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Watanabe K, Wilmanski T, Baloni P, Robinson M, Garcia GG, Hoopmann MR, Midha MK, Baxter DH, Maes M, Morrone SR, Crebs KM, Kapil C, Kusebauch U, Wiedrick J, Lapidus J, Pflieger L, Lausted C, Roach JC, Glusman G, Cummings SR, Schork NJ, Price ND, Hood L, Miller RA, Moritz RL, Rappaport N. Author Correction: Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers. Commun Biol 2023; 6:1208. [PMID: 38012377 PMCID: PMC10682460 DOI: 10.1038/s42003-023-05549-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Affiliation(s)
| | | | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Gonzalo G Garcia
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | | | | | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Jack Wiedrick
- Oregon Health and Science University, Portland, OR, USA
| | - Jodi Lapidus
- Oregon Health and Science University, Portland, OR, USA
| | - Lance Pflieger
- Institute for Systems Biology, Seattle, WA, USA
- Phenome Health, Seattle, WA, USA
| | | | | | | | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nicholas J Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA.
- Phenome Health, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Richard A Miller
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI, USA
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2
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Roach JC, Freidin MB. Editorial: Insights in human and medical genomics: 2022. Front Genet 2023; 14:1287894. [PMID: 37818104 PMCID: PMC10561311 DOI: 10.3389/fgene.2023.1287894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Affiliation(s)
- Jared C. Roach
- Institute for Systems Biology, Seattle, WA, United States
| | - Maxim B. Freidin
- Department of Biology, School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
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3
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Watanabe K, Wilmanski T, Baloni P, Robinson M, Garcia GG, Hoopmann MR, Midha MK, Baxter DH, Maes M, Morrone SR, Crebs KM, Kapil C, Kusebauch U, Wiedrick J, Lapidus J, Pflieger L, Lausted C, Roach JC, Glusman G, Cummings SR, Schork NJ, Price ND, Hood L, Miller RA, Moritz RL, Rappaport N. Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers. Commun Biol 2023; 6:768. [PMID: 37481675 PMCID: PMC10363145 DOI: 10.1038/s42003-023-05128-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/10/2023] [Indexed: 07/24/2023] Open
Abstract
Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of biological processes under multiple lifespan-extending interventions. Differential Rank Conservation (DIRAC) analyses of mouse liver proteomics and transcriptomics data show that mechanistically distinct lifespan-extending interventions (acarbose, 17α-estradiol, rapamycin, and calorie restriction) generally tighten the regulation of biological modules. These tightening patterns are similar across the interventions, particularly in processes such as fatty acid oxidation, immune response, and stress response. Differences in DIRAC patterns between proteins and transcripts highlight specific modules which may be tightened via augmented cap-independent translation. Moreover, the systemic shifts in fatty acid metabolism are supported through integrated analysis of liver transcriptomics data with a mouse genome-scale metabolic model. Our findings highlight the power of systems-level approaches for identifying and characterizing the biological processes involved in aging and longevity.
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Affiliation(s)
| | | | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Gonzalo G Garcia
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | | | | | | | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Jack Wiedrick
- Oregon Health and Science University, Portland, OR, USA
| | - Jodi Lapidus
- Oregon Health and Science University, Portland, OR, USA
| | - Lance Pflieger
- Institute for Systems Biology, Seattle, WA, USA
- Phenome Health, Seattle, WA, USA
| | | | | | | | - Steven R Cummings
- San Francisco Coordinating Center, California Pacific Medical Center Research Institute, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Nicholas J Schork
- Department of Quantitative Medicine, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
- Department of Population Sciences and Molecular and Cell Biology, The City of Hope National Medical Center, Duarte, CA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA.
- Phenome Health, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
| | - Richard A Miller
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
- University of Michigan Geriatrics Center, Ann Arbor, MI, USA
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4
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Glen AK, Ma C, Mendoza L, Womack F, Wood EC, Sinha M, Acevedo L, Kvarfordt LG, Peene RC, Liu S, Hoffman AS, Roach JC, Deutsch EW, Ramsey SA, Koslicki D. ARAX: a graph-based modular reasoning tool for translational biomedicine. Bioinformatics 2023; 39:7031241. [PMID: 36752514 PMCID: PMC10027432 DOI: 10.1093/bioinformatics/btad082] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/17/2022] [Accepted: 02/07/2023] [Indexed: 04/12/2023] Open
Abstract
MOTIVATION With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but progress has been hindered by the lack of an expressive analysis workflow language for translational reasoning and by the lack of a reasoning engine-supporting that language-that federates semantically integrated knowledge-bases. RESULTS We introduce ARAX, a new reasoning system for translational biomedicine that provides a web browser user interface and an application programming interface (API). ARAX enables users to encode translational biomedical questions and to integrate knowledge across sources to answer the user's query and facilitate exploration of results. For ARAX, we developed new approaches to query planning, knowledge-gathering, reasoning and result ranking and dynamically integrate knowledge providers for answering biomedical questions. To illustrate ARAX's application and utility in specific disease contexts, we present several use-case examples. AVAILABILITY AND IMPLEMENTATION The source code and technical documentation for building the ARAX server-side software and its built-in knowledge database are freely available online (https://github.com/RTXteam/RTX). We provide a hosted ARAX service with a web browser interface at arax.rtx.ai and a web API endpoint at arax.rtx.ai/api/arax/v1.3/ui/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Luis Mendoza
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Finn Womack
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA
| | - E C Wood
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Meghamala Sinha
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Liliana Acevedo
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Lindsey G Kvarfordt
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Ross C Peene
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Shaopeng Liu
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA 16802, USA
| | - Andrew S Hoffman
- Interdisciplinary Hub for Digitalization and Society, Radboud University, Nijmegen 6500GL, The Netherlands
| | - Jared C Roach
- Institute for Systems Biology, Seattle, WA 98109, USA
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5
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Roach JC, Rapozo MK, Hara J, Glusman G, Lovejoy J, Shankle WR, Hood L. A Remotely Coached Multimodal Lifestyle Intervention for Alzheimer's Disease Ameliorates Functional and Cognitive Outcomes. J Alzheimers Dis 2023; 96:591-607. [PMID: 37840487 DOI: 10.3233/jad-230403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
BACKGROUND Comprehensive treatment of Alzheimer's disease and related dementias (ADRD) requires not only pharmacologic treatment but also management of existing medical conditions and lifestyle modifications including diet, cognitive training, and exercise. Personalized, multimodal therapies are needed to best prevent and treat Alzheimer's disease (AD). OBJECTIVE The Coaching for Cognition in Alzheimer's (COCOA) trial was a prospective randomized controlled trial to test the hypothesis that a remotely coached multimodal lifestyle intervention would improve early-stage AD. METHODS Participants with early-stage AD were randomized into two arms. Arm 1 (N = 24) received standard of care. Arm 2 (N = 31) additionally received telephonic personalized coaching for multiple lifestyle interventions. The primary outcome was a test of the hypothesis that the Memory Performance Index (MPI) change over time would be better in the intervention arm than in the control arm. The Functional Assessment Staging Test was assessed for a secondary outcome. COCOA collected psychometric, clinical, lifestyle, genomic, proteomic, metabolomic, and microbiome data at multiple timepoints (dynamic dense data) across two years for each participant. RESULTS The intervention arm ameliorated 2.1 [1.0] MPI points (mean [SD], p = 0.016) compared to the control over the two-year intervention. No important adverse events or side effects were observed. CONCLUSION Multimodal lifestyle interventions are effective for ameliorating cognitive decline and have a larger effect size than pharmacological interventions. Dietary changes and exercise are likely to be beneficial components of multimodal interventions in many individuals. Remote coaching is an effective intervention for early stage ADRD. Remote interventions were effective during the COVID pandemic.
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Affiliation(s)
| | | | - Junko Hara
- Pickup Family Neurosciences Institute, Hoag Memorial Hospital Presbyterian, Newport Beach, CA, USA
| | | | | | - William R Shankle
- Pickup Family Neurosciences Institute, Hoag Memorial Hospital Presbyterian, Newport Beach, CA, USA
- Department of Cognitive Sciences, University of California, Irvine, CA, USA
- Shankle Clinic, Newport Beach, CA, USA
- EMBIC Corporation, Newport Beach, CA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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6
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Bramen JE, Siddarth P, Popa ES, Kress GT, Rapozo MK, Hodes JF, Ganapathi AS, Slyapich CB, Glatt RM, Pierce K, Porter VR, Wong C, Kim M, Dye RV, Panos S, Bookheimer T, Togashi T, Loong S, Raji CA, Bookheimer SY, Roach JC, Merrill DA. Impact of Eating a Carbohydrate-Restricted Diet on Cortical Atrophy in a Cross-Section of Amyloid Positive Patients with Alzheimer's Disease: A Small Sample Study. J Alzheimers Dis 2023; 96:329-342. [PMID: 37742646 PMCID: PMC10657694 DOI: 10.3233/jad-230458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND A carbohydrate-restricted diet aimed at lowering insulin levels has the potential to slow Alzheimer's disease (AD). Restricting carbohydrate consumption reduces insulin resistance, which could improve glucose uptake and neural health. A hallmark feature of AD is widespread cortical thinning; however, no study has demonstrated that lower net carbohydrate (nCHO) intake is linked to attenuated cortical atrophy in patients with AD and confirmed amyloidosis. OBJECTIVE We tested the hypothesis that individuals with AD and confirmed amyloid burden eating a carbohydrate-restricted diet have thicker cortex than those eating a moderate-to-high carbohydrate diet. METHODS A total of 31 patients (mean age 71.4±7.0 years) with AD and confirmed amyloid burden were divided into two groups based on a 130 g/day nCHO cutoff. Cortical thickness was estimated from T1-weighted MRI using FreeSurfer. Cortical surface analyses were corrected for multiple comparisons using cluster-wise probability. We assessed group differences using a two-tailed two-independent sample t-test. Linear regression analyses using nCHO as a continuous variable, accounting for confounders, were also conducted. RESULTS The lower nCHO group had significantly thicker cortex within somatomotor and visual networks. Linear regression analysis revealed that lower nCHO intake levels had a significant association with cortical thickness within the frontoparietal, cingulo-opercular, and visual networks. CONCLUSIONS Restricting carbohydrates may be associated with reduced atrophy in patients with AD. Lowering nCHO to under 130 g/day would allow patients to follow the well-validated MIND diet while benefiting from lower insulin levels.
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Affiliation(s)
- Jennifer E. Bramen
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
- Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Prabha Siddarth
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Emily S. Popa
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Gavin T. Kress
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Molly K. Rapozo
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - John F. Hodes
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Aarthi S. Ganapathi
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Colby B. Slyapich
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Ryan M. Glatt
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Kyron Pierce
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Verna R. Porter
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
- Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Claudia Wong
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Mihae Kim
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Providence Saint John’s Health Center, Santa Monica, CA, USA
| | - Richelin V. Dye
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Loma Linda University, School of Medicine and School of Behavioral Health, Loma Linda, CA, USA
| | - Stella Panos
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Tess Bookheimer
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
| | - Tori Togashi
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Loma Linda University, School of Medicine and School of Behavioral Health, Loma Linda, CA, USA
| | - Spencer Loong
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Loma Linda University, School of Medicine and School of Behavioral Health, Loma Linda, CA, USA
| | - Cyrus A. Raji
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Mallinckrodt Institute of Radiology, Washington University, St. Louis, MO, USA
| | - Susan Y. Bookheimer
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | | | - David A. Merrill
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA, USA
- Providence Saint John’s Health Center, Santa Monica, CA, USA
- David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
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7
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Hadlock J, Chen D, Dai CL, Yuan D, Su Y, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel) 2022; 11:5. [PMID: 36679852 PMCID: PMC9861578 DOI: 10.3390/vaccines11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a different strain harboring the spike variant D614G. This case of reinfection was one of the first cases of reinfection reported in 2020. With antibody, B cell and T cell analytics, we show correlates of adaptive immunity at reinfection, including a differential response in neutralizing antibodies to a D614G pseudovirus. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kelly Chun
- LabCorp Esoterix, Calabasas, CA 91301, USA
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Kim M. Murray
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA 98057, USA
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Joshua Jeharajah
- Division of Infectious Diseases, Polyclinic, Seattle, WA 98104, USA
| | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA 98104, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, DC 98109, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94304, USA
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8
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Meysami S, Raji CA, Chwa WJ, Popa ES, Ganapathi AS, Bookheimer T, Slyapich CB, Pierce KP, Richards CJ, Gill JM, Lampa MG, Rapozo MK, Hodes JF, Glatt RM, Tongson YM, Wong CL, Kim M, Porter VR, Kaiser SA, Panos SE, Dye RV, Miller KJ, Bookheimer SY, Martin NA, Kesari S, Kelly DF, Siddarth P, Roach JC, Bramen JE, Merrill DA. Preliminary Evaluation of Longitudinal Brain MRI Volumetric Quantification in Persons with Cognitive Decline and Confirmed Amyloid Burden Undergoing Multi‐Modal Interventions at an Outpatient Memory Clinic. Alzheimers Dement 2022. [DOI: 10.1002/alz.063695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Somayeh Meysami
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | - Cyrus A. Raji
- Mallinckrodt Institute of Radiology, Washington University St. Louis MO USA
| | - Won Jong Chwa
- Mallinckrodt Institute of Radiology, Washington University St. Louis MO USA
| | - Emily S. Popa
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Aarthi S. Ganapathi
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Tess Bookheimer
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Colby B. Slyapich
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Kyron P. Pierce
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Casey J. Richards
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Jaya M. Gill
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Melanie G. Lampa
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Molly K. Rapozo
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - John F. Hodes
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Drexel University College of Medicine Philadelphia PA USA
| | - Ryan M. Glatt
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
| | | | - Claudia L. Wong
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
| | - Mihae Kim
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
| | - Verna R. Porter
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
- Providence Saint John's Health Center Santa Monica CA USA
| | - Scott A. Kaiser
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
| | - Stella E. Panos
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
| | - Richelin V. Dye
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Behavioral Health Institute, Loma Linda University School of Medicine Loma Linda CA USA
| | - Karen J. Miller
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | - Susan Y. Bookheimer
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | - Neil A. Martin
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
| | - Santosh Kesari
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
| | - Daniel F. Kelly
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John's Health Center Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
| | - Prabha Siddarth
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | | | - Jennifer E. Bramen
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
| | - David A. Merrill
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
- Providence Saint John's Health Center Santa Monica CA USA
- Saint John's Cancer Institute at Providence Saint John's Health Center Santa Monica CA USA
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9
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Bramen JE, Popa ES, Rapozo MK, Siddarth P, Hodes JF, Ganapathi AS, Slyapich CB, Glatt RM, Porter VR, Wong CL, Bookheimer SY, Roach JC, Merrill DA. Net Carbohydrate Consumption is Associated with Cortical Thickness in Cognitively Impaired Older Adults with Confirmed Amyloid Burden. Alzheimers Dement 2022. [DOI: 10.1002/alz.062649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jennifer E. Bramen
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center Santa Monica CA USA
| | - Emily S. Popa
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Molly K. Rapozo
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Prabha Siddarth
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | - John F. Hodes
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Drexel University College of Medicine Philadelphia PA USA
| | - Aarthi S. Ganapathi
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Colby B. Slyapich
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Ryan M. Glatt
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | - Verna R. Porter
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | - Claudia L. Wong
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | - Susan Y. Bookheimer
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | | | - David A. Merrill
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Cancer Institute Santa Monica CA USA
- David Geffen School of Medicine at UCLA Los Angeles CA USA
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10
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Roach JC, Hara J, Edens L, Rajbhandari S, Dill L, Romansik R, Rapozo MK, Funk C, Jade K, Merrill DA, Bramen JE, Panos SE, Porter VR, Dye RV, Ganapathi AS, Hodes JF, Slyapich CB, Glatt RM, Wong CL, Fortier D, Shankle WR. Frequent Cognitive Tests Increase Power for Alzheimer’s Disease Clinical Trials. Alzheimers Dement 2022. [DOI: 10.1002/alz.063995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Junko Hara
- Hoag Memorial Hospital Presbyterian Newport Beach CA USA
| | - Lance Edens
- Institute for Systems Biology Seattle WA USA
- Oregon Health and Science University Portland OR USA
| | - Sophiya Rajbhandari
- Institute for Systems Biology Seattle WA USA
- Oregon Health and Science University Portland OR USA
| | - Lauren Dill
- Hoag Memorial Hospital Presbyterian Newport Beach CA USA
- VA Long Beach Healthcare System Long Beach CA USA
| | | | - Molly K. Rapozo
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Cory Funk
- Institute for Systems Biology Seattle WA USA
| | | | - David A. Merrill
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center Santa Monica CA USA
- David Geffen School of Medicine at UCLA Los Angeles CA USA
| | - Jennifer E. Bramen
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Saint John’s Cancer Institute at Providence Saint John’s Health Center Santa Monica CA USA
| | - Stella E. Panos
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | - Verna R. Porter
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
- David Geffen School of Medicine at University of California Los Angeles Los Angeles CA USA
| | - Richelin V. Dye
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Behavioral Health Institute Loma Linda University School of Medicine Loma Linda CA USA
| | - Aarthi S. Ganapathi
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - John F. Hodes
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Drexel University College of Medicine Philadelphia PA USA
| | - Colby B. Slyapich
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
| | - Ryan M. Glatt
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | - Claudia L. Wong
- Pacific Brain Health Center, Pacific Neuroscience Institute Foundation Santa Monica CA USA
- Providence Saint John’s Health Center Santa Monica CA USA
| | | | - William R Shankle
- Hoag Memorial Hospital Presbyterian Newport Beach CA USA
- Embic Newport Beach CA USA
- Shankle Clinic Newport Beach CA USA
- University of California at Irvine Irvine CA USA
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11
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Wood EC, Glen AK, Kvarfordt LG, Womack F, Acevedo L, Yoon TS, Ma C, Flores V, Sinha M, Chodpathumwan Y, Termehchy A, Roach JC, Mendoza L, Hoffman AS, Deutsch EW, Koslicki D, Ramsey SA. RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. BMC Bioinformatics 2022; 23:400. [PMID: 36175836 PMCID: PMC9520835 DOI: 10.1186/s12859-022-04932-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 03/25/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API). RESULTS To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building-and hosting a web API for querying-a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink. CONCLUSION RTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json . The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2 .
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Affiliation(s)
- E C Wood
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Amy K Glen
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.
| | - Lindsey G Kvarfordt
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Finn Womack
- Computer Science and Engineering, Penn State University, State College, PA, USA
| | - Liliana Acevedo
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Timothy S Yoon
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Chunyu Ma
- Huck Institutes of the Life Sciences, Penn State University, State College, PA, USA
| | - Veronica Flores
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Meghamala Sinha
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | | | - Arash Termehchy
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | | | | | - Andrew S Hoffman
- Interdisciplinary Hub for Digitalization and Society, Radboud University, Nijmegen, The Netherlands
| | | | - David Koslicki
- Computer Science and Engineering, Penn State University, State College, PA, USA.,Huck Institutes of the Life Sciences, Penn State University, State College, PA, USA.,Department of Biology, Penn State University, State College, PA, USA
| | - Stephen A Ramsey
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.,Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
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12
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Hasin N, Riggs LM, Shekhtman T, Ashworth J, Lease R, Oshone RT, Humphries EM, Badner JA, Thomson PA, Glahn DC, Craig DW, Edenberg HJ, Gershon ES, McMahon FJ, Nurnberger JI, Zandi PP, Kelsoe JR, Roach JC, Gould TD, Ament SA. Rare variants implicate NMDA receptor signaling and cerebellar gene networks in risk for bipolar disorder. Mol Psychiatry 2022; 27:3842-3856. [PMID: 35546635 DOI: 10.1038/s41380-022-01609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/19/2021] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023]
Abstract
Bipolar disorder is an often-severe mental health condition characterized by alternation between extreme mood states of mania and depression. Despite strong heritability and the recent identification of 64 common variant risk loci of small effect, pathophysiological mechanisms remain unknown. Here, we analyzed genome sequences from 41 multiply-affected pedigrees and identified variants in 741 genes with nominally significant linkage or association with bipolar disorder. These 741 genes overlapped known risk genes for neurodevelopmental disorders and clustered within gene networks enriched for synaptic and nuclear functions. The top variant in this analysis - prioritized by statistical association, predicted deleteriousness, and network centrality - was a missense variant in the gene encoding D-amino acid oxidase (DAOG131V). Heterologous expression of DAOG131V in human cells resulted in decreased DAO protein abundance and enzymatic activity. In a knock-in mouse model of DAOG131, DaoG130V/+, we similarly found decreased DAO protein abundance in hindbrain regions, as well as enhanced stress susceptibility and blunted behavioral responses to pharmacological inhibition of N-methyl-D-aspartate receptors (NMDARs). RNA sequencing of cerebellar tissue revealed that DaoG130V resulted in decreased expression of two gene networks that are enriched for synaptic functions and for genes expressed, respectively, in Purkinje neurons or granule neurons. These gene networks were also down-regulated in the cerebellum of patients with bipolar disorder compared to healthy controls and were enriched for additional rare variants associated with bipolar disorder risk. These findings implicate dysregulation of NMDAR signaling and of gene expression in cerebellar neurons in bipolar disorder pathophysiology and provide insight into its genetic architecture.
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Affiliation(s)
- Naushaba Hasin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Lace M Riggs
- Program in Neuroscience and Training Program in Integrative Membrane Biology, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Robert Lease
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rediet T Oshone
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - 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
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical College, Chicago, IL, USA
| | - Pippa A Thomson
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, UK
| | - David C Glahn
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, CA, USA
| | - Howard J Edenberg
- Departments of Biochemistry and Molecular Biology and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elliot S Gershon
- Departments of Psychiatry and Human Genetics, University of Chicago, Chicago, IL, USA
| | - Francis J McMahon
- Intramural Research Program, National Institute of Mental Health, Bethesda, MD, USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - John R Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | | | - Todd D Gould
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
- Departments of Pharmacology and Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Veterans Affairs Maryland Health Care System, Baltimore, MD, USA
| | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA.
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13
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Abstract
Projections of the near future of daily case incidence of COVID-19 are valuable for informing public policy. Near-future estimates are also useful for outbreaks of other diseases. Short-term predictions are unlikely to be affected by changes in herd immunity. In the absence of major net changes in factors that affect reproduction number (R), the two-parameter exponential model should be a standard model - indeed, it has been standard for epidemiological analysis of pandemics for a century but in recent decades has lost popularity to more complex compartmental models. Exponential models should be routinely included in reports describing epidemiological models as a reference, or null hypothesis. Exponential models should be fitted separately for each epidemiologically distinct jurisdiction. They should also be fitted separately to time intervals that differ by any major changes in factors that affect R. Using an exponential model, incidence-count half-life (t1/2) is a better statistic than R. Here an example of the exponential model is applied to King County, Washington during Spring 2020. During the pandemic, the parameters and predictions of this model have remained stable for intervals of one to four months, and the accuracy of model predictions has outperformed models with more parameters. The COVID pandemic can be modeled as a series of exponential curves, each spanning an interval ranging from one to four months. The length of these intervals is hard to predict, other than to extrapolate that future intervals will last about as long as past intervals.
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14
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Roach JC, Hodes JF, Funk CC, Shankle WR, Merrill DA, Hood L, Bramen J. Dense data enables 21st century clinical trials. A&D Transl Res & Clin Interv 2022; 8:e12297. [PMID: 35733645 PMCID: PMC9191823 DOI: 10.1002/trc2.12297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/12/2022] [Indexed: 11/12/2022]
Affiliation(s)
| | - John F. Hodes
- Pacific Brain Health Center Pacific Neuroscience Institute Foundation Santa Monica California USA
| | - Cory C. Funk
- Institute for Systems Biology Seattle Washington USA
| | - William R Shankle
- Pickup Family Neurosciences Institute Hoag Memorial Hospital Presbyterian Newport Beach California USA
- Department of Cognitive Sciences University of California, Irvine Irvine California USA
- Shankle Clinic Newport Beach California USA
- EMBIC Corporation Newport Beach California USA
| | - David A. Merrill
- Pacific Brain Health Center Pacific Neuroscience Institute Foundation Santa Monica California USA
- Department of Translational Neurosciences and Neurotherapeutics Saint John's Cancer Institute Santa Monica California USA
| | - Leroy Hood
- Institute for Systems Biology Seattle Washington USA
- Providence St. Joseph Health Renton Washington USA
| | - Jennifer Bramen
- Pacific Brain Health Center Pacific Neuroscience Institute Foundation Santa Monica California USA
- Department of Translational Neurosciences and Neurotherapeutics Saint John's Cancer Institute Santa Monica California USA
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15
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Roach JC, Hara J, Fridman D, Lovejoy JC, Jade K, Heim L, Romansik R, Swietlikowski A, Phillips S, Rapozo MK, Shay MA, Fischer D, Funk C, Dill L, Brant‐Zawadzki M, Hood L, Shankle WR. The Coaching for Cognition in Alzheimer's (COCOA) trial: Study design. A&D Transl Res & Clin Interv 2022; 8:e12318. [PMID: 35910672 PMCID: PMC9322829 DOI: 10.1002/trc2.12318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/07/2022] [Accepted: 05/13/2022] [Indexed: 11/15/2022]
Abstract
Comprehensive treatment of Alzheimer's disease (AD) requires not only pharmacologic treatment but also management of existing medical conditions and lifestyle modifications including diet, cognitive training, and exercise. We present the design and methodology for the Coaching for Cognition in Alzheimer's (COCOA) trial. AD and other dementias result from the interplay of multiple interacting dysfunctional biological systems. Monotherapies have had limited success. More interventional studies are needed to test the effectiveness of multimodal multi‐domain therapies for dementia prevention and treatment. Multimodal therapies use multiple interventions to address multiple systemic causes and potentiators of cognitive decline and functional loss; they can be personalized, as different sets of etiologies and systems responsive to therapy may be present in different individuals. COCOA is designed to test the hypothesis that coached multimodal interventions beneficially alter the trajectory of cognitive decline for individuals on the spectrum of AD and related dementias (ADRD). COCOA is a two‐arm prospective randomized controlled trial (RCT). COCOA collects psychometric, clinical, lifestyle, genomic, proteomic, metabolomic, and microbiome data at multiple timepoints across 2 years for each participant. These data enable systems biology analyses. One arm receives standard of care and generic healthy aging recommendations. The other arm receives standard of care and personalized data‐driven remote coaching. The primary outcome measure is the Memory Performance Index (MPI), a measure of cognition. The MPI is a summary statistic of the MCI Screen (MCIS). Secondary outcome measures include the Functional Assessment Staging Test (FAST), a measure of function. COCOA began enrollment in January 2018. We hypothesize that multimodal interventions will ameliorate cognitive decline and that data‐driven health coaching will increase compliance, assist in personalizing multimodal interventions, and improve outcomes for patients, particularly for those in the early stages of the AD spectrum.
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Affiliation(s)
| | - Junko Hara
- Pickup Family Neurosciences Institute Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | - Deborah Fridman
- Hoag Center for Research and Education Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | | | - Kathleen Jade
- Institute for Systems Biology Seattle Washington USA
| | - Laura Heim
- Hoag Center for Research and Education Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | - Rachel Romansik
- Hoag Center for Research and Education Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | - Adrienne Swietlikowski
- Hoag Center for Research and Education Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | - Sheree Phillips
- Hoag Center for Research and Education Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | | | - Maria A. Shay
- Institute for Systems Biology Seattle Washington USA
| | - Dan Fischer
- Institute for Systems Biology Seattle Washington USA
- Oregon Health & Science University Portland Oregon USA
| | - Cory Funk
- Institute for Systems Biology Seattle Washington USA
| | - Lauren Dill
- Pickup Family Neurosciences Institute Hoag Memorial Hospital Presbyterian Newport Beach California USA
- VA Long Beach Healthcare System Long Beach California USA
| | - Michael Brant‐Zawadzki
- Pickup Family Neurosciences Institute Hoag Memorial Hospital Presbyterian Newport Beach California USA
| | - Leroy Hood
- Institute for Systems Biology Seattle Washington USA
- Providence St. Joseph Health Renton Washington USA
| | - William R. Shankle
- Pickup Family Neurosciences Institute Hoag Memorial Hospital Presbyterian Newport Beach California USA
- Department of Cognitive Sciences University of California Irvine California USA
- Shankle Clinic Newport Beach California USA
- EMBIC Corporation Newport Beach California USA
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16
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Ross MK, Raji C, Lokken KL, Bredesen DE, Roach JC, Funk CC, Price N, Rappaport N, Hood L, Heath JR. Case Study: A Precision Medicine Approach to Multifactorial Dementia and Alzheimer's Disease. J Alzheimers Dis Parkinsonism 2021; 11:018. [PMID: 35237464 PMCID: PMC8887953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We report a case of a patient with mixed dementia successfully treated with a personalized multimodal therapy. Monotherapeutics are inadequate for the treatment of Alzheimer's disease (AD) and mixed dementia; therefore, we approach treatment through an adaptive personalized multimodal program. Many multimodal programs are pre-determined, and thus may not address the underlying contributors to cognitive decline in each particular individual. The combination of a targeted, personalized, precision medicine approach using a multimodal program promises advantages over monotherapies and untargeted multimodal therapies for multifactorial dementia. In this case study, we describe successful treatment for a patient diagnosed with AD, using a multimodal, programmatic, precision medicine intervention encompassing therapies targeting multiple dementia diastheses. We describe specific interventions used in this case that are derived from a comprehensive protocol for AD precision medicine. After treatment, our patient demonstrated improvements in quantitative neuropsychological testing, volumetric neuroimaging, PET scans, and serum chemistries, accompanied by symptomatic improvement over a 3.5-year period. This case outcome supports the need for rigorous trials of comprehensive, targeted combination therapies to stabilize, restore, and prevent cognitive decline in individuals with potentially many underlying causes of such decline and dementia. Our multimodal therapy included personalized treatments to address each potential perturbation to neuroplasticity. In particular, neuroinflammation and metabolic subsystems influence cognitive function and hippocampal volume. In this patient with a primary biliary cholangitis (PBC) multimorbidity component, we introduced a personalized diet that helped reduce liver inflammation. Together, all these components of multimodal therapy showed a sustained functional and cognitive benefit. Multimodal therapies may have systemwide benefits on all dementias, particularly in the context of multimorbidity. Furthermore, these therapies provide generalized health benefits, as many of the factors - such as inflammation - that impact cognitive function also impact other systems.
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Affiliation(s)
- Mary Kay Ross
- Brain Health and Research Institute, Seattle, WA, USA
| | - Cyrus Raji
- Washington University School of Medicine, St. Louis, MO, USA
| | - Kristine L Lokken
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama-Birmingham, Birmingham, AL, USA
| | - Dale E Bredesen
- Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, USA
| | - Jared C Roach
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
| | - Cory C Funk
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
| | - Nathan Price
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
| | - Noa Rappaport
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
| | - Leroy Hood
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
| | - James R Heath
- Institute for Systems Biology, 401 Terry Ave N, Seattle, WA, USA, 98109
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17
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McEwen SC, Merrill DA, Bramen J, Porter V, Panos S, Kaiser S, Hodes J, Ganapathi A, Bell L, Bookheimer T, Glatt R, Rapozo M, Ross MK, Price ND, Kelly D, Funk CC, Hood L, Roach JC. A systems-biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer's disease. Alzheimers Dement (N Y) 2021; 7:e12191. [PMID: 34295960 PMCID: PMC8290633 DOI: 10.1002/trc2.12191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/29/2021] [Accepted: 05/12/2021] [Indexed: 02/01/2023]
Abstract
INTRODUCTION There is an urgent need to develop effective interventional treatments for people with Alzheimer's disease (AD). AD results from a complex multi-decade interplay of multiple interacting dysfunctional biological systems that have not yet been fully elucidated. Epidemiological studies have linked several modifiable lifestyle factors with increased incidence for AD. Because monotherapies have failed to prevent or ameliorate AD, interventional studies should deploy multiple, targeted interventions that address the dysfunctional systems that give rise to AD. METHODS This randomized controlled trial (RCT) will examine the efficacy of a 12-month personalized, multimodal, lifestyle intervention in 60 mild cognitive impairment (MCI) and early stage AD patients (aged 50+, amyloid positivity). Both groups receive data-driven, lifestyle recommendations designed to target multiple systemic pathways implicated in AD. One group receives these personalized recommendations without coaching. The other group receives personalized recommendations with health coaching, dietary counseling, exercise training, cognitive stimulation, and nutritional supplements. We collect clinical, proteomic, metabolomic, neuroimaging, and genetic data to fuel systems-biology analyses. We will examine effects on cognition and hippocampal volume. The overarching goal of the study is to longitudinally track biological systems implicated in AD to reveal the dynamics between these systems during the intervention to understand differences in treatment response. RESULTS We have developed and implemented a protocol for a personalized, multimodal intervention program for early AD patients. We began enrollment in September 2019; we have enrolled a third of our target (20 of 60) with a 95% retention and 86% compliance rate. DISCUSSION This study presents a paradigm shift in designing multimodal, lifestyle interventions to reduce cognitive decline, and how to elucidate the biological systems being targeted. Analytical efforts to explain mechanistic or causal underpinnings of individual trajectories and the interplay between multi-omic variables will inform the design of future hypotheses and development of effective precision medicine trials.
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Affiliation(s)
- Sarah C. McEwen
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - David A. Merrill
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Jennifer Bramen
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Verna Porter
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Stella Panos
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Scott Kaiser
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - John Hodes
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
| | - Aarthi Ganapathi
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Lesley Bell
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
| | - Tess Bookheimer
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
| | - Ryan Glatt
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
| | - Molly Rapozo
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
| | - Mary Kay Ross
- Brain Health and Research InstituteSeattleWashingtonUSA
| | | | - Daniel Kelly
- Pacific Neuroscience InstitutePacific Brain Health CenterSanta MonicaCaliforniaUSA
- Providence Saint John's Cancer InstituteDepartment of Translational Neurosciences and NeurotherapeuticsSanta MonicaCaliforniaUSA
| | - Cory C. Funk
- Institute for Systems BiologySeattleWashingtonUSA
| | - Leroy Hood
- Providence St. Joseph HealthRentonWashingtonUSA
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18
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Su Y, Hadlock J, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. medRxiv 2020:2020.09.22.20192443. [PMID: 32995830 PMCID: PMC7523175 DOI: 10.1101/2020.09.22.20192443] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a new strain harboring the spike variant D614G. With antibody and B cell analytics, we show correlates of adaptive immunity, including a differential response to D614G. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA
| | | | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | | | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, WA, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
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19
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Roach JC, Hara J, Lovejoy JC, Fridman D, Funk C, Heath LM, Price ND, Hood L, Heim L, Brant-Zawadski M, Shankle WR. P4-017: COACHING FOR COGNITION IN ALZHEIMER'S (COCOA) TRIAL. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.06.3676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Junko Hara
- Medical Care Corporation; Newport Beach CA USA
- Hoag Memorial Hospital Presbyterian; Newport Beach CA USA
| | | | | | - Cory Funk
- Institute for Systems Biology; Seattle WA USA
| | | | | | - Leroy Hood
- Institute for Systems Biology; Seattle WA USA
| | - Laura Heim
- Hoag Memorial Hospital Presbyterian; Newport Beach CA USA
| | | | - William R. Shankle
- Medical Care Corporation; Newport Beach CA USA
- Hoag Memorial Hospital Presbyterian; Newport Beach CA USA
- Shankle Clinic; Newport Beach CA USA
- University of California at Irvine; Irvine CA USA
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20
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Budde M, Friedrichs S, Alliey-Rodriguez N, Ament S, Badner JA, Berrettini WH, Bloss CS, Byerley W, Cichon S, Comes AL, Coryell W, Craig DW, Degenhardt F, Edenberg HJ, Foroud T, Forstner AJ, Frank J, Gershon ES, Goes FS, Greenwood TA, Guo Y, Hipolito M, Hood L, Keating BJ, Koller DL, Lawson WB, Liu C, Mahon PB, McInnis MG, McMahon FJ, Meier SM, Mühleisen TW, Murray SS, Nievergelt CM, Nurnberger JI, Nwulia EA, Potash JB, Quarless D, Rice J, Roach JC, Scheftner WA, Schork NJ, Shekhtman T, Shilling PD, Smith EN, Streit F, Strohmaier J, Szelinger S, Treutlein J, Witt SH, Zandi PP, Zhang P, Zöllner S, Bickeböller H, Falkai PG, Kelsoe JR, Nöthen MM, Rietschel M, Schulze TG, Malzahn D. Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder. Eur Neuropsychopharmacol 2019; 29:156-170. [PMID: 30503783 DOI: 10.1016/j.euroneuro.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/16/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022]
Abstract
Genome-wide association studies of case-control status have advanced the understanding of the genetic basis of psychiatric disorders. Further progress may be gained by increasing sample size but also by new analysis strategies that advance the exploitation of existing data, especially for clinically important quantitative phenotypes. The functionally-informed efficient region-based test strategy (FIERS) introduced herein uses prior knowledge on biological function and dependence of genotypes within a powerful statistical framework with improved sensitivity and specificity for detecting consistent genetic effects across studies. As proof of concept, FIERS was used for the first genome-wide single nucleotide polymorphism (SNP)-based investigation on bipolar disorder (BD) that focuses on an important aspect of disease course, the functional outcome. FIERS identified a significantly associated locus on chromosome 15 (hg38: chr15:48965004 - 49464789 bp) with consistent effect strength between two independent studies (GAIN/TGen: European Americans, BOMA: Germans; n = 1592 BD patients in total). Protective and risk haplotypes were found on the most strongly associated SNPs. They contain a CTCF binding site (rs586758); CTCF sites are known to regulate sets of genes within a chromatin domain. The rs586758 - rs2086256 - rs1904317 haplotype is located in the promoter flanking region of the COPS2 gene, close to microRNA4716, and the EID1, SHC4, DTWD1 genes as plausible biological candidates. While implication with BD is novel, COPS2, EID1, and SHC4 are known to be relevant for neuronal differentiation and function and DTWD1 for psychopharmacological side effects. The test strategy FIERS that enabled this discovery is equally applicable for tag SNPs and sequence data.
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Affiliation(s)
- Monika Budde
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany
| | - Stefanie Friedrichs
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, United States
| | - Seth Ament
- Institute for Systems Biology, Seattle, WA 98109, United States
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical Center, Chicago, IL 60612, United States
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Cinnamon S Bloss
- University of California San Diego, La Jolla, CA 92093, United States
| | - William Byerley
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA 94103, United States
| | - Sven Cichon
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland; Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich 52425, Germany
| | - Ashley L Comes
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany; International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - William Coryell
- University of Iowa Hospitals and Clinics, Iowa City, IA 52242, United States
| | - David W Craig
- The Translational Genomics Research Institute, Phoenix, AZ 85004, United States
| | - Franziska Degenhardt
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Andreas J Forstner
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany; Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland; Department of Psychiatry (UPK), University of Basel, Basel 4012, Switzerland
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, United States
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States
| | - Tiffany A Greenwood
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, United States; Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
| | - Maria Hipolito
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC 20060, United States
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, United States
| | - Brendan J Keating
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-5159, United States; Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5158, United States
| | - Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - William B Lawson
- Dell Medical School, University of Texas at Austin, Austin, TX 78723, United States
| | - Chunyu Liu
- SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Pamela B Mahon
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48105, United States
| | - Francis J McMahon
- U.S. Department of Health & Human Services, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20894, United States
| | - Sandra M Meier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany; National Centre for Register-Based Research, Aarhus University, Aarhus V 8210, Denmark
| | - Thomas W Mühleisen
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich 52425, Germany; Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland
| | - Sarah S Murray
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA 92037, United States; Department of Pathology, University of California San Diego, La Jolla, CA 92093, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Evaristus A Nwulia
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC 20060, United States
| | - James B Potash
- Department of Psychiatry, Carver College of Medicine, University of Iowa School of Medicine, Iowa City, IA 52242, United States
| | - Danjuma Quarless
- J. Craig Venter Institute, La Jolla, CA 92037, United States; University of California San Diego, La Jolla, CA 92093, United States
| | - John Rice
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, United States
| | - Jared C Roach
- Institute for Systems Biology, Seattle, WA 98109, United States
| | | | - Nicholas J Schork
- J. Craig Venter Institute, La Jolla, CA 92037, United States; The Translational Genomics Research Institute, Phoenix, AZ 85004, United States; University of California San Diego, La Jolla, CA 92093, United States
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Paul D Shilling
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Erin N Smith
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA 92037, United States; Department of Pediatrics and Rady's Children's Hospital, School of Medicine, University of California San Diego, La Jolla, CA 92037, United States
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Szabolcs Szelinger
- The Translational Genomics Research Institute, Phoenix, AZ 85004, United States
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Peter P Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States
| | - Peng Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sebastian Zöllner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States; Department of Psychiatry, University of Michigan, Ann Arbor, MI 48105, United States
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany
| | - Peter G Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich 80336, Germany
| | - John R Kelsoe
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany; Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States; U.S. Department of Health & Human Services, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20894, United States.
| | - Dörthe Malzahn
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany.
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21
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Goldmann JM, Wong WSW, Pinelli M, Farrah T, Bodian D, Stittrich AB, Glusman G, Vissers LELM, Hoischen A, Roach JC, Vockley JG, Veltman JA, Solomon BD, Gilissen C, Niederhuber JE. Author Correction: Parent-of-origin-specific signatures of de novo mutations. Nat Genet 2018; 50:1615. [PMID: 30291356 DOI: 10.1038/s41588-018-0226-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article published, the P values for the enrichment of single mutation categories were inadvertently not corrected for multiple testing. After multiple-testing correction, only two of the six mutation categories mentioned are still statistically significant. To reflect this, the text "More specifically, paternally derived DNMs are enriched in transitions in A[.]G contexts, especially ACG>ATG and ATG>ACG (Bonferroni-corrected P = 1.3 × 10-2 and P = 1 × 10-3, respectively). Additionally, we observed overrepresentation of ATA>ACA mutations (Bonferroni-corrected P = 4.28 × 10-2) for DNMs of paternal origin. Among maternally derived DNMs, CCA>CTA, GCA>GTA and TCT>TGT mutations were significantly overrepresented (Bonferroni-corrected P = 4 × 10-4, P = 5 × 10-4, P = 1 × 10-3, respectively)" should read "More specifically, CCA>CTA and GCA>GTA mutations were significantly overenriched on the maternal allele (Bonferroni-corrected P = 0.0192 and P = 0.048, respectively)." Additionally, the last sentence to the legend for Fig. 3b should read "Green boxes highlight the mutation categories that differ significantly" instead of "Green boxes highlight the mutation categories that differ more than 1% of mutation load with a bootstrapping P value <0.05." Corrected versions of Fig. 3b and Supplementary Table 25 appear with the Author Correction.
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Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Terry Farrah
- Institute for Systems Biology, Seattle, Washington, USA
| | - Dale Bodian
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA
| | | | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jared C Roach
- Institute for Systems Biology, Seattle, Washington, USA
| | - Joseph G Vockley
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Benjamin D Solomon
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA.,Department of Pediatrics, Inova Children's Hospital, Inova Health System, Falls Church, Virginia, USA.,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - John E Niederhuber
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, Virginia, USA. .,Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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22
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Hou L, Kember RL, Roach JC, O'Connell JR, Craig DW, Bucan M, Scott WK, Pericak-Vance M, Haines JL, Crawford MH, Shuldiner AR, McMahon FJ. Author Correction: A population-specific reference panel empowers genetic studies of Anabaptist populations. Sci Rep 2018; 8:6771. [PMID: 29691419 PMCID: PMC5915589 DOI: 10.1038/s41598-018-24604-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Liping Hou
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, 20892, USA.
| | - Rachel L Kember
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jared C Roach
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David W Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jonathan L Haines
- Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michael H Crawford
- Department of Anthropology, University of Kansas, Lawrence, KS, 66045, USA
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Francis J McMahon
- Human Genetics Branch, National Institute of Mental Health Intramural Research Program, Bethesda, MD, 20892, USA.
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23
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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24
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Stittrich AB, Ashworth J, Shi M, Robinson M, Mauldin D, Brunkow ME, Biswas S, Kim JM, Kwon KS, Jung JU, Galas D, Serikawa K, Duerr RH, Guthery SL, Peschon J, Hood L, Roach JC, Glusman G. Genomic architecture of inflammatory bowel disease in five families with multiple affected individuals. Hum Genome Var 2016; 3:15060. [PMID: 27081563 PMCID: PMC4785573 DOI: 10.1038/hgv.2015.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 01/06/2023] Open
Abstract
Currently, the best clinical predictor for inflammatory bowel disease (IBD) is family history. Over 163 sequence variants have been associated with IBD in genome-wide association studies, but they have weak effects and explain only a fraction of the observed heritability. It is expected that additional variants contribute to the genomic architecture of IBD, possibly including rare variants with effect sizes larger than the identified common variants. Here we applied a family study design and sequenced 38 individuals from five families, under the hypothesis that families with multiple IBD-affected individuals harbor one or more risk variants that (i) are shared among affected family members, (ii) are rare and (iii) have substantial effect on disease development. Our analysis revealed not only novel candidate risk variants but also high polygenic risk scores for common known risk variants in four out of the five families. Functional analysis of our top novel variant in the remaining family, a rare missense mutation in the ubiquitin ligase TRIM11, suggests that it leads to increased nuclear factor of kappa light chain enhancer in B-cells (NF-κB) signaling. We conclude that an accumulation of common weak-effect variants accounts for the high incidence of IBD in most, but not all families we analyzed and that a family study design can identify novel rare variants conferring risk for IBD with potentially large effect size, such as the TRIM11 p.H414Y mutation.
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Affiliation(s)
| | | | - Mude Shi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | | | | | | | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Korea
| | - Ki-Sun Kwon
- Aging Intervention Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Jae U Jung
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, WA, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen L Guthery
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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25
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Lalli MA, Bettcher BM, Arcila ML, Garcia G, Guzman C, Madrigal L, Ramirez L, Acosta-Uribe J, Baena A, Wojta KJ, Coppola G, Fitch R, de Both MD, Huentelman MJ, Reiman EM, Brunkow ME, Glusman G, Roach JC, Kao AW, Lopera F, Kosik KS. Whole-genome sequencing suggests a chemokine gene cluster that modifies age at onset in familial Alzheimer's disease. Mol Psychiatry 2015; 20:1294-300. [PMID: 26324103 PMCID: PMC4759097 DOI: 10.1038/mp.2015.131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/10/2015] [Accepted: 07/23/2015] [Indexed: 12/22/2022]
Abstract
We have sequenced the complete genomes of 72 individuals affected with early-onset familial Alzheimer's disease caused by an autosomal dominant, highly penetrant mutation in the presenilin-1 (PSEN1) gene, and performed genome-wide association testing to identify variants that modify age at onset (AAO) of Alzheimer's disease. Our analysis identified a haplotype of single-nucleotide polymorphisms (SNPs) on chromosome 17 within a chemokine gene cluster associated with delayed onset of mild-cognitive impairment and dementia. Individuals carrying this haplotype had a mean AAO of mild-cognitive impairment at 51.0 ± 5.2 years compared with 41.1 ± 7.4 years for those without these SNPs. This haplotype thus appears to modify Alzheimer's AAO, conferring a large (~10 years) protective effect. The associated locus harbors several chemokines including eotaxin-1 encoded by CCL11, and the haplotype includes a missense polymorphism in this gene. Validating this association, we found plasma eotaxin-1 levels were correlated with disease AAO in an independent cohort from the University of California San Francisco Memory and Aging Center. In this second cohort, the associated haplotype disrupted the typical age-associated increase of eotaxin-1 levels, suggesting a complex regulatory role for this haplotype in the general population. Altogether, these results suggest eotaxin-1 as a novel modifier of Alzheimer's disease AAO and open potential avenues for therapy.
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Affiliation(s)
- M A Lalli
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - B M Bettcher
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - M L Arcila
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
| | - G Garcia
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - C Guzman
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - L Madrigal
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - L Ramirez
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - J Acosta-Uribe
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - A Baena
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - K J Wojta
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - G Coppola
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - R Fitch
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - M D de Both
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - M J Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - E M Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, USA
- Banner Alzheimer's Institute, Department of Psychiatry, University of Arizona, Tucson, AZ, USA
| | - M E Brunkow
- Institute for Systems Biology, Seattle, WA, USA
| | - G Glusman
- Institute for Systems Biology, Seattle, WA, USA
| | - J C Roach
- Institute for Systems Biology, Seattle, WA, USA
| | - A W Kao
- Memory and Aging Center, Department of Neurology, University of California at San Francisco, San Francisco, CA, USA
| | - F Lopera
- Grupo de Neurociencias, Universidad de Antioquia, Medellín, Colombia
| | - K S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara, Santa Barbara, CA, USA
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26
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Viollet L, Glusman G, Murphy KJ, Newcomb TM, Reyna SP, Sweney M, Nelson B, Andermann F, Andermann E, Acsadi G, Barbano RL, Brown C, Brunkow ME, Chugani HT, Cheyette SR, Collins A, DeBrosse SD, Galas D, Friedman J, Hood L, Huff C, Jorde LB, King MD, LaSalle B, Leventer RJ, Lewelt AJ, Massart MB, Mérida MR, Ptáček LJ, Roach JC, Rust RS, Renault F, Sanger TD, Sotero de Menezes MA, Tennyson R, Uldall P, Zhang Y, Zupanc M, Xin W, Silver K, Swoboda KJ. Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry. PLoS One 2015; 10:e0127045. [PMID: 25996915 PMCID: PMC4440742 DOI: 10.1371/journal.pone.0127045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 04/11/2015] [Indexed: 11/21/2022] Open
Abstract
Mutations in ATP1A3 cause Alternating Hemiplegia of Childhood (AHC) by disrupting function of the neuronal Na+/K+ ATPase. Published studies to date indicate 2 recurrent mutations, D801N and E815K, and a more severe phenotype in the E815K cohort. We performed mutation analysis and retrospective genotype-phenotype correlations in all eligible patients with AHC enrolled in the US AHC Foundation registry from 1997-2012. Clinical data were abstracted from standardized caregivers’ questionnaires and medical records and confirmed by expert clinicians. We identified ATP1A3 mutations by Sanger and whole genome sequencing, and compared phenotypes within and between 4 groups of subjects, those with D801N, E815K, other ATP1A3 or no ATP1A3 mutations. We identified heterozygous ATP1A3 mutations in 154 of 187 (82%) AHC patients. Of 34 unique mutations, 31 (91%) are missense, and 16 (47%) had not been previously reported. Concordant with prior studies, more than 2/3 of all mutations are clustered in exons 17 and 18. Of 143 simplex occurrences, 58 had D801N (40%), 38 had E815K (26%) and 11 had G937R (8%) mutations. Patients with an E815K mutation demonstrate an earlier age of onset, more severe motor impairment and a higher prevalence of status epilepticus. This study further expands the number and spectrum of ATP1A3 mutations associated with AHC and confirms a more deleterious effect of the E815K mutation on selected neurologic outcomes. However, the complexity of the disorder and the extensive phenotypic variability among subgroups merits caution and emphasizes the need for further studies.
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Affiliation(s)
- Louis Viollet
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Kelley J. Murphy
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Tara M. Newcomb
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Sandra P. Reyna
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew Sweney
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Benjamin Nelson
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Frederick Andermann
- Neurogenetics Unit, Montreal Neurologic Institute and Hospital, McGill University, Montreal Quebec, Canada
| | - Eva Andermann
- Neurogenetics Unit, Montreal Neurologic Institute and Hospital, McGill University, Montreal Quebec, Canada
| | - Gyula Acsadi
- Departments of Pediatrics and Neurology, Connecticut Children's Medical Center and University of Connecticut School of Medicine, Hartford, CT, United States of America
| | - Richard L. Barbano
- Department of Neurology, University of Rochester School of Medicine, Rochester, New York, United States of America
| | - Candida Brown
- Diablo Valley Child Neurology, an affiliate of Stanford Health Alliance, Pleasant Hill, California, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Harry T. Chugani
- Division of Pediatric Neurology, Children's Hospital of Michigan, Wayne State University, Detroit, Michigan, United States of America
| | - Sarah R. Cheyette
- Department of Child Neurology, Palo Alto Medical Foundation Redwood City Clinic, Redwood City, California, United States of America
| | - Abigail Collins
- Department of Pediatric Neurology, Children’s Hospital Colorado, University of Colorado Hospital, Aurora, Colorado, United States of America
| | - Suzanne D. DeBrosse
- Departments of Genetics and Genome Sciences, Pediatrics, and Neurology, Case Western Reserve University and University Hospitals Case Medical Center, Cleveland, Ohio, United States of America
| | - David Galas
- Pacific Northwest Diabetes Research Institute, Seattle, Washington, United States of America
| | - Jennifer Friedman
- Departments of Neuroscience and Pediatrics, University of California San Diego, San Diego, California, United States of America
| | - Lee Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Chad Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary D. King
- Departments of Pediatrics and Neurology, University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Bernie LaSalle
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Richard J. Leventer
- Children’s Neuroscience Centre, Murdoch Childrens Research Institute, University of Melbourne Department of Paediatrics, The Royal Children’s Hospital Melbourne, Parkville Victoria, Australia
| | - Aga J. Lewelt
- Department of Pediatrics, College of Medicine Jacksonville, University of Florida, Jacksonville, Florida, United States of America
| | - Mylynda B. Massart
- Department of Family Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Mario R. Mérida
- Stevens Henager College, Salt Lake City, Utah, United States of America
| | - Louis J. Ptáček
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Robert S. Rust
- Center for Medical Ethics and Humanities in Medicine, University Of Virginia UVA health system, Charlottesville, Virginia, United States of America
| | - Francis Renault
- Departement de Neurophysiologie. Hopital Armand Trousseau APHP, Paris, France
| | - Terry D. Sanger
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California, United States of America
| | | | - Rachel Tennyson
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter Uldall
- Department of Paediatrics and Adolescent Medicine, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Yue Zhang
- Study Design and Biostatistics Center, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary Zupanc
- Department of Neurology, Children’s Hospital Orange County, and Department of Pediatrics, University of California, Orange, California, United States of America
| | - Winnie Xin
- Center for Human Genetic Research, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kenneth Silver
- Departments of Pediatrics and Neurology, University of Chicago and Comer Children's Hospital, Chicago, Illinois, United States of America
| | - Kathryn J. Swoboda
- Pediatric Motor Disorders Research Program, Departments of Neurology and Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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27
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Glusman G, Severson A, Dhankani V, Robinson M, Farrah T, Mauldin DE, Stittrich AB, Ament SA, Roach JC, Brunkow ME, Bodian DL, Vockley JG, Shmulevich I, Niederhuber JE, Hood L. Identification of copy number variants in whole-genome data using Reference Coverage Profiles. Front Genet 2015; 6:45. [PMID: 25741365 PMCID: PMC4330915 DOI: 10.3389/fgene.2015.00045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 11/30/2014] [Accepted: 01/30/2015] [Indexed: 12/20/2022] Open
Abstract
The identification of DNA copy numbers from short-read sequencing data remains a challenge for both technical and algorithmic reasons. The raw data for these analyses are measured in tens to hundreds of gigabytes per genome; transmitting, storing, and analyzing such large files is cumbersome, particularly for methods that analyze several samples simultaneously. We developed a very efficient representation of depth of coverage (150–1000× compression) that enables such analyses. Current methods for analyzing variants in whole-genome sequencing (WGS) data frequently miss copy number variants (CNVs), particularly hemizygous deletions in the 1–100 kb range. To fill this gap, we developed a method to identify CNVs in individual genomes, based on comparison to joint profiles pre-computed from a large set of genomes. We analyzed depth of coverage in over 6000 high quality (>40×) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC. To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used. Normalization of the scaled coverage to the RCP followed by hidden Markov model (HMM) segmentation enables efficient detection of CNVs and large deletions in individual genomes. Use of pre-computed multi-genome coverage profiles improves our ability to analyze each individual genome. We make available RCPs and tools for performing these analyses on personal genomes. We expect the increased sensitivity and specificity for individual genome analysis to be critical for achieving clinical-grade genome interpretation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Dale L Bodian
- Inova Translational Medicine Institute, Inova Health System Falls Church, VA, USA
| | - Joseph G Vockley
- Inova Translational Medicine Institute, Inova Health System Falls Church, VA, USA
| | | | - John E Niederhuber
- Inova Translational Medicine Institute, Inova Health System Falls Church, VA, USA
| | - Leroy Hood
- Institute for Systems Biology Seattle, WA, USA
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28
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Gierman HJ, Fortney K, Roach JC, Coles NS, Li H, Glusman G, Markov GJ, Smith JD, Hood L, Coles LS, Kim SK. Whole-genome sequencing of the world's oldest people. PLoS One 2014; 9:e112430. [PMID: 25390934 PMCID: PMC4229186 DOI: 10.1371/journal.pone.0112430] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022] Open
Abstract
Supercentenarians (110 years or older) are the world's oldest people. Seventy four are alive worldwide, with twenty two in the United States. We performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity. We found no significant evidence of enrichment for a single rare protein-altering variant or for a gene harboring different rare protein altering variants in supercentenarian compared to control genomes. We followed up on the gene most enriched for rare protein-altering variants in our cohort of supercentenarians, TSHZ3, by sequencing it in a second cohort of 99 long-lived individuals but did not find a significant enrichment. The genome of one supercentenarian had a pathogenic mutation in DSC2, known to predispose to arrhythmogenic right ventricular cardiomyopathy, which is recommended to be reported to this individual as an incidental finding according to a recent position statement by the American College of Medical Genetics and Genomics. Even with this pathogenic mutation, the proband lived to over 110 years. The entire list of rare protein-altering variants and DNA sequence of all 17 supercentenarian genomes is available as a resource to assist the discovery of the genetic basis of extreme longevity in future studies.
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Affiliation(s)
- Hinco J. Gierman
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Kristen Fortney
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Natalie S. Coles
- Gerontology Research Group, Los Angeles, CA, United States of America
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Hong Li
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Glenn J. Markov
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Justin D. Smith
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, United States of America
| | - L. Stephen Coles
- Gerontology Research Group, Los Angeles, CA, United States of America
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Stuart K. Kim
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
- * E-mail:
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29
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Schubert J, Siekierska A, Langlois M, May P, Huneau C, Becker F, Muhle H, Suls A, Lemke JR, de Kovel CGF, Thiele H, Konrad K, Kawalia A, Toliat MR, Sander T, Rüschendorf F, Caliebe A, Nagel I, Kohl B, Kecskés A, Jacmin M, Hardies K, Weckhuysen S, Riesch E, Dorn T, Brilstra EH, Baulac S, Møller RS, Hjalgrim H, Koeleman BPC, Jurkat-Rott K, Lehmann-Horn F, Roach JC, Glusman G, Hood L, Galas DJ, Martin B, de Witte PAM, Biskup S, De Jonghe P, Helbig I, Balling R, Nürnberg P, Crawford AD, Esguerra CV, Weber YG, Lerche H. Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nat Genet 2014; 46:1327-32. [DOI: 10.1038/ng.3130] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/06/2014] [Indexed: 01/12/2023]
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30
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Abstract
Genomic information reported as haplotypes rather than genotypes will be increasingly important for personalized medicine. Current technologies generate diploid sequence data that is rarely resolved into its constituent haplotypes. Furthermore, paradigms for thinking about genomic information are based on interpreting genotypes rather than haplotypes. Nevertheless, haplotypes have historically been useful in contexts ranging from population genetics to disease-gene mapping efforts. The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference. Long-read sequencing technologies are enabling longer molecular haplotypes, and decreases in the cost of whole-genome sequencing are enabling the sequencing of whole-chromosome genetic haplotypes. Hybrid approaches combining high-throughput short-read assembly with strategic approaches that enable physical or virtual binning of reads into haplotypes are enabling multi-gene haplotypes to be generated from single individuals. These techniques can be further combined with genetic and population approaches. Here, we review advances in whole-genome haplotyping approaches and discuss the importance of haplotypes for genomic medicine. Clinical applications include diagnosis by recognition of compound heterozygosity and by phasing regulatory variation to coding variation. Haplotypes, which are more specific than less complex variants such as single nucleotide variants, also have applications in prognostics and diagnostics, in the analysis of tumors, and in typing tissue for transplantation. Future advances will include technological innovations, the application of standard metrics for evaluating haplotype quality, and the development of databases that link haplotypes to disease.
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Affiliation(s)
- Gustavo Glusman
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Hannah C Cox
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
| | - Jared C Roach
- Institute for Systems Biology, Terry Avenue North, Seattle, WA 98109 USA
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31
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Lehman A, Stittrich AB, Glusman G, Zong Z, Li H, Eydoux P, Senger C, Lyons C, Roach JC, Patel M. Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations. Am J Med Genet A 2014; 164A:2656-62. [PMID: 25091416 DOI: 10.1002/ajmg.a.36685] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 06/18/2014] [Indexed: 11/11/2022]
Abstract
Adams-Oliver syndrome (AOS) is a rare malformation syndrome characterized by the presence of two anomalies: aplasia cutis congenita of the scalp and transverse terminal limb defects. Many affected individuals also have additional malformations, including a variety of intracranial anomalies such as periventricular calcification in keeping with cerebrovascular microbleeds, impaired neuronal migration, epilepsy, and microcephaly. Cardiac malformations can be present, as can vascular dysfunction in the forms of cutis marmorata telangiectasia congenita, pulmonary vein stenoses, and abnormal hepatic microvasculature. Elucidated genetic causes include four genes in different pathways, leading to a model of AOS as a multi-pathway disorder. We identified an infant with mild aplasia cutis congenita and terminal transverse limb defects, developmental delay and a severe, diffuse angiopathy with incomplete microvascularization. Whole-genome sequencing documented two rare truncating variants in DOCK6, a gene associated with a type of autosomal recessive AOS that recurrently features periventricular calcification and impaired neurodevelopment. We highlight an unexpectedly high frequency of likely deleterious mutations in this gene in the general population, relative to the rarity of the disease, and discuss possible explanations for this discrepancy.
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Affiliation(s)
- Anna Lehman
- Department of Medical Genetics and Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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32
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Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol 2014; 32:663-9. [PMID: 24837662 DOI: 10.1038/nbt.2895] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/04/2014] [Indexed: 01/02/2023]
Abstract
High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Jared C Roach
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Karl V Voelkerding
- 1] Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA. [2] ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Rebecca L Margraf
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Jacob D Durtschi
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Shankaracharya
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Wilfred Wu
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Shuoguo Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA
| | | | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington, USA
| | - Hong Li
- Institute for Systems Biology, Seattle, Washington, USA
| | - Vidu Garg
- 1] Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA. [2] Center for Cardiovascular and Pulmonary Research, Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Barry Moore
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, USA
| | - David J Galas
- 1] Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg. [2] Pacific Northwest Diabetes Research Institute, Seattle, Washington, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California, San Francisco, San Francisco, California, USA
| | | | - Lynn B Jorde
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Li H, Glusman G, Huff C, Caballero J, Roach JC. Accurate and robust prediction of genetic relationship from whole-genome sequences. PLoS One 2014; 9:e85437. [PMID: 24586241 PMCID: PMC3938395 DOI: 10.1371/journal.pone.0085437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 11/27/2013] [Indexed: 12/02/2022] Open
Abstract
Computing the genetic relationship between two humans is important to studies in genetics, genomics, genealogy, and forensics. Relationship algorithms may be sensitive to noise, such as that arising from sequencing errors or imperfect reference genomes. We developed an algorithm for estimation of genetic relationship by averaged blocks (GRAB) that is designed for whole-genome sequencing (WGS) data. GRAB segments the genome into blocks, calculates the fraction of blocks sharing identity, and then uses a classification tree to infer 1st- to 5th- degree relationships and unrelated individuals. We evaluated GRAB on simulated and real sequenced families, and compared it with other software. GRAB achieves similar performance, and does not require knowledge of population background or phasing. GRAB can be used in workflows for identifying unreported relationships, validating reported relationships in family-based studies, and detection of sample-tracking errors or duplicate inclusion. The software is available at familygenomics.systemsbiology.net/grab.
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Affiliation(s)
- Hong Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Chad Huff
- Department of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Juan Caballero
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail:
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35
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Li H, Glusman G, Hu H, Shankaracharya, Caballero J, Hubley R, Witherspoon D, Guthery SL, Mauldin DE, Jorde LB, Hood L, Roach JC, Huff CD. Relationship estimation from whole-genome sequence data. PLoS Genet 2014; 10:e1004144. [PMID: 24497848 PMCID: PMC3907355 DOI: 10.1371/journal.pgen.1004144] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 12/02/2022] Open
Abstract
The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected false-positive relationships among controls compared to high-density microarray datasets. To address this issue, we developed a new method to identify and mask genomic regions with excess IBD. This method, implemented in ERSA 2.0, fully resolved the inflated cryptic relationship detection rates while improving relationship estimation accuracy. ERSA 2.0 detected all 1(st) through 6(th) degree relationships, and 55% of 9(th) through 11(th) degree relationships in the 30 families. We estimate that WGS data provides a 5% to 15% increase in relationship detection power relative to high-density microarray data for distant relationships. Our results identify regions of the genome that are highly problematic for IBD mapping and introduce new software to accurately detect 1(st) through 9(th) degree relationships from whole-genome sequence data.
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Affiliation(s)
- Hong Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Hao Hu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shankaracharya
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Juan Caballero
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - David Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Stephen L. Guthery
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Denise E. Mauldin
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Chad D. Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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36
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Higdon R, Stewart E, Roach JC, Dombrowski C, Stanberry L, Clifton H, Kolker N, van Belle G, Del Beccaro MA, Kolker E. Predictive Analytics In Healthcare: Medications as a Predictor of Medical Complexity. Big Data 2013; 1:237-244. [PMID: 27447256 DOI: 10.1089/big.2013.0024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Children with special healthcare needs (CSHCN) require health and related services that exceed those required by most hospitalized children. A small but growing and important subset of the CSHCN group includes medically complex children (MCCs). MCCs typically have comorbidities and disproportionately consume healthcare resources. To enable strategic planning for the needs of MCCs, simple screens to identify potential MCCs rapidly in a hospital setting are needed. We assessed whether the number of medications used and the class of those medications correlated with MCC status. Retrospective analysis of medication data from the inpatients at Seattle Children's Hospital found that the numbers of inpatient and outpatient medications significantly correlated with MCC status. Numerous variables based on counts of medications, use of individual medications, and use of combinations of medications were considered, resulting in a simple model based on three different counts of medications: outpatient and inpatient drug classes and individual inpatient drug names. The combined model was used to rank the patient population for medical complexity. As a result, simple, objective admission screens for predicting the complexity of patients based on the number and type of medications were implemented.
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Affiliation(s)
- Roger Higdon
- 1 Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
- 2 Predictive Analytics, Seattle Children's Hospital , Seattle, Washington
- 3 Data Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
| | - Elizabeth Stewart
- 1 Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
- 3 Data Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
| | - Jared C Roach
- 4 Institute for Systems Biology , Seattle, Washington
| | | | - Larissa Stanberry
- 1 Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
- 2 Predictive Analytics, Seattle Children's Hospital , Seattle, Washington
- 3 Data Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
| | - Holly Clifton
- 6 Center for Children with Special Needs , Seattle Children's Research Institute, Seattle, Washington
| | - Natali Kolker
- 2 Predictive Analytics, Seattle Children's Hospital , Seattle, Washington
- 3 Data Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
| | - Gerald van Belle
- 7 Departments of Biostatistics and Environmental and Occupational Health Sciences, University of Washington , Seattle, Washington
| | - Mark A Del Beccaro
- 8 Department of Pediatrics, University of Washington , Seattle, Washington
- 9 Medical Affairs, Seattle Children's Hospital , Seattle, Washington
- 10 Department of Biomedical Informatics & Medical Education, University of Washington , Seattle, Washington
| | - Eugene Kolker
- 1 Bioinformatics and High-Throughput Data Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
- 2 Predictive Analytics, Seattle Children's Hospital , Seattle, Washington
- 3 Data Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
- 8 Department of Pediatrics, University of Washington , Seattle, Washington
- 10 Department of Biomedical Informatics & Medical Education, University of Washington , Seattle, Washington
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Abstract
SUMMARY With the rapidly expanding availability of data from personal genomes, exomes and transcriptomes, medical researchers will frequently need to test whether observed genomic variants are novel or known. This task requires downloading and handling large and diverse datasets from a variety of sources, and processing them with bioinformatics tools and pipelines. Alternatively, researchers can upload data to online tools, which may conflict with privacy requirements. We present here Kaviar, a tool that greatly simplifies the assessment of novel variants. Kaviar includes: (i) an integrated and growing database of genomic variation from diverse sources, including over 55 million variants from personal genomes, family genomes, transcriptomes, SNV databases and population surveys; and (ii) software for querying the database efficiently.
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38
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Roach JC, Glusman G, Smit AF, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, Shendure J, Drmanac R, Jorde LB, Hood L, Galas DJ. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 2010; 328:636-9. [PMID: 20220176 PMCID: PMC3037280 DOI: 10.1126/science.1186802] [Citation(s) in RCA: 729] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in this family have two recessive disorders: Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families.
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Affiliation(s)
| | | | | | - Chad D. Huff
- Institute for Systems Biology, Seattle, WA 98103
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | | - Lee Rowen
- Institute for Systems Biology, Seattle, WA 98103
| | | | | | - Michael Bamshad
- Department of Pediatrics, University of Washington, Seattle WA 98195
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle WA 98195
| | | | - Lynn B. Jorde
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98103
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39
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Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R. TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 2009; 10:R29. [PMID: 19284633 PMCID: PMC2691000 DOI: 10.1186/gb-2009-10-3-r29] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 02/26/2009] [Accepted: 03/12/2009] [Indexed: 11/20/2022] Open
Abstract
TFCat is a catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review of the scientific literature Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal .
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Affiliation(s)
- Debra L Fulton
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.
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40
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Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2009; 6:e311. [PMID: 19090620 PMCID: PMC2602723 DOI: 10.1371/journal.pbio.0060311] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/31/2008] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis. Tuberculosis remains a worldwide public health emergency. The emergence of drug-resistant forms of tuberculosis in many parts of the world is threatening to make this important human disease incurable. Even though many resources are being invested into the development of new tuberculosis control tools, we still do not know the extent of genetic diversity in tuberculosis bacteria, nor do we understand the evolutionary forces that shape this diversity. To address these questions, we studied a large collection of human tuberculosis strains using DNA sequencing. We found that strains originating in different parts of the world are more genetically diverse than previously recognized. Our results also suggest that much of this diversity has functional consequences and could affect the efficacy of new tuberculosis diagnostics, drugs, and vaccines. Furthermore, we found that the global diversity in tuberculosis strains can be linked to the ancient human migrations out of Africa, as well as to more recent movements that followed the increases of human populations in Europe, India, and China during the past few hundred years. Taken together, our findings suggest that the evolutionary characteristics of tuberculosis bacteria could synergize with the effects of increasing globalization and human travel to enhance the global spread of drug-resistant tuberculosis. DNA sequence analysis of a global collection ofM. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.
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Affiliation(s)
- Ruth Hershberg
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Mikhail Lipatov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Peter M Small
- Institute for Systems Biology, Seattle, Washington, United States of America
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Hadar Sheffer
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Stefan Niemann
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Susanne Homolka
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Jared C Roach
- Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
| | - Kristin Kremer
- Mycobacteria Reference Unit (CIb-LIS), National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sebastien Gagneux
- Institute for Systems Biology, Seattle, Washington, United States of America
- MRC National Institute for Medical Research, London, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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41
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Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I. Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics. PLoS Comput Biol 2008; 4:e1000021. [PMID: 18369420 PMCID: PMC2265556 DOI: 10.1371/journal.pcbi.1000021] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 02/04/2008] [Indexed: 01/04/2023] Open
Abstract
Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a transcriptional network underlying TLR-stimulated murine macrophage activation. Microarray-based expression profiling and transcription factor binding site motif scanning were used to infer a network of associations between transcription factor genes and clusters of co-expressed target genes. The time-lagged correlation was used to analyze temporal expression data in order to identify potential causal influences in the network. A novel statistical test was developed to assess the significance of the time-lagged correlation. Several associations in the resulting inferred network were validated using targeted ChIP-on-chip experiments. The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation. Macrophages play a vital role in host defense against infection by recognizing pathogens through pattern recognition receptors, such as the Toll-like receptors (TLRs), and mounting an immune response. Stimulation of TLRs initiates a complex transcriptional program in which induced transcription factor genes dynamically regulate downstream genes. Microarray-based transcriptional profiling has proved useful for mapping such transcriptional programs in simpler model organisms; however, mammalian systems present difficulties such as post-translational regulation of transcription factors, combinatorial gene regulation, and a paucity of available gene-knockout expression data. Additional evidence sources, such as DNA sequence-based identification of transcription factor binding sites, are needed. In this work, we computationally inferred a transcriptional network for TLR-stimulated murine macrophages. Our approach combined sequence scanning with time-course expression data in a probabilistic framework. Expression data were analyzed using the time-lagged correlation. A novel, unbiased method was developed to assess the significance of the time-lagged correlation. The inferred network of associations between transcription factor genes and co-expressed gene clusters was validated with targeted ChIP-on-chip experiments, and yielded insights into the macrophage activation program, including a potential novel regulator. Our general approach could be used to analyze other complex mammalian systems for which time-course expression data are available.
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Affiliation(s)
- Stephen A. Ramsey
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (SR); (AA); (IS)
| | - Sandy L. Klemm
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Daniel E. Zak
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Kathleen A. Kennedy
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vesteinn Thorsson
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Bin Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Mark Gilchrist
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Elizabeth S. Gold
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Carrie D. Johnson
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vladimir Litvak
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Garnet Navarro
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | | | - Alistair G. Rust
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Natalya Yudkovsky
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Alan Aderem
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (SR); (AA); (IS)
| | - Ilya Shmulevich
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (SR); (AA); (IS)
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42
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Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H. The Innate Immune Database (IIDB). BMC Immunol 2008; 9:7. [PMID: 18321385 PMCID: PMC2268913 DOI: 10.1186/1471-2172-9-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 03/05/2008] [Indexed: 02/04/2023] Open
Abstract
Background As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site . Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens. Description We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser. Conclusion We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at .
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Affiliation(s)
- Martin Korb
- Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103-8904, USA.
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Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A. Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A 2007; 104:16245-50. [PMID: 17913878 PMCID: PMC2042192 DOI: 10.1073/pnas.0707757104] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Transcription factors play a key role in integrating and modulating biological information. In this study, we comprehensively measured the changing abundances of mRNAs over a time course of activation of human peripheral-blood-derived mononuclear cells ("macrophages") with lipopolysaccharide. Global and dynamic analysis of transcription factors in response to a physiological stimulus has yet to be achieved in a human system, and our efforts significantly advanced this goal. We used multiple global high-throughput technologies for measuring mRNA levels, including massively parallel signature sequencing and GeneChip microarrays. We identified 92 of 1,288 known human transcription factors as having significantly measurable changes during our 24-h time course. At least 42 of these changes were previously unidentified in this system. Our data demonstrate that some transcription factors operate in a functional range below 10 transcripts per cell, whereas others operate in a range three orders of magnitude greater. The highly reproducible response of many mRNAs indicates feedback control. A broad range of activation kinetics was observed; thus, combinatorial regulation by small subsets of transcription factors would permit almost any timing input to cis-regulatory elements controlling gene transcription.
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Affiliation(s)
- Jared C. Roach
- *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
- To whom correspondence may be addressed. E-mail: or
| | - Kelly D. Smith
- *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Katie L. Strobe
- *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
| | | | | | - Daixing Zhou
- Illumina, 25861 Industrial Boulevard, Hayward, CA 94545
| | | | - G. A. Held
- IBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598
| | | | - Leroy E. Hood
- *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
- To whom correspondence may be addressed. E-mail: or
| | - Alan Aderem
- *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103
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Roach JC, Deutsch K, Li S, Siegel AF, Bekris LM, Einhaus DC, Sheridan CM, Glusman G, Hood L, Lernmark A, Janer M. Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet 2006; 79:614-27. [PMID: 16960798 PMCID: PMC1592562 DOI: 10.1086/507876] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 07/18/2006] [Indexed: 01/15/2023] Open
Abstract
We mapped the genetic influences for type 1 diabetes (T1D), using 2,360 single-nucleotide polymorphism (SNP) markers in the 4.4-Mb human major histocompatibility complex (MHC) locus and the adjacent 493 kb centromeric to the MHC, initially in a survey of 363 Swedish T1D cases and controls. We confirmed prior studies showing association with T1D in the MHC, most significantly near HLA-DR/DQ. In the region centromeric to the MHC, we identified a peak of association within the inositol 1,4,5-triphosphate receptor 3 gene (ITPR3; formerly IP3R3). The most significant single SNP in this region was at the center of the ITPR3 peak of association (P=1.7 x 10(-4) for the survey study). For validation, we typed an additional 761 Swedish individuals. The P value for association computed from all 1,124 individuals was 1.30 x 10(-6) (recessive odds ratio 2.5; 95% confidence interval [CI] 1.7-3.9). The estimated population-attributable risk of 21.6% (95% CI 10.0%-31.0%) suggests that variation within ITPR3 reflects an important contribution to T1D in Sweden. Two-locus regression analysis supports an influence of ITPR3 variation on T1D that is distinct from that of any MHC class II gene.
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Affiliation(s)
- Jared C Roach
- Institute for Systems Biology, Seattle, WA 98103, USA.
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Gilchrist M, Thorsson V, Li B, Rust AG, Korb M, Roach JC, Kennedy K, Hai T, Bolouri H, Aderem A. Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 2006; 441:173-8. [PMID: 16688168 DOI: 10.1038/nature04768] [Citation(s) in RCA: 611] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 03/29/2006] [Indexed: 11/09/2022]
Abstract
The innate immune system is absolutely required for host defence, but, uncontrolled, it leads to inflammatory disease. This control is mediated, in part, by cytokines that are secreted by macrophages. Immune regulation is extraordinarily complex, and can be best investigated with systems approaches (that is, using computational tools to predict regulatory networks arising from global, high-throughput data sets). Here we use cluster analysis of a comprehensive set of transcriptomic data derived from Toll-like receptor (TLR)-activated macrophages to identify a prominent group of genes that appear to be regulated by activating transcription factor 3 (ATF3), a member of the CREB/ATF family of transcription factors. Network analysis predicted that ATF3 is part of a transcriptional complex that also contains members of the nuclear factor (NF)-kappaB family of transcription factors. Promoter analysis of the putative ATF3-regulated gene cluster demonstrated an over-representation of closely apposed ATF3 and NF-kappaB binding sites, which was verified by chromatin immunoprecipitation and hybridization to a DNA microarray. This cluster included important cytokines such as interleukin (IL)-6 and IL-12b. ATF3 and Rel (a component of NF-kappaB) were shown to bind to the regulatory regions of these genes upon macrophage activation. A kinetic model of Il6 and Il12b messenger RNA expression as a function of ATF3 and NF-kappaB promoter binding predicted that ATF3 is a negative regulator of Il6 and Il12b transcription, and this hypothesis was validated using Atf3-null mice. ATF3 seems to inhibit Il6 and Il12b transcription by altering chromatin structure, thereby restricting access to transcription factors. Because ATF3 is itself induced by lipopolysaccharide, it seems to regulate TLR-stimulated inflammatory responses as part of a negative-feedback loop.
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Affiliation(s)
- Mark Gilchrist
- Institute for Systems Biology, Seattle, Washington 98103, USA
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Glusman G, Qin S, El-Gewely MR, Siegel AF, Roach JC, Hood L, Smit AFA. A third approach to gene prediction suggests thousands of additional human transcribed regions. PLoS Comput Biol 2006; 2:e18. [PMID: 16543943 PMCID: PMC1391917 DOI: 10.1371/journal.pcbi.0020018] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Accepted: 01/25/2006] [Indexed: 12/26/2022] Open
Abstract
The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome. Many algorithms for computational gene prediction have been described, ultimately derived from two basic concepts: (1) modeling gene structure and (2) recognizing sequence similarity. Successful hybrid methods combining these two concepts have also been developed. We present a third orthogonal approach to gene prediction, based on detecting the genomic signatures of transcription, accumulated over evolutionary time. We discuss four algorithms based on this third concept: Greens and CHOWDER, which quantify mutational strand biases caused by transcription-coupled DNA repair, and ROAST and PASTA, which are based on strand-specific selection against polyadenylation signals. We combined these algorithms into an integrated method called FEAST, which we used to predict the location and orientation of thousands of putative transcription units not overlapping known genes. Many of the newly predicted transcriptional units do not appear to code for proteins. The new algorithms are particularly apt at detecting genes with long introns and lacking sequence conservation. They therefore complement existing gene prediction methods and will help identify functional transcripts within many apparent "genomic deserts."
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Purcell MK, Smith KD, Hood L, Winton JR, Roach JC. Conservation of Toll-Like Receptor Signaling Pathways in Teleost Fish. Comp Biochem Physiol Part D Genomics Proteomics 2006; 1:77-88. [PMID: 17330145 PMCID: PMC1524722 DOI: 10.1016/j.cbd.2005.07.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In mammals, Toll-like receptors (TLR) recognize ligands, including pathogen-associated molecular patterns (PAMPs), and respond with ligand-specific induction of genes. In this study, we establish evolutionary conservation in teleost fish of key components of the TLR-signaling pathway that act as switches for differential gene induction, including MYD88, TIRAP, TRIF, TRAF6, IRF3, and IRF7. We further explore this conservation with a molecular phylogenetic analysis of MYD88. To the extent that current genomic analysis can establish, each vertebrate has one ortholog to each of these genes. For molecular tree construction and phylogeny inference, we demonstrate a methodology for including genes with only partial primary sequences without disrupting the topology provided by the high-confidence full-length sequences. Conservation of the TLR-signaling molecules suggests that the basic program of gene regulation by the TLR-signaling pathway is conserved across vertebrates. To test this hypothesis, leukocytes from a model fish, rainbow trout (Oncorhynchus mykiss), were stimulated with known mammalian TLR agonists including: diacylated and triacylated forms of lipoprotein, flagellin, two forms of LPS, synthetic double-stranded RNA, and two imidazoquinoline compounds (loxoribine and R848). Trout leukocytes responded in vitro to a number of these agonists with distinct patterns of cytokine expression that correspond to mammalian responses. Our results support the key prediction from our phylogenetic analyses that strong selective pressure of pathogenic microbes has preserved both TLR recognition and signaling functions during vertebrate evolution.
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Affiliation(s)
- Maureen K. Purcell
- School of Aquatic and Fishery Sciences; University of Washington, Seattle, WA, 98195, USA
- Western Fisheries Research Center/USGS, Seattle, WA, 98115, USA
| | - Kelly D. Smith
- Department of Pathology; University of Washington, Seattle, WA 98195, USA
- Institute for Systems Biology, Seattle, WA, 98103, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, 98103, USA
| | - James R. Winton
- Western Fisheries Research Center/USGS, Seattle, WA, 98115, USA
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, WA, 98103, USA
- *Corresponding author: Jared Roach, Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA, Office: (206) 732-1290,
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Iliev DB, Roach JC, Mackenzie S, Planas JV, Goetz FW. Endotoxin recognition: in fish or not in fish? FEBS Lett 2005; 579:6519-28. [PMID: 16297386 PMCID: PMC1365396 DOI: 10.1016/j.febslet.2005.10.061] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 10/17/2005] [Accepted: 10/27/2005] [Indexed: 11/24/2022]
Abstract
The interaction between pathogens and their multicellular hosts is initiated by activation of pathogen recognition receptors (PRRs). These receptors, that include most notably members of the toll-like receptor (TLR) family, recognize specific pathogen-associated molecular patterns (PAMPs). TLR4 is a central part of the receptor complex that is involved in the activation of the immune system by lipopolysaccharide (LPS) through the specific recognition of its endotoxic moiety (Lipid A). This is a critical event that is essential for the immune response to Gram-negative bacteria as well as the etiology of endotoxic shock. Interestingly, compared to mammals, fish are resistant to endotoxic shock. This in vivo resistance concurs with in vitro studies demonstrating significantly lowered sensitivity of fish leukocytes to LPS activation. Further, our in vitro analyses demonstrate that in trout mononuclear phagocytes, LPS fails to induce antiviral genes, an event that occurs downstream of TLR4 and is required for the development of endotoxic shock. Finally, an in silico approach that includes mining of different piscine genomic and EST databases, reveals the presence in fish of all of the major TLR signaling elements except for the molecules specifically involved in TLR4-mediated endotoxin recognition and signaling in mammals. Collectively, our analysis questions the existence of TLR4-mediated cellular responses to LPS in fish. We further speculate that other receptors, in particular beta-2 integrins, may play a primary role in the activation of piscine leukocytes by LPS.
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Affiliation(s)
- Dimitar B Iliev
- Great Lakes WATER Institute, University of Wisconsin-Milwaukee, 600 E. Greenfield Ave., Milwaukee, WI 53204, USA.
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Oudes AJ, Roach JC, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY. Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. BMC Cancer 2005; 5:86. [PMID: 16042785 PMCID: PMC1187880 DOI: 10.1186/1471-2407-5-86] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 07/22/2005] [Indexed: 11/24/2022] Open
Abstract
Background Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. Methods Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. Results Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. Conclusion Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases.
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Affiliation(s)
| | | | | | | | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, USA
| | | | - Alvin Y Liu
- Institute for Systems Biology, Seattle, USA
- Department of Urology, University of Washington, Seattle, USA
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Abstract
The complete sequences of Takifugu Toll-like receptor (TLR) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. Strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging TLR recognition in all vertebrates. There are six major families of vertebrate TLRs. This repertoire is distinct from that of invertebrates. TLRs within a family recognize a general class of pathogen-associated molecular patterns. Most vertebrates have exactly one gene ortholog for each TLR family. The family including TLR1 has more species-specific adaptations than other families. A major family including TLR11 is represented in humans only by a pseudogene. Coincidental evolution plays a minor role in TLR evolution. The sequencing phase of this study produced finished genomic sequences for the 12 Takifugu rubripes TLRs. In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt.
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Affiliation(s)
- Jared C Roach
- Institute for Systems Biology, Seattle, WA 98103, USA.
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