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Article ; Online: A year of COVID-19 GWAS results from the GRASP portal reveals potential genetic risk factors.

Thibord, Florian / Chan, Melissa V / Chen, Ming-Huei / Johnson, Andrew D

HGG advances

2022 Volume 3, Issue 2, Page(s) 100095

Abstract: Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of genetic associations with coronavirus disease 2019 (COVID-19) phenotypes could help to develop new therapeutic strategies to decrease its ...

Abstract	Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of genetic associations with coronavirus disease 2019 (COVID-19) phenotypes could help to develop new therapeutic strategies to decrease its burden. Between May 2020 and June 2021, we used COVID-19 data released periodically by UK Biobank and performed 65 genome-wide association studies in up to 18 releases of COVID-19 susceptibility (n = 18,481 cases in June 2021), hospitalization (n = 3,260), severe outcomes (n = 1,244), and deaths (n = 1,104), stratified by sex and ancestry. In coherence with previous studies, we observed two independent signals at the chr3p21.31 locus (rs73062389-A, odds ratio [OR], 1.21 (P = 4.26 × 10
Language	English
Publishing date	2022-02-22
Publishing country	United States
Document type	Journal Article
ISSN	2666-2477
ISSN (online)	2666-2477
DOI	10.1016/j.xhgg.2022.100095
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: An evaluation of approaches for rare variant association analyses of binary traits in related samples.

Chen, Ming-Huei / Pitsillides, Achilleas / Yang, Qiong

Scientific reports

2021 Volume 11, Issue 1, Page(s) 3145

Abstract: Recognizing that family data provide unique advantage of identifying rare risk variants in genetic association studies, many cohorts with related samples have gone through whole genome sequencing in large initiatives such as the NHLBI Trans-Omics for ... ...

Abstract	Recognizing that family data provide unique advantage of identifying rare risk variants in genetic association studies, many cohorts with related samples have gone through whole genome sequencing in large initiatives such as the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. Analyzing rare variants poses challenges for binary traits in that some genotype categories may have few or no observed events, causing bias and inflation in commonly used methods. Several methods have recently been proposed to better handle rare variants while accounting for family relationship, but their performances have not been thoroughly evaluated together. Here we compare several existing approaches including SAIGE but not limited to related samples using simulations based on the Framingham Heart Study samples and genotype data from Illumina HumanExome BeadChip where rare variants are the majority. We found that logistic regression with likelihood ratio test applied to related samples was the only approach that did not have inflated type I error rates in both single variant test (SVT) and gene-based tests, followed by Firth logistic regression that had inflation in its direction insensitive gene-based test at prevalence 0.01 only, applied to either related or unrelated samples, though theoretically logistic regression and Firth logistic regression do not account for relatedness in samples. SAIGE had inflation in SVT at prevalence 0.1 or lower and the inflation was eliminated with a minor allele count filter of 5. As for power, there was no approach that outperformed others consistently among all single variant tests and gene-based tests.
MeSH term(s)	Alleles ; Computer Simulation ; Gene Frequency ; Genome, Human ; Genome-Wide Association Study ; Genotype ; Humans ; Logistic Models ; Longitudinal Studies ; Models, Genetic ; Multifactorial Inheritance ; Polymorphism, Single Nucleotide ; Precision Medicine/methods ; Precision Medicine/statistics & numerical data ; Software
Language	English
Publishing date	2021-02-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-82547-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Role of Transformational Leadership and Knowledge Management and Learning Organization on Vocational Schools Performance During Digital Era.

Firmansyah, Arif / Chen, Ming-Huei / Junaedi, I Wayan Ruspendi / Arwani, Mokhammad / Kistyanto, Anang

Frontiers in psychology

2022 Volume 13, Page(s) 895341

Language	English
Publishing date	2022-05-06
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2563826-9
ISSN	1664-1078
ISSN	1664-1078
DOI	10.3389/fpsyg.2022.895341
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Article ; Online: Alcohol intake including wine drinking is associated with decreased platelet reactivity in a large population sample.

Pashek, Robin E / Nkambule, Bongani B / Chan, Melissa V / Thibord, Florian / Lachapelle, Amber R / Cunha, Jason / Chen, Ming-Huei / Johnson, Andrew D

International journal of epidemiology

2023 Volume 52, Issue 6, Page(s) 1939–1950

Abstract: Background: Alcohol consumption is linked to decreased platelet function. Whether this link is dependent on sex or type of beverage remains unclear.: Methods: Cross-sectional data were obtained from the Framingham Heart Study (N = 3427). Alcohol ... ...

Abstract	Background: Alcohol consumption is linked to decreased platelet function. Whether this link is dependent on sex or type of beverage remains unclear. Methods: Cross-sectional data were obtained from the Framingham Heart Study (N = 3427). Alcohol consumption was assessed by using standardized medical history and Harvard semi-quantitative food frequency questionnaires. Five bioassays measured 120 platelet reactivity traits across agonists in whole-blood and platelet-rich plasma samples. Linear mixed-effects models adjusted for age, sex and aspirin use, hypertension, body mass index, cholesterol, high-density lipoprotein, triglycerides, smoking and diabetes evaluated associations between platelet reactivity and alcohol consumption. Beta effects, the regression coefficients that estimate the amount of change in each unit of the predictor variable whereas all other predictor variables remain fixed, for heavy alcohol consumption were compared with effects of aspirin use. Results: Alcohol consumption was associated with decreased platelet reactivity, with more associations among wine and liquor compared with beer. Many platelet-alcohol associations in the full sample (86%, P < 0.01) had larger effect sizes in females. Lower light transmission aggregometry adenosine diphosphate (1.82 µM) maximum aggregation (P = 2.6E-3, 95% CI = -0.07, -0.02, β = -0.042) and area under the curve (P = 7.7E-3, 95% CI = -0.07, -0.01, β = -0.039) were associated with white wine consumption; however, red wine had no associations with platelet reactivity. The effect of aspirin use was on average 11.3 (±4.0) times greater than that of heavy drinking in our full sample. Conclusions: We confirm associations between alcohol consumption and decreased platelet reactivity. Effects appeared larger for liquor and wine intake and in our female cohort. Red wine consumption is not associated with lower platelet function, contrasting with prior population studies. Although we report an inhibitory relationship between alcohol intake and platelet function, these effects appear much smaller than that of aspirin use.
MeSH term(s)	Humans ; Female ; Wine ; Cross-Sectional Studies ; Alcohol Drinking/epidemiology ; Alcoholic Beverages ; Beer ; Aspirin
Chemical Substances	Aspirin (R16CO5Y76E)
Language	English
Publishing date	2023-08-04
Publishing country	England
Document type	Journal Article
ZDB-ID	187909-1
ISSN	1464-3685 ; 0300-5771
ISSN (online)	1464-3685
ISSN	0300-5771
DOI	10.1093/ije/dyad099
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Zs.A 893: Show issues

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Article ; Online: The association between platelet reactivity and lipoprotein levels in Framingham Heart Study participants.

Nkambule, Bongani Brian / Chan, Melissa Victoria / Lachapelle, Amber Rose / Grech, Joseph / Thibord, Florian / Chen, Ming-Huei / Johnson, Andrew Danner

Thrombosis research

2023 Volume 225, Page(s) 103–109

Abstract: Background: Hypertriglyceridemia is an independent risk factor for major adverse cardiovascular events, though the mechanisms linking triglycerides and platelet function with thrombosis, remain elusive. The aim of this study was to assess the ... ...

Abstract	Background: Hypertriglyceridemia is an independent risk factor for major adverse cardiovascular events, though the mechanisms linking triglycerides and platelet function with thrombosis, remain elusive. The aim of this study was to assess the association between platelet function and triglyceride levels. Methods: We included participants from the Framingham Heart Study Third Generation cohort, OMNI, and New Offspring Spouse cohort who attended the third examination cycle (2016-2019). Eligible participants were categorized into four triglyceride subgroups. Results: The study comprised a total of 1897 (55.53 %) participants with normal TG levels; 883 (25.85 %) participants with high-normal TGs; 378 (11.07 %) with borderline high TGs; and 258 (7.55 %) participants with hypertriglyceridemia. After adjusting for age, sex, alcohol consumption, aspirin, statin and P2Y Conclusion: Triglyceride levels are associated with altered platelet activation and aggregation. Furthermore, increased platelet-driven thrombogenicity is directly associated with triglyceride levels after adjusting for medications and other covariates.
MeSH term(s)	Humans ; Triglycerides/therapeutic use ; Lipoproteins, LDL ; Longitudinal Studies ; Hypertriglyceridemia/drug therapy ; Cholesterol
Chemical Substances	Triglycerides ; Lipoproteins, LDL ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2023-03-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	121852-9
ISSN	1879-2472 ; 0049-3848
ISSN (online)	1879-2472
ISSN	0049-3848
DOI	10.1016/j.thromres.2023.03.013
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Zs.A 863: Show issues

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Article ; Online: RVFam: an R package for rare variant association analysis with family data.

Chen, Ming-Huei / Yang, Qiong

Bioinformatics (Oxford, England)

2016 Volume 32, Issue 4, Page(s) 624–626

Abstract: Unlabelled: Family-based designs offer unique advantage for identifying rare risk variants in genetic association studies. There are existing tools for analyzing rare variants in families but lacking components to handle binary traits properly and ... ...

Abstract	Unlabelled: Family-based designs offer unique advantage for identifying rare risk variants in genetic association studies. There are existing tools for analyzing rare variants in families but lacking components to handle binary traits properly and survival traits. In this report, we introduce an R software package RVFam (Rare Variant association analysis with Family data) designed to analyze continuous, binary and survival traits against rare and common sequencing variants in genome-wide association studies (GWAS) involving family data. Single and multiple variant association tests were implemented while accounting for arbitrary family structures. Extensive simulation studies were performed to evaluate all the approaches implemented in RVFam. Availability and implementation: http://cran.r-project.org/web/packages/RVFam/.
MeSH term(s)	Family ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Software
Language	English
Publishing date	2016-02-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv609
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Zs.A 2374: Show issues

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Article: RVFam: an R package for rare variant association analysis with family data

Chen, Ming-Huei / Yang, Qiong

Bioinformatics. 2016 Feb. 15, v. 32, no. 4

2016

Abstract: Summary: Family-based designs offer unique advantage for identifying rare risk variants in genetic association studies. There are existing tools for analyzing rare variants in families but lacking components to handle binary traits properly and survival ... ...

Abstract	Summary: Family-based designs offer unique advantage for identifying rare risk variants in genetic association studies. There are existing tools for analyzing rare variants in families but lacking components to handle binary traits properly and survival traits. In this report, we introduce an R software package RVFam (Rare Variant association analysis with Family data) designed to analyze continuous, binary and survival traits against rare and common sequencing variants in genome-wide association studies (GWAS) involving family data. Single and multiple variant association tests were implemented while accounting for arbitrary family structures. Extensive simulation studies were performed to evaluate all the approaches implemented in RVFam. Availability and Implementation: http://cran.r-project.org/web/packages/RVFam/ Contact: qyang@bu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Keywords	bioinformatics ; computer software ; genome-wide association study ; risk
Language	English
Dates of publication	2016-0215
Size	p. 624-626.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4811 ; 1367-4803
ISSN (online)	1460-2059 ; 1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv609
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A year of COVID-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers

Thibord, Florian / Chan, Melissa V. / Chen, Ming-Huei / Johnson, Andrew D.

medRxiv

Abstract: Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of novel genetic associations with Covid-19 phenotypes could help developing new therapeutic strategies to reduce its burden. Between May ... ...

Abstract	Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of novel genetic associations with Covid-19 phenotypes could help developing new therapeutic strategies to reduce its burden. Between May 2020 and February 2021, we used Covid-19 data released periodically by UK Biobank and performed over 400 Genome-Wide Association Studies (GWAS) of Covid-19 susceptibility (N=15,738 cases), hospitalization (N=1,916), severe outcomes (N=935) and death (N=828), stratified by ancestry and sex. In coherence with previous studies, we observed 2 independent signals at the chr3p21.31 locus (rs73062389-A, OR=1.22, P=7.64E-14 and rs13092887-A, OR=1.73, P=2.38E-8, in Europeans) modulating susceptibility and severity, respectively, and a signal influencing susceptibility at the ABO locus (rs9411378-A, OR=1.10, P =7.36E-10, in Europeans), which was more significant in men than in women (P=0.01). In addition, we detected 7 genome-wide significant signals in the last data release analyzed (on February 24th 2021), of which 4 were associated with susceptibility (SCRT2, LRMDA, chr15q24.2, MIR3681HG), 2 with hospitalization (ANKS1A, chr12p13.31) and 1 for severity (ADGRE1). Finally, we identified over 300 associations which increased in significance over time, and reached at least P<10-5 in the last data release analyzed. We replicated 2 of these signals in an independent dataset: a variant downstream of CCL3 (rs2011959) associated with severity in men, and a variant located in an ATP5PO intron (rs12482569) associated with hospitalization. These results, freely available on the GRASP portal, provide new insights on the host genetic architecture of Covid-19 phenotypes.
Keywords	covid19
Language	English
Publishing date	2021-06-11
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.06.08.21258507
Database	COVID19

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Article ; Online: Trends among platelet function, arterial calcium, and vascular function measures.

Cunha, Jason / Chan, Melissa V / Nkambule, Bongani B / Thibord, Florian / Lachapelle, Amber / Pashek, Robin E / Vasan, Ramachandran S / Rong, Jian / Benjamin, Emelia J / Hamburg, Naomi M / Chen, Ming-Huei / Mitchell, Gary F / Johnson, Andrew D

Platelets

2023 Volume 34, Issue 1, Page(s) 2238835

Abstract: Arterial tonometry and vascular calcification measures are useful in cardiovascular disease (CVD) risk assessment. Prior studies found associations between tonometry measures, arterial calcium, and CVD risk. Activated platelets release angiopoietin-1 and ...

Abstract	Arterial tonometry and vascular calcification measures are useful in cardiovascular disease (CVD) risk assessment. Prior studies found associations between tonometry measures, arterial calcium, and CVD risk. Activated platelets release angiopoietin-1 and other factors, which may connect vascular structure and platelet function. We analyzed arterial tonometry, platelet function, aortic, thoracic and coronary calcium, and thoracic and abdominal aorta diameters measured in the Framingham Heart Study Gen3/NOS/OMNI-2 cohorts (
MeSH term(s)	Female ; Male ; Humans ; Calcium ; Pulse Wave Analysis ; Blood Pressure ; Platelet Activation ; Atherosclerosis
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-08-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1034283-7
ISSN	1369-1635 ; 0953-7104
ISSN (online)	1369-1635
ISSN	0953-7104
DOI	10.1080/09537104.2023.2238835
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Zs.A 2888: Show issues

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Article: Opportunity recognition, entrepreneurial creativity and new venture performance in Taiwan

Chen, Ming-Huei

The making of Taiwan's economic miracle : successful entrepreneurship in theories and practices , p. 24-45

2012 , Page(s) 24–45

Author's details	Ming-Huei Chen
Language	English
Publisher	Global Research Publ.
Publishing place	New Delhi
Document type	Article
ISBN	978-81-8963045-4 ; 81-8963045-8
Database	ECONomics Information System

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