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Test Code NAT2O N-Acetyltransferase 2 Gene (NAT2), Full Gene Sequence, Saliva

Reporting Name

NAT2 Full Gene Sequence, Saliva

Useful For

Identifying patients who may require isoniazid dosing adjustments

 

Genotyping patients who prefer not to have venipuncture done

Profile Information

Test ID Reporting Name Available Separately Always Performed
NT2FO NAT2, Full Gene Sequence No Yes
NAT2S NAT2, Gene Sequencing No Yes

Method Name

Polymerase Chain Reaction (PCR) Followed by DNA Sequence Analysis

Performing Laboratory

Mayo Medical Laboratories in Rochester

Specimen Type

Saliva


Specimen Required


Multiple saliva genotype tests can be performed on a single specimen after a single extraction. See Multiple Saliva Genotype Tests in Special Instructions for a list of tests that can be ordered together.

 

Container/Tube: Oragene DNA Self-Collection Kit (T651: fees apply)

Specimen Volume: Full tube

Collection Instructions:

1. Fill tube to line.

2. Send specimen in original container per kit instructions.


Specimen Minimum Volume

1 mL

Specimen Stability Information

Specimen Type Temperature Time
Saliva Ambient

Reject Due To

Hemolysis

NA

Lipemia

NA

Icterus

NA

Other

NA

Reference Values

An interpretive report will be provided.

Day(s) and Time(s) Performed

Varies

CPT Code Information

81479-Unlisted molecular pathology procedure

LOINC Code Information

Test ID Test Order Name Order LOINC Value
NAT2O NAT2 Full Gene Sequence, Saliva In Process

 

Result ID Test Result Name Result LOINC Value
NAT2S NAT2, Gene Sequencing In Process
32985 Haplotype 1 84414-2
32986 Haplotype 2 84414-2
32987 Haplotype 3 84414-2
32988 Haplotype 4 84414-2
32989 111T>C 82939-0
32990 190C>T 82939-0
32991 191G>A 82939-0
32992 282C>T 82939-0
32993 341T>C 82939-0
32994 364G>A 82939-0
32995 411T>A 82939-0
32996 434A>C 82939-0
32997 481C>T 82939-0
32998 499G>A 82939-0
32999 590G>A 82939-0
33000 759C>T 82939-0
33001 803A>G 82939-0
33002 845A>C 82939-0
33003 857G>A 82939-0
33004 859T>C/del 82939-0
33005 Reviewed By 18771-6
33006 NAT2 Full Gene Interpretation 69047-9

Test Classification

See Individual Test IDs

Cautions

Saliva samples may contain donor DNA if obtained from patients who received heterologous blood transfusions or allogeneic blood or marrow transplantation. Results from samples obtained under these circumstances may not accurately reflect the recipient’s genotype. For individuals who have received blood transfusions, the genotype usually reverts to that of the recipient within 6 weeks. For individuals who have received allogeneic blood or marrow transplantation, a pretransplant DNA specimen is recommended for testing.

 

NAT2 genetic test results in patients who have undergone liver transplantation may not accurately reflect the patient's NAT2 status.

 

This test sequences the entire NAT2 gene. All variants, including novel variants not listed, should be detected. However, novel variants not described in the literature may be of unknown significance.

 

Mutations in the primer binding regions can affect the testing and, ultimately, the genotyping interpretation made.

 

Drug-drug interactions and drug or metabolite inhibition must be considered when dealing with heterozygous individuals. Drug or metabolite inhibition can reduce residual functional NAT2 catalytic activity. Acetaminophen is a significant inhibitor of NAT2.

 

Patients may develop isoniazid toxicity problems if liver and kidney function are impaired, even in the absence of slow or intermediate acetylator status.

Method Description

Genomic DNA is extracted from saliva. The entire NAT2 gene is amplified by PCR. The single amplicon is sequenced in 4 positions in both directions for a total of 8 sequences. These 8 sequencing reactions provide complete bidirectional sequencing coverage of NAT2.(Unpublished Mayo method)

Analytic Time

7 days (not reported on Saturday or Sunday)

Specimen Retention Time

2 weeks

Clinical Information

Arylamine N-acetyltransferase type 2 (NAT2) is a highly polymorphic phase 2 metabolic enzyme that conjugates hydrazine derivatives and aromatic amine drugs with acetyl-groups. NAT2 also is involved in the acetylation and activation of some procarcinogens.(1)

 

Individuals acetylate drugs at different rates by NAT2, and are described as having slow, intermediate, or fast acetylator phenotypes. A gradient exists in which the prevalence of slow acetylator phenotypes increases with decreasing distance to the equator. Near the equator, up to 80% of individuals may be slow acetylators, while in some more northern countries, as few as 10% of the population may have the slow acetylator phenotype.

 

A number of drugs are metabolized by NAT2 including procainamide, dapsone, nitrazepam, hydralazine, zonisamide, and isoniazid. Isoniazid is used to treat and prevent tuberculosis, and is still used as a primary treatment agent. Adverse reactions with isoniazid, which include nausea, drug-induced hepatitis, peripheral neuropathy, and sideroblastic anemia, are associated more often with a slow NAT2 acetylator phenotype. These individuals may require a lower dose to avoid adverse reactions.

 

The NAT2 gene contains a single intronless exon of 870 base pairs and encodes 290 amino acids. NAT2 is highly polymorphic and contains 16 known single nucleotide polymorphisms and 1 single base-pair deletion. These polymorphisms are combined into 36 known haplotype alleles. Each individual haplotype is predictive of either a fast or slow acetylator phenotype. Individuals with 2 fast haplotypes are predicted to be extensive (normal) metabolizers, while those with 1 fast and 1 slow haplotype are intermediate metabolizers, and those with 2 slow haplotypes are poor metabolizers.(2,3) Studies with patients who have different acetylator haplotypes have correlated the ratio of plasma N-acetylisoniazid/isoniazid drug concentrations with haplotypes, with slow and intermediate acetylators having lower ratios than fast acetylators.(4)

 

NAT2 Allele

Nucleotide Change

Amino Acid Change

Predicted Acetylator Phenotype

*4

None

None

Fast

*5A

341T->C
481C->T

I114T

Slow

*5B

341T->C
481C->T
803A->G

I114T

K268R

Slow

*5C

341T->C
803A->G

I114T
K268R

Slow

*5D

341T->C

I114T

Slow

*5E

341T->C
590G->A

I114T
R197Q

Slow

*5F

341T->C
481C->T
759C->T
803A->G

I114T
K268R

Slow

*5G

282C->T
341T->C
481C->T
803A->G

I114T

K268R

Slow

*5H

341T->C

481C->T

803A->G

859Del

I114T
K268R

S287 Frameshift

Slow

*5I

341T->C

411A->T

481C->T

803A->G

I114T
L137F
K268R

Slow

*5J

282C->T
341T->C
590G->A

I114T

R197Q

Slow

*6A

282C->T
590G->A

R197Q

Slow

*6B

590G->A

R197Q

Slow

*6C

282C->T
590G->A
803A->G

R197Q
K268R

Slow

*6D

111T->C
282C->T
590G->A

R197Q

Slow

*6E

481C->T
590G->A

R197Q

Slow

*7A

857G->A

G286E

Slow

*7B

282C->T
857G->A

 G286E

Slow

*10

499G->A

E167K

Undetermined

*11A

481C->T

None

Undetermined

*11B

481C->T

859Del

S287 Frameshift

Undetermined

*12A

803A->G

K268R

Fast

*12B

282C->T
803A->G

 K268R

Fast

*12C

481C->T
803A->G

K268R

Fast

*12D

364G->A
803A->G

D122N
K268R

Undetermined

*13

282C->T

None

Fast

*14A

191G->A

R64Q

Slow

*14B

191G->A
282C->T

R64Q

Slow

*14C

191G->A
341T->C
481C->T
803A->G

R64Q
I114T
K268R

Slow

*14D

191G->A
282C->T
590G->A

R64Q
R197Q

Slow

*14E

191G->A
803A->G

R64Q
K268R

Slow

*14F

191G->A
341T->C
803A->G

R64Q
I114T
K268R

Slow

*14G

191G->A
282C->T
803A->G

R64Q
K268R

Slow

*17

434A->C

Q145P

Undetermined

*18

845A->C

K282T

Undetermined

*19

190C->T

R64W

Undetermined

 

Interpretation

The wild-type (normal) genotype for NAT2 is *4. This is the most commonly occurring allele in some, but not all, ethnic groups.(5)

 

Individuals are classified as being slow, intermediate, or fast acetylators depending on their diplotype. Slow acetylators have 2 slow haplotypes, fast acetylators have 2 fast haplotypes, and intermediate acetylators have 1 of each.

 

Slow acetylators receiving isoniazid therapy should be monitored for signs of toxicity.

 

Dose reductions may be considered for both slow and intermediate acetylators. However, it should be verified that the reduced isoniazid dose produces serum levels within the therapeutic range.

Forms

1. New York Clients-Informed consent is required. Please document on the request form or electronic order that a copy is on file. An Informed Consent for Genetic Testing (T576) is available in Special Instructions.

2. If not ordering electronically, complete, print, and send a Pharmacogenomics Test Request Form (T797) with the specimen (https://www.mayomedicallaboratories.com/it-mmfiles/pharmacogenomics-test-request-form-mc0767-15.pdf)