“A” or “An” with

abbreviations? It depends.
Scientific papers tend to contain lots of abbreviations—acronyms,
initialisms,* gene symbols and protein designations, element and
isotope symbols, chemical formulas, and so on—and authors sometimes
have difficulty choosing the correct indefinite article (“a” or “an”) to use
with abbreviations. The general rule is that the choice depends on how
the abbreviation would be pronounced if read aloud: if the
pronunciation starts with a vowel sound, use “an,” and if it starts with a
consonant sound, use “a.” Let’s look at some examples:

The UTR lengths were calculated as the number of reads in a UTR

divided by the number of reads in the CDS multiplied by the CDS
length.

Here “UTR,” pronounced letter-by-letter, starts with a consonant sound

(\y\ as y in yet), so “a” is the best choice. Note, however, that a Google
Scholar search of “an UTR” turns up a number of hits (about 1/6 as
many as “a UTR”): for example,

The blocked copy can then be replaced with an UTR-specific primer

pair.

My guess is that this author read this sentence as if the abbreviation

were spelled out—“with an untranslated region–specific primer pair”†—
and thus I would argue that “an” is not incorrect, as long as it is used
consistently throughout the manuscript.

Here are two example sentences with abbreviations pronounced as

words:

Therefore, calcium ion–dependent glutamate release from astrocytes is

a SNARE protein–dependent process that requires the presence of
functional vesicle–associated proteins.

All the antisera reacted with p240 in an HDAC-specific manner

“SNARE” is pronounced with an initial consonant sound and thus gets

“a,” and “HDAC” starts with the vowel sound “aitch” (“aitch-dak”) and
thus gets “an.”

Some abbreviations are pronounced as words by some people and

letter-by-letter by others; SNP (for single nucleotide polymorphism) is
an example, and you’ll find both “a” and “an” used in the literature:

Here we report the results of an SNP [pronounced “s-n-p”] survey of 21

maize loci.

The most common cause of the loss of hepatic CYP3A5 expression is a

SNP [pronounced “snip”] at nt 22,893 in intron 3 of CYP3A5*3.

The same is true for some gene symbols:

KmycJ are K562 cells with a MYC gene [pronounced “mik gene”]
inducible by ZnSO4.

The cells show L3 morphology. . .with coexpression of TdT and surface

light chains in addition to an MYC gene [pronounced “m-y-c gene”]
translocation.

I would argue that both are correct; just be consistent throughout your
manuscript.

What about element symbols? The ACS Style Guide states that element
names are pronounced even when element symbols are used, and
therefore the choice of article depends on the pronunciation of the
element name:

The analyzed DNA is hybridized with a primer nucleic acid that is

associated with a Au surface [pronounced “a gold surface” not “an a-u
surface”].

TGA-DSC measurements were performed under a He flow

[pronounced “a helium flow” not “an h-e flow”].

The same guidance applies to simple chemical formulas:

Indomethacin, a nonsteroidal inhibitor of prostaglandin synthetase, was

diluted in a Na2CO3 buffer [pronounced “sodium carbonate buffer”].

Isotopes are treated differently. The ACS Style Guide calls for the
element symbol to be pronounced before the number (e.g., “14C” is
pronounced “c fourteen”), and thus the pronunciation of the element
symbol should determine the choice of article:

As N-1 becomes pyramidal, an 15N [pronounced “en fifteen”] isotope

effect of up to 2–3% is observed.

Note, however, that this “rule” does not appear to be followed

universally. I found that “a 15N isotope” is much more common than “an
15N isotope”: for example,

Reaction of hydroxide ion with the neutral phosphotriester exhibits a

15
N-isotope effect consistent with only 25% bond fission

Perhaps most people read this as if the element name were spelled out
—“a nitrogen-15 isotope”—in which case “a” is in fact correct. Again,
make a choice and stick to it consistently.

*Acronyms are abbreviations that are pronounced as words (e.g.,

ANOVA, SNARE, GABA), and initialisms are abbreviations that are
pronounced letter-by-letter (e.g., DNA, UTR, EDTA).

†
Or he or she speaks a language (e.g., German or French) in which the
letter “u” is pronounced starting with a vowel sound.