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Article: Assessment of the current status of real-world pharmacogenomic testing: informed consent, patient education, and related practices.

Pereira, Lucas / Haidar, Cyrine-Eliana / Haga, Susanne B / Cisler, Anna G / Hall, April / Shukla, Sanjay K / Hebbring, Scott J / Leary, Emili J W

Frontiers in pharmacology

2024 Volume 15, Page(s) 1355412

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2024-02-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2024.1355412
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Article: Estimating the efficacy of pharmacogenomics over a lifetime.

Ye, Zhan / Mayer, John / Leary, Emili J / Kitchner, Terrie / Dart, Richard A / Brilliant, Murray H / Hebbring, Scott J

Frontiers in medicine

2023 Volume 10, Page(s) 1006743

Abstract: It is well known that common variants in specific genes influence drug metabolism and response, but it is currently unknown what fraction of patients are given prescriptions over a lifetime that could be contraindicated by their pharmacogenomic profiles. ...

Abstract	It is well known that common variants in specific genes influence drug metabolism and response, but it is currently unknown what fraction of patients are given prescriptions over a lifetime that could be contraindicated by their pharmacogenomic profiles. To determine the clinical utility of pharmacogenomics over a lifetime in a general patient population, we sequenced the genomes of 300 deceased Marshfield Clinic patients linked to lifelong medical records. Genetic variants in 33 pharmacogenes were evaluated for their lifetime impact on drug prescribing using extensive electronic health records. Results show that 93% of the 300 deceased patients carried clinically relevant variants. Nearly 80% were prescribed approximately three medications on average that may have been impacted by these variants. Longitudinal data suggested that the optimal age for pharmacogenomic testing was prior to age 50, but the optimal age is greatly influenced by the stability of the population in the healthcare system. This study emphasizes the broad clinical impact of pharmacogenomic testing over a lifetime and demonstrates the potential application of genomic medicine in a general patient population for the advancement of precision medicine.
Language	English
Publishing date	2023-10-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2023.1006743
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Article ; Online: The challenges, advantages and future of phenome-wide association studies.

Hebbring, Scott J

Immunology

2013 Volume 141, Issue 2, Page(s) 157–165

Abstract: Over the last decade, significant technological breakthroughs have revolutionized human genomic research in the form of genome-wide association studies (GWASs). GWASs have identified thousands of statistically significant genetic variants associated with ...

Abstract	Over the last decade, significant technological breakthroughs have revolutionized human genomic research in the form of genome-wide association studies (GWASs). GWASs have identified thousands of statistically significant genetic variants associated with hundreds of human conditions including many with immunological aetiologies (e.g. multiple sclerosis, ankylosing spondylitis and rheumatoid arthritis). Unfortunately, most GWASs fail to identify clinically significant associations. Identifying biologically significant variants by GWAS also presents a challenge. The GWAS is a phenotype-to-genotype approach. As a complementary/alternative approach to the GWAS, investigators have begun to exploit extensive electronic medical record systems to conduct a genotype-to-phenotype approach when studying human disease - specifically, the phenome-wide association study (PheWAS). Although the PheWAS approach is in its infancy, this method has already demonstrated its capacity to rediscover important genetic associations related to immunological diseases/conditions. Furthermore, PheWAS has the advantage of identifying genetic variants with pleiotropic properties. This is particularly relevant for HLA variants. For example, PheWAS results have demonstrated that the HLA-DRB1 variant associated with multiple sclerosis may also be associated with erythematous conditions including rosacea. Likewise, PheWAS has demonstrated that the HLA-B genotype is not only associated with spondylopathies, uveitis, and variability in platelet count, but may also play an important role in other conditions, such as mastoiditis. This review will discuss and compare general PheWAS methodologies, describe both the challenges and advantages of the PheWAS, and provide insight into the potential directions in which PheWAS may lead.
MeSH term(s)	Animals ; Genome-Wide Association Study ; Genotype ; Humans ; International Classification of Diseases ; Phenotype ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2013-11-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	80124-0
ISSN	1365-2567 ; 0019-2805 ; 0953-4954
ISSN (online)	1365-2567
ISSN	0019-2805 ; 0953-4954
DOI	10.1111/imm.12195
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Article ; Online: Estimating the efficacy of pharmacogenomics over a lifetime

Zhan Ye / John Mayer / Emili J. Leary / Terrie Kitchner / Richard A. Dart / Murray H. Brilliant / Scott J. Hebbring

Frontiers in Medicine, Vol

2023 Volume 10

Abstract	It is well known that common variants in specific genes influence drug metabolism and response, but it is currently unknown what fraction of patients are given prescriptions over a lifetime that could be contraindicated by their pharmacogenomic profiles. To determine the clinical utility of pharmacogenomics over a lifetime in a general patient population, we sequenced the genomes of 300 deceased Marshfield Clinic patients linked to lifelong medical records. Genetic variants in 33 pharmacogenes were evaluated for their lifetime impact on drug prescribing using extensive electronic health records. Results show that 93% of the 300 deceased patients carried clinically relevant variants. Nearly 80% were prescribed approximately three medications on average that may have been impacted by these variants. Longitudinal data suggested that the optimal age for pharmacogenomic testing was prior to age 50, but the optimal age is greatly influenced by the stability of the population in the healthcare system. This study emphasizes the broad clinical impact of pharmacogenomic testing over a lifetime and demonstrates the potential application of genomic medicine in a general patient population for the advancement of precision medicine.
Keywords	Pharmacogenenomics and personalised medicine ; electronic health record (EHR) ; drug responce ; precision medicine ; individualized medicine ; Medicine (General) ; R5-920
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Kidney failure in Bardet-Biedl syndrome.

Meyer, Jennifer R / Krentz, Anthony D / Berg, Richard L / Richardson, Jesse G / Pomeroy, Jeremy / Hebbring, Scott J / Haws, Robert M

Clinical genetics

2022 Volume 101, Issue 4, Page(s) 429–441

Abstract: The aim of this study was to explore kidney failure (KF) in Bardet-Biedl syndrome (BBS), focusing on high-risk gene variants, demographics, and morbidity. We employed the Clinical Registry Investigating BBS (CRIBBS) to identify 44 (7.2%) individuals with ...

Abstract	The aim of this study was to explore kidney failure (KF) in Bardet-Biedl syndrome (BBS), focusing on high-risk gene variants, demographics, and morbidity. We employed the Clinical Registry Investigating BBS (CRIBBS) to identify 44 (7.2%) individuals with KF out of 607 subjects. Molecularly confirmed BBS was identified in 37 KF subjects and 364 CRIBBS registrants. KF was concomitant with recessive causal variants in 12 genes, with BBS10 the most predominant causal gene (26.6%), while disease penetrance was highest in SDCCAG8 (100%). Two truncating variants were present in 67.6% of KF cases. KF incidence was increased in genes not belonging to the BBSome or chaperonin-like genes (p < 0.001), including TTC21B, a new candidate BBS gene. Median age of KF was 12.5 years, with the vast majority of KF occurring by 30 years (86.3%). Females were disproportionately affected (77.3%). Diverse uropathies were identified, but were not more common in the KF group (p = 0.672). Kidney failure was evident in 11 of 15 (73.3%) deaths outside infancy. We conclude that KF poses a significant risk for premature morbidity in BBS. Risk factors for KF include female sex, truncating variants, and genes other than BBSome/chaperonin-like genes highlighting the value of comprehensive genetic investigation.
MeSH term(s)	Bardet-Biedl Syndrome/complications ; Bardet-Biedl Syndrome/genetics ; Chaperonins/genetics ; Child ; Female ; Humans ; Male ; Mutation ; Penetrance ; Renal Insufficiency/genetics
Chemical Substances	Chaperonins (EC 3.6.1.-)
Language	English
Publishing date	2022-02-02
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	221209-2
ISSN	1399-0004 ; 0009-9163
ISSN (online)	1399-0004
ISSN	0009-9163
DOI	10.1111/cge.14119
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Article ; Online: E-Pedigrees: a large-scale automatic family pedigree prediction application.

Huang, Xiayuan / Tatonetti, Nicholas / LaRow, Katie / Delgoffee, Brooke / Mayer, John / Page, David / Hebbring, Scott J

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 21, Page(s) 3966–3968

Abstract: Motivation: The use and functionality of Electronic Health Records (EHR) have increased rapidly in the past few decades. EHRs are becoming an important depository of patient health information and can capture family data. Pedigree analysis is a ... ...

Abstract	Motivation: The use and functionality of Electronic Health Records (EHR) have increased rapidly in the past few decades. EHRs are becoming an important depository of patient health information and can capture family data. Pedigree analysis is a longstanding and powerful approach that can gain insight into the underlying genetic and environmental factors in human health, but traditional approaches to identifying and recruiting families are low-throughput and labor-intensive. Therefore, high-throughput methods to automatically construct family pedigrees are needed. Results: We developed a stand-alone application: Electronic Pedigrees, or E-Pedigrees, which combines two validated family prediction algorithms into a single software package for high throughput pedigrees construction. The convenient platform considers patients' basic demographic information and/or emergency contact data to infer high-accuracy parent-child relationship. Importantly, E-Pedigrees allows users to layer in additional pedigree data when available and provides options for applying different logical rules to improve accuracy of inferred family relationships. This software is fast and easy to use, is compatible with different EHR data sources, and its output is a standard PED file appropriate for multiple downstream analyses. Availability and implementation: The Python 3.3+ version E-Pedigrees application is freely available on: https://github.com/xiayuan-huang/E-pedigrees.
MeSH term(s)	Humans ; Pedigree ; Software ; Algorithms ; Electronic Health Records
Language	English
Publishing date	2021-06-02
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/btab419
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Article ; Online: An independently validated, portable algorithm for the rapid identification of COPD patients using electronic health records.

Chu, Su H / Wan, Emily S / Cho, Michael H / Goryachev, Sergey / Gainer, Vivian / Linneman, James / Scotty, Erica J / Hebbring, Scott J / Murphy, Shawn / Lasky-Su, Jessica / Weiss, Scott T / Smoller, Jordan W / Karlson, Elizabeth

Scientific reports

2021 Volume 11, Issue 1, Page(s) 19959

Abstract: Electronic health records (EHR) provide an unprecedented opportunity to conduct large, cost-efficient, population-based studies. However, the studies of heterogeneous diseases, such as chronic obstructive pulmonary disease (COPD), often require labor- ... ...

Abstract	Electronic health records (EHR) provide an unprecedented opportunity to conduct large, cost-efficient, population-based studies. However, the studies of heterogeneous diseases, such as chronic obstructive pulmonary disease (COPD), often require labor-intensive clinical review and testing, limiting widespread use of these important resources. To develop a generalizable and efficient method for accurate identification of large COPD cohorts in EHRs, a COPD datamart was developed from 3420 participants meeting inclusion criteria in the Mass General Brigham Biobank. Training and test sets were selected and labeled with gold-standard COPD classifications obtained from chart review by pulmonologists. Multiple classes of algorithms were built utilizing both structured (e.g. ICD codes) and unstructured (e.g. medical notes) data via elastic net regression. Models explicitly including and excluding spirometry features were compared. External validation of the final algorithm was conducted in an independent biobank with a different EHR system. The final COPD classification model demonstrated excellent positive predictive value (PPV; 91.7%), sensitivity (71.7%), and specificity (94.4%). This algorithm performed well not only within the MGBB, but also demonstrated similar or improved classification performance in an independent biobank (PPV 93.5%, sensitivity 61.4%, specificity 90%). Ancillary comparisons showed that the classification model built including a binary feature for FEV1/FVC produced substantially higher sensitivity than those excluding. This study fills a gap in COPD research involving population-based EHRs, providing an important resource for the rapid, automated classification of COPD cases that is both cost-efficient and requires minimal information from unstructured medical records.
MeSH term(s)	Algorithms ; Databases, Factual ; Electronic Health Records ; Forced Expiratory Volume ; Humans ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Vital Capacity
Language	English
Publishing date	2021-10-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-98719-w
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Article ; Online: Genetic and clinical determinants of telomere length.

Allaire, Patrick / He, Jing / Mayer, John / Moat, Luke / Gerstenberger, Peter / Wilhorn, Reynor / Strutz, Sierra / Kim, David S L / Zeng, Chenjie / Cox, Nancy / Shay, Jerry W / Denny, Joshua / Bastarache, Lisa / Hebbring, Scott

HGG advances

2023 Volume 4, Issue 3, Page(s) 100201

Abstract: Many epidemiologic studies have identified important relationships between leukocyte telomere length (LTL) with genetics and health. Most of these studies have been significantly limited in scope by focusing predominantly on individual diseases or ... ...

Abstract	Many epidemiologic studies have identified important relationships between leukocyte telomere length (LTL) with genetics and health. Most of these studies have been significantly limited in scope by focusing predominantly on individual diseases or restricted to GWAS analysis. Using two large patient populations derived from Vanderbilt University and Marshfield Clinic biobanks linked to genomic and phenomic data from medical records, we investigated the inter-relationship between LTL, genomics, and human health. Our GWAS confirmed 11 genetic loci previously associated with LTL and two novel loci in
MeSH term(s)	Humans ; Aged ; Leukocytes ; Telomere/genetics ; Calcium-Binding Proteins/genetics ; Eye Proteins/genetics ; Membrane Proteins/genetics
Chemical Substances	PITPNM1 protein, human ; Calcium-Binding Proteins ; Eye Proteins ; Membrane Proteins
Language	English
Publishing date	2023-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2666-2477
ISSN (online)	2666-2477
DOI	10.1016/j.xhgg.2023.100201
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Article ; Online: Ancestry-specific polygenic scores and SNP heritability of 25(OH)D in African- and European-ancestry populations.

Hatchell, Kathryn E / Lu, Qiongshi / Hebbring, Scott J / Michos, Erin D / Wood, Alexis C / Engelman, Corinne D

Human genetics

2019 Volume 138, Issue 10, Page(s) 1155–1169

Abstract: Vitamin D inadequacy, assessed by 25-hydroxyvitamin D [25(OH)D], affects around 50% of adults in the United States and is associated with numerous adverse health outcomes. Blood 25(OH)D concentrations are influenced by genetic factors that may determine ... ...

Abstract	Vitamin D inadequacy, assessed by 25-hydroxyvitamin D [25(OH)D], affects around 50% of adults in the United States and is associated with numerous adverse health outcomes. Blood 25(OH)D concentrations are influenced by genetic factors that may determine how much vitamin D intake is required to reach optimal 25(OH)D. Despite large genome-wide association studies (GWASs), only a small portion of the genetic factors contributing to differences in 25(OH)D has been discovered. Therefore, knowledge of a fuller set of genetic factors could be useful for risk prediction of 25(OH)D inadequacy, personalized vitamin D supplementation, and prevention of downstream morbidity and mortality. Using PRSice and weights from published African- and European-ancestry GWAS summary statistics, ancestry-specific polygenic scores (PGSs) were created to capture a more complete set of genetic factors in those of European (n = 9569) or African ancestry (n = 2761) from three cohort studies. The PGS for African ancestry was derived using all input SNPs (a p value cutoff of 1.0) and had an R
MeSH term(s)	Black People/genetics ; Cohort Studies ; Databases, Genetic ; Dietary Supplements ; Female ; Genetics, Population ; Genome-Wide Association Study ; Humans ; Inheritance Patterns ; Male ; Middle Aged ; Multifactorial Inheritance ; Polymorphism, Single Nucleotide ; Ultraviolet Rays ; Vitamin D/analogs & derivatives ; Vitamin D/blood ; White People/genetics
Chemical Substances	Vitamin D (1406-16-2) ; 25-hydroxyvitamin D (A288AR3C9H)
Language	English
Publishing date	2019-07-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-019-02049-x
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Article ; Online: Pleiotropy of systemic lupus erythematosus risk alleles and cardiometabolic disorders: A phenome-wide association study and inverse-variance weighted meta-analysis.

Kawai, Vivian K / Shi, Mingjian / Liu, Ge / Feng, QiPing / Wei, WeiQi / Chung, Cecilia P / Walunas, Theresa L / Gordon, Adam S / Linneman, James G / Hebbring, Scott J / Harley, John B / Cox, Nancy J / Roden, Dan M / Stein, C Michael / Mosley, Jonathan D

Lupus

2021 Volume 30, Issue 8, Page(s) 1264–1272

Abstract: Objectives: To test the hypothesis that genetic predisposition to systemic lupus erythematosus (SLE) increases the risk of cardiometabolic disorders.: Methods: Using 41 single nucleotide polymorphisms (SNPs) associated with SLE, we calculated a ... ...

Abstract	Objectives: To test the hypothesis that genetic predisposition to systemic lupus erythematosus (SLE) increases the risk of cardiometabolic disorders. Methods: Using 41 single nucleotide polymorphisms (SNPs) associated with SLE, we calculated a weighted genetic risk score (wGRS) for SLE. In a large biobank we tested the association between this wGRS and 9 cardiometabolic phenotypes previously associated with SLE: atrial fibrillation, ischemic stroke, coronary artery disease, type 1 and type 2 diabetes, obesity, chronic kidney disease, hypertension, and hypercholesterolemia. Additionally, we performed a phenome-wide association analysis (pheWAS) to discover novel clinical associations with a genetic predisposition to SLE. Findings were replicated in the Electronic Medical Records and Genomics (eMERGE) Network. To further define the association between SLE-related risk alleles and the selected cardiometabolic phenotypes, we performed an inverse variance weighted regression (IVWR) meta-analysis. Results: The wGRS for SLE was calculated in 74,759 individuals of European ancestry. Among the pre-selected phenotypes, the wGRS was significantly associated with type 1 diabetes (OR [95%CI] =1.11 [1.06, 1.17], P-value = 1.05x10 Conclusion: A weighted GRS for SLE was associated with an increased risk of several autoimmune-related phenotypes including type I diabetes but not with cardiometabolic disorders.
MeSH term(s)	Alleles ; Cardiovascular Diseases/genetics ; Diabetes Mellitus, Type 1/genetics ; Diabetes Mellitus, Type 2 ; Genetic Predisposition to Disease ; Humans ; Lupus Erythematosus, Systemic/genetics ; Metabolic Diseases ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article ; Meta-Analysis
ZDB-ID	1154407-7
ISSN	1477-0962 ; 0961-2033
ISSN (online)	1477-0962
ISSN	0961-2033
DOI	10.1177/09612033211014952
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