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Longevity debate: Chips to blame?

Posted by Jennifer Welsh
[Entry posted at 14th July 2010 02:24 PM GMT]
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At the heart of a feverish debate over the validity of a recent genome-wide

association study (GWAS) of centenarians is the authors' possible misuse of gene
chips in different testing groups, part of an ongoing issue affecting other GWAS
research.

How this variation might impact the validity of the longevity findings, however,
including the 150 SNPs associated with extreme longevity, is unclear.

The initially heralded study, published in

Science Express July 2, examined the
genomes of about 1,000 centenarians,
those rare humans that have reached
the age of 100, and compared them to
those of controls.

However, the authors used two different

gene chips to analyze their centenarian
population, with one gathering about 10 SNP chips are at the center of the longevity study's faults
percent of the data. The data from the Image: Wikimedia Commons, Magnus Manske

control population was also gathered using a total of four different chips.

Each chip has its own special quirks, even if it's made by the same
manufacturer, so comparing the results from two different chips can be a
challenge. If a chip has an issue with a particular SNP, it could produce faulty
results, such as incorrectly significant alleles. If scientists compare those data to
results from a chip that does not have a problem with that particular SNP, it may
look as if one sample is genetically different from the other, when it's simply a
misreading from one chip.

The authors of the longevity study -- Thomas Perls, the director of the New
England Centenarian Study, and Boston University biostatistician Paola
Sebastiani used Illumina's HumanCNV370 chips to analyze the first 90 percent of
centenarians, and the company's Human610-quad chip for the last 10 percent.
(After the Human610-quad chip was introduced, Illumina stopped making the
Human CNV370.)

Scientists such as GWAS experts David Goldstein, a researcher at Duke

University, and DeCODE founder Kári Stefánsson claim that the Human610-quad
chip has been plagued with these quirks. Consequently, it's possible that some of
the results -- namely, that the 150 selected SNPs can predict if a person is a
centenarian with 77 percent accuracy -- are not valid, Goldstein said.

"When you have an imbalance in the chips that you use between cases and
controls, any of the polymorphisms that are genotyped differently between the
chips appear to be different between the chips," said Goldstein.

However, Perls argues that the results are valid, since he and Sebastiani used
both kinds of chips on both the centenarian and control groups.

For some SNPs, it's impossible to tell if the chip is accurately reporting the
identity of the nucleotide at the SNP correctly, unless the scientists look at the
distribution of each of the possible responses at the SNP. A normal distribution
would have results distributed among the three possibilities -- two copies of
allele one, two copies of allele two, or one copy of each allele -- without the
results clustered around one possibility.

Some faulty SNPs can look like they are giving a good reading, because the chip
is giving a signal that it is detecting something at the location of the SNP, but
the reading might be inaccurate, said Goldstein. He explained that sometimes
the chip can be 'blind' to one of the two possible alleles, so reads the SNP as
containing two copies of the other allele, no matter what nucleotide is actually
contained in the sample.

"It is now known that that is exactly what happened for the two most associated
SNPs" in the longevity study -- namely, 2 SNPs most associated with an
increased chance of reaching 100. Those markers, called rs1036819 and
rs9576827, are known to give an incorrect reading on the 610-quad chip, said
Goldstein. "We have checked on our own data and we see those problems on our
own data too."

"Everyone who works with [these chips] is complaining," said Barzilai. "On one
hand you are trying to wait for this best new technology but on the other hand it
could be your biggest nightmare."

The company, Illumina, Inc., which makes the chips, has done its own quality
control and has information on which of the SNPs give faulty readouts on each of
the chips. "Most of our customer communication is through newsletters and our
support team," said Daniel Peiffer, senior product manager for Illumina's
genotyping applications. "Perhaps from our side this could have been better
communicated, but the information was there."

Both experts and Illumina agree that if scientists find something interesting,
they always need to double-check their results with some other method, like
Taqman. "If it looks OK you can't be certain it's OK," said Goldstein. "For really
important findings you want to separately genotype it."

When asked if he contacted Illumina tech support or verified his data using
another technology, Perls said he was "unaware of a problem with these two
SNPs (out of 150). And now that we are, we are following up."

Even with the two most significant SNPs out of the game, some still have faith in
the remaining 148 SNPs that the original study found. "It doesn't mean that
what they found was not real," said Nir Barzilai, who is conducting a very similar
study of the genetics of extreme longevity in a group of Ashkenazi Jews.

"For the moment, I do not see any serious evidence that all the paper's
conclusions are wrong," Jan Vijg, a gerontological geneticist, said in an email.

Perls and Sebastiani are currently working to determine if any of the SNPs need
to be re-genotyped. "It is a big mistake to make premature judgments about
what the data will end up showing," Perls said. "I'm not going to say what the
magnitude of the problem is one way or the other until the issue is looked at
rigorously."

The reanalysis "should be finished within the week, and it will be passed on to
the editors at Science," he noted.

"It's a study that took 15 years to get to where it is today and a few more
weeks isn't too long to wait," said Perls. "Don't rush it, get the right answer."

P. Sebastiani, et al. "Genetic signatures of exceptional longevity in

humans," Science Express, July 2010

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