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May 27, 2014

It’s in My Blood

We be of one blood, thou and I.

So says Mowgli, the boy raised by wolves in Rudyard Kipling’s The Jungle Book. From Cain and Abel to Twilight’s Edward and Jacob, the human race's very existence has been vitally dependent on that fascinating fluid that flows thicker than water. The ultimate importance of lifeblood has been recognized by science and medicine from their inception, but only relatively recently have some of its deeper technical mysteries been revealed. We’re all familiar with the critical value of a single drop in a forensic case.

In Nature Genetics this month, one of our longtime collaborators, Greg Gibson, and his student, Youssef Idaghdour, effectively analyze blood samples from an exotic location to provide some key insights into the mysteries of human genetics and its relationship to the environment and disease. [NOTE: The research project described here had its roots in a 2007 project that is described in a JMP customer story.]

Blood nourishes, cleans and defends our primary organs and is an integral component of vital body systems. As one of our most renewable and readily available tissues, it is a very natural target for large-scale genomics studies. An extensive number of clinical trials now routinely collect samples and freeze them away for future investigation.

Blood-based biomarkers are highly prized, ranging from basic types (A,B,O were some of the first-used, and various panels are now routinely used in medical labs) to advanced screening of millions of alterations in DNA, RNA, protein, metabolites and other analytes. But there are difficulties: Certain elements of blood fluctuate widely, and some overabundant components like albumin can mask truly discriminating markers. Modern technologies are providing steady progress, and there is even a scientific journal Blood that reports on “bleeding edge” research.

Gibson and Idaghdour risked some of their own precious plasma and ventured on camelback into the Moroccan desert to take blood samples from members of two different rural villages. They also collected samples from a nearby urban area. Using bead-based technology from Illumina, they measured more than 500,000 single nucleotide polymorphisms (SNPs, variations in DNA) and 16,000 gene expression levels (RNA transcript abundance) on around 200 individuals. Data analysis was performed in JMP Genomics with help from experts Wendy Czika and Kelci Miclaus in the JMP group. Their findings? Two distinct population ancestries, the Amazigh Berber and Arab, are very apparent in principal component plots of the SNPs, along with individuals in between having an admixture of the two; for a few of them their genetic profiles contradicted their self-reported ancestry! Around a third of the gene expression measurements differ between rural and urban, and 356 are strongly associated with variation in SNPs, so-called expression SNPs (eSNPs). Gender interactions are also apparent, as males tend to travel much more frequently between urban and rural locations than do females. Perhaps most importantly, several of the key eSNPs have direct associations with important diseases like Type 1 diabetes. Gibson is already conducting similar experiments worldwide and is looking to make more extensive connections between genes, environment and disease.

While awaiting the next hematological breakthrough, I guess I don’t need to warn you to watch out for viruses, mosquitoes, ticks, leeches, sharks, 18th-century physicians and vampires (any century). You can donate with help from wonderful organizations like the Red Cross, and of course keep tabs on your systolic and diastolic pressure. If you ever find yourself in a desert or jungle and get asked why you like genomics, just reply with a sanguine smile that “It’s in my blood”!

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