Genome-Wide Analysis of Protein-Coding Variants in Leprosy

Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding...

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Published inJournal of investigative dermatology Vol. 137; no. 12; pp. 2544 - 2551
Main Authors Liu, Hong, Wang, Zhenzhen, Li, Yi, Yu, Gongqi, Fu, Xi’an, Wang, Chuan, Liu, Wenting, Yu, Yongxiang, Bao, Fangfang, Irwanto, Astrid, Liu, Jian, Chu, Tongsheng, Andiappan, Anand Kumar, Maurer-Stroh, Sebastian, Limviphuvadh, Vachiranee, Wang, Honglei, Mi, Zihao, Sun, Yonghu, Sun, Lele, Wang, Ling, Wang, Chaolong, You, Jiabao, Li, Jinghui, Foo, Jia Nee, Liany, Herty, Meah, Wee Yang, Niu, Guiye, Yue, Zhenhua, Zhao, Qing, Wang, Na, Yu, Meiwen, Yu, Wenjun, Cheng, Xiujun, Khor, Chiea Chuen, Sim, Kar Seng, Aung, Tin, Wang, Ningli, Wang, Deyun, Shi, Li, Ning, Yong, Zheng, Zhongyi, Yang, Rongde, Li, Jinlan, Yang, Jun, Yan, Liangbin, Shen, Jianping, Zhang, Guocheng, Chen, Shumin, Liu, Jianjun, Zhang, Furen
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 01.12.2017
Subjects
Alleles
Asian Continental Ancestry Group
Autophagy
CARD Signaling Adaptor Proteins - genetics
Case-Control Studies
China
Cohort Studies
Endocytosis
Exome
Female
Gene Frequency
Genetic Predisposition to Disease
Genetic Variation
Genome-Wide Association Study
Genotype
Humans
Leprosy - ethnology
Leprosy - genetics
Male
Phagocytosis
Polymorphism, Single Nucleotide
Reproducibility of Results
Skin - metabolism
GO
GWAS
MAF
OR
SNP
Online AccessGet full text
ISSN0022-202X
1523-1747
1523-1747
DOI10.1016/j.jid.2017.08.004

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Abstract Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10–9, odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10–8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10–10, OR = 1.36), rs146466242 in FLG (P = 3.39 × 10–12, OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10–6, OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10–9, OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10–7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.
AbstractList Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10-9, odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10-8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10-10, OR = 1.36), rs146466242 in FLG (P = 3.39 × 10-12, OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10-6, OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10-9, OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10-7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10-9, odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10-8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10-10, OR = 1.36), rs146466242 in FLG (P = 3.39 × 10-12, OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10-6, OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10-9, OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10-7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.
Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10–9, odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10–8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10–10, OR = 1.36), rs146466242 in FLG (P = 3.39 × 10–12, OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10–6, OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10–9, OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10–7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.
Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10 , odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10 , OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10 , OR = 1.36), rs146466242 in FLG (P = 3.39 × 10 , OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10 , OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10 , OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10 , OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.
Author Liu, Jianjun
Yu, Gongqi
Chu, Tongsheng
Wang, Chaolong
Niu, Guiye
Sun, Yonghu
Yang, Rongde
Zheng, Zhongyi
Liu, Wenting
Bao, Fangfang
Zhao, Qing
Irwanto, Astrid
Andiappan, Anand Kumar
Yu, Yongxiang
Wang, Ling
Liany, Herty
Wang, Deyun
You, Jiabao
Zhang, Guocheng
Chen, Shumin
Wang, Honglei
Limviphuvadh, Vachiranee
Wang, Ningli
Cheng, Xiujun
Li, Jinlan
Foo, Jia Nee
Li, Yi
Yu, Meiwen
Meah, Wee Yang
Li, Jinghui
Liu, Jian
Shi, Li
Wang, Chuan
Maurer-Stroh, Sebastian
Wang, Na
Khor, Chiea Chuen
Fu, Xi’an
Yan, Liangbin
Ning, Yong
Zhang, Furen
Yang, Jun
Shen, Jianping
Liu, Hong
Aung, Tin
Sun, Lele
Yu, Wenjun
Mi, Zihao
Yue, Zhenhua
Sim, Kar Seng
Wang, Zhenzhen
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/28842327$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
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1523-1747
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Issue 12
Keywords GO
GWAS
MAF
OR
SNP
Language English
License This is an open access article under the CC BY-NC-ND license.
Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
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Snippet Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility,...
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SubjectTerms Alleles
Asian Continental Ancestry Group
Autophagy
CARD Signaling Adaptor Proteins - genetics
Case-Control Studies
China
Cohort Studies
Endocytosis
Exome
Female
Gene Frequency
Genetic Predisposition to Disease
Genetic Variation
Genome-Wide Association Study
Genotype
Humans
Leprosy - ethnology
Leprosy - genetics
Male
Phagocytosis
Polymorphism, Single Nucleotide
Reproducibility of Results
Skin - metabolism
Title Genome-Wide Analysis of Protein-Coding Variants in Leprosy
URI https://dx.doi.org/10.1016/j.jid.2017.08.004
https://www.ncbi.nlm.nih.gov/pubmed/28842327
https://www.proquest.com/docview/1932840574
Volume 137
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