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Scientists rename human genes to stop Microsoft Excel from misreading them as
dates

   [87]New, [88]77 comments

   Sometimes it’s easier to rewrite genetics than update Excel
   By [89]James Vincent Aug 6, 2020, 8:44am EDT

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   Illustration by Alex Castro / The Verge

   There are tens of thousands of genes in the human genome: minuscule
   twists of DNA and RNA that combine to express all of the traits and
   characteristics that make each of us unique. Each gene is given a name
   and alphanumeric code, known as a symbol, which scientists use to
   coordinate research. But over the past year or so, some 27 human genes
   have been renamed, all because Microsoft Excel kept misreading their
   symbols as dates.

   The problem isn’t as unexpected as it first sounds. Excel is a behemoth
   in the spreadsheet world and is regularly used by scientists to track
   their work and even conduct clinical trials. But its default settings
   were designed with more mundane applications in mind, so when a user
   inputs a gene’s alphanumeric symbol into a spreadsheet, like MARCH1 —
   short for “[98]Membrane Associated Ring-CH-Type Finger 1” — Excel
   converts that into a date: 1-Mar.

   "Studies found a fifth of genetic data in papers was affected by Excel
   errors"

   This is extremely frustrating, even dangerous, corrupting data that
   scientists have to sort through by hand to restore. It’s also
   surprisingly widespread and affects even peer-reviewed scientific work.
   One study [99]from 2016 examined genetic data shared alongside 3,597
   published papers and found that roughly one-fifth had been affected by
   Excel errors.

   “It’s really, really annoying,” Dezső Módos, a systems biologist at the
   Quadram Institute in the UK, told The Verge. Módos, whose job involves
   analyzing freshly sequenced genetic data, says Excel errors happen all
   the time, simply because the software is often the first thing to hand
   when scientists process numerical data. “It’s a widespread tool and if
   you are a bit computationally illiterate you will use it,” he says.
   “During my PhD studies I did as well!”
   Examples of gene symbols being rendered as dates in Microsoft Excel.
   GIF: The Verge

   There’s no easy fix, either. Excel doesn’t offer the option to turn off
   this auto-formatting, and the only way to avoid it is to [100]change
   the data type for individual columns. Even then, a scientist might fix
   their data but export it as a CSV file without saving the formatting.
   Or, another scientist might load the data without the correct
   formatting, changing gene symbols back into dates. The end result is
   that while knowledgeable Excel users can avoid this problem, it’s easy
   for mistakes to be introduced.

   Help has arrived, though, in the form of the scientific body in charge
   of standardizing the names of genes, the HUGO Gene Nomenclature
   Committee, or HGNC. This week, the HGNC published new [101]guidelines
   for gene naming, including for “symbols that affect data handling and
   retrieval.” From now on, they say, human genes and the proteins they
   expressed will be named with one eye on Excel’s auto-formatting. That
   means the symbol MARCH1 has now become MARCHF1, while SEPT1 has become
   SEPTIN1, and so on. A record of old symbols and names will be stored by
   HGNC to avoid confusion in the future.

   So far, the names of some 27 genes have been changed like this over the
   past year, Elspeth Bruford, the coordinator of HGNC, tells The Verge,
   but the guidelines themselves weren’t formally announced until this
   week. “We consulted the respective research communities to discuss the
   proposed updates, and we also notified researchers who had published on
   these genes specifically when the changes were being put into effect,”
   says Bruford.

   As Bruford makes clear, the art of naming genes is very much driven by
   consensus. Like the lexicographers charged with updating dictionaries,
   the Gene Nomenclature Committee has to be sensitive to the needs of
   those individuals who will be most affected by their work.

     THRILLED by this announcement by the Human Gene Nomenclature
     Committee. [102]pic.twitter.com/BqLIOMm69d
     — Janna Hutz (@jannahutz) [103]August 4, 2020

   This wasn’t always the case, mind. In the early, frontier days of
   genetics, gene naming was often a [104]playground for creative
   scientists, leading to notorious genes like “sonic hedgehog” (yes,
   named for that Sonic) and “Indy” (short for “I’m not dead yet”; a
   reference to the gene’s function, which can double the life span of
   fruit flies when mutated).

   Now, though, the HGNC has taken matters firmly in hand, and current
   guidelines don’t cede much ground to whimsy or ego. The focus is on
   practical concerns: how do we minimize confusion? For that reason, gene
   symbols should be unique, and gene names should be brief and specific,
   says the committee. They cannot use subscript or superscript; can only
   contain Latin letters and Arabic numerals; and should not spell out
   names or words, particularly offensive ones (a rule that should hold
   true “ideally in any language”).

   "Gene names should avoid offense “ideally in any language”"

   And while the decision to rename genes is not taken lightly, it’s not
   unusual, says Bruford. Many gene symbols that can be read as nouns have
   been renamed to avoid false positives during searches, for example. In
   the past, CARS has become CARS1, WARS changed to WARS1, and MARS
   tweaked to MARS1. Other changes have been made to avoid insult.

   “We always have to imagine a clinician having to explain to a parent
   that their child has a mutation in a particular gene,” says Bruford.
   “For example, HECA used to have the gene name ‘headcase homolog
   (Drosophila),’ named after the equivalent gene in fruit fly, but we
   changed it to ‘hdc homolog, cell cycle regulator’ to avoid potential
   offense.”

   But Bruford says this is the first time that the guidelines have been
   rewritten specifically to counter the problems caused by software. So
   far, the reactions seem to be extremely positive — some would even say
   joyous.

   After geneticist Janna Hutz shared the relevant section of HGNC’s new
   guidelines on Twitter, the response from the community was jubilant.
   “THRILLED by this announcement by the Human Gene Nomenclature
   Committee,” [105]tweeted Hutz herself. “Finally!!!” [106]responded
   Mudra Hegde, a computational biologist at the Broad Institute in
   Massachusetts. “Greatest news of the day!” [107]said a pseudonymous
   Twitter user.

   "Why did Microsoft win in a fight against human genetics?"

   Bruford notes that there has been some dissent about the decision, but
   it mostly seems to be focused on a single question: why was it easier
   to rename human genes than it was to change how Excel works? Why,
   exactly, in a fight between Microsoft and the entire genetics
   community, was it the scientists who had to back down?

   Microsoft did not respond to a request for comment, but Bruford’s
   theory is that it’s simply not worth the trouble to change. “This is
   quite a limited use case of the Excel software,” she says. “There is
   very little incentive for Microsoft to make a significant change to
   features that are used extremely widely by the rest of the massive
   community of Excel users.”

   Bruford doesn’t seem bitter about the situation, though. After all, she
   says, it wouldn’t do to wait on a hypothetical Excel update to fix
   these problems when a long-term solution can be introduced by
   scientists themselves. Microsoft Excel may be fleeting, but human genes
   will be around for as long as we are. It’s best to give them names that
   work.

   Correction: The story has been corrected to clarify that Excel users
   can save spreadsheets that retain their formatting, avoiding the
   mistake where gene symbols are changed into dates. We regret the error.

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