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Humphries EM, Ahn K, Kember RL, Lopes FL, Mocci E, Peralta JM, Blangero J, Glahn DC, Goes FS, Zandi PP, Kochunov P, Van Hout C, Shuldiner AR, Pollin TI, Mitchell BD, Bucan M, Hong LE, McMahon FJ, Ament SA. Genome-wide significant risk loci for mood disorders in the Old Order Amish founder population. Mol Psychiatry 2023; 28:5262-5271. [PMID: 36882501 PMCID: PMC10483025 DOI: 10.1038/s41380-023-02014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Genome-wide association studies (GWAS) of mood disorders in large case-control cohorts have identified numerous risk loci, yet pathophysiological mechanisms remain elusive, primarily due to the very small effects of common variants. We sought to discover risk variants with larger effects by conducting a genome-wide association study of mood disorders in a founder population, the Old Order Amish (OOA, n = 1,672). Our analysis revealed four genome-wide significant risk loci, all of which were associated with >2-fold relative risk. Quantitative behavioral and neurocognitive assessments (n = 314) revealed effects of risk variants on sub-clinical depressive symptoms and information processing speed. Network analysis suggested that OOA-specific risk loci harbor novel risk-associated genes that interact with known neuropsychiatry-associated genes via gene interaction networks. Annotation of the variants at these risk loci revealed population-enriched, non-synonymous variants in two genes encoding neurodevelopmental transcription factors, CUX1 and CNOT1. Our findings provide insight into the genetic architecture of mood disorders and a substrate for mechanistic and clinical studies.
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Affiliation(s)
- Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kwangmi Ahn
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Rachel L Kember
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Fabiana L Lopes
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Evelina Mocci
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Juan M Peralta
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - John Blangero
- University of Texas Rio Grande Valley, Harlingen, TX, USA
| | | | - Fernando S Goes
- Departments of Epidemiology and Mental Health, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter P Zandi
- Departments of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Peter Kochunov
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cristopher Van Hout
- Regeneron Genetics Center, Tarrytown, NY, USA
- Laboratorio Internacional de Investigatión sobre el Genoma Humano, Campus Juriquilla de la Universidad Nacional Autónoma de México, Querétaro, Querétaro, 76230, Mexico
| | - Alan R Shuldiner
- Regeneron Genetics Center, Tarrytown, NY, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maja Bucan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - L Elliot Hong
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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Smolyak D, Humphries EM, Parikh A, Gopalakrishnan M, Aycan F, Bjarnadóttir M, Ament SA, El-Metwally D, Beitelshees A, Agarwal R. Predicting Heterogeneity in Patient Response to Morphine Treatment for Neonatal Opioid Withdrawal Syndrome. Clin Pharmacol Ther 2023; 114:1015-1022. [PMID: 37470135 DOI: 10.1002/cpt.3007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023]
Abstract
Infants with neonatal opioid withdrawal syndrome commonly receive morphine treatment to manage their withdrawal signs. However, the effectiveness of this pharmacotherapy in managing the infants' withdrawal signs vary widely. We sought to understand how information available early in infant monitoring can anticipate this treatment response, focusing on early modified Finnegan Neonatal Abstinence Scoring System (FNASS) scores, polygenic risk for opioid dependence (polygenic risk score (PRS)), and drug exposure. Using k-means clustering, we divided the 213 infants in our cohort into 3 groups based on their FNASS scores in the 12 hours before and after the initiation of pharmacotherapy. We found that these groups were pairwise significantly different for risk factors, including methadone exposure, and for in-hospital outcomes, including total morphine received, length of stay, and highest FNASS score. Whereas PRS was not predictive of receipt of treatment, PRS was pairwise significantly different between a subset of the groups. Using tree-based machine learning methods, we then constructed network graphs of the relationships among these groups, FNASS scores, PRS, drug exposures, and in-hospital outcomes. The resulting networks also showed meaningful connection between early FNASS scores and PRS, as well as between both of those and later in-hospital outcomes. These analyses present clinicians with the opportunity to better anticipate infant withdrawal progression and prepare accordingly, whether with expedited morphine treatment or non-pharmacotherapeutic alternative treatments.
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Affiliation(s)
- Daniel Smolyak
- Department of Computer Science, University of Maryland, College Park, Maryland, USA
| | - Elizabeth M Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Abhinav Parikh
- Department of Pediatrics, New York Presbyterian Brooklyn Methodist Hospital, Brooklyn, New York, USA
| | - Mathangi Gopalakrishnan
- Department of Practice, Science, and Health Outcomes Research, University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - Fulden Aycan
- Department of Pediatrics, Division of Neonatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Margrét Bjarnadóttir
- Robert H. Smith School of Business, University of Maryland, College Park, Maryland, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dina El-Metwally
- Department of Pediatrics, Division of Neonatology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amber Beitelshees
- University of Maryland - Medicine Institute for Neuroscience Discovery (UM-MIND), Baltimore, Maryland, USA
| | - Ritu Agarwal
- Carey Business School, Center for Digital Health and Artificial Intelligence, Johns Hopkins University, Baltimore, Maryland, USA
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Humphries EM, Wright C, Hoffman AM, Savonen C, Leek JT. What's the best chatbot for me? Researchers put LLMs through their paces. Nature 2023:10.1038/d41586-023-03023-4. [PMID: 37759110 DOI: 10.1038/d41586-023-03023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
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Li LL, Liu N, Humphries EM, Yu JM, Li S, Lindsay BR, Stine OC, Duan ZJ. Aetiology of diarrhoeal disease and evaluation of viral-bacterial coinfection in children under 5 years old in China: a matched case-control study. Clin Microbiol Infect 2015; 22:381.e9-381.e16. [PMID: 26724990 PMCID: PMC4865875 DOI: 10.1016/j.cmi.2015.12.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 01/21/2023]
Abstract
Globally, diarrhoeal diseases are the second leading cause of death among children under 5 years old. Few case-control studies on the aetiology of diarrhoea have been conducted in China. A case-control study on 922 children under 5 years old who presented with diarrhoea and individually matched controls was conducted in China between May 2011 and January 2013. Quantitative PCR was used to analyze stool samples for 10 diarrhoeal pathogens. Potential enteric pathogens were detected in 377 (81.8%) of 461 children with diarrhoea and 215 controls (46.6%, p <0.001). Rotavirus, norovirus GII, Shigella and adenovirus were qualitatively associated with diarrhoea. Using receiver operating characteristic curves, the optimal cutoff threshold for defining a symptomatic individual was 72, 5840, and 10(4) copies per reaction for rotavirus (odds ratio 259), norovirus GII (odds ratio 10.6) and Shigella (odds ratio 5.1). The attributable fractions were 0.18 for rotavirus, 0.08 for norovirus GII, 0.01 for Shigella and 0.04 for adenovirus. Coinfections between pathogens were common. Two pairs, rotavirus and adenovirus, and norovirus GII and Salmonella were positively associated. The co-occurrence of rotavirus and sapovirus, astrovirus, enterotoxigenic Escherichia coli or Campylobacter jejuni only occurred in children with disease. Coinfection was not correlated with clinical symptoms. Quantitative data are critical. Our results indicate that increased pathogen loads increase the OR between diarrhoea and rotavirus, norovirus GII and Shigella. Coinfections with rotavirus and norovirus GII are common and occur in a nonrandom distribution. Despite testing for ten diarrhoeal pathogens, over two-thirds of cases do not have a recognized attributable cause.
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Affiliation(s)
- L L Li
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - N Liu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - E M Humphries
- University of Maryland, School of Medicine, Baltimore, MD, USA
| | - J M Yu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - S Li
- University of Maryland, School of Medicine, Baltimore, MD, USA
| | - B R Lindsay
- University of Maryland, School of Medicine, Baltimore, MD, USA; Merck & Co. Inc., North Wales, PA, USA
| | - O C Stine
- University of Maryland, School of Medicine, Baltimore, MD, USA.
| | - Z J Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
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Abstract
Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.
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Affiliation(s)
- Elizabeth M Humphries
- Department of Biology and Wildlife, Institute of Arctic Biology, University of Alaska Museum, 907 Yukon Drive, Fairbanks, AK 99775, USA
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Humphries EM, Winker K. Working through polytomies: auklets revisited. Mol Phylogenet Evol 2009; 54:88-96. [PMID: 19643194 DOI: 10.1016/j.ympev.2009.07.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Revised: 07/21/2009] [Accepted: 07/22/2009] [Indexed: 11/26/2022]
Abstract
Polytomies, or phylogenetic "bushes", are the result of a series of internodes occurring in a short period of evolutionary time (which can result in data that do not contain enough information), or data that have too much homoplasy to resolve a bifurcating branching pattern. In this study we used the Aethia auklet polytomy to explore the effectiveness of different methods for resolving polytomies: mitochondrial DNA gene choice, number of individuals per species sampled, model of molecular evolution, and AFLP loci. We recovered a fully-resolved phylogeny using NADH dehydrogenase subunit 2 (ND2) sequence data under two different Bayesian models. We were able to corroborate this tree under one model with an expanded mtDNA dataset. Effectiveness of additional intraspecific sampling varied with node, and fully 20% of the subsampled datasets failed to return a congruent phylogeny when we sampled only one or two individuals per species. We did not recover a resolved phylogeny using AFLP data. Conflict in the AFLP dataset showed that nearly all possible relationships were supported at low levels of confidence, suggesting that either AFLPs are not useful at the genetic depth of the Aethia auklet radiation (7-9% divergent in the mtDNA ND2 gene), perhaps resulting in too much homoplasy, or that the Aethia auklets have experienced incomplete lineage sorting at many nuclear loci.
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Affiliation(s)
- Elizabeth M Humphries
- University of Alaska Museum, Department of Biology & Wildlife, Institute of Arctic Biology, Fairbanks, AK 99775, USA.
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Peters JL, Zhuravlev YN, Fefelov I, Humphries EM, Omland KE. Multilocus phylogeography of a holarctic duck: colonization of north america from eurasia by gadwall (Anas strepera). Evolution 2008; 62:1469-83. [PMID: 18346221 DOI: 10.1111/j.1558-5646.2008.00372.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
More than 100 species of birds have Holarctic distributions extending across Eurasia and North America, and many of them likely achieved these distributions by recently colonizing one continent from the other. Mitochondrial DNA (mtDNA) and five nuclear introns were sequenced to test the direction and timing of colonization for a Holarctic duck, the gadwall (Anas strepera). Three lines of evidence suggest gadwalls colonized North America from Eurasia. First, New World (NW) gadwalls had fewer alleles at every locus and 61% of the allelic richness found in Old World (OW) gadwalls. Second, NW gadwalls had lower mtDNA allelic richness than other NW ducks. Third, coalescent analysis suggested that less than 5% of the ancestral population contributed to NW gadwalls at the time of divergence. Gadwalls likely colonized North America during the Late Pleistocene (approximately 81,000 years ago), but the confidence interval on that estimate was large (8500-450,000 years ago). Intercontinental gene flow and selection also likely contributed to genetic diversity in gadwalls. This study illustrates the use of multiple loci and coalescent analyses for critically testing a priori hypotheses regarding dispersal and colonization and provides an independent datapoint supporting an OW to NW bias in the direction of colonization.
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Affiliation(s)
- Jeffrey L Peters
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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Humphries EM, Savidge K, Tyler RM. Occurrence Workgroup Poster Abstracts. Advances in Experimental Medicine and Biology 2008. [DOI: 10.1007/978-0-387-75865-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Humphries EM. A child care experiment. Nurs Times 1967; 63:1424. [PMID: 6075647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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