中国汉族人群脸部特征相关SNP位点研究

doi:10.16288/j.yczz.19-355

遗传 ›› 2020, Vol. 42 ›› Issue (7): 680-690.doi: 10.16288/j.yczz.19-355

中国汉族人群脸部特征相关SNP位点研究

刘明^1,², 李祎³, 杨亚芳^2,⁴, 晏于文², 刘凡³, 李彩霞², 曾发明^1,⁵(), 赵雯婷²()

^1. 昆明医科大学法医学院,昆明 650500
^2. 公安部物证鉴定中心,现场物证溯源技术国家工程实验室,法医遗传学公安部重点实验室,北京 100038
^3. 中国科学院北京基因组研究所,中国科学院精准基因组医学重点实验室,北京 100101
^4. 山西医科大学法医学院,太原 030001
^5. 云南省公安厅刑事侦查总队,昆明 650021

收稿日期:2020-03-09 修回日期:2020-05-20 出版日期:2020-07-20 发布日期:2020-05-21
通讯作者: 曾发明,赵雯婷 E-mail:zfm1964@126.com;wtzhao@sibs.ac.cn
作者简介:刘明,在读硕士研究生,专业方向：法医物证学。E-mail: mingliu2019@foxmail.com
基金资助:
国家重点研发项目编号(2017YFC0803501);中央级公益类科研院所基本科研业务费专项资金编号(2018JB046);项目和国家科技资源共享服务平台计划项目资助编号(YCZYPT[2017]01-3);项目和国家科技资源共享服务平台计划项目资助编号(2017JB025)

Human facial shape related SNP analysis in Han Chinese populations

Ming Liu^1,², Yi Li³, Yafang Yang^2,⁴, Yuwen Yan², Fan Liu³, Caixia Li², Faming Zeng^1,⁵(), Wenting Zhao²()

^1. School of Forensic Medicine, Kuming Medical University, Kunming 650500, China
^2. National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
^3. CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100101, China
^4. School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China
^5. Criminal Investigation Police Corps, Yunnan Provincial Public Security Department, Kunming 650021, China

Received:2020-03-09 Revised:2020-05-20 Online:2020-07-20 Published:2020-05-21
Contact: Zeng Faming,Zhao Wenting E-mail:zfm1964@126.com;wtzhao@sibs.ac.cn
Supported by:
Supported by the National Key R&D Program of China No(2017YFC0803501);Central Public-Interest Scientific Institution Basal Research Fund No(2018JB046);Central Public-Interest Scientific Institution Basal Research Fund (No. 2018JB046), and the National Science and Technological Resources Platform Nos(YCZYPT[2017]01-3);Central Public-Interest Scientific Institution Basal Research Fund (No. 2018JB046), and the National Science and Technological Resources Platform Nos(2017JB025)

摘要/Abstract

摘要：

脸部形态是人类重要的生物特征之一,了解脸部形态特征的遗传基础在群体遗传学、发育生物学和法庭科学中具有重要意义。本研究针对中国汉族成年男性人群1177名个体,在高分辨率三维人脸图像的17个脸部特征点中提取出136组欧几里德距离(Euclidean distance)表型。结合3×低深度测序数据,用线性回归分析了125个已报道的与脸部形态显著相关的SNP位点和136组脸部表型之间的相关性。结果表明,在经过多重校正后,来自10个不同基因区域的12个SNP位点与一个或多个脸部特征显著相关(显著性阈值P<1.35×10 ^-3),解释了年龄和BMI指数校正后3.89%脸部表型差异。相关SNP位点包括TEX41 rs17479393,PAX3 rs974448、RAB7A/ACAD9 rs2977562、DCHS2 rs9995821、DCHS2 rs2045323、C5orf50 rs6555969、SUPT3H/RUNX2 rs1852985、MSRA rs11782517、EYA1 rs10504499、GSC rs2224309、DICER1 rs7161418和DHX35 rs2206437。本研究结果对揭示中国汉族人群脸部形态的遗传机制和脸部特征的遗传推断提供了参考数据。

关键词: 脸部形态, 线性回归, 中国汉族人群, 脸部特征相关SNP位点

Abstract:

Human facial morphology is one of the important visible biological characteristics. Understanding the genetic basis underlying facial shape traits has important implications in population genetics, developmental biology, and forensic science. This study extracted 136 Euclidean distance phenotypes from 17 facial features of high-resolution 3D facial images in 1177 Chinese Han adult males. Based on 3× low-depth sequencing data, linear regression was used to analyze the correlation between 125 reported SNPs significantly associated with facial morphology and 136 facial phenotypes. As a result, a total of twelve SNPs from ten genes demonstrated significant association with one or more facial shape traits after adjusting for multiple testing (significance threshold P < 1.35 × 10 ^-3 )_, together explaining up to 3.89% of age-, and BMI-adjusted facial phenotype variance. These included TEX41 rs17479393, PAX3 rs974448, RAB7A/ACAD9 rs2977562, DCHS2 rs9995821, DCHS2 rs2045323, C5orf50 rs6555969, SUPT3H/RUNX2 rs1852985, MSRA rs11782517, EYA1 rs10504499, GSC rs2224309, DICER1 rs7161418 and DHX35 rs2206437.These results revealed the genetics basis of facial morphology of Han Chinese population, and provided reference data for DNA-based face prediction.

Key words: facial morphology, linear regression, Chinese Han population, facial feature associated SNPs

刘明, 李祎, 杨亚芳, 晏于文, 刘凡, 李彩霞, 曾发明, 赵雯婷. 中国汉族人群脸部特征相关SNP位点研究[J]. 遗传, 2020, 42(7): 680-690.

Ming Liu, Yi Li, Yafang Yang, Yuwen Yan, Fan Liu, Caixia Li, Faming Zeng, Wenting Zhao. Human facial shape related SNP analysis in Han Chinese populations[J]. Hereditas(Beijing), 2020, 42(7): 680-690.

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参考文献 41

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			已有研究						本研究
染色体区段	基因	SNP	表型	参考文献	BETA	OR	SE	P值	EA/OA	EAF	BETA	SE	P值	定量表型
4q31.3	DCHS2	rs9995821	小柱/鼻尖	[13]	0.39	-	0.04	7.33E-19	C/T	0.21	-0.25	0.04	1.58E-08	ChL~AlL
4q31	DCHS2	rs2045323	小柱倾斜; 鼻子突出; 鼻尖角度	[11]	-	-	-	3.00E-09	A/G	0.20	-0.24	0.04	4.40E-08	ChL~AlL
8q13.3	EYA1	rs10504499	下巴	[19]	-	1.292	-	7.90E-34	G/T	0.01	-0.89	0.24	2.03E-04	EnL~ChR
6p21	SUPT3H/ RUNX2	rs1852985	鼻梁宽度	[11]	-	-	-	2.00E-08	T/C	0.28	0.15	0.04	3.05E-04	EnR~ExL
2q22.3	TEX41	rs17479393	下巴	[19]	-	0.832	-	8.10E-30	T/A	0.20	-0.17	0.05	3.29E-04	ExL~Prn
3q21.3	RAB7A/ ACAD9	rs2977562	鼻翼宽度	[13]	0.20	-	0.04	8.63E-07	G/A	0.45	0.12	0.03	3.52E-04	ExR~EnR
14q32.13	DICER1	rs7161418	下巴	[19]	-	1.106	-	1.40E-09	T/G	0.02	0.47	0.13	3.96E-04	Ls~Li
20q12	DHX35	rs2206437	鼻翼宽度	[12]	-0.28	-	0.05	1.61E-09	T/A	0.26	-0.16	0.04	4.90E-04	Prn~Sn
5q35.1	C5orf50	rs6555969	右侧颧点到鼻根点	[17]	0.41	-	0.07	1.17E-09	T/C	0.34	0.14	0.04	6.15E-04	EnR~N
14q32.13	GSC	rs2224309	鼻子大小	[19]	-	-	-	3.80E-09	A/C	0.15	-0.18	0.05	1.02E-03	Sto~Li
8p23.1	MSRA	rs11782517	鼻子大小	[19]	-	-	-	3.80E-07	C/T	0.29	-0.13	0.04	1.21E-03	ChR~Li
2q35	PAX3	rs974448	右眼到鼻根点	[17]	0.29	-	0.05	1.56E-08	G/A	0.08	-0.22	0.07	1.35E-03	ExL~Prn

染色体区段	基因	SNP	效应等位基因	其他等位基因	东亚	南亚	非洲	欧洲	美洲
2q22.3	TEX41	rs17479393	T	A	0.17	0.16	0.07	0.22	0.27
2q35	PAX3	rs974448	G	A	0.07	0.14	0.12	0.20	0.16
3q21.3	RAB7A/ACAD9	rs2977562	G	A	0.48	0.40	0.73	0.25	0.44
4q31.3	DCHS2	rs9995821	C	T	0.22	0.32	0.20	0.22	0.35
4q31	DCHS2	rs2045323	A	G	0.20	0.23	0.03	0.09	0.27
5q35.1	C5orf50	rs6555969	T	C	0.34	0.36	0.07	0.31	0.36
6p21	SUPT3H/RUNX2	rs1852985	T	C	0.24	0.11	0.17	0.13	0.27
8p23.1	MSRA	rs11782517	C	T	0.30	0.28	0.02	0.23	0.35
8q13.3	EYA1	rs10504499	G	T	0.00	0.16	0.04	0.11	0.04
14q32.13	GSC	rs2224309	A	C	0.13	0.16	0.25	0.22	0.13
14q32.13	DICER1	rs7161418	T	G	0.02	0.11	0.19	0.25	0.20
20q12	DHX35	rs2206437	T	A	0.23	0.22	0.25	0.48	0.27

中国汉族人群脸部特征相关SNP位点研究

Human facial shape related SNP analysis in Han Chinese populations

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