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Integrative Network Analysis of Multi-Omics Data in the Link between Plasma Carotenoid Concentrations and Lipid Profile 血浆类胡萝卜素浓度与脂质图谱之间联系的多密克戎数据的综合网络分析
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-11-26 DOI: 10.1159/000503828
Bénédicte L. Tremblay, F. Guénard, B. Lamarche, L. Pérusse, M. Vohl
Introduction: Carotenoids, which are a reliable biomarker of fruit and vegetable consumption, are positively associated with the lipid profile. Circulating carotenoid concentrations may interact with several omics profiles including genome, transcriptome, and epigenome. Few studies have used multi-omics approaches, and they rarely include environmental factors, such as diet. Objective: The objective of this observational study was to examine the potential role of multi-omics data in the interconnection between diet, represented by total carotenoids, and lipid profile using weighted gene correlation network analysis (WGCNA). Methods: Blood leukocyte DNA methylation levels of 472,245 CpG sites and whole blood gene expression levels of 18,160 transcripts were tested for associations with total carotenoid concentrations using regressions in 48 healthy subjects. WGCNA was used to identify co-omics modules and hub genes related to the lipid profile. Results: Among genes associated with total carotenoid concentrations, a total of 236 genes were identified at both DNA methylation and gene expression levels. Using WGCNA, six modules, consisting of groups of highly correlated genes represented by colors, were identified and linked to the lipid profile. Probes clustered in the turquoise and green modules correlated with plasma lipid concentrations. A total of 28 hub genes were identified. Conclusions: Genome-wide DNA methylation and gene expression levels were both associated with plasma total carotenoid concentrations. Several hub genes, mostly involved in lipid metabolism and inflammatory response with several genetic variants associated with plasma lipid concentrations, came out of the integrative analysis. This provides a comprehensive understanding of the interactive molecular system between carotenoids, omics, and plasma lipid profile.
引言:类胡萝卜素是水果和蔬菜消费的可靠生物标志物,与脂质状况呈正相关。循环类胡萝卜素浓度可能与几种组学特征相互作用,包括基因组、转录组和表观基因组。很少有研究使用多组学方法,也很少包括饮食等环境因素。目的:本观察性研究的目的是使用加权基因相关网络分析(WGCNA)来检验以总类胡萝卜素为代表的多组学数据在饮食和脂质图谱之间的相互联系中的潜在作用。方法:在48名健康受试者中,使用回归法检测472245个CpG位点的血液白细胞DNA甲基化水平和18160个转录物的全血基因表达水平与总类胡萝卜素浓度的相关性。WGCNA用于鉴定与脂质图谱相关的共组学模块和枢纽基因。结果:在与总类胡萝卜素浓度相关的基因中,共有236个基因在DNA甲基化和基因表达水平上被鉴定。使用WGCNA,鉴定了六个模块,由以颜色表示的高度相关的基因组组成,并将其与脂质图谱联系起来。聚集在绿松石和绿色模块中的探针与血浆脂质浓度相关。共鉴定出28个枢纽基因。结论:全基因组DNA甲基化和基因表达水平均与血浆总类胡萝卜素浓度有关。综合分析得出了几个中枢基因,主要参与脂质代谢和炎症反应,并有几个与血脂浓度相关的遗传变异。这提供了对类胡萝卜素、组学和血脂谱之间相互作用的分子系统的全面理解。
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引用次数: 5
Adiponectin Gene Variant rs266729 Interacts with Different Macronutrient Distribution of Two Different Hypocaloric Diets 脂联素基因变体rs266729与两种不同低热量饮食中不同常量营养素分布的相互作用
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-11-20 DOI: 10.1159/000503863
D. D. de Luis, D. Primo, O. Izaola, R. Aller
Background: The role of ADIPOQ gene variants in weight loss after different dietary fat amounts remains unclear. Objective: Our aim was to analyze the effects of ADIPOQ gene polymorphism rs266729 on metabolic changes after two different amounts of dietary fat in two hypocaloric diets. Design: A population of 283 obese patients was recruited in a randomized clinical trial with two diets: Diet HF (high-fat diet: 38% carbohydrates, 24% proteins, and 38% fats) versus Diet LF (low-fat diet: 53% carbohydrates, 20% proteins, and 27% fats). Before and after 3 months, an anthropometric evaluation, an assessment of nutritional intake, and a biochemical analysis were carried out. The variant of the ADIPOQgene was assessed by real-time PCR. Results: Weight loss was similar with both diets in both genotypes (CC vs. CG+GG). After dietary intervention with Diet HF, only subjects with CC genotype showed a significant improvement in insulin levels (–3.3 ± 0.6 vs. –1.8 ± 0.9 mU/L; p = 0.03) and the homeostasis model assessment for insulin resistance (HOMA-IR) (–1.3 ± 0.1 vs. –0.8 ± 0.2 units; p = 0.02). After Diet LF, subjects with CC genotype showed a significant improvement in total cholesterol levels (CC vs. CG+GG) (–15.3 ± 1.4 vs. –6.4 ± 1.3 mg/dL; p = 0.01), LDL cholesterol (–14.6 ± 1.8 vs. –6.4 ± 1.3 mg/dL; p = 0.01), insulin levels (–4.6 ± 1.0 vs. –1.6 ± 0.5 mU/L; p = 0.01), and HOMA-IR (–1.6 ± 0.1 vs. –1.0 ± 0.2 units; p = 0.02). Only subjects with CC genotype showed a significant increase of adiponectin levels after both diets (CC vs. CG+GG): Diet HF (10.6 ± 2.0 vs. 1.8 ± 1.0 ng/dL; p = 0.01) and Diet LF (16.1 ± 2.8 vs. 1.3 ± 1.0 ng/dL: p = 0.03). Conclusion: CC genotype of ADIPOQgene variantrs266729 was associated with a better metabolic response after both diets. Additionally, Diet LF produced a significant improvement in lipid profile in noncarriers of allele G.
背景:ADIPOQ基因变异在不同膳食脂肪量后减肥中的作用尚不清楚。目的:分析ADIPOQ基因多态性rs266729对两种低热量日粮中添加两种不同量脂肪后代谢变化的影响。设计:在一项随机临床试验中,招募了283名肥胖患者,采用两种饮食:饮食HF(高脂肪饮食:38%碳水化合物、24%蛋白质和38%脂肪)和饮食LF(低脂饮食:53%碳水化合物、20%蛋白质和27%脂肪)。在3个月之前和之后,进行了人体测量评估、营养摄入评估和生化分析。通过实时PCR评估ADIPOQ基因的变体。结果:在两种基因型中,两种饮食的减肥效果相似(CC与CG+GG)。饮食HF干预后,只有CC基因型受试者的胰岛素水平(-3.3±0.6 vs.-1.8±0.9 mU/L;p=0.03)和胰岛素抵抗稳态模型评估(HOMA-IR)(-1.3±0.1 vs.-0.8±0.2单位;p=0.02)有显著改善。饮食LF后,CC基因型受试者的总胆固醇水平(CC vs.CG+GG)(–15.3±1.4 vs.–6.4±1.3 mg/dL;p=0.01)、低密度脂蛋白胆固醇(–14.6±1.8 vs.–6.4+1.3 mg/dL,p=0.01)和胰岛素水平(–4.6±1.0 vs.–1.6±0.5 mU/L,p=0.001)显著改善,HOMA-IR(-1.6±0.1 vs.-1.0±0.2单位;p=0.02)。只有CC基因型受试者在两种饮食后脂联素水平显著升高(CC vs。CG+GG):日粮HF(10.6±2.0 vs.1.8±1.0 ng/dL;p=0.01)和日粮LF(16.1±2.8 vs.1.3±1.0 ng/dL:p=0.03)。此外,饮食LF显著改善了G等位基因非携带者的脂质状况。
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引用次数: 5
Front & Back Matter 正面和背面事项
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-10-01 DOI: 10.1159/000504004
María Elizabeth Tejero Barrera
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引用次数: 0
Epigenetic Modifications as Outcomes of Exercise Interventions Related to Specific Metabolic Alterations: A Systematic Review 表观遗传修饰作为运动干预与特定代谢改变相关的结果:一项系统综述
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-09-23 DOI: 10.1159/000503289
E. Barrón-Cabrera, O. Ramos-López, Karina González-Becerra, J. Riezu-Boj, F. Milagro, E. Martínez-López, J. A. Martínez
Background: Chronic diseases arise as a consequence of an unhealthy lifestyle primarily characterized by physical inactivity and unbalanced diets. Regular physical activity can improve health, and there is consistent evidence that these improvements may be the result of epigenetic modifications. Objective: To identify epigenetic modificationsas outcomes of exercise interventions related to specific metabolic alterations. Methods: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) methodology for manuscript research and preparation was followed using PubMed and EBSCO databases for literature review. Out of 2,638 articles identified, only 34 articles met the inclusion criteria. Results: The sections of the review were organized by metabolic alterations in which studies were grouped according to healthy, diseased, and trained individuals. Resistance exercise in humans induced epigenetic changes in pathways associated with energy metabolism and insulin sensitivity, contributing to healthy skeletal muscle. Endurance exercise also caused modifications in biomarkers associated to metabolic alterations through changes in DNA methylation and the expression of specific miRNAs. However, both resistance and endurance exercise are necessary to obtain a better physiological adaptation and a combination of both seems to be needed to properly tackle the increasing prevalence of non-communicable pathologies. Conclusion: Given the heterogeneity and complexity of the existing literature, it is currently not possible to propose a specific recommendation about the type, intensity, or duration of exercise that could be beneficial for different subsets of the population (healthy, diseased, and/or trained). Nevertheless, this review highlights the importance of exercise for health and shows the need to perform more research in this emerging area to identify epigenetic biomarkers that could serve as indicators of exercise adaptations.
背景:慢性病是由不健康的生活方式引起的,主要表现为缺乏运动和饮食不均衡。有规律的体育活动可以改善健康,有一致的证据表明,这些改善可能是表观遗传学修饰的结果。目的:确定表观遗传学修饰是与特定代谢改变相关的运动干预的结果。方法:使用PubMed和EBSCO数据库进行文献综述,采用系统评价和荟萃分析方案(PRISMA-P)方法进行手稿研究和准备。在确定的2638篇文章中,只有34篇符合纳入标准。结果:综述的各部分按代谢变化进行组织,其中研究根据健康、患病和受过训练的个体进行分组。人类的抵抗运动诱导了与能量代谢和胰岛素敏感性相关的途径的表观遗传学变化,有助于骨骼肌的健康。耐力运动还通过改变DNA甲基化和特定miRNA的表达,导致与代谢改变相关的生物标志物发生改变。然而,为了获得更好的生理适应,抵抗力和耐力运动都是必要的,而且似乎需要将两者结合起来,以适当应对非传染性疾病日益普遍的情况。结论:鉴于现有文献的异质性和复杂性,目前尚不可能就运动的类型、强度或持续时间提出对不同人群(健康、患病和/或受过训练)有益的具体建议。尽管如此,这篇综述强调了运动对健康的重要性,并表明有必要在这一新兴领域进行更多的研究,以确定可以作为运动适应指标的表观遗传学生物标志物。
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引用次数: 35
Four-Week Omega-3 Supplementation in Carriers of the Prosteatotic PNPLA3 p.I148M Genetic Variant: An Open-Label Study 前列腺癌PNPLA3 p.I148M基因变异携带者补充四周Omega-3:一项开放标签研究
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-08-27 DOI: 10.1159/000502008
C. Kuttner, R. Mancina, G. Wagenpfeil, F. Lammert, C. Stokes
Background/Aims: The PNPLA3 loss-of-function variant p.I148M is a strong genetic determinant of nonalcoholic fatty liver disease. The PNPLA3 protein functions as an intracellular lipase in the liver, with a greater activity on unsaturated fatty acids. This study aimed to determine whether short-term supplementation with omega-3 fatty acids impacts hepatic steatosis differently in PNPLA3 p.148I wild-type individuals as compared to homozygous carriers of the PNPLA3 p.148M variant. Methods: Twenty subjects with hepatic steatosis (50% women, age 18–77 years) were included. Ten subjects homozygous for the PNPLA3 148M variant were matched to 10 wild-type individuals. The subjects received 4 g omega-3 fatty acids (1,840 mg eicosapentaenoic acid and 1,520 mg docosahexaenoic acid) a day for 4 weeks. Transient elastography with a controlled attenuation parameter (CAP) was used to quantify liver fat before and after the intervention. Body composition, fibrosis, liver function tests, serum free fatty acids (FFA) and glucose markers were compared. Results: Patients homozygous for the PNPLA3 p.148M variant (risk group) demonstrated no significant changes in CAP compared to baseline (284 ± 55 vs. 287 ± 65 dB/m) as did the control group (256 ± 56 vs. 262 ± 55 dB/m). While serum liver enzyme activities remained unchanged in both groups, the risk group displayed significantly (p = 0.02) lower baseline FFA concentrations (334.5 [range 281.0–431.0] vs. 564.5 [range 509.0–682.0] μmol/L), which markedly increased by 9.1% after the intervention. In contrast, FFA concentrations decreased significantly (p = 0.01) by 28.3% in the wild-type group. Conclusions: Short-term omega-3 fatty acid supplementation did not significantly alter hepatic steatosis. The nutrigenomic and metabolic effects of omega-3 fatty acids should be investigated further in carriers of the PNPLA3 148M risk variant.
背景/目的:PNPLA3功能丧失变体p.I148M是非酒精性脂肪肝的一个强大的遗传决定因素。PNPLA3蛋白在肝脏中起细胞内脂肪酶的作用,对不饱和脂肪酸具有较大的活性。本研究旨在确定短期补充omega-3脂肪酸对pnpla3p . 148i野生型个体的肝脏脂肪变性的影响是否与pnpla3p . 148m变体纯合携带者不同。方法:纳入20例肝脂肪变性患者(50%为女性,年龄18-77岁)。10个PNPLA3 148M变异纯合子与10个野生型个体匹配。受试者每天服用4 g omega-3脂肪酸(1,840 mg二十碳五烯酸和1,520 mg二十二碳六烯酸),持续4周。采用控制衰减参数的瞬时弹性成像(CAP)来量化干预前后的肝脏脂肪。比较体成分、纤维化、肝功能、血清游离脂肪酸(FFA)和血糖指标。结果:纯合子PNPLA3 p.148M变异的患者(风险组)与基线(284±55比287±65 dB/m)和对照组(256±56比262±55 dB/m)相比,CAP没有显著变化。两组的血清肝酶活性保持不变,但危险组的基线FFA浓度显著(p = 0.02)降低(334.5 μmol/L[范围281.0-431.0]vs. 564.5 μmol/L[范围509.0-682.0]),干预后显著升高9.1%。相比之下,野生型组FFA浓度显著下降28.3% (p = 0.01)。结论:短期补充omega-3脂肪酸不会显著改变肝脏脂肪变性。omega-3脂肪酸对PNPLA3 148M风险变异携带者的营养基因组学和代谢影响有待进一步研究。
{"title":"Four-Week Omega-3 Supplementation in Carriers of the Prosteatotic PNPLA3 p.I148M Genetic Variant: An Open-Label Study","authors":"C. Kuttner, R. Mancina, G. Wagenpfeil, F. Lammert, C. Stokes","doi":"10.1159/000502008","DOIUrl":"https://doi.org/10.1159/000502008","url":null,"abstract":"Background/Aims: The PNPLA3 loss-of-function variant p.I148M is a strong genetic determinant of nonalcoholic fatty liver disease. The PNPLA3 protein functions as an intracellular lipase in the liver, with a greater activity on unsaturated fatty acids. This study aimed to determine whether short-term supplementation with omega-3 fatty acids impacts hepatic steatosis differently in PNPLA3 p.148I wild-type individuals as compared to homozygous carriers of the PNPLA3 p.148M variant. Methods: Twenty subjects with hepatic steatosis (50% women, age 18–77 years) were included. Ten subjects homozygous for the PNPLA3 148M variant were matched to 10 wild-type individuals. The subjects received 4 g omega-3 fatty acids (1,840 mg eicosapentaenoic acid and 1,520 mg docosahexaenoic acid) a day for 4 weeks. Transient elastography with a controlled attenuation parameter (CAP) was used to quantify liver fat before and after the intervention. Body composition, fibrosis, liver function tests, serum free fatty acids (FFA) and glucose markers were compared. Results: Patients homozygous for the PNPLA3 p.148M variant (risk group) demonstrated no significant changes in CAP compared to baseline (284 ± 55 vs. 287 ± 65 dB/m) as did the control group (256 ± 56 vs. 262 ± 55 dB/m). While serum liver enzyme activities remained unchanged in both groups, the risk group displayed significantly (p = 0.02) lower baseline FFA concentrations (334.5 [range 281.0–431.0] vs. 564.5 [range 509.0–682.0] μmol/L), which markedly increased by 9.1% after the intervention. In contrast, FFA concentrations decreased significantly (p = 0.01) by 28.3% in the wild-type group. Conclusions: Short-term omega-3 fatty acid supplementation did not significantly alter hepatic steatosis. The nutrigenomic and metabolic effects of omega-3 fatty acids should be investigated further in carriers of the PNPLA3 148M risk variant.","PeriodicalId":18030,"journal":{"name":"Lifestyle Genomics","volume":"12 1","pages":"10 - 17"},"PeriodicalIF":2.6,"publicationDate":"2019-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1159/000502008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42991143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Front & Back Matter 正面和背面
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-08-01 DOI: 10.1159/000502462
B. Koletzko, R. Shamir, D. Turck, M. Phillip
169 13th Congress of the International Society of Nutrigenetics/Nutrigenomics (ISNN) July 12–13, 2019, Cambridge, UK Guest Editors: Kohlmeier, M. (Kannapolis, NC, USA); Chirita, A. (Timisoara, Romania); Beckett, E. (New Lambton Heights, NSW, Australia); Angelino, D. (Parma, Italy); Del Rio, D. (Parma, Italy); Niculescu, M. (Hillsborough, NC, USA) 168 Erratum 194
169国际营养遗传学/营养基因组学学会第十三届大会(ISNN),2019年7月12日至13日,英国剑桥,客座编辑:Kohlmeier,M.(美国北卡罗来纳州坎纳波利斯);Chirita,A.(罗马尼亚蒂米什瓦拉);Beckett,E.(澳大利亚新南威尔士州新兰顿高地);Angelino,D.(意大利帕尔马);德尔里奥,D.(意大利帕尔马);Niculescu,M.(美国北卡罗来纳州希尔斯堡)168勘误表194
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引用次数: 0
Contents 内容
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-08-01 DOI: 10.1159/000502164
Iwona Rudkowska, M. E. Tejero
Selected Abstracts from the 19 3rd European Summer School on Nutrigenomics Jesi, June 25–29, 2018
2018年6月25日至29日,第19届欧洲营养基因组学暑期学校节选
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引用次数: 0
Genetic and Oral Tests for the Diagnosis of Lactose Intolerance in Mixed-Ancestry Brazilians with Metabolic Syndrome 遗传和口腔测试诊断巴西混血儿代谢综合征乳糖不耐受
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-07-26 DOI: 10.1159/000501690
E. Araújo, Luama Araujo dos Santos, Radamés Coutinho, Viviane Assis, N. Brandao, Daniela Almeida, G. Conceição, C. Figueredo, H. Fonseca, Maria de Lourdes Lima, D. Lemaire, D. Rios
Background/Aims: Metabolic syndrome (MetS) comprises a cluster of physiological and anthropometric abnormalities. MetS has been linked to lactose intolerance (LI). The aim of this study was to compare the sensitivity and specificity to detect LI using 2 different tests: (1) a genetic test and (2) an oral lactose tolerance test (OLTT). Methods: Two hundred and fifty-four MetS patients, ≥20 years of age, of both genders, were recruited for this comparative study. Nine single nucleotide polymorphisms (SNPs) were selected for genetic investigation: rs182549and rs4988235(both considered “gold standard”); rs56064699; rs148142676; rs562211644; rs59533246; rs3754689; rs2278544,and rs10552864(as potential novel SNPs). Sensitivity and specificity, as well as positive and negative predictive values, were calculated for each genotype using WINPEPI version 11.65. Differences between positive and negative OLTT groups were considered statistically significant when p ≤ 0.05. Results: Among the selected SNPs, only rs182549(p < 0.001) and rs4988235(p < 0.001) gave similar results compared to an OLTT. The sensitivity of both SNPs to detect LI was 87 and 86%, and specificity was 83 and 82.5%, respectively. Conclusion: Genetic tests using rs182549and rs4988235SNPs showed high agreement with OLTT. These genetic tests may be a good option to replace OLTT in MetS patients.
背景/目的:代谢综合征(MetS)包括一系列生理和人体测量异常。MetS与乳糖不耐症(LI)有关。本研究的目的是比较两种不同检测方法检测LI的敏感性和特异性:(1)基因检测和(2)口服乳糖耐量试验(OLTT)。方法:这项比较研究招募了254名年龄≥20岁的MetS患者,男女不限。选择9个单核苷酸多态性(snp)进行遗传研究:rs182549和rs4988235(均被认为是“金标准”);rs56064699;rs148142676;rs562211644;rs59533246;rs3754689;rs2278544和rs10552864(作为潜在的新snp)。使用WINPEPI version 11.65计算每种基因型的敏感性和特异性以及阳性和阴性预测值。当p≤0.05时,认为OLTT阳性组与阴性组之间差异有统计学意义。结果:在所选snp中,只有rs182549(p < 0.001)和rs4988235(p < 0.001)的结果与OLTT相似。两种snp检测LI的敏感性分别为87%和86%,特异性分别为83%和82.5%。结论:rs182549和rs4988235snp基因检测结果与OLTT高度一致。在met患者中,这些基因检测可能是替代OLTT的一个很好的选择。
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引用次数: 2
Erratum 勘误
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-05-29 DOI: 10.1159/000499733
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引用次数: 0
Front & Back Matter 正面和背面
IF 2.6 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2019-02-01 DOI: 10.1159/000499123
María Elizabeth Tejero Barrera
109 12th Congress of the International Society of Nutrigenetics/Nutrigenomics (ISNN) September 30 to October 3, 2018, Winnipeg, MB, Canada Guest Editors: Jones, P.J.H.; Myrie, S. (Winnipeg, MB) (available online only)
国际营养遗传学/营养基因组学学会(ISNN)第12届大会2018年9月30日至10月3日,加拿大温尼伯,MB,客座编辑:Jones, P.J.H.;Myrie, S.(温尼伯,MB)(只在网上提供)
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引用次数: 0
期刊
Lifestyle Genomics
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