Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans
For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pha...
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MDPI AG
2021-01-01
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| Series: | Journal of Personalized Medicine |
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| Online Access: | https://www.mdpi.com/2075-4426/11/1/33 |
| _version_ | 1797415432126201856 |
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| author | Nayoung Han Jung Mi Oh In-Wha Kim |
| author_facet | Nayoung Han Jung Mi Oh In-Wha Kim |
| author_sort | Nayoung Han |
| collection | DOAJ |
| description | For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (<i>N</i> = 72,299) and CNV data (<i>N</i> = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. <i>CYP2D6</i> rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. <i>DMD</i> ranked the highest in frequency for gene gain (64.52%), while <i>TPMT</i> ranked the highest in frequency for gene loss (51.80%). Copy number gain of <i>CYP4F2</i> was observed in 22 subjects; 13 of those subjects were carriers with <i>CYP4F2</i>*3 gain. In the case of <i>TPMT</i>, approximately one-half of the participants (<i>N</i> = 308) had loss of the <i>TPMT</i>*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study. |
| first_indexed | 2024-03-09T05:47:33Z |
| format | Article |
| id | doaj.art-d757c57bbcf04860ac87fb5b726ce7f4 |
| institution | Directory Open Access Journal |
| issn | 2075-4426 |
| language | English |
| last_indexed | 2024-03-09T05:47:33Z |
| publishDate | 2021-01-01 |
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| series | Journal of Personalized Medicine |
| spelling | doaj.art-d757c57bbcf04860ac87fb5b726ce7f42023-12-03T12:19:59ZengMDPI AGJournal of Personalized Medicine2075-44262021-01-011113310.3390/jpm11010033Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in KoreansNayoung Han0Jung Mi Oh1In-Wha Kim2College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, KoreaCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, KoreaCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, KoreaFor predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (<i>N</i> = 72,299) and CNV data (<i>N</i> = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. <i>CYP2D6</i> rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. <i>DMD</i> ranked the highest in frequency for gene gain (64.52%), while <i>TPMT</i> ranked the highest in frequency for gene loss (51.80%). Copy number gain of <i>CYP4F2</i> was observed in 22 subjects; 13 of those subjects were carriers with <i>CYP4F2</i>*3 gain. In the case of <i>TPMT</i>, approximately one-half of the participants (<i>N</i> = 308) had loss of the <i>TPMT</i>*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.https://www.mdpi.com/2075-4426/11/1/33polymorphismspharmacogenes |
| spellingShingle | Nayoung Han Jung Mi Oh In-Wha Kim Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans Journal of Personalized Medicine polymorphisms pharmacogenes |
| title | Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans |
| title_full | Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans |
| title_fullStr | Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans |
| title_full_unstemmed | Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans |
| title_short | Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans |
| title_sort | combination of genome wide polymorphisms and copy number variations of pharmacogenes in koreans |
| topic | polymorphisms pharmacogenes |
| url | https://www.mdpi.com/2075-4426/11/1/33 |
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