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Widely Used Reference for the Human Genome is Missing 300 Million Bits of DNA
Known as the GRCh38 reference genome, it is periodically updated with DNA sequences from other individuals, but in a new analysis, Johns Hopkins scientists now say that the collective genomes of 910 people of African descent have a large chunk — about 300 million bits — of genetic material that is missing from the basic reference genome.
“There’s so much more human DNA than we originally thought,” says Steven Salzberg, Ph.D., the Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at The Johns Hopkins University.
Knowing the variations in genomes across populations is essential to research design to reveal why certain people or groups of people may be more or less susceptible to common health conditions, such as heart disease, cancer and diabetes, and Salzberg says that scientists need to build more reference genomes that more closely reflect different populations.
“The whole world is relying on what is essentially a single reference genome, and when a particular DNA analysis doesn’t match the reference and you throw away those non-matching sequences, those discarded bits may in fact hold the answers and clues you are seeking,” says Salzberg.
(Score: 1) by shrewdsheep on Wednesday November 21 2018, @03:27PM (1 child)
This article goes to show that huge chunks of science hinge on some critical assumptions that go unchecked/unquestioned for long periods of time. Apart from the reference genome in genetics all fields have their version of a "reference genome". The standard model in physics or the frequentist/Bayesian paradigms in statistics come to mind.
I do not believe that this is a problem as these "axioms" are there for a reason, it just makes us aware of how little we know and how naive we are.
(Score: 2, Insightful) by Anonymous Coward on Wednesday November 21 2018, @08:42PM
Meh, I tried to use the reference genome to check for a sequence once and immediately came across that huge swaths were missing. Then I wanted to compare a difference sequence between human and cows and found the human genome had been used to "scaffold" the cow genome so they were not independent. If you don't figure this stuff out really quickly when working with it there is something wrong with you.