1
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Dantzer B, Mabry KE, Bernhardt JR, Cox RM, Francis CD, Ghalambor CK, Hoke KL, Jha S, Ketterson E, Levis NA, McCain KM, Patricelli GL, Paull SH, Pinter-Wollman N, Safran RJ, Schwartz TS, Throop HL, Zaman L, Martin LB. Understanding Organisms Using Ecological Observatory Networks. Integr Org Biol 2023; 5:obad036. [PMID: 37867910 PMCID: PMC10586040 DOI: 10.1093/iob/obad036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 06/07/2023] [Accepted: 09/21/2023] [Indexed: 10/24/2023] Open
Abstract
Human activities are rapidly changing ecosystems around the world. These changes have widespread implications for the preservation of biodiversity, agricultural productivity, prevalence of zoonotic diseases, and sociopolitical conflict. To understand and improve the predictive capacity for these and other biological phenomena, some scientists are now relying on observatory networks, which are often composed of systems of sensors, teams of field researchers, and databases of abiotic and biotic measurements across multiple temporal and spatial scales. One well-known example is NEON, the US-based National Ecological Observatory Network. Although NEON and similar networks have informed studies of population, community, and ecosystem ecology for years, they have been minimally used by organismal biologists. NEON provides organismal biologists, in particular those interested in NEON's focal taxa, with an unprecedented opportunity to study phenomena such as range expansions, disease epidemics, invasive species colonization, macrophysiology, and other biological processes that fundamentally involve organismal variation. Here, we use NEON as an exemplar of the promise of observatory networks for understanding the causes and consequences of morphological, behavioral, molecular, and physiological variation among individual organisms.
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Affiliation(s)
- B Dantzer
- Department of Psychology, University of Michigan, Ann Arbor, MI 48109,USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
| | - K E Mabry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
- Department of Biology, New Mexico State University, Las Cruces, NM 88003,USA
| | - J R Bernhardt
- Department of Biology, New Mexico State University, Las Cruces, NM 88003,USA
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - R M Cox
- Department of Biology, University of Virginia, Charlottesville, VA 22940,USA
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407,USA
| | - C D Francis
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407,USA
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N‐7491 Trondheim, Norway
| | - C K Ghalambor
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N‐7491 Trondheim, Norway
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - K L Hoke
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - S Jha
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712,USA
| | - E Ketterson
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405,USA
| | - N A Levis
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405,USA
| | - K M McCain
- Global Health and Infectious Disease Research Center, College of Public Health, University of South Florida, Tampa, FL 33612,USA
| | - G L Patricelli
- Department of Evolution and Ecology, University of California, Davis, CA 95616,USA
| | - S H Paull
- Battelle, National Ecological Observatory Network, 1685 38th Street, Boulder, CO 80301, USA
| | - N Pinter-Wollman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - R J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309,USA
| | - T S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - H L Throop
- School of Earth and Space Exploration and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - L Zaman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109,USA
- Center for the Study of Complex Systems, University of Michigan, Ann Arbor, MI 48109, USA
| | - L B Martin
- Global Health and Infectious Disease Research Center and Center for Genomics, College of Public Health, University of South Florida, Tampa, FL 33612,USA
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Green RC, Shah N, Genetti CA, Yu T, Zettler B, Uveges MK, Ceyhan-Birsoy O, Lebo MS, Pereira S, Agrawal PB, Parad RB, McGuire AL, Christensen KD, Schwartz TS, Rehm HL, Holm IA, Beggs AH. Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. Am J Hum Genet 2023; 110:1034-1045. [PMID: 37279760 PMCID: PMC10357495 DOI: 10.1016/j.ajhg.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Newborn genomic sequencing (NBSeq) to screen for medically important genetic information is of considerable interest but data characterizing the actionability of such findings, and the downstream medical efforts in response to discovery of unanticipated genetic risk variants, are lacking. From a clinical trial of comprehensive exome sequencing in 127 apparently healthy infants and 32 infants in intensive care, we previously identified 17 infants (10.7%) with unanticipated monogenic disease risks (uMDRs). In this analysis, we assessed actionability for each of these uMDRs with a modified ClinGen actionability semiquantitative metric (CASQM) and created radar plots representing degrees of penetrance of the condition, severity of the condition, effectiveness of intervention, and tolerability of intervention. In addition, we followed each of these infants for 3-5 years after disclosure and tracked the medical actions prompted by these findings. All 17 uMDR findings were scored as moderately or highly actionable on the CASQM (mean 9, range: 7-11 on a 0-12 scale) and several distinctive visual patterns emerged on the radar plots. In three infants, uMDRs revealed unsuspected genetic etiologies for existing phenotypes, and in the remaining 14 infants, uMDRs provided risk stratification for future medical surveillance. In 13 infants, uMDRs prompted screening for at-risk family members, three of whom underwent cancer-risk-reducing surgeries. Although assessments of clinical utility and cost-effectiveness will require larger datasets, these findings suggest that large-scale comprehensive sequencing of newborns will reveal numerous actionable uMDRs and precipitate substantial, and in some cases lifesaving, downstream medical care in newborns and their family members.
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Affiliation(s)
- Robert C Green
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ariadne Labs, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Nidhi Shah
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Dartmouth Health Children's, Lebanon, NH 03756, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Timothy Yu
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Bethany Zettler
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Ariadne Labs, Boston, MA 02215, USA
| | - Melissa K Uveges
- William F. Connell School of Nursing, Boston College, Chestnut Hill, MA 02467, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew S Lebo
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Pankaj B Agrawal
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Richard B Parad
- Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Kurt D Christensen
- Harvard Medical School, Boston, MA 02215, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Talia S Schwartz
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alan H Beggs
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
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3
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Schwartz TS, Christensen KD, Uveges MK, Waisbren SE, McGuire AL, Pereira S, Robinson JO, Beggs AH, Green RC, Bachmann GA, Rabson AB, Holm IA. Effects of participation in a U.S. trial of newborn genomic sequencing on parents at risk for depression. J Genet Couns 2022; 31:218-229. [PMID: 34309124 PMCID: PMC8789951 DOI: 10.1002/jgc4.1475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/14/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 02/03/2023]
Abstract
Much emphasis has been placed on participant's psychological safety within genomic research studies; however, few studies have addressed parental psychological health effects associated with their child's participation in genomic studies, particularly when parents meet the threshold for clinical concern for depression. We aimed to determine if parents' depressive symptoms were associated with their child's participation in a randomized-controlled trial of newborn exome sequencing. Parents completed the Edinburgh Postnatal Depression Scale (EPDS) at baseline, immediately post-disclosure, and 3 months post-disclosure. Mothers and fathers scoring at or above thresholds for clinical concern on the EPDS, 12 and 10, respectively, indicating possible Major Depressive Disorder with Peripartum Onset, were contacted by study staff for mental health screening. Parental concerns identified in follow-up conversations were coded for themes. Forty-five parents had EPDS scores above the clinical threshold at baseline, which decreased by an average of 2.9 points immediately post-disclosure and another 1.1 points 3 months post-disclosure (both p ≤ .014). For 28 parents, EPDS scores were below the threshold for clinical concern at baseline, increased by an average of 4.7 points into the elevated range immediately post-disclosure, and decreased by 3.8 points at 3 months post-disclosure (both p < .001). Nine parents scored above thresholds only at 3 months post-disclosure after increasing an average of 5.7 points from immediately post-disclosure (p < .001). Of the 82 parents who scored above the threshold at any time point, 43 (52.4%) were reached and 30 (69.7%) of these 43 parents attributed their elevated scores to parenting stress, balancing work and family responsibilities, and/or child health concerns. Only three parents (7.0%) raised concerns about their participation in the trial, particularly their randomization to the control arm. Elevated scores on the EPDS were typically transient and parents attributed their symptomatology to life stressors in the postpartum period rather than participation in a trial of newborn exome sequencing.
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Affiliation(s)
- Talia S Schwartz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa K Uveges
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Connell School of Nursing, Boston College, Chestnut Hill, Massachusetts, USA
| | - Susan E Waisbren
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Robert C Green
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Gloria A Bachmann
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Arnold B Rabson
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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4
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Wojcik MH, Schwartz TS, Thiele KE, Paterson H, Stadelmaier R, Mullen TE, VanNoy GE, Genetti CA, Madden JA, Gubbels CS, Yu TW, Tan WH, Agrawal PB. Infant mortality: the contribution of genetic disorders. J Perinatol 2019; 39:1611-1619. [PMID: 31395954 PMCID: PMC6879816 DOI: 10.1038/s41372-019-0451-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine the proportion of infant deaths occurring in the setting of a confirmed genetic disorder. STUDY DESIGN A retrospective analysis of the electronic medical records of infants born from 1 January, 2011 to 1 June, 2017, who died prior to 1 year of age. RESULTS Five hundred and seventy three deceased infants were identified. One hundred and seventeen were confirmed to have a molecular or cytogenetic diagnosis in a clinical diagnostic laboratory and an additional seven were diagnosed by research testing for a total of 124/573 (22%) diagnosed infants. A total of 67/124 (54%) had chromosomal disorders and 58/124 (47%) had single gene disorders (one infant had both). The proportion of diagnoses made by sequencing technologies, such as exome sequencing, increased over the years. CONCLUSIONS The prevalence of confirmed genetic disorders within our cohort of infant deaths is higher than that previously reported. Increased efforts are needed to further understand the mortality burden of genetic disorders in infancy.
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Affiliation(s)
- Monica H. Wojcik
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Neonatal Genomics Program, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Talia S. Schwartz
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Katri E. Thiele
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Brody School of Medicine at East Carolina University, Greenville, NC, USA, 27834
| | - Heather Paterson
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Rachel Stadelmaier
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Thomas E. Mullen
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Grace E. VanNoy
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Casie A. Genetti
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Jill A. Madden
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Cynthia S. Gubbels
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Timothy W. Yu
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115,The Neonatal Genomics Program, Department of Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA, 02142
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5
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Genetti CA, Schwartz TS, Robinson JO, VanNoy GE, Petersen D, Pereira S, Fayer S, Peoples HA, Agrawal PB, Betting WN, Holm IA, McGuire AL, Waisbren SE, Yu TW, Green RC, Beggs AH, Parad RB. Parental interest in genomic sequencing of newborns: enrollment experience from the BabySeq Project. Genet Med 2019; 21:622-630. [PMID: 30209271 PMCID: PMC6420384 DOI: 10.1038/s41436-018-0105-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Newborn genomic sequencing (nGS) has great potential to improve pediatric care. Parental interest and concerns about genomics are relatively unexplored. Understanding why parents decline research consent for nGS may reveal implementation barriers. METHODS We evaluated parental interest in a randomized trial of nGS in well-baby and intensive care unit nursery settings. Interested families attended an informational enrollment session (ES) with a genetic counselor prior to consenting. Reason(s) for declining participation and sociodemographic associations were analyzed. RESULTS Of 3860 eligible approached families, 10% attended ES, 67% of whom enrolled. Of 1760 families queried for decline reasons, 58% were uninterested in research. Among 499 families considering research, principal reasons for decline prior to ES included burdensome study logistics (48%), feeling overwhelmed postpartum (17%), and lack of interest/discomfort with genetic testing (17%). Decliners after ES more often cited concerns about privacy/insurability (41%) and uncertain/unfavorable results (23%). CONCLUSION Low interest in research and study logistics were major initial barriers to postpartum enrollment and are likely generic to many postpartum research efforts. Concerns over privacy and result implications were most commonly cited in decliners after ES. Understanding parental concerns around research nGS may inform future integration of nGS into newborn screening, predictive testing, and pediatric diagnostics.
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Affiliation(s)
- Casie A Genetti
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Talia S Schwartz
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Grace E VanNoy
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Devan Petersen
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Shawn Fayer
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Hayley A Peoples
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Wendi N Betting
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Susan E Waisbren
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Timothy W Yu
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Robert C Green
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alan H Beggs
- Division of Genetics and Genomics and The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Richard B Parad
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts, USA.
- Harvard Medical School, Boston, Massachusetts, USA.
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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6
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Pereira S, Robinson JO, Gutierrez AM, Petersen DK, Hsu RL, Lee CH, Schwartz TS, Holm IA, Beggs AH, Green RC, McGuire AL. Perceived Benefits, Risks, and Utility of Newborn Genomic Sequencing in the BabySeq Project. Pediatrics 2019; 143:S6-S13. [PMID: 30600265 PMCID: PMC6480393 DOI: 10.1542/peds.2018-1099c] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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] [Accepted: 07/03/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES There is interest in applying genomic sequencing (GS) to newborns' clinical care. Here we explore parents' and clinicians' attitudes toward and perceptions of the risks, benefits, and utility of newborn GS compared with newborn screening (NBS) prior to receiving study results. METHODS The BabySeq Project is a randomized controlled trial used to explore the impact of integrating GS into the clinical care of newborns. Parents (n = 493) of enrolled infants (n = 309) and clinicians (n = 144) completed a baseline survey at enrollment. We examined between-group differences in perceived utility and attitudes toward NBS and GS. Open-ended responses about risks and benefits of each technology were categorized by theme. RESULTS The majority of parents (71%) and clinicians (51%) agreed that there are health benefits of GS, although parents and clinicians agreed more that there are risks associated with GS (35%, 70%) than with NBS (19%, 39%; all P < .05). Parents perceived more benefit and less risk of GS than did clinicians. Clinicians endorsed concerns about privacy and discrimination related to genomic information more strongly than did parents, and parents anticipated benefits of GS that clinicians did not. CONCLUSIONS Parents and clinicians are less confident in GS than NBS, but parents perceive a more favorable risk/benefit ratio of GS than do clinicians. Clinicians should be aware that parents' optimism may stem from their perceived benefits beyond clinical utility.
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Affiliation(s)
- Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Devan K Petersen
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Rebecca L Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Caroline H Lee
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Talia S Schwartz
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital
- Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Ingrid A Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital
- Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital
- Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Robert C Green
- Department of Medicine, Harvard Medical School, Harvard University, Boston, Massachusetts
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
- Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; and
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas;
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Holm IA, Agrawal PB, Ceyhan-Birsoy O, Christensen KD, Fayer S, Frankel LA, Genetti CA, Krier JB, LaMay RC, Levy HL, McGuire AL, Parad RB, Park PJ, Pereira S, Rehm HL, Schwartz TS, Waisbren SE, Yu TW, Green RC, Beggs AH. The BabySeq project: implementing genomic sequencing in newborns. BMC Pediatr 2018; 18:225. [PMID: 29986673 PMCID: PMC6038274 DOI: 10.1186/s12887-018-1200-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 06/27/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The greatest opportunity for lifelong impact of genomic sequencing is during the newborn period. The "BabySeq Project" is a randomized trial that explores the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. METHODS Families of newborns are enrolled from Boston Children's Hospital and Brigham and Women's Hospital nurseries, and half are randomized to receive genomic sequencing and a report that includes monogenic disease variants, recessive carrier variants for childhood onset or actionable disorders, and pharmacogenomic variants. All families participate in a disclosure session, which includes the return of results for those in the sequencing arm. Outcomes are collected through review of medical records and surveys of parents and health care providers and include the rationale for choice of genes and variants to report; what genomic data adds to the medical management of sick and healthy babies; and the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. DISCUSSION The BabySeq Project will provide empirical data about the risks, benefits and costs of newborn genomic sequencing and will inform policy decisions related to universal genomic screening of newborns. TRIAL REGISTRATION The study is registered in ClinicalTrials.gov Identifier: NCT02422511 . Registration date: 10 April 2015.
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Affiliation(s)
- Ingrid A. Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Pankaj B. Agrawal
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Ozge Ceyhan-Birsoy
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Kurt D. Christensen
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Shawn Fayer
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Leslie A. Frankel
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
- Department of Psychological, Health and Learning Sciences, University of Houston College of Education, Houston, TX USA
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
| | - Rebecca C. LaMay
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Harvey L. Levy
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
| | - Richard B. Parad
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA USA
| | - Peter J. Park
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX USA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA USA
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Talia S. Schwartz
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
| | - Susan E. Waisbren
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
| | - Timothy W. Yu
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA USA
- Harvard Medical School, Boston, MA USA
- The Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Alan H. Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA USA
- Department of Pediatrics, Harvard Medical School, Boston, MA USA
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Schwartz TS, Wojcik MH, Pelletier RC, Edward HL, Picker JD, Holm IA, Towne MC, Beggs AH, Agrawal PB. Expanding the phenotypic spectrum associated with OPHN1 variants. Eur J Med Genet 2018; 62:137-143. [PMID: 29960046 DOI: 10.1016/j.ejmg.2018.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 01/19/2018] [Revised: 05/02/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
Genomic sequencing has allowed for the characterization of new gene-to-disease relationships, as well as the identification of variants in established disease genes in patients who do not fit the classically-described phenotype. This is especially true in rare syndromes where the clinical spectrum is not fully known. After a lengthy and costly diagnostic odyssey, patients with atypical presentations may be left with many questions even after a genetic diagnosis is identified. We present a 22-year old male with hypotonia, developmental delay, seizure disorder, and dysmorphic facial features who enrolled in our rare disease research center at 18 years of age, where exome sequencing revealed a novel, likely pathogenic variant in the OPHN1 gene. Through efforts by the study team and collaborations with the larger genetics community, contacts with other families with OPHN1 variants were eventually made, and outreach by these families expanded the patient network. This partnership between families and researchers facilitated the gathering of phenotypic information, allowing for comparison of clinical presentations among three new patients and those previously reported in the literature. These comparisons found previously unreported commonalities between the newly identified patients, such as the presence of otitis media and the lack of genitourinary abnormalities (i.e. hypoplastic scrotum, microphallus, cryptorchidism), which had been noted to be classic features of patients with OPHN1 variants. As genomic sequencing becomes more common, connecting patients with novel variants in the same gene will facilitate phenotypic analysis and continue to refine the clinical spectrum associated with that gene.
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Affiliation(s)
- Talia S Schwartz
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Monica H Wojcik
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Renee C Pelletier
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Center for Cancer Risk Assessment, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Heather L Edward
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Jonathan D Picker
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Ingrid A Holm
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Meghan C Towne
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Ambry Genetics, Aliso Viejo, CA, USA
| | - Alan H Beggs
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics & Genomics, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; The Manton Center for Orphan Disease Research, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA; Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital and Harvard Medical School Boston, MA, 02115, USA.
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Shaddick K, Burridge CP, Jerry DR, Schwartz TS, Truong K, Gilligan DM, Beheregaray LB. A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum. J Fish Biol 2011; 79:1214-1235. [PMID: 22026603 DOI: 10.1111/j.1095-8649.2011.03105.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The presence and distribution of hybrid individuals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the total sample) with varying levels of introgression. Most hybrids were observed in an area extending from the Snowy River to the Albert River suggesting a hybrid zone in the eastern Bass Strait region. Sixteen hybrids, however, were found outside this zone, possibly reflecting the movement of hybrid offspring between estuaries or their inadvertent release during fish stocking programmes. Biparental backcrossing was found to occur suggesting that hybrids were fertile. These results have implications for the management of the extensive stocking programme in M. novemaculeata and for understanding the potential role of habitat degradation and reduced water flow in facilitating hybridization in species with migratory life histories.
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Affiliation(s)
- K Shaddick
- Molecular Ecology Lab., Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Abstract
Hox genes are recognized for their explanatory power of bilateral development. However, relatively little is known about natural variation in, and the evolutionary dynamics of, Hox genes within wild populations. Utilizing a natural population of sand lizards (Lacerta agilis), we screened HoxA13 for genetic variation and an association with incidence of offspring malformations. We found significant effects of parental genetic similarity and offspring sex, and their interaction, on risk of hatching malformed as an offspring. We also found within population genetic variation in HoxA13, and identified a significant effect of a three-way interaction among Hox genotype, parental genetic similarity, and offspring sex on the risk of hatching malformation. Since malformed offspring in this population do not survive to maturity, this study reveals complex and ongoing selection associated with Hox genes in a wild reptile population. Importantly, this demonstrates the utility of natural populations in unveiling microevolutionary processes shaping variation in highly conserved genes.
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Affiliation(s)
- T S Schwartz
- School of Biological Sciences, University of Wollongong, Wollongong, NSW, Australia.
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Gadsby JE, Keyes PL, Schwartz TS, Bill CH, Lucchesi B. Do catecholamines play a physiologic role in regulating corpus luteum function in the pseudopregnant rabbit? Biol Reprod 1985; 32:907-15. [PMID: 3890970 DOI: 10.1095/biolreprod32.4.907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In these studies the beta-adrenergic receptor antagonist propranolol was administered to estrogen-treated hypophysectomized pseudopregnant rabbits in vivo, and serum progesterone concentrations were measured to monitor luteal function. In Experiment 1, which was designed to determine an effective dose of propranolol, 1 mg/(kg X h) s.c. propranolol for 3 h (integral of 80 ng/ml in serum) gave an adequate level of beta-adrenergic receptor blockade, i.e., a 1000-fold inhibition of the blood pressure/isoproterenol dose-response relationship. In Experiment 2, "acute" administration of propranolol (P; 1 mg/(kg X h) s.c.) or saline (control, C) for 24 h on Days 7-8, 10-11, and 13-14 of pseudopregnancy did not produce any marked differences in serum progesterone concentrations in P or C animals on any of the days tested, although hourly fluctuations were observed. In Experiment 3, "chronic" (4-day) treatment with propranolol was achieved by the use of propranolol-containing pellets placed s.c. (integral of 200-600 ng/ml in serum), on Days 13-17. Control animals received pellets of vehicle only. Serum progesterone concentrations were very similar in P and C animals throughout the period of treatment (Days 13-17) and on Days 18 and 20. We conclude that endogenous catecholamines play no major role in regulating luteal steroidogenesis or corpus luteum regression in the pseudopregnant rabbit.
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