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Article ; Online: Bilateral medial medullary syndrome-a rare case report.

Patwardhan, Saket / Pawar, Shefali S / Gavali, Prachi

2023

Language	English
Publishing date	2023-11-24
Publishing country	Italy
Document type	Letter
ZDB-ID	127315-2
ISSN	2240-2993 ; 0300-9009
ISSN (online)	2240-2993
ISSN	0300-9009
DOI	10.1007/s13760-023-02414-8
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Article: Titin-Truncating variants Predispose to Dilated Cardiomyopathy in Diverse Populations.

DePaolo, John / Bornstein, Marc / Judy, Renae / Abramowitz, Sarah / Verma, Shefali S / Levin, Michael G / Arany, Zoltan / Damrauer, Scott M

medRxiv : the preprint server for health sciences

2024

Abstract: Importance: The effect of high percentage spliced in (hiPSI) : Objective: To determine the effect of TTNtvs on risk of DCM in diverse population as measured by genetic distance (GD) in principal component (PC) space.: Design: Cohort study.: ... ...

Abstract	Importance: The effect of high percentage spliced in (hiPSI) Objective: To determine the effect of TTNtvs on risk of DCM in diverse population as measured by genetic distance (GD) in principal component (PC) space. Design: Cohort study. Setting: Penn Medicine Biobank (PMBB) is a large, diverse biobank. Participants: Participants were recruited from across the Penn Medicine healthcare system and volunteered to have their electronic health records linked to biospecimen data including DNA which has undergone whole exome sequencing. Main outcomes and measures: Risk of DCM among individuals carrying a hiPSI TTNtv. Results: Carrying a hiPSI TTNtv was associated with DCM among PMBB participants across a range of GD deciles from the 1000G European centroid; the effect estimates ranged from odds ratio (OR) = 3.29 (95% confidence interval [CI] 1.26 to 8.56) to OR = 9.39 (95% CI 3.82 to 23.13). When individuals were assigned to population subgroups based on genetic similarity to the 1000G reference populations, hiPSI TTNtvs conferred significant risk of DCM among those genetically similar to the 1000G European reference population (OR = 7.55, 95% CI 4.99 to 11.42, Conclusions and relevance: TTNtvs are associated with increased risk of DCM among a diverse cohort. There is no significant difference in effect of TTNtvs on DCM risk across deciles of GD from the 1000G European centroid, suggesting genetic background should not be considered when screening individuals for titin-related DCM.
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.17.24301405
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Article ; Online: Leveraging electronic health record data for endometriosis research.

Penrod, Nadia / Okeh, Chelsea / Velez Edwards, Digna R / Barnhart, Kurt / Senapati, Suneeta / Verma, Shefali S

Frontiers in digital health

2023 Volume 5, Page(s) 1150687

Abstract: ... ...

Abstract	Endometriosis
Language	English
Publishing date	2023-06-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2673-253X
ISSN (online)	2673-253X
DOI	10.3389/fdgth.2023.1150687
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Article ; Online: Leveraging electronic health record data for endometriosis research

Nadia Penrod / Chelsea Okeh / Digna R. Velez Edwards / Kurt Barnhart / Suneeta Senapati / Shefali S. Verma

Frontiers in Digital Health, Vol

2023 Volume 5

Abstract: Endometriosis is a chronic, complex disease for which there are vast disparities in diagnosis and treatment between sociodemographic groups. Clinical presentation of endometriosis can vary from asymptomatic disease—often identified during (in)fertility ... ...

Abstract	Endometriosis is a chronic, complex disease for which there are vast disparities in diagnosis and treatment between sociodemographic groups. Clinical presentation of endometriosis can vary from asymptomatic disease—often identified during (in)fertility consultations—to dysmenorrhea and debilitating pelvic pain. Because of this complexity, delayed diagnosis (mean time to diagnosis is 1.7–3.6 years) and misdiagnosis is common. Early and accurate diagnosis of endometriosis remains a research priority for patient advocates and healthcare providers. Electronic health records (EHRs) have been widely adopted as a data source in biomedical research. However, they remain a largely untapped source of data for endometriosis research. EHRs capture diverse, real-world patient populations and care trajectories and can be used to learn patterns of underlying risk factors for endometriosis which, in turn, can be used to inform screening guidelines to help clinicians efficiently and effectively recognize and diagnose the disease in all patient populations reducing inequities in care. Here, we provide an overview of the advantages and limitations of using EHR data to study endometriosis. We describe the prevalence of endometriosis observed in diverse populations from multiple healthcare institutions, examples of variables that can be extracted from EHRs to enhance the accuracy of endometriosis prediction, and opportunities to leverage longitudinal EHR data to improve our understanding of long-term health consequences for all patients.
Keywords	reproductive health ; women’s health ; electronic health records—EHR ; endometriosis ; obstetric & gynecologic ; Medicine ; R ; Public aspects of medicine ; RA1-1270 ; Electronic computers. Computer science ; QA75.5-76.95
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: A rapid self-assembled hybrid bio-microflowers of alpha-amylase with enhanced activity.

Maurya, Shefali S / Nadar, Shamraja S / Rathod, Virendra K

Journal of biotechnology

2020 Volume 317, Page(s) 27–33

Abstract: In conventional preparation of enzyme embedded organic-inorganic hybrid flower-like nanostructures, usually it requires three days which is time-consuming and limits their widespread applications. In this context, alpha-amylase hybrid bio-microflowers ... ...

Abstract	In conventional preparation of enzyme embedded organic-inorganic hybrid flower-like nanostructures, usually it requires three days which is time-consuming and limits their widespread applications. In this context, alpha-amylase hybrid bio-microflowers were prepared by simple, efficient and rapid method in the presence of chitosan via inotropic gelation and biomineralization approach. The hybrid bio-microflowers was synthesized within 6 h with ∼140 % enhanced catalytic activity. The prepared hybrid bio-microflowers were characterized by FT-IR, SEM, and PXRD. The hybrid bio-microflowers exhibited higher rate of reaction (V
MeSH term(s)	Calcium/chemistry ; Chitosan/chemistry ; Enzyme Stability ; Enzymes, Immobilized/chemistry ; Enzymes, Immobilized/metabolism ; Equipment Reuse ; Hydrolysis ; Nanostructures/chemistry ; Nanostructures/ultrastructure ; Spectroscopy, Fourier Transform Infrared ; Starch/chemistry ; Starch/metabolism ; alpha-Amylases/chemistry ; alpha-Amylases/metabolism
Chemical Substances	Enzymes, Immobilized ; Starch (9005-25-8) ; Chitosan (9012-76-4) ; alpha-Amylases (EC 3.2.1.1) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2020-04-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	843647-2
ISSN	1873-4863 ; 0168-1656 ; 1389-0352
ISSN (online)	1873-4863
ISSN	0168-1656 ; 1389-0352
DOI	10.1016/j.jbiotec.2020.04.010
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Article ; Online: Polygenic risk scores for cardiometabolic traits demonstrate importance of ancestry for predictive precision medicine.

Kember, Rachel L / Verma, Shefali S / Verma, Anurag / Xiao, Brenda / Lucas, Anastasia / Kripke, Colleen M / Judy, Renae / Chen, Jinbo / Damrauer, Scott M / Rader, Daniel J / Ritchie, Marylyn D

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

2024 Volume 29, Page(s) 611–626

Abstract: Polygenic risk scores (PRS) have predominantly been derived from genome-wide association studies (GWAS) conducted in European ancestry (EUR) individuals. In this study, we present an in-depth evaluation of PRS based on multi-ancestry GWAS for five ... ...

Abstract	Polygenic risk scores (PRS) have predominantly been derived from genome-wide association studies (GWAS) conducted in European ancestry (EUR) individuals. In this study, we present an in-depth evaluation of PRS based on multi-ancestry GWAS for five cardiometabolic phenotypes in the Penn Medicine BioBank (PMBB) followed by a phenome-wide association study (PheWAS). We examine the PRS performance across all individuals and separately in African ancestry (AFR) and EUR ancestry groups. For AFR individuals, PRS derived using the multi-ancestry LD panel showed a higher effect size for four out of five PRSs (DBP, SBP, T2D, and BMI) than those derived from the AFR LD panel. In contrast, for EUR individuals, the multi-ancestry LD panel PRS demonstrated a higher effect size for two out of five PRSs (SBP and T2D) compared to the EUR LD panel. These findings underscore the potential benefits of utilizing a multi-ancestry LD panel for PRS derivation in diverse genetic backgrounds and demonstrate overall robustness in all individuals. Our results also revealed significant associations between PRS and various phenotypic categories. For instance, CAD PRS was linked with 18 phenotypes in AFR and 82 in EUR, while T2D PRS correlated with 84 phenotypes in AFR and 78 in EUR. Notably, associations like hyperlipidemia, renal failure, atrial fibrillation, coronary atherosclerosis, obesity, and hypertension were observed across different PRSs in both AFR and EUR groups, with varying effect sizes and significance levels. However, in AFR individuals, the strength and number of PRS associations with other phenotypes were generally reduced compared to EUR individuals. Our study underscores the need for future research to prioritize 1) conducting GWAS in diverse ancestry groups and 2) creating a cosmopolitan PRS methodology that is universally applicable across all genetic backgrounds. Such advances will foster a more equitable and personalized approach to precision medicine.
MeSH term(s)	Humans ; Genetic Risk Score ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Precision Medicine ; Multifactorial Inheritance ; Computational Biology ; Phenotype ; Hypertension/genetics ; Diabetes Mellitus, Type 2/genetics ; Risk Factors
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2335-6936
ISSN (online)	2335-6936
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Article ; Online: The caspase-like Gpi8 subunit of Candida albicans GPI transamidase is a metal-dependent endopeptidase.

Sah, Sudisht Kumar / Shefali, Shailja / Yadav, Anshuman / Som, Punnag / Komath, Sneha Sudha

Biochemical and biophysical research communications

2020

Abstract: GPI anchored proteins (GPI-APs) act at the frontiers of cells, decoding environmental cues and determining host-pathogen interactions in several lower eukaryotes. They are also essential for viability in lower eukaryotes. The GPI biosynthetic pathway ... ...

Abstract	GPI anchored proteins (GPI-APs) act at the frontiers of cells, decoding environmental cues and determining host-pathogen interactions in several lower eukaryotes. They are also essential for viability in lower eukaryotes. The GPI biosynthetic pathway begins at the ER and follows a roughly linear pathway to generate the complete precursor (CP) glycolipid. The GPI transamidase (GPIT) transfers this glycolipid to the C-terminal end of newly translated proteins after removing their GPI attachment signal sequence (SS). The GPIT subunit that cleaves SS is Gpi8, a protein with a conserved Cys/His catalytic dyad typical of cysteine proteases. A CaGPI8 heterozygous mutant accumulates CPs and has reduced cell surface GPI-APs. Using a simple cell-free assay, we demonstrate that the heterozygous CaGPI8 strain has low endopeptidase activity as well. The revertant strain is restored in all these phenotypes. CaGpi8 is also shown to be a metalloenzyme, whose protease activity is sensitive to agents that modify Cys/His residues.
Language	English
Publishing date	2020-02-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2020.02.008
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Article ; Online: Evaluating the frequency and the impact of pharmacogenetic alleles in an ancestrally diverse Biobank population

Shefali S. Verma / Karl Keat / Binglan Li / Glenda Hoffecker / Marjorie Risman / Regeneron Genetics Center / Katrin Sangkuhl / Michelle Whirl-Carrillo / Scott Dudek / Anurag Verma / Teri E. Klein / Marylyn D. Ritchie / Sony Tuteja

Journal of Translational Medicine, Vol 20, Iss 1, Pp 1-

2022 Volume 15

Abstract: Abstract Background Pharmacogenomics (PGx) aims to utilize a patient’s genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for ...

Abstract	Abstract Background Pharmacogenomics (PGx) aims to utilize a patient’s genetic data to enable safer and more effective prescribing of medications. The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides guidelines with strong evidence for 24 genes that affect 72 medications. Despite strong evidence linking PGx alleles to drug response, there is a large gap in the implementation and return of actionable pharmacogenetic findings to patients in standard clinical practice. In this study, we evaluated opportunities for genetically guided medication prescribing in a diverse health system and determined the frequencies of actionable PGx alleles in an ancestrally diverse biobank population. Methods A retrospective analysis of the Penn Medicine electronic health records (EHRs), which includes ~ 3.3 million patients between 2012 and 2020, provides a snapshot of the trends in prescriptions for drugs with genotype-based prescribing guidelines (‘CPIC level A or B’) in the Penn Medicine health system. The Penn Medicine BioBank (PMBB) consists of a diverse group of 43,359 participants whose EHRs are linked to genome-wide SNP array and whole exome sequencing (WES) data. We used the Pharmacogenomics Clinical Annotation Tool (PharmCAT), to annotate PGx alleles from PMBB variant call format (VCF) files and identify samples with actionable PGx alleles. Results We identified ~ 316.000 unique patients that were prescribed at least 2 drugs with CPIC Level A or B guidelines. Genetic analysis in PMBB identified that 98.9% of participants carry one or more PGx actionable alleles where treatment modification would be recommended. After linking the genetic data with prescription data from the EHR, 14.2% of participants (n = 6157) were prescribed medications that could be impacted by their genotype (as indicated by their PharmCAT report). For example, 856 participants received clopidogrel who carried CYP2C19 reduced function alleles, placing them at increased risk for major adverse cardiovascular events. When we stratified ...
Keywords	Pharmacogenomics ; Electronic Health Records ; Genomic analyses ; Genetic testing ; CPIC guidelines ; Medicine ; R
Subject code	610
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Genetic liability for substance use associated with medical comorbidities in electronic health records of African- and European-ancestry individuals.

Hartwell, Emily E / Merikangas, Alison K / Verma, Shefali S / Ritchie, Marylyn D / Kranzler, Henry R / Kember, Rachel L

Addiction biology

2021 Volume 27, Issue 1, Page(s) e13099

Abstract: Polygenic risk scores (PRS) represent an individual's summed genetic risk for a trait and can serve as biomarkers for disease. Less is known about the utility of PRS as a means to quantify genetic risk for substance use disorders (SUDs) than for many ... ...

Abstract	Polygenic risk scores (PRS) represent an individual's summed genetic risk for a trait and can serve as biomarkers for disease. Less is known about the utility of PRS as a means to quantify genetic risk for substance use disorders (SUDs) than for many other traits. Nonetheless, the growth of large, electronic health record-based biobanks makes it possible to evaluate the association of SUD PRS with other traits. We calculated PRS for smoking initiation, alcohol use disorder (AUD), and opioid use disorder (OUD) using summary statistics from the Million Veteran Program sample. We then tested the association of each PRS with its primary phenotype in the Penn Medicine BioBank (PMBB) using all available genotyped participants of African or European ancestry (AFR and EUR, respectively) (N = 18,612). Finally, we conducted phenome-wide association analyses (PheWAS) separately by ancestry and sex to test for associations across disease categories. Tobacco use disorder was the most common SUD in the PMBB, followed by AUD and OUD, consistent with the population prevalence of these disorders. All PRS were associated with their primary phenotype in both ancestry groups. PheWAS results yielded cross-trait associations across multiple domains, including psychiatric disorders and medical conditions. SUD PRS were associated with their primary phenotypes; however, they are not yet predictive enough to be useful diagnostically. The cross-trait associations of the SUD PRS are indicative of a broader genetic liability. Future work should extend findings to additional population groups and for other substances of abuse.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Alcoholism/ethnology ; Alcoholism/genetics ; Blacks/genetics ; Comorbidity ; Electronic Health Records/statistics & numerical data ; Female ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Genotype ; Humans ; Male ; Middle Aged ; Multifactorial Inheritance ; Opioid-Related Disorders/ethnology ; Opioid-Related Disorders/genetics ; Phenotype ; Risk Factors ; Sex Factors ; Substance-Related Disorders/ethnology ; Substance-Related Disorders/genetics ; Tobacco Use Disorder/ethnology ; Tobacco Use Disorder/genetics ; Whites/genetics
Language	English
Publishing date	2021-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1324314-7
ISSN	1369-1600 ; 1355-6215
ISSN (online)	1369-1600
ISSN	1355-6215
DOI	10.1111/adb.13099
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Article ; Online: Uncovering myocardial infarction genetic signatures using GWAS exploration in Saudi and European cohorts.

Al-Ali, Amein K / Al-Rubaish, Abdullah M / Alali, Rudaynah A / Almansori, Mohammed S / Al-Jumaan, Mohammed A / Alshehri, Abdullah M / Al-Madan, Mohammed S / Vatte, ChittiBabu / Cherlin, Tess / Young, Sylvia / Verma, Shefali S / Morahan, Grant / Koeleman, Bobby P C / Keating, Brendan J

Scientific reports

2023 Volume 13, Issue 1, Page(s) 21866

Abstract: Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover ... ...

Abstract	Genome-wide association studies (GWAS) have yielded significant insights into the genetic architecture of myocardial infarction (MI), although studies in non-European populations are still lacking. Saudi Arabian cohorts offer an opportunity to discover novel genetic variants impacting disease risk due to a high rate of consanguinity. Genome-wide genotyping (GWG), imputation and GWAS followed by meta-analysis were performed based on two independent Saudi Arabian studies comprising 3950 MI patients and 2324 non-MI controls. Meta-analyses were then performed with these two Saudi MI studies and the CardioGRAMplusC4D and UK BioBank GWAS as controls. Meta-analyses of the two Saudi MI studies resulted in 17 SNPs with genome-wide significance. Meta-analyses of all 4 studies revealed 66 loci with genome-wide significance levels of p < 5 × 10
MeSH term(s)	Humans ; Genome-Wide Association Study/methods ; Saudi Arabia ; Genotype ; Myocardial Infarction/genetics ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease
Language	English
Publishing date	2023-12-10
Publishing country	England
Document type	Meta-Analysis ; Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-49105-1
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