When is a gene really an allele?

The way some sections of the media use the word “gene” has become a bit of a pet peeve of mine.  Here’s an example from ScienceDaily:

Tibetans Developed Genes to Help Them Adapt to Life at High Elevations

Researchers have long wondered why the people of the Tibetan Highlands can live at elevations that cause some humans to become life-threateningly ill — and a new study answers that mystery, in part, by showing that through thousands of years of natural selection, those hardy inhabitants of south-central Asia evolved 10 unique oxygen-processing genes that help them live in higher climes.

Closer inspection of this research, which was published in Science last week, reveals that Tibetans don’t actually have 10 genes that are missing in the rest of humanity, what they have are different variants of the same genes.  These variants are called alleles, or haplotypes (there is a subtle difference between these two terms which I won’t go into here – but they both basically refer to different forms of the same gene or chromosomal region).  When geneticists refer to genetic variation in a species or population they are referring to the changes in the DNA sequence that results in multiple variant forms (alleles) of any given gene, the stuff that natural selection works on.

This study found that the Tibetan population have DNA changes in 10 genes that appear to be the result of natural selection.  Two of these genes, EGLN1 and PPARA have haplotypes that are significantly associated with the “decreased hemoglobin phenotype”, which is thought to be an adaptation to high altitude living.  These haplotypes appear to be selected for in the Tibetan population.  We all have EGLN1 and PPARA, but the Tibetan populations have unique haplotypes of these genes that help them live in higher climes.

This sort of incorrect usage of the word gene is pervasive in the popular media.  The phrase “the gene for” seems to be everywhere – the gene for breast cancer, the gene for schizophrenia, the gene for diabetes etc etc.  This gives the wrong impression of what these studies actually show, and is just plain incorrect.  What is actually being referred to in these studies is an allele or haplotype of a gene that we all have, and usually it is an allele that is correlated with a slightly higher incidence of the disease, not necessarily one that causes the disease.  Perhaps its time for for biologists to be more clear about what they mean by the word “gene”, and for journalists to incorporate the word “allele” or even just “genetic variant” into their vernacular.

If you want to read more about the Tibetans, the original paper is here, and an excellent summary of it by Razib Khan at Discover Magazine is here.

2 Responses to When is a gene really an allele?

  1. razib says:

    recently i listened to david reich of harvard on a radio show. he was talking, and he said, “the alle-, uh, variant.” i laughed.

  2. Jo Thompson says:

    Will you write a blog / post about the difference between an allele and haplotypes / haplogroups? Is there any reference that has clear explanations ? And is there a way to illustrate the difference between allele, gene, haplotype?
    Thanks!

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