Screening for pathogenic variants in obese cohort using whole-exome sequencing

doi:10.3969/j.issn.1674-8115.2023.07.010

Abstract

Abstract:

Objective ·To screen mutations of key genes in the leptin-melanocyte stimulating hormone (LEP-MSH) pathway by whole-exome sequencing (WES) in the obese cohort. Methods ·A total of 119 obese patients aged 17－65 years old with body mass index (BMI)≥34 kg/m², who underwent laparoscopic sleeve gastrectomy from January 2011 to July 2019 at Shanghai Sixth People′s Hospital, Shanghai Jiao Tong University School of Medicine were collected. The peripheral blood samples of the research subjects were collected, and whole genome DNA was extracted to perform WES. Bioinformatic methods were applied to detect the mutations in 16 genes in the LEP-MSH pathway (ADCY3, AGRP, BDNF, KSR2, LEP, LEPR, MC3R, MC4R, MCHR1, MRAP2, NTRK2, PCSK1, PHIP, POMC, SH2B1,and SIM1). Rare variants with the minor allele frequency in the total population less than 0.02 and in the East Asian population less than 0.01 in the 1000 Genome (1000G), Exome Aggregation Consortium (ExAC) and Genome Aggregation Database (gnomAD) were selected for subsequent analysis. Six pieces of prediction software were used to evaluate the deleteriousness of the mutations. Finally, based on the clinical information of each patient, the pathogenicity of all variants was determined according to the guidelines of America College of Medical Genetics and Genomics (ACMG), and only the "pathogenic", "likely pathogenic", and "uncertain significance" variants were retained. Results ·A total of 26 variants, 22 kinds of variants were detected in 24 patients from 119 subjects, all of which were heterozygous mutations. The detected variants included 7 in SH2B1 gene (accounting for 26.92% of the total variants), 4 in MCHR1 gene (accounting for 15.38%), 3 in PHIP gene (accounting for 11.53%), 2 in ADCY3 and LEPR genes (accounting for 7.69%, respectively), and 1 in LEP, NTRK2, AGRP, KSR2, MC3R, MC4R, BDNF, and PCSK1 genes, respectively (accounting for 3.85%, respectively). There were 3 patients having the same mutation site in SH2B1 gene, and 2 patients having the same mutation sites in LEPR gene and MCHR1 gene, respectively. In addition, among these mutations, there were 12 ones not included in the East Asian population in 3 public databases, which were novel mutations in the East Asian population, located in SH2B1 (p.V209I, p.R67C, and p.L149F), KSR2 (p.P155T), LEP (p.D106N), LEPR (p.W132R), PHIP (p.K1461R), BDNF (p.N84S), PCSK1 (p.R282W), NTRK2 (p.T732M), MC3R (p.S71P), and MC4R (p.W174X). Conclusion ·A total of 22 kinds of rare variations possibly associated with obesity in the LEP-MSH pathway are detected, 12 of which are novel in the East Asian population.

Key words: obesity, whole-exome sequencing (WES), leptin-melanocyte stimulating hormone pathway, gene mutation

CLC Number:

R589.2

WANG Jinghui, ZHANG Hong, ZHANG Rong, PENG Danfeng, YU Hairong, CHEN Xianghui, XUAN Ye, HU Cheng, GU Yunjuan. Screening for pathogenic variants in obese cohort using whole-exome sequencing[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2023, 43(7): 882-889.

Figures/Tables 3

TrendMD

References 32

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Sample ID	ACMG	Gene	Chromosome	Position	dbSNP	MAF in EAS	SNV class	DNA/AA change	Degree of damage	GERP score
1	Pathogenic	NTRK2	chr9	87635191	rs367769334	Novel	Nonsynonymous	c.C2195T/p.T732M	DVS	6.16
2	Likely pathogenic	MCHR1	chr22	41077612	rs182594063	0.001 0	Nonsynonymous	c.C949T/p.R317W	DS	4.19
3	VUS	MCHR1	chr22	41077832	rs190547628	0.007 4	Nonsynonymous	c.G1169A/p.R390H	D	5.40
4	VUS	SH2B1	chr16	28878040	‒	Novel	Nonsynonymous	c.G625A/p.V209I	B	-1.84
5	Pathogenic	AGRP	chr16	67516606	rs199927717	0.001 0	Nonsynonymous	c.G332A/p.R111H	DS	6.17
6	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
7	VUS	KSR2	chr12	118199252	‒	Novel	Nonsynonymous	c.C463A/p.P155T	B	2.72
8	Likely pathogenic	LEP	chr7	127894628	‒	Novel	Nonsynonymous	c.G316A/p.D106N	D	3.86
9	Pathogenic	LEPR	chr1	66038032	‒	Novel	Nonsynonymous	c.T394C/p.W132R	DS	4.17
10	Pathogenic	LEPR	chr1	66038032	‒	Novel	Nonsynonymous	c.T394C/p.W132R	DS	4.17
11	VUS	ADCY3	chr2	25050847	rs78678013	0.000 6	Nonsynonymous	c.G2356A/p.A786T	DW	4.50
12	Pathogenic	PHIP	chr6	79655966	‒	Novel	Nonsynonymous	c.A4382G/p.K1461R	D	6.17
13	Pathogenic	MC3R	chr20	54824110	‒	Novel	Nonsynonymous	c.T211C/p.S71P	D	4.00
14	Pathogenic	SH2B1	chr16	28877614	rs781063312	Novel	Nonsynonymous	c.C199T/p.R67C	DS	4.71
	Pathogenic	SH2B1	chr16	28878223	rs561413284	0.001 9	Nonsynonymous	c.C808T/p.R270W	DS	3.96
15	Likely pathogenic	MCHR1	chr22	41077283	rs188147970	0.003 0	Nonsynonymous	c.C620T/p.A207V	D	5.02
16	VUS	BDNF	chr11	27679861	‒	Novel	Nonsynonymous	c.A251G/p.N84S	B	-9.56
17	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
18	Pathogenic	PCSK1	chr5	95748060	rs773564429	Novel	Nonsynonymous	c.C844T/p.R282W	DVS	0.38
19	Pathogenic	SH2B1	chr16	28877860	‒	Novel	Nonsynonymous	c.C445T/p.L149F	D	3.47
20	Likely pathogenic	PHIP	chr6	79650578	rs182783944	0.001 0	Nonsynonymous	c.G5298A/p.M1766I	D	5.92
21	VUS	MCHR1	chr22	41077832	rs190547628	0.007 4	Nonsynonymous	c.G1169A/p.R390H	D	5.40
22	Pathogenic	MC4R	chr18	58039062	rs878909905	Novel	Stopgain	c.G521A/p.W174X	D	5.85
23	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
24	Pathogenic	ADCY3	chr2	25042876	rs750100505	0.000 1	Nonsynonymous	c.G3363C/p.K1121N	DS	3.81
	VUS	PHIP	chr6	79655019	rs769344926	0.000 1	Nonsynonymous	c.A4826C/p.Q1609P	B	4.77

Sample ID	ACMG	Gene	Chromosome	Position	dbSNP	MAF in EAS	SNV class	DNA/AA change	Degree of damage	GERP score
1	Pathogenic	NTRK2	chr9	87635191	rs367769334	Novel	Nonsynonymous	c.C2195T/p.T732M	DVS	6.16
2	Likely pathogenic	MCHR1	chr22	41077612	rs182594063	0.001 0	Nonsynonymous	c.C949T/p.R317W	DS	4.19
3	VUS	MCHR1	chr22	41077832	rs190547628	0.007 4	Nonsynonymous	c.G1169A/p.R390H	D	5.40
4	VUS	SH2B1	chr16	28878040	‒	Novel	Nonsynonymous	c.G625A/p.V209I	B	-1.84
5	Pathogenic	AGRP	chr16	67516606	rs199927717	0.001 0	Nonsynonymous	c.G332A/p.R111H	DS	6.17
6	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
7	VUS	KSR2	chr12	118199252	‒	Novel	Nonsynonymous	c.C463A/p.P155T	B	2.72
8	Likely pathogenic	LEP	chr7	127894628	‒	Novel	Nonsynonymous	c.G316A/p.D106N	D	3.86
9	Pathogenic	LEPR	chr1	66038032	‒	Novel	Nonsynonymous	c.T394C/p.W132R	DS	4.17
10	Pathogenic	LEPR	chr1	66038032	‒	Novel	Nonsynonymous	c.T394C/p.W132R	DS	4.17
11	VUS	ADCY3	chr2	25050847	rs78678013	0.000 6	Nonsynonymous	c.G2356A/p.A786T	DW	4.50
12	Pathogenic	PHIP	chr6	79655966	‒	Novel	Nonsynonymous	c.A4382G/p.K1461R	D	6.17
13	Pathogenic	MC3R	chr20	54824110	‒	Novel	Nonsynonymous	c.T211C/p.S71P	D	4.00
14	Pathogenic	SH2B1	chr16	28877614	rs781063312	Novel	Nonsynonymous	c.C199T/p.R67C	DS	4.71
	Pathogenic	SH2B1	chr16	28878223	rs561413284	0.001 9	Nonsynonymous	c.C808T/p.R270W	DS	3.96
15	Likely pathogenic	MCHR1	chr22	41077283	rs188147970	0.003 0	Nonsynonymous	c.C620T/p.A207V	D	5.02
16	VUS	BDNF	chr11	27679861	‒	Novel	Nonsynonymous	c.A251G/p.N84S	B	-9.56
17	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
18	Pathogenic	PCSK1	chr5	95748060	rs773564429	Novel	Nonsynonymous	c.C844T/p.R282W	DVS	0.38
19	Pathogenic	SH2B1	chr16	28877860	‒	Novel	Nonsynonymous	c.C445T/p.L149F	D	3.47
20	Likely pathogenic	PHIP	chr6	79650578	rs182783944	0.001 0	Nonsynonymous	c.G5298A/p.M1766I	D	5.92
21	VUS	MCHR1	chr22	41077832	rs190547628	0.007 4	Nonsynonymous	c.G1169A/p.R390H	D	5.40
22	Pathogenic	MC4R	chr18	58039062	rs878909905	Novel	Stopgain	c.G521A/p.W174X	D	5.85
23	VUS	SH2B1	chr16	28883185	rs200463987	0.005 1	Nonsynonymous	c.T386C/p.M129T	DW	5.14
24	Pathogenic	ADCY3	chr2	25042876	rs750100505	0.000 1	Nonsynonymous	c.G3363C/p.K1121N	DS	3.81
	VUS	PHIP	chr6	79655019	rs769344926	0.000 1	Nonsynonymous	c.A4826C/p.Q1609P	B	4.77

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