Monday, February 15, 2010

Predicting lactase persistence from genetic data ... not yet!

...especially in Africa, SE Europe, and parts of Asia.
It seems like their genetic information consists of the four SNPs that are so far known to be associated with lactase persistence.

A worldwide correlation of lactase persistence phenotype and genotypes

Itan Y, Jones BL, Ingram CJ, Swallow DM, Thomas MG
BMC Evol Biol. 2010 Feb 9;10(1):36. [Epub ahead of print]
ABSTRACT: BACKGROUND: The ability of adult humans to digest the milk sugar lactose - lactase persistence - is a dominant Mendelian trait that has been a subject of extensive genetic, medical and evolutionary research. Lactase persistence is common in people of European ancestry as well as some African, Middle Eastern and Southern Asian groups, but is rare or absent elsewhere in the world. The recent identification of independent nucleotide changes that are strongly associated with lactase persistence in different populations worldwide has led to the possibility of genetic tests for the trait. However, it is highly unlikely that all lactase persistence-associated variants are known. Using an extensive database of lactase persistence phenotype frequencies, together with information on how those data were collected and data on the frequencies of lactase persistence variants, we present a global summary of the extent to which current genetic knowledge can explain lactase persistence phenotype frequency. RESULTS: We used surface interpolation of Old World lactase persistence genotype and phenotype frequency estimates obtained from all available literature and perform a comparison between predicted and observed trait frequencies in continuous space. By accommodating additional data on sample numbers and known false negative and false positive rates for the various lactase persistence phenotype tests (blood glucose and breath hydrogen), we also apply a Monte Carlo method to estimate the probability that known lactase persistence-associated allele frequencies can explain observed trait frequencies in different regions. CONCLUSION: Lactase persistence genotype data is currently insufficient to explain lactase persistence phenotype frequency in much of western and southern Africa, southeastern Europe, the Middle East and parts of central and southern Asia. We suggest that further studies of genetic variation in these regions should reveal additional nucleotide variants that are associated with lactase persistence.


wreaver said...

I believe you have an error in your title.

The title is currently: "Predicting lactose persistence from genetic data ... not yet!". Note that it says "lactOse persistence" and not "lactAse persistence". (I.e., change to "O" to an "A".)

Yann Klimentidis said...

Thanks for catching that!

Maju said...

Very interesting, thanks for posting this. I have mirrored this (in my own style) at Leherensuge (FYI).

bioinformatics training said...

Yah...really this article is so nice. i appreciate it..

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