Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants
Abstract
:1. Introduction
2. Materials and Methods
2.1. The 1000 Genomes Project
2.2. Functional Variant Determination
2.3. Constructing Haplogroups
2.4. Assignment of Star Alleles
2.5. Evaluation
2.6. Enrichment Analysis
2.7. Genomic Features of Star Alleles
3. Results
3.1. Haplogroup Construction
3.2. Evaluate Haplogroup Construction
3.3. Genomic Characterization of Star Alleles by Haplogroups
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Correction Statement
References
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Gene | Gene Length a | Haplogroups (Variant) | Observed Star Alleles b (Variant) | TotalStar Alleles c (Variant) | VI |
---|---|---|---|---|---|
IFNL3 | 1.40 | 8 (4) | 2 (1) | 4 (3) | 0.98 |
GSTP1 | 3.06 | 4 (2) | 3 (2) | 4 (2) | 1.37 |
CYP2D6 | 4.42 | 13 (4) | 38 (37) | 131 (125) | 1.76 |
VKORC1 | 5.14 | 7 (5) | 2 (1) | 2 (1) | 1.04 |
NUDT15 | 9.66 | 2 (1) | 7 (5) | 20 (18) | 1.23 |
NAT2 | 9.97 | 8 (3) | 11 (10) | 18 (17) | 0.96 |
UGT1A1 | 13.05 | 4 (2) | 5 (3) | 9 (6) | 1.36 |
G6PD | 16.18 | 2 (1) | 21 (19) | 186 (182) | 1.38 |
CYP4F2 | 20.10 | 4 (2) | 3 (2) | 4 (2) | 2.00 |
GSTM1 | 21.23 | 16 (4) | 2 (1) | 3 (1) | 3.24 |
UGT2B15 | 24.00 | 12 (4) | 5 (3) | 11 (4) | 1.35 |
TPMT | 26.76 | 4 (2) | 13 (12) | 46 (45) | 1.47 |
CYP2B6 | 27.10 | 13 (4) | 15 (7) | 37 (35) | 2.10 |
CYP3A4 | 27.29 | 8 (3) | 20 (19) | 33 (32) | 2.28 |
CYP3A5 | 31.81 | 5 (3) | 4 (3) | 9 (8) | 0.88 |
CYP2C8 | 32.73 | 7 (3) | 11 (11) | 18 (18) | 2.40 |
CYP2C9 | 50.73 | 4 (2) | 21 (20) | 71 (69) | 1.57 |
NAT1 | 53.21 | 14 (5) | 7 (6) | 11 (10) | 2.27 |
UGT1A4 | 54.52 | 4 (2) | 7 (10) | 12 (12) | 1.98 |
CACNA1S | 73.05 | 8 (3) | 1 (0) | 3 (2) | 2.37 |
SLCO1B1 | 108.05 | 16 (4) | 23 (16) | 44 (31) | 3.06 |
RYR1 | 153.87 | 8 (3) | 2 (1) | 49 (48) | 1.27 |
CYP2C19 | 165.11 | 8 (3) | 17 (17) | 36 (33) | 2.15 |
CFTR | 250.19 | 9 (4) | 9 (8) | 41 (40) | 2.05 |
DPYD | 843.31 | 4 (2) | 39 (39) | 83 (83) | 4.08 |
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Ahn, S.H.; Park, Y.; Kim, J.H. Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants. Genes 2024, 15, 521. https://doi.org/10.3390/genes15040521
Ahn SH, Park Y, Kim JH. Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants. Genes. 2024; 15(4):521. https://doi.org/10.3390/genes15040521
Chicago/Turabian StyleAhn, Se Hwan, Yoomi Park, and Ju Han Kim. 2024. "Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants" Genes 15, no. 4: 521. https://doi.org/10.3390/genes15040521
APA StyleAhn, S. H., Park, Y., & Kim, J. H. (2024). Contradiction in Star-Allele Nomenclature of Pharmacogenes between Common Haplotypes and Rare Variants. Genes, 15(4), 521. https://doi.org/10.3390/genes15040521