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Scientific Nomenclature

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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), 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