What’s wrong with these genotypes?

During a correspondence with a colleague about the validity of genotyping rare variants I became aware of a paper in Science that I missed initially. It is about genetic signatures in longevity:

Using these data, we built a genetic model that includes 150 single-nucleotide polymorphisms (SNPs) and found that it could predict EL with 77% accuracy in an independent set of centenarians and controls.

That’s an extremely difficult enterprise given our recent results of the heritability of life span. But that’s not the point, reading now the editorial expression of concern by Bruce Alberts.

In their study, Sebastiani et al. used a number of different genotyping platforms and neglected to perform data quality-control steps, which resulted in their reporting several false-positive single-nucleotide polymorphism (SNP) associations. In particular, one of the platforms used in their work, the Illumina 610-Quad array, has been shown in unpublished studies by other investigators to produce artifactual genotype data at a subset of SNPs.

No idea, what’s bad with the Illumina 610-Quad. Retraction watch points to a Newsweek article

“Unfortunately, different chips have their own little problems for specific [genetic variants],” he says. The key to keeping false positives at bay is to ensure that cases and control groups are analyzed using exactly the same techniques. If you use one type of chip to analyze your cases and a different type to analyze your control group, “you can see any [variants] that are genotyped differently on the different chips ‘lighting up’ as apparently associated with the trait,” says Goldstein, when in fact that pattern is just an experimental artifact …

That phenomenon would indeed point to a experimental design error and not so much to a chip error as the editorial concern suggests. We will see…