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As far as I understand, the human genome sample called NA12878 provides high confidence variants for a human sample. It is being used as a benchmark for many genomic research projects.

Q: Why exactly the NA12878 is such a popular benchmark dataset? Just because we have a set of high confidence variants? But we can also get some high confidence variants from the 1000 Genome project. Does that have something to do with the sequencing technology? Anything to do with the sample itself? Why do we want to benchmark our experiments with NA12878?

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    $\begingroup$ @Chris NA12878 is the name. It is not abbreviation of anything. $\endgroup$
    – SmallChess
    Commented Mar 30, 2017 at 5:51
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    $\begingroup$ First: This has nothing to do with me being a mod. Then: It is well known to people from the field, but questions/answers here are expected to stand on their own without reading further literature. $\endgroup$
    – Chris ♦
    Commented Mar 30, 2017 at 5:59
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    $\begingroup$ @Chris I still disagree. This is like explaining DNA for any question related to genetics. Prior knowledge is assumed and required for most questions in this site. Anyway, I did give a brief introduction on what NA12878 is in my first sentence. The title and the question could be a potential useful resource for anyone googling NA128278. $\endgroup$
    – SmallChess
    Commented Mar 30, 2017 at 6:03
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    $\begingroup$ No it isn't. I work with NA12878 daily, so I happen to recognize it, but that doesn't mean that everyone who could answer your question would know the code on sight. I have been working in genomics for almost 10 years now but didn't know what NA12878 was until last year when I started doing variant calling. More to the point, if another user, let alone a mod, suggests that your question could be clearer, why don't you just clarify instead of arguing? Obviously it seems clear to you, but equally obviously, it isn't so clear to everyone. $\endgroup$
    – terdon
    Commented Mar 30, 2017 at 11:08
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    $\begingroup$ It's not about closing, it's about making the question easier to understand. And nobody said it was inappropriate. The only thing inappropriate here is your reaction to a helpful suggestion telling you how to improve your question and increase your chances of getting an answer. You took it as criticism and started arguing when all you needed to do is provide a link as I just did. That way, people can click on it and see that you are referring to a DNA sequencing sample and can look up information about it. $\endgroup$
    – terdon
    Commented Mar 30, 2017 at 11:20

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So to clarify for people unfamiliar with NA12878, that's the sample identification for a particular Utah woman. Her parents are NA12891 and NA12892. In human variation data-sets that's what we are given to identify individuals, an ID, sex and population. All the other data is removed to protect patient privacy. So the question is why was NA12878 (this Utah woman) chosen as the reference patient in genomic analysis...

I don't know the real practical answer but from what I gather it's inertia.

I don't have a full history for her but I do know somethings which make her genome a good choice for a benchmark. NA12878 is a fairly old to geneticists and her DNA is included in multiple legacy projects, specifically HapMap.

She has a genetic disease (CYP2D6 mutation) which is probably what initially included her and her family genetic analysis. This is a better reason to study this genome in detail instead of it simply being someone famous (i.e. Venter).

She's Utah mormon (small founder population with extensive pedigree information), has 11 children (can do recombination/inheritance analysis). What this means is that a deep understanding of her genome will have applications to this population.

Her lymphoblastoid cell line GM12878 was included as tier-1 ENCODE cell of study. This means there's terabytes of epignomic data for her as well.

When I choose to do human genome analysis, NA12878 is the obvious choice because of how much data is already available, which also means more data is going to be available. Thus I think the answer is largely inertia.

Also consider it this way, if you're trying to say your pipeline or sequencing technology is better then other ones, and everyone uses NA12878 to benchmark their technology, then it's wise to also use NA12878 so the results can be comparable.

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