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Scientific Nomenclature


Nucleotides

Blood generally follows the Human Genome Variation Society’s mutation nomenclature recommendations for nucleotides.

Nucleotides are represented by the letters A, C, G, and T; lowercase letters are allowed (to indicate uncertainty in the base call).

Denote nucleotide substitutions and polymorphisms by putting the nucleotide number first and then using a greater-than symbol between the replaced nucleotide and the new nucleotide; all elements should be closed up.

1691G>A
G>A 


To indicate that a genomic DNA or complementary DNA sequence is used, include “(gDNA [or cDNA] sequence, first described by _____ ref#)”; do not preface nucleotide substitutions with the letter g or c.

Denote nucleotide insertions by putting the 2 surrounding nucleotide numbers in front, separated by a hyphen, followed by "ins" and the inserted nucleotide.

186-187insC

Denote nucleotide deletions by specifying the nucleotide number deleted, followed by "del" and the deleted nucleotide.

1997delT

Denote nucleotide codon changes using the substitution scheme above:

GAG>TAG

See the Human Genome Variation Society website for how to handle other situations (eg, intron mutations and IVS-intervening sequences).

Amino acids

In mutation notation, it is acceptable to use abbreviations without expansion (see Amino acid abbreviations below), but follow abbreviations rules elsewhere.

Amino acids may be abbreviated with 1-letter abbreviations or 3-letter abbreviations. Amino acid abbreviations details both abbreviation schemes. Authors should try to use the same scheme consistently throughout an article, though variation is allowed.

A codon number may be used to describe a mutation.

Arg506
Arg506Gln
R506
R506Q

If the codon number is not used, then denote the mutation with a full arrow.

Arg→Gln
R→Q


If a stop codon is discussed, note that it is sometimes denoted by an abbreviation for unspecified amino acid (Xaa or X); if so, ensure that this abbreviation is consistent with surrounding amino acid abbreviations. Note that other notation is sometimes used (eg, “Stop”).

Arg506Xaa
Arg506Stop
R506X
R506Stop

Amino acid abbreviations

alanine


Ala


A


arginine


Arg


R


asparagine


Asn


N


aspartic acid


Asp


D


cysteine


Cys


C


glutamic acid


Glu


E


glutamine


Gln


Q


glycine


Gly


G


histidine


His


H


isoleucine


Ile


I


leucine


Leu


L


lysine


Lys


K


methionine


Met


M


phenylalanine


Phe


F


proline


Pro


P


serine


Ser


S


threonine


Thr


T


tryptophan


Trp


W


tyrosine


Tyr


Y


valine


Val


V


unspecified aa


Xaa


X


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