Program (GSP) http://www.genome.gov/sequencingcosts/  The cost of DNA sequencing has rapidly dropped in the last 15 years. In 2001 it cost about $10,000 to sequence a million base pairs of DNA. In 2014 it costs under 10 cents to sequence a million base pairs. This rapid drop in the price of DNA sequencing has enabled researchers to tackle questions that we previously could not address. With this sequencing data we are identifying loss-of-function variants (broken genes) that...

MAGNUM - AMGV38 Picture from search.gelbvieh.org On January 14th, Dr. Jon Beever of the University of Illinois sent a letter to the Board of Directors of the American Gelbvieh Association informing them that his lab had resolved issues with odd results when testing fullblood Gelbvieh animals with the DNA test for Contractural Arachnodactyly (CA, “fawn calf”). One of the oldest fullblood Gelbvieh bulls, Magnum (AMGV38) tested as a carrier of the CA abnormality, and several other Gelbvieh animals with little Angus influence tested as either affected or carrier. Dr. Beever took several lines of action to evaluate what was producing the odd results and after DNA sequencing the region in the Gelbvieh animals found that the protein sequence was still functional in the Gelbvieh animals. But, the DNA base pair used in the diagnostic test was the same in affected Angus and normal Gelbvieh. Thus, the test was producing false positives in Gelbvieh animals. Dr. Beever originally designed...

Here is a link to my article in the BEEF Cow-Calf Weekly. I know there may be some questions (and disagreement) about my article. Please comment with questions or contact me by email. Luckily, we now have the tools to manage these broken genes.