Copy number variations of cytochrome P450 genes in Kinh Vietnamese Cover

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Copy number variations of cytochrome P450 genes in Kinh Vietnamese

Asian Biomedicine

Volume 17 (2023): Issue 2 (April 2023)

By: Nhung Phuong Vu, Ton Dang Nguyen, Binh Huy Nguyen, Duong Thuy Nguyen, Hai Van Nong and Ha Hai Nguyen

Open Access

|Sep 2023

Figures & Tables

Graphical illustration of CYP450 CNVs identified in current study. (A) Reference gen locus of CYP1B1 (up) and CYP1B1Dup allele (down). CYP1B1 located on chromosome 2 and represented by yellow boxes. (B) Reference gen locus on chromosome 19 of CYP2A6 (orange box) and pseudogene CYP2A7 (grey box) (up) and CYP2A6Del allele (down), downstream of exon 9 of CYP2A6 is denoted by the black boxes. Primers position and strategy used for CYP2A6 del allele detection are also shown. (C) Reference gene cluster on chromosome 10 including CYP2C9 (blue box), CYP2C8 (green box) (up), and CYP2C9 Del allele (down). (D) Reference gen locus of CYP2E1 (pink box) on chromosome 10 (up), CYP2E1Del allele (middle), and CYP2E1Dup allele with 2 copies of the gene (down). CNVs, copy number variations.

Copy number confirmation of CYP2A6Del. (A) Amplification of a part of CYP2A6 gene or hybrid CYP2A7/2A6 using primer pair 2AE7F/2A6R1 resulting in approximately 2 kb products. (B) Detection of CYP2A6Del allele, Wt: Wild-type allele, Del: Deletion allele. CYP2A6 genotype of tested samples were as follows: FVN48: Wt/Del, FVN74: Del/Del, FVN79: Wt/Wt.

Copy number confirmation of CYP1B1, CYP2C9, and CYP2E1. Primers for real-time PCR located in exon 1 and exon 2 of CYP1B1, exons 4 and 7 of CYP2C9, exons 8 and 9 of CYP2E1 were used to confirm CNVs detected by MLPA in these genes. REF: reference samples, in which MLPA showing 2 copies of gene of interest. (A) Heterozygous duplications of CYP1B1 detected in both FVN 96 and MVN 21. (B) Heterozygous deletions of CYP2C9 were found in both MVN 21 and MVN 23. (C) Copy number confirmation of CYP2E1 showed that heterozygous deletion was detected in FVN 73 while heterozygous duplications were identified in FVN 46, FVN 98, Kinh 712 and DB98. CNVs, copy number variations; MLPA, multiplex ligation-dependent probe amplification.

Comparison of CYP450 CNVs frequency between Kinh Vietnamese and worldwide populations

Population	N	Alleles/copy number of CYP2A6			References

		Dup (2)	Wt (1)	Del (0)
CYP2A6 copy number alleles frequency
Kinh Vietnamese	154	ND	0.89	0.11	Present study
Chinese	96	-	0.849	0.151	[9]
Finns	100	-	0.96	0.001^***
Spaniards	100	-	0.965	0.005^***
Korean	209	-	0.885	0.11	[10]
Japanese	92	-	0.799	0.201^**	[11]
African-American	105	0.01	0.952	0.038^**	[2]
Asian	102	0.015	0.902	0.083^**
Caucasian	103	ND	0.985	0.015^***
Hispanic	109	ND	0.986	0.014^***
Ashkenazi Jews	123	0.02^*	0.98	ND^***
Colombian	123	0.004	0.976	0.02^***	[12]

Primers sequence for real-time PCR detecting copy number of CYP1B1, CYP2C9, and CYP2E1

Gene-region	Primer name	Sequence (5′-3′)
CYP1B1 Exon 1	CYP1B1 E1F	CTG CGACTCCAGTTGTGAGAG C
CYP1B1 Exon 1	CYP1B1 E1R	AGTCTCTTGGCGTCG TCAGTG
CYP1B1 Exon 2	CYP1B1 E2F	CACAGCATGATGCGCAACTTC
CYP1B1 Exon 2	CYP1B1 E2R	CACTCATGACGTTGGCCA CG
CYP2C9 Exon 4	CYP2C9 E4F	ATGCATGCCGAACTCTTTTT
CYP2C9 Exon 4	CYP2C9 E4R2	AGGATGAAAGTGGGATCACAGG
CYP2C9 Exon 7	CYP2C9 E7F	CACATTTGTGCATCTGTAACCA
CYP2C9 Exon 7	CYP2C9 E7R3	CCGGTTTCTGCCAATCACACG
CYP2E1 Exon 8	CYP2E1 E8F	GGCACAGTCGTAGTGCCAACTC
CYP2E1 Exon 8	CYP2E1 E8R	CTGCCTCTGATCTTTCTCACCTG
CYP2E1 Exon 9	CYP2E1 E9F	TGGAGAAGGCCTGGCTCGCATG
CYP2E1 Exon 9	CYP2E1 E9R	GTTCAGGGTGTCCTCCACACAC

Primer used for genotyping the CYP2A6 deletion and duplication alleles [9]

Primer name	Sequence (5′-3′)
2A E7F	GRC CAA CAT GCC CTA CAT G
2A6R1	GCA CTT ATG TTT TGT GAG ACA TCA GAG ACA A
2A6E8F	CAC TTC CTG AAT GAG
2A7E8F	CAT TTC CTG GAT GAC
2A6R2	AAA ATG GGC ATG AAC GCC C

Final probe ratio from MLPA of representative samples carrying CYP450 copy number alterations

Samples	*CYP1B1*		*CYP2A6*				*CYP2C9*					*CYP2E1*

	Exon 2	Exon 3	Exon 1	Exon 2	Exon 3	Exon 5	Exon 1	Exon 7	Exon 8-1	Exon 8-2	Exon 9	Exon 5	Exon 6	Exon 8
FVN48	0.89	0.87	0.41	0.42	0.5	0.43	1.1	1.18	1.16	1.06	0.92	0.95	0.93	0.88
FVN74	0.89	0.85	0	0	0	0	1	1	1	0.96	0.99	1.02	0.94	1.11
MVN23	1.34	1.53	1.15	1.14	1.16	1.15	0.47	0.55	0.61	0.56	0.58	1.09	1.08	0.99
FVN73	1.08	0.99	1.05	1.07	1.04	1.08	1	0.99	0.98	0.92	0.96	0.51	0.51	0.47
FVN46	1.04	1.1	0.94	0.92	1.17	1.2	1.17	1.03	1.1	0.82	0.93	1.37	1.38	1.63
FVN98	0.86	0.86	0.97	0.98	1.16	0.91	1.06	0.96	1.02	1.28	1.11	1.36	1.37	1.37

Alleles frequency of CYP450 copy number variability

Allele/copies	Gene/alleles frequency (n = 308)

	*CYP1B1*		*CYP2A6*		*CYP2C9*		*CYP2E1*

	Freq.	95% CI	Freq.	95% CI	Freq.	95% CI	Freq.	95% CI
Dup (2)	0.010	0.000–0.010	-	-	-	-	0.010	0.000–0.021
Wt (1)	0.990	0.980–1.000	0.890	0.852–0.927	0.990	0.980–1.000	0.987	0.974–1.000
Del (0)	-	-	0.110	0.073–0.148	0.010	0.000–0.021	0.003	0.000–0.010

Genotypes frequency of CYP450 copy number variability

Genotype	Gene/genotypes frequency

	*CYP1B1*		*CYP2A6*		*CYP2C9*		*CYP2E1*

	N	Freq. (%)	N	Freq. (%)	N	Freq. (%)	N	Freq. (%)
Wt/Del	0	0	26/154	16.88	3/154	1.95	1/154	0.65
Del/Del	0	0.00	4/154	2.60	0	0.00	0	0.00
Wt/Dup	3/154	1.95	0/154	0.00	0	0.00	3/154	1.95
Wt/Wt	151/154	98.05	124/154	80.52	151/154	98.05	150/54	97.40

DOI: https://doi.org/10.2478/abm-2023-0048 | Journal eISSN: 1875-855X | Journal ISSN: 1905-7415

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Language: English

Page range: 84 - 92

Published on: Sep 17, 2023

Published by: Chulalongkorn University

In partnership with: Paradigm Publishing Services

Publication frequency: 6 issues per year

Keywords:

drug metabolism,

genetic variants,

pharmacogenetics

Related subjects:

Assistive professions, nursing,

Basic medical science,

Basic medical science, other,

Clinical medicine,

Clinical medicine, other

© 2023 Nhung Phuong Vu, Ton Dang Nguyen, Binh Huy Nguyen, Duong Thuy Nguyen, Hai Van Nong, Ha Hai Nguyen, published by Chulalongkorn University
This work is licensed under the Creative Commons Attribution 4.0 License.

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