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Table 2 Genotype’s counts for the 13 variants described as related to breast cancer medications in Italian isolated populations

From: Pharmacogenetics driving personalized medicine: analysis of genetic polymorphisms related to breast cancer medications in Italian isolated populations

Snp Id

(gene)

Functional

annotation

Level of evidence

Druga

Minor

Major

Parameters

Risk allele

Genotype

(A1A1-A1A2-A2A2)

A

 rs4244285

(CYP2C19)

exonic,

synonymous

4

Doxorubicin, cyclophosphamide, tamoxifen

A

G

Efficacy

A (FVG freq <1000G/ExAC)

3AA-48AG-265GG

 rs714368

(SLC22A16 )

exonic,

nonsynonymous

4

Doxorubicin, doxorubicinol, cyclophosphamide

C

T

Toxicity

T (FVG freq >1000G/ExAC)

118CC-618CT-836TT

 rs4880

(SOD2)

exonic,

nonsynonymous

2B/3*

Cyclophosphamide/tamoxifen

A

G

Efficacy

G (FVG freq >1000G/ExAC)

110GG-157GA-49AA

 rs1801274

(FCGR2A)

exonic,

nonsynonymous

2B

Trastuzumab, doxorubicin, paclitaxel, cyclophosphamide

G

A

Efficacy

G (FVG freq <1000G/ExAC)

289GG-741GA-542AA

 rs1136201

(ERBB2)

exonic,

nonsynonymous

3

Trastuzumab

G

A

Toxicity

G (FVG freq <1000G/ExAC)

49GG - 437GA - 1095AA

 rs2297595

(DPYD)

exonic,

nonsynonymous

2A

Capecitabine, fluorouracil

C

T

Toxicity

C (FVG freq <1000G/ExAC)

20CC-247CT-1314TT

 rs3918290

(DPYD)

splicing,

NA

1

Capecitabine, fluorouracil

T

C

Toxicity

T (FVG freq <1000G/ExAC)

0TT-2TC-1579CC

 rs1048943

(CYP1A1)

exonic,

nonsynonymous

3

Docetaxel, capecitabine

C

T

Efficacy

T (FVG freq >1000G/ExAC)

6CC-189CT-1386TT

 rs776746b

(CYP3A5)

splicing,

NA

3/Not reported

Paclitaxel/tamoxifene

T

C

Toxicity

T (FVG freq >1000G)

18TT-216TC-1337CC

B

 rs2369049

(TCL1A)

intergenic,

NA

Not reported

Exemestane, anastrozole

G

A

Not defined

Not defined

18GG-315GA-1247AA

 rs2072671

(CDA)

exonic,

nonsynonymous

Not reported

Capecitabine

C

A

Not defined

Not defined

255CC-721CA-605AA

 rs180  1159

(DPYD)

exonic,

nonsynonymous

Not reported

Capecitabine

C

T

Not defined

Not defined

84CC-518CT-979TT

 rs6214

(IGF1)

UTR3,NA

Not reported

Tamoxifen

T

C

Not defined

Not defined

198TT-707TC-666CC

  1. A) variants that show significant difference in frequency between FVG sample set and EUR/ExAC populations in terms of level of association with drug response
  2. B) variants that don’t show a level of evidence for drug response
  3. As in most case the association has been evaluated in the context of polychemotherapeutic regimens, the most likely drug related to the target polymorphism is reported in italic
  4. Snp id (gene) variant name, gene name, Functional annotation functional annotation for the variant, Level of evidence based on the amount of evidence reported at https://www.pharmgkb.org/that supports the association, Drug a medication reported to be correlated with a variant/gene after checking the literature thus filtering out the non-significative association reported in PharmGKB database, Minor minor allele, Major major allele, Genotype genotype’s count for FVG population
  5. Most of the studies were conduced in the context of polychemitherapeutic regimens; in such studies the drugs most likely related to the targeted polymorphisms according to the available literature are highlighted in italics; Parameters reported by PharmaGKB database. efficacy poor outcome, toxicity significant side effects, Risk allele risk allele reported in literature.b for variant rs776746 data for this variant was not available in the ExAC database at the time of the analysis, Genotype genotype’s counts
  6. Level 1A: annotation for a variant-drug combination in a CPIC or medical society-endorsed PGx guideline, or implemented at a PGRN site or in another major health system; Level 1B: annotation for a variant-drug combination where the preponderance of evidence shows an association. The association must be replicated in more than one cohort with significant p-values, and preferably will have a strong effect size; Level 2A: annotation for a variant-drug combination that qualifies for level 2B where the variant is within a VIP (very important pharmacogene) as defined by PharmGKB. The variants in level 2A are in known pharmacogenes, so functional significance is more likely; Level 2B: annotation for a variant-drug combination with moderate evidence of an association. The association must be replicated but there may be some studies that do not show statistical significance, and/or the effect size may be small; Level 3: annotation for a variant-drug combination based on a single significant (not yet replicated) or annotation for a variant-drug combination evaluated in multiple studies but lacking clear evidence of an association; Level 4: annotation based on a case report, non-significant study or in vitro, molecular or functional assay evidence only
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Journal of Translational Medicine

ISSN: 1479-5876

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