Supplementary Table. Common Names and Corresponding HGVS Nomenclature of Major Variant

Supplementary Table. Common Names and Corresponding HGVS Nomenclature of Major Variant CYP2D6 Alleles

Major Nucleotide Variation
Variant
Allelea / Common Name
(GenBank Accession Number M33388) / dbSNP
Numberb / HGVS
(NCBI RefSeq NM_000106.4) / Effect on Protein
(NCBI RefSeq NP_000097.2)
*2c / 2850C>T; 4180G>C / rs16947; rs1135840 / c.886C>T; c.1457G>C / p.Arg296Cys; p.Ser486Thr
*3 / 2549delA / rs35742686 / c.775delA / p.Arg259Glyfs
*4 / 1846G>A / rs3892097 / c.506-1G>A / Splicing defect
*5 / full gene deletion / - / - / -
*6 / 1707delT / rs5030655 / c.454delT / p.Trp152Glyfs
*7 / 2935A>C / rs5030867 / c.971A>C / p.His324Pro
*8 / 1758G>T / - / c.505G>T / p.Gly169X
*9 / 2615_2617delAAG / rs5030656 / c.841_843delAAG / p.Lys281delLys
*10 / 100C>T / rs1065852 / c.100C>T / p.Pro34Ser
*11 / 883G>C / rs5030863 / c.181-1G>C / Splicing defect
*12 / 124G>A / rs5030862 / c.124G>A / p.Gly42Arg
*14 / 1758G>A / rs5030865 / c.505G>A / p.Gly169Arg
*15 / 137_138insT / rs72549357 / c.137delTinsTT / p.Leu46Argfs
*17 / 1023C>T / rs28371706 / c.320C>T / p.Thr107Ile
*19 / 2539_2542delAACT / rs72549353 / c.765_768delAACT / p.Leu255_Thr256?fs
*20 / 1973_1974insG / rs72549354 / c.632_633insG / p.Glu211?fs
*29 / 3183G>A / rs59421388 / c.1012G>A / p.Val338Met
*35 / 31G>A / rs769258 / c.31G>A / p.Val11Met
*36 / 100C>T; exon 9 gene conversion to CYP2D7 / rs1065852 / c.100C>T / p.Pro34Ser
*40 / 1863_1864ins(TTT CGC CCC)2 / rs72549356 / c.522_523insTTTCGCCCCTTTCGCCCC / p.Pro174_Asn175?
*41 / 2988G>A / rs28371725 / c.985+39G>A / Splicing defect

HGVS: Human Genome Variation Society

a Only the major SNP of the haplotype is given in this table. See the Cytochrome P450 Nomenclature Database website for complete haplotype definitions ()

b RefSNP accession ID number ()

c The CYP2D6*2 nucleotide variants (rs16947; rs1135840) also occur on several other CYP2D6 alleles.

Appendix A.

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal History:

Date of Report:June 15, 2010Concurrent Medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: No Variants Detected

Interpretation:Consistent with an Extensive (Normal) Metabolizer Phenotype.

No cytochrome P450 2D6 mutations were detected. This result is consistent with two copies of functional alleles and predicts an extensive (normal) metabolizer phenotype.

Drug metabolism may be affected by genetic and non-genetic factors not detected by this assay. For example, co-administration of drugs that inhibit CYP2D6 activity (e.g. some antidepressants) could impair or prevent metabolism of drugs metabolized by CYP2D6 (e.g. tamoxifen).

This result does not rule out the presence of other mutations within the cytochrome P450 family or other genetic changes that can affect drug metabolism. It is possible that the individual has a rare variant in the CYP2D6 gene that is not examined by this assay.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

With an extensive metabolizer phenotype, Tamoxifen treatment can follow standard dosing procedures.
Patient may need to avoid CYP2D6 inhibitors, such as Fluoxetine, Paroxetine, Quinidine, or Bupropion. A list of CY2D6 metabolizing drugs is available at
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Laboratory

Supplemental Information For Cytochrome P450 2D6 (CYP2D6):

The cytochrome P450 gene products are responsible for metabolizing a large number of widely prescribed drugs. Tamoxifen is metabolized by CYP2D6 to its active form endoxifen. Individuals with poor metabolizer phenotype for CYP2D6 will require alternative therapies to Tamoxifen such as aromatase inhibitors, while those with ultra-extensive metabolizer phenotype will require a decreased Tamoxifen dosage due to higher than normal rates of drug metabolism*.

Variants Tested: All common and most rare alleles with known clinical significance. Allele defining variant is in bold.

VARIANTS TESTED:

Functional / Nonfunctional / Decreased Function / Duplicated Functional / Duplicated
Decreased/
NonFunctional
Cyp2D6*1 (presumed)
Cyp2D6*2ABD
-1584C>G (*2A only), 1039C>T, 1661G>C, 2850C>T, 4180G>C
Cyp2D6*35
-1584C, 31G>A, 1661G>C, 2850C>T, 4180G>C / Cyp2D6*4ABDJK
100C>T, 1039C>T, 1661G>C, 1846G>A, 2850C>T, 4180G>C
Cyp2D6*5
(deletion)
Cyp2D6*6ABC
1707delT, 1976G>A, 4180G>C
Cyp2D6*7
2935A>C
Cyp2D6*8
1661G>C, 1758G>T, 2850C>T, 4180G>C
Cyp2D6*11
883G>C, 1661G>C, 2850C>T, 4180G>C
Cyp2D6*15
138insT
Cyp2D6*19
1661G>C, 2539-2542delAACT, 2850C>T, 4180G>C
Cyp2D6*20
1661G>C, 1973insG, 1978C>T, 1979T>C, 2850C>T, 4180G>C
Cyp2D6*36
100C>T, 1039C>T, 1661G>C, 4180G>C, (gene conversion to CYP2D7 in exon 9)
Cyp2D6*40
1023C>T, 1661G>C, 1863ins(TTTCGCCCC)2, 2850C>T, 4180G>C / Cyp2D6*9
2613-2615delAGA
Cyp2D6*10
100C>T, 1039C>T, 1661G>C, 4180G>C
Cyp2D6*17
1023C>T, 1661G>C, 2850C>T, 4180G>C
Cyp2D6*20
1661G>C, 1973insG, 1978C>T, 1979T>C, 2850C>T, 4180G>C
Cyp2D6*29
1659G>A, 1661G>C, 2850C>T, 3183G>A, 4180G>C
Cyp2D6*41
,1661G>C, 2850C>T, 2988G>A, 4180G>C / Cyp2D6*1xN
(presumed)
Cyp2D6*2xN
-1584C>G (*2A only),
1039C>T,
1661G>C, 2850C>T, 4180G>C
Cyp2D6*35xN
-1584C,
31G>A, 1661G>C, 2850C>T, 4180G>C / Cyp2D6*4xN
100C>T, 1039C>T, 1661G>C, 1846G>A, 2850C>T, 4180G>C
Cyp2D6*10xN
100C>T, 1039C>T, 1661G>C, 4180G>C
Cyp2D6*17xN
1023C>T, 1661G>C, 2850C>T, 4180G>C
Cyp2D6*36xN
100C>T, 1039C>T, 1661G>C, 4180G>C, (gene conversion to CYP2D7 in exon 9)
Cyp2D6*41xN
1661G>C, 2850C>T, 2988G>A, 4180G>C

Incidence of Poor Metabolizer Phenotype: 10 percent ofCaucasians and Hispanics, 2 percent of African Americans, and 1 percent of Asians.

Clinical Sensitivity: Greater than 95 percent of deleterious CYP2D6 variants are detected in Caucasians; sensitivity is unknown in other ethnicities.
Methodology: multiplex polymerase chain reaction (PCR) followed by hybridization to a microarray.

Analytical sensitivity**: 99% (95% CI 90%-100% when compared against referent method).

Analytical specificity**: 100% (95% CI 94%-100% when compared against referent method).
Limitations: Only the targeted CYP2D6variants will be detected. Mutations or variants in other genes will not be detected. Rare diagnostic errors can occur due to primer site mutations. Mutation detection is not a substitute for therapeutic drug monitoring. Non-genetic factors may also affect drug metabolism. These results should be interpreted in light of clinical and familial data.

* FDA-clearance of a particular assay may dictate the phenotype.

**Analytical sensitivity and specificity will be laboratory specific based on internal validation data.

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent Medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: *4/*4

Interpretation:Consistent with a Poor Metabolizer Phenotype.

Two copies of non-functional alleles were detected, consistent with a poor metabolizer phenotype. This individual’s ability to metabolize Tamoxifen is predicted to be markedly reduced, rendering tamoxifen therapy less effective. She is also at increased risk for drug-induced side effects due to diminished drug metabolism for other drugs metabolized by CYP2D6.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

Alternative therapies, such as aromatase inhibitors, could be considered.
Consultation with a clinical pharmacy professional to discuss drug and dose selection is recommended.
Additional information regarding this test is available from the laboratory (phone number)
Increased risk of drug-induced side effects; drug therapies should be closely monitored

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent Medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: Duplication: No Other Mutations Detected

Interpretation: Consistent with an Ultra-Rapid Metabolizer Phenotype.

More than two copies of the cytochrome P450 2D6 gene were detected. No other mutations were detected. This result is consistent with the duplication of a functional allele predicting an ultra-rapid metabolizer phenotype and increased Tamoxifen metabolism.

Drug metabolism may be affected by non-genetic factors. For example, co-administration of drugs that inhibit CYP2D6 activity (e.g. some antidepressants) could impair or prevent metabolism of drugs metabolized by CYP2D6 (e.g. tamoxifen).

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

This individual may require decreased dosage of Tamoxifen to obtain therapeutic response.
Treating with drugs that inhibit CYP2D6 metabolism may be effective.
Consultation with a clinical pharmacy professional to discuss drug and dose selection is recommended.
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent Medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: *2/*4xN

Interpretation: Consistent with an Extensive (Normal)-to-Intermediate* Phenotype.

One non-functional allele and one functional allele were detected in the cytochrome P450 2D6 gene, consistent with normal-to-intermediate CYP2D6activity. Some reduction in Tamoxifen metabolism is possible.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

This individual may require a higher than normal drug dosage for optimal therapeutic response.
Patient should avoid CYP2D6 inhibitors, such as Fluoxetine, Paroxetine, Quinidine, or Bupropion. A list of drugs is available at
Multiple drug therapies should be monitored closely.
Consultation with a clinical pharmacy professional to discuss drug and dose selection is recommended.
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: *10/*4

Interpretation: Consistent with an Intermediate-to-Poor Phenotype.

One non-functional allele and one decreased function allele were detected in the cytochrome P450 2D6 gene, consistent with impaired CYP2D6 metabolism (intermediate-to-poor metabolizer). This individual may have decreased Tamoxifen metabolism and at an increased risk for drug-induced side effects due to diminished drug metabolism for other drugs metabolized by CYP2D6.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

This individual may require a higher than normal drug dosage for optimal therapeutic response.
Patient should avoid CYP2D6 inhibitors, such as Fluoxetine, Paroxetine, Quinidine, or Bupropion. A list of drugs is available at
Multiple drug therapies should be monitored closely.
Consultation with a clinical pharmacy professional to discuss drug and dose selection is recommended.
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: *10XN/*41

Interpretation: Consistent with Intermediate-to-Extensive Metabolizer Phenotype.

More than two copies of the cytochrome P450 2D6 gene were detected, including two decreased function alleles. Duplication of decreased function alleles may enhance overall enzyme function leading to normal CYP2D6 activity and normal Tamoxifen metabolism.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

This individual may require a higher than normal drug dosage for optimal therapeutic response.
Patient should avoid CYP2D6 inhibitors, such as Fluoxetine, Paroxetine, Quinidine, or Bupropion. A list of drugs is available at
Multiple drug therapies should be monitored closely.
Consultation with a clinical pharmacy professional to discuss drug and dose selection is recommended.
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory

The Laboratory

1111 Laboratory Avenue

Nowhere, State 00839

(555) 920-3333

Patient Name:Jane D.

ID number: 057398468Patient and Family Information

DOB:04/05/2007Race/Ethnicity:

Gender:FemaleFamily History:

Ordering Physician: Dr. GoodPersonal history:

Date of Report:June 15, 2010Concurrent medications:

Test Performed:CYP2D6

Indication for testing: Predictive response to tamoxifen

Specimen Type: Blood

Result: *41/-

Interpretation: Consistent with an Extensive Metabolizer Phenotype.

One decreased function allele was detected in the cytochrome P450 2D6 gene. Because a functional allele may compensate for the presence of a decreased function allele, this result is consistent with normal CYP2D6activity.

Reference: Ingelman-Sundberg M, Daly AK, Nebert DW, Eds. 2009. Available in:

Guidance:

With an extensive metabolizer phenotype, Tamoxifen treatment can follow standard dosing procedures.
Patient should avoid CYP2D6 inhibitors, such as Fluoxetine, Paroxetine, Quinidine, or Bupropion. A list of drugs is available at
Additional information regarding this test is available from the laboratory (phone number)

This report was reviewed and approved by:

______

John Doe, M.D., Ph.D. Date

Director, The Molecular Laboratory