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Outram SM, Brown JEH, Norstad M, Zamora AN, Ackerman SL. Experts' Views on Children's Access to Community-Based Therapeutic and Education Services After Genomic Sequencing Results. J Dev Behav Pediatr 2024:00004703-990000000-00187. [PMID: 38990145 DOI: 10.1097/dbp.0000000000001299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/13/2024] [Indexed: 07/12/2024]
Abstract
OBJECTIVE To evaluate how community-based experts respond to families seeking therapeutic and educational support services after pediatric genomic sequencing for rare conditions. METHODS We interviewed 15 experts in the provision of community-based services for children with intellectual differences, developmental differences, or both, as part of a large study examining the utility of exome sequencing. RESULTS Interviewees highlighted the complexity of the overall referral and assessment system for therapeutic or educational needs, that genetic diagnoses are secondary to behavioral observations in respect to eligibility for the provision of services, and that social capital drives service acquisition. Although emphasizing that genetic results do not currently provide sufficient information for determining service eligibility, interviewees also highlighted their hopes that genetics would be increasingly relevant in the future. CONCLUSION Genomic results do not usually provide information that directly impacts service provision. However, a positive genomic test result can strengthen evidence for behavioral diagnoses and the future trajectory of a child's condition and support needs. Interviewees' comments suggest a need to combine emerging genetic knowledge with existing forms of therapeutic and educational needs assessment, and for additional supports for families struggling to navigate social and therapeutic services.
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Affiliation(s)
- Simon M Outram
- Division of Prevention Science, University of California San Francisco, San Francisco, CA
| | - Julia E H Brown
- Program in Bioethics, Institute for Health and Aging, University of California San Francisco, San Francisco, CA
| | - Matthew Norstad
- Program in Bioethics, Institute for Health and Aging, University of California San Francisco, San Francisco, CA
| | - Astrid N Zamora
- Maternal and Child Health Research Institute, School of Medicine, Stanford University, Stanford, CA
| | - Sara L Ackerman
- Division of Prevention Science, University of California San Francisco, San Francisco, CA
- Department of Social and Behavioral Sciences, University of California San Francisco, San Francisco, CA
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Martschenko DO, Granucci A, Cho MK. "Ethical Responsibility Very Often Gets Drowned Out": A Qualitative Interview Study of Genome Scientists' and ELSI Scholars' Perspectives on the Role and Relevance of ELSI Expertise. AJOB Empir Bioeth 2024:1-12. [PMID: 38916600 DOI: 10.1080/23294515.2024.2370769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
BACKGROUND Genome scientists and Ethical, Legal, and Social Implications of genetics (ELSI) scholars commonly inhabit distinct research cultures - utilizing different research methods, asking different research questions, and valuing different types of knowledge. Collaborations between these two communities are frequently called for to enhance the ethical conduct of genomics research. Yet, little has been done to qualitatively compare genome scientists' and ELSI scholars' perspectives on collaborations with each other and the factors that may affect these collaborations. METHODS 20 semi-structured interviews with US-based genome scientists and ELSI scholars were conducted between June-September 2021. Interviews were analyzed using inductive thematic analysis. RESULTS Genome scientists and ELSI scholars provided different understandings of the value and goals of their collaborations with each other. Genome scientists largely perceived ELSI expertise to be relevant for human subjects research; they described ELSI scholars as communicators who help the public and/or study participants better understand genomics research. In comparison, ELSI scholars viewed themselves as developing and implementing policies; they expressed frustration at how scientists can misunderstand their research methods or negatively perceive them. A combination of factors - both structural (e.g., criteria for promotion) and cultural (e.g., perceptions of what colleagues value and respect) - seemed to shape these diverging perspectives. CONCLUSION Academic institutions, funders, and researchers commonly call for collaborations between genome scientists and ELSI scholars, but under-consider how their different conceptual frameworks, research methods, goals, norms, and values, conjoin to affect such partnerships. Acknowledging, exploring, and addressing the complex interplay between these factors could help to more effectively facilitate collaborations between genome scientists and ELSI scholars.
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Affiliation(s)
- Daphne O Martschenko
- Stanford Center for Biomedical Ethics and Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Anna Granucci
- Stanford Center for Biomedical Ethics and Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics and Department of Pediatrics, Stanford University, Stanford, CA, USA
- Stanford Center for Biomedical Ethics and Department of Medicine, Stanford University, Stanford, CA, USA
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3
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Martinez KL, Klein A, Martin JR, Sampson CU, Giles JB, Beck ML, Bhakta K, Quatraro G, Farol J, Karnes JH. Disparities in ABO blood type determination across diverse ancestries: a systematic review and validation in the All of Us Research Program. J Am Med Inform Assoc 2024:ocae161. [PMID: 38917427 DOI: 10.1093/jamia/ocae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
OBJECTIVES ABO blood types have widespread clinical use and robust associations with disease. The purpose of this study is to evaluate the portability and suitability of tag single-nucleotide polymorphisms (tSNPs) used to determine ABO alleles and blood types across diverse populations in published literature. MATERIALS AND METHODS Bibliographic databases were searched for studies using tSNPs to determine ABO alleles. We calculated linkage between tSNPs and functional variants across inferred continental ancestry groups from 1000 Genomes. We compared r2 across ancestry and assessed real-world consequences by comparing tSNP-derived blood types to serology in a diverse population from the All of Us Research Program. RESULTS Linkage between functional variants and O allele tSNPs was significantly lower in African (median r2 = 0.443) compared to East Asian (r2 = 0.946, P = 1.1 × 10-5) and European (r2 = 0.869, P = .023) populations. In All of Us, discordance between tSNP-derived blood types and serology was high across all SNPs in African ancestry individuals and linkage was strongly correlated with discordance across all ancestries (ρ = -0.90, P = 3.08 × 10-23). DISCUSSION Many studies determine ABO blood types using tSNPs. However, tSNPs with low linkage disequilibrium promote misinference of ABO blood types, particularly in diverse populations. We observe common use of inappropriate tSNPs to determine ABO blood type, particularly for O alleles and with some tSNPs mistyping up to 58% of individuals. CONCLUSION Our results highlight the lack of transferability of tSNPs across ancestries and potential exacerbation of disparities in genomic research for underrepresented populations. This is especially relevant as more diverse cohorts are made publicly available.
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Affiliation(s)
- Kiana L Martinez
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Andrew Klein
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Jennifer R Martin
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
- Department of the University of Arizona Health Sciences Library, The University of Arizona, Tucson, AZ 85721, United States
| | - Chinwuwanuju U Sampson
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Jason B Giles
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Madison L Beck
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Krupa Bhakta
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Gino Quatraro
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
| | - Juvie Farol
- Department of Clinical and Translational Science, The University of Arizona College of Medicine, Tucson, AZ 85721, United States
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, The University of Arizona R. Ken Coit College of Pharmacy, Tucson, AZ 85721, United States
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, United States
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4
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Greiner AM, Mehdi H, Cevan C, Gutmann R, London B. The role of GPD1L, a sodium channel interacting gene, in the pathogenesis of Brugada Syndrome. Front Med (Lausanne) 2024; 10:1159586. [PMID: 38962240 PMCID: PMC11221213 DOI: 10.3389/fmed.2023.1159586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/06/2023] [Indexed: 07/05/2024] Open
Abstract
Background Brugada Syndrome (BrS) is an inherited arrhythmia syndrome in which mutations in the cardiac sodium channel SCN5A (NaV1.5) account for approximately 20% of cases. Mutations in sodium channel-modifying genes may account for additional BrS cases, though BrS may be polygenic given common SNPs associated with BrS have been identified. Recent analysis, however, has suggested that SCN5A should be regarded as the sole monogenic cause of BrS. Objective We sought to re-assess the genetic underpinnings of BrS in a large mutligenerational family with a putative mutation in GPD1L that affects surface membrane expression of NaV1.5 in vitro. Methods Fine linkage mapping was performed in the family using the Illumina Global Screening Array. Whole exome sequencing of the proband was performed to identify rare variants and mutations, and Sanger sequencing was used to assay previously-reported risk single nucleotide polymorphsims (SNPs) for BrS. Results Linkage analysis decreased the size of the previously-reported microsatellite linkage region to approximately 3 Mb. GPD1L-A280V was the only coding non-synonymous variation present at less than 1% allele frequency in the proband within the linkage region. No rare non-synonymous variants were present outside the linkage area in affected individuals in genes associated with BrS. Risk SNPs known to predispose to BrS were overrepresented in affected members of the family. Conclusion Together, our data suggest GPD1L-A280V remains the most likely cause of BrS in this large multigenerational family. While care should be taken in interpreting variant pathogenicity given the genetic uncertainty of BrS, our data support inclusion of other putative BrS genes in clinical genetic panels.
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Affiliation(s)
- Alexander M. Greiner
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- University of Iowa Interdisciplinary Graduate Program in Genetics, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
| | - Haider Mehdi
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Chloe Cevan
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Rebecca Gutmann
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Barry London
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- Department of Internal Medicine, Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
- University of Iowa Interdisciplinary Graduate Program in Genetics, Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, United States
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Amer K, Soliman NA, Soror S, Gad YZ, Moustafa A, Elmonem MA, Amer M, Ragheb A, Kotb A, Taha T, Ali W, Sakr M, Ghaffar KA. Egypt Genome: Towards an African new genomic era. J Adv Res 2024:S2090-1232(24)00227-3. [PMID: 38844121 DOI: 10.1016/j.jare.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/14/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future. AIM OF REVIEW The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG. KEY SCIENTIFIC CONCEPTS EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.
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Affiliation(s)
- Khaled Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt.
| | - Neveen A Soliman
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Sameh Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Yehia Z Gad
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Center, Cairo, Egypt; Ancient DNA Laboratory, National Museum of Egyptian Civilization, Egypt
| | - Ahmed Moustafa
- Department of Biology, and Bioinformatics and Integrative Genomics Lab, American University in Cairo, Cairo, Egypt
| | - Mohamed A Elmonem
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Ameera Ragheb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Amira Kotb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Tarek Taha
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Wael Ali
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Mahmoud Sakr
- Academy of Scientific Research & Technology, Egypt
| | - Khaled Abdel Ghaffar
- Department of Oral Medicine, Periodontolgy and Diagnosis, Faculty of Dentistry, Ain Shams University, Cairo, Egypt; Ministry of Health and Population, Cairo, Egypt
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6
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Chung WK, Dasgupta S, Regier DS, Solomon BD. The clinical geneticist workforce: Community forums to address challenges and opportunities. Genet Med 2024; 26:101121. [PMID: 38469792 DOI: 10.1016/j.gim.2024.101121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Shoumita Dasgupta
- Department of Medicine, Biomedical Genetics Section, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA
| | - Debra S Regier
- Children's National Rare Disease Institute, Children's National Hospital, Washington, DC
| | - Benjamin D Solomon
- Office of the Clinical Director and Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MA.
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7
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Muhammad A, Calandranis ME, Li B, Yang T, Blackwell DJ, Harvey ML, Smith JE, Daniel ZA, Chew AE, Capra JA, Matreyek KA, Fowler DM, Roden DM, Glazer AM. High-throughput functional mapping of variants in an arrhythmia gene, KCNE1, reveals novel biology. Genome Med 2024; 16:73. [PMID: 38816749 PMCID: PMC11138074 DOI: 10.1186/s13073-024-01340-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/26/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND KCNE1 encodes a 129-residue cardiac potassium channel (IKs) subunit. KCNE1 variants are associated with long QT syndrome and atrial fibrillation. However, most variants have insufficient evidence of clinical consequences and thus limited clinical utility. METHODS In this study, we leveraged the power of variant effect mapping, which couples saturation mutagenesis with high-throughput sequencing, to ascertain the function of thousands of protein-coding KCNE1 variants. RESULTS We comprehensively assayed KCNE1 variant cell surface expression (2554/2709 possible single-amino-acid variants) and function (2534 variants). Our study identified 470 loss- or partial loss-of-surface expression and 574 loss- or partial loss-of-function variants. Of the 574 loss- or partial loss-of-function variants, 152 (26.5%) had reduced cell surface expression, indicating that most functionally deleterious variants affect channel gating. Nonsense variants at residues 56-104 generally had WT-like trafficking scores but decreased functional scores, indicating that the latter half of the protein is dispensable for protein trafficking but essential for channel function. 22 of the 30 KCNE1 residues (73%) highly intolerant of variation (with > 70% loss-of-function variants) were in predicted close contact with binding partners KCNQ1 or calmodulin. Our functional assay data were consistent with gold standard electrophysiological data (ρ = - 0.64), population and patient cohorts (32/38 presumed benign or pathogenic variants with consistent scores), and computational predictors (ρ = - 0.62). Our data provide moderate-strength evidence for the American College of Medical Genetics/Association of Molecular Pathology functional criteria for benign and pathogenic variants. CONCLUSIONS Comprehensive variant effect maps of KCNE1 can both provide insight into I Ks channel biology and help reclassify variants of uncertain significance.
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Affiliation(s)
- Ayesha Muhammad
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA
- Medical Scientist Training Program, Vanderbilt University, Nashville, TN, 37232, USA
| | - Maria E Calandranis
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bian Li
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Tao Yang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Daniel J Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - M Lorena Harvey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jeremy E Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zerubabell A Daniel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ashli E Chew
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - John A Capra
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, 94143, USA
| | - Kenneth A Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Dan M Roden
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Andrew M Glazer
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, 1235 Medical Research Building IV, 2215B Garland Avenue, Nashville, TN, 37232, USA.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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8
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Pak CM, Gilmore MJ, Bulkley JE, Chakraborty P, Dagan-Rosenfeld O, Foreman AKM, Gollob MH, Jenkins CL, Katz AE, Lee K, Meeks N, O'Daniel JM, Posey JE, Rego SM, Shah N, Steiner RD, Stergachis AB, Subramanian SL, Trotter T, Wallace K, Williams MS, Goddard KAB, Buchanan AH, Manickam K, Powell B, Ezzell Hunter J. Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group. Genet Med 2024; 26:101164. [PMID: 38757444 DOI: 10.1016/j.gim.2024.101164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
PURPOSE The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions. METHODS Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs. RESULTS The resulting rubric has a 4-point scale (limited, moderate, strong, and definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, predefined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs. CONCLUSION The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.
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Affiliation(s)
- Christine M Pak
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR.
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, and Division of Metabolics University of Ottawa, Ottawa, ON, Canada
| | | | | | - Michael H Gollob
- Division of Cardiology, University of Toronto, Toronto, ON, Canada
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | - Alexander E Katz
- Division of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Naomi Meeks
- Section of Genetics, Department of Pediatrics, University of Colorado, Aurora, CO
| | | | - Jennifer E Posey
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX
| | - Shannon M Rego
- Institute for Human Genetics, University of California, San Francisco, CA
| | - Neethu Shah
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX
| | - Robert D Steiner
- University of Wisconsin and Marshfield Clinic, Marshfield and Madison, WI
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Sai Lakshmi Subramanian
- Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX; Roche Diagnostics, Santa Clara, CA
| | - Tracy Trotter
- Department of Pediatrics, John Muir Health, Walnut Creek, CA
| | - Kathleen Wallace
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | | | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Kaiser Permanente Center for Health Research, Portland, OR
| | | | - Kandamurugu Manickam
- Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH
| | - Bradford Powell
- Department of Genetics, University of North Carolina, Chapel Hill, NC
| | - Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, NC
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9
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Aljabali AAA, Obeid MA, El-Tanani M, Mishra V, Mishra Y, Tambuwala MM. Precision epidemiology at the nexus of mathematics and nanotechnology: Unraveling the dance of viral dynamics. Gene 2024; 905:148174. [PMID: 38242374 DOI: 10.1016/j.gene.2024.148174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/21/2024]
Abstract
The intersection of mathematical modeling, nanotechnology, and epidemiology marks a paradigm shift in our battle against infectious diseases, aligning with the focus of the journal on the regulation, expression, function, and evolution of genes in diverse biological contexts. This exploration navigates the intricate dance of viral transmission dynamics, highlighting mathematical models as dual tools of insight and precision instruments, a theme relevant to the diverse sections of Gene. In the context of virology, ethical considerations loom large, necessitating robust frameworks to protect individual rights, an aspect essential in infectious disease research. Global collaboration emerges as a critical pillar in our response to emerging infectious diseases, fortified by the predictive prowess of mathematical models enriched by nanotechnology. The synergy of interdisciplinary collaboration, training the next generation to bridge mathematical rigor, biology, and epidemiology, promises accelerated discoveries and robust models that account for real-world complexities, fostering innovation and exploration in the field. In this intricate review, mathematical modeling in viral transmission dynamics and epidemiology serves as a guiding beacon, illuminating the path toward precision interventions, global preparedness, and the collective endeavor to safeguard human health, resonating with the aim of advancing knowledge in gene regulation and expression.
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Affiliation(s)
- Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan.
| | - Mohammad A Obeid
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid 21163, Jordan
| | - Mohamed El-Tanani
- College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Yachana Mishra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, United Kingdom.
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Echeverría-Garcés G, Ramos-Medina MJ, Vargas R, Cabrera-Andrade A, Altamirano-Colina A, Freire MP, Montalvo-Guerrero J, Rivera-Orellana S, Echeverría-Espinoza P, Quiñones LA, López-Cortés A. Gastric cancer actionable genomic alterations across diverse populations worldwide and pharmacogenomics strategies based on precision oncology. Front Pharmacol 2024; 15:1373007. [PMID: 38756376 PMCID: PMC11096557 DOI: 10.3389/fphar.2024.1373007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/10/2024] [Indexed: 05/18/2024] Open
Abstract
Introduction: Gastric cancer is one of the most prevalent types of cancer worldwide. The World Health Organization (WHO), the International Agency for Research on Cancer (IARC), and the Global Cancer Statistics (GLOBOCAN) reported an age standardized global incidence rate of 9.2 per 100,000 individuals for gastric cancer in 2022, with a mortality rate of 6.1. Despite considerable progress in precision oncology through the efforts of international consortia, understanding the genomic features and their influence on the effectiveness of anti-cancer treatments across diverse ethnic groups remains essential. Methods: Our study aimed to address this need by conducting integrated in silico analyses to identify actionable genomic alterations in gastric cancer driver genes, assess their impact using deleteriousness scores, and determine allele frequencies across nine global populations: European Finnish, European non-Finnish, Latino, East Asian, South Asian, African, Middle Eastern, Ashkenazi Jewish, and Amish. Furthermore, our goal was to prioritize targeted therapeutic strategies based on pharmacogenomics clinical guidelines, in silico drug prescriptions, and clinical trial data. Results: Our comprehensive analysis examined 275,634 variants within 60 gastric cancer driver genes from 730,947 exome sequences and 76,215 whole-genome sequences from unrelated individuals, identifying 13,542 annotated and predicted oncogenic variants. We prioritized the most prevalent and deleterious oncogenic variants for subsequent pharmacogenomics testing. Additionally, we discovered actionable genomic alterations in the ARID1A, ATM, BCOR, ERBB2, ERBB3, CDKN2A, KIT, PIK3CA, PTEN, NTRK3, TP53, and CDKN2A genes that could enhance the efficacy of anti-cancer therapies, as suggested by in silico drug prescription analyses, reviews of current pharmacogenomics clinical guidelines, and evaluations of phase III and IV clinical trials targeting gastric cancer driver proteins. Discussion: These findings underline the urgency of consolidating efforts to devise effective prevention measures, invest in genomic profiling for underrepresented populations, and ensure the inclusion of ethnic minorities in future clinical trials and cancer research in developed countries.
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Affiliation(s)
- Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Rodrigo Vargas
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Department of Molecular Biology, Galileo University, Guatemala City, Guatemala
| | - Alejandro Cabrera-Andrade
- Escuela de Enfermería, Facultad de Ciencias de La Salud, Universidad de Las Américas, Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
| | | | - María Paula Freire
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - Luis A. Quiñones
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology (DOBC), Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Pharmaceutical Sciences and Technology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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11
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Cohen ASA, Berrios CD, Zion TN, Barrett CM, Moore R, Boillat E, Belden B, Farrow EG, Thiffault I, Zuccarelli BD, Pastinen T. Genomic Answers for Kids: Toward more equitable access to genomic testing for rare diseases in rural populations. Am J Hum Genet 2024; 111:825-832. [PMID: 38636509 PMCID: PMC11080604 DOI: 10.1016/j.ajhg.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Next-generation sequencing has revolutionized the speed of rare disease (RD) diagnoses. While clinical exome and genome sequencing represent an effective tool for many RD diagnoses, there is room to further improve the diagnostic odyssey of many RD patients. One recognizable intervention lies in increasing equitable access to genomic testing. Rural communities represent a significant portion of underserved and underrepresented individuals facing additional barriers to diagnosis and treatment. Primary care providers (PCPs) at local clinics, though sometimes suspicious of a potential benefit of genetic testing for their patients, have significant constraints in pursuing it themselves and rely on referrals to specialists. Yet, these referrals are typically followed by long waitlists and significant delays in clinical assessment, insurance clearance, testing, and initiation of diagnosis-informed care management. Not only is this process time intensive, but it also often requires multiple visits to urban medical centers for which distance may be a significant barrier to rural families. Therefore, providing early, "direct-to-provider" (DTP) local access to unrestrictive genomic testing is likely to help speed up diagnostic times and access to care for RD patients in rural communities. In a pilot study with a PCP clinic in rural Kansas, we observed a minimum 5.5 months shortening of time to diagnosis through the DTP exome sequencing program as compared to rural patients receiving genetic testing through the "traditional" PCP-referral-to-specialist scheme. We share our experience to encourage future partnerships beyond our center. Our efforts represent just one step in fostering greater diversity and equity in genomic studies.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
| | - Courtney D Berrios
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Cassandra M Barrett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Riley Moore
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emelia Boillat
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Britton D Zuccarelli
- Salina Pediatric Care, Salina Regional Health Center, Salina, KS 67401, USA; Department of Pediatrics, University of Kansas School of Medicine - Salina Campus, Salina, KS 67401, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO 64108, USA
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12
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Wang Y, He Y, Shi Y, Qian DC, Gray KJ, Winn R, Martin AR. Aspiring toward equitable benefits from genomic advances to individuals of ancestrally diverse backgrounds. Am J Hum Genet 2024; 111:809-824. [PMID: 38642557 PMCID: PMC11080611 DOI: 10.1016/j.ajhg.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
Advancements in genomic technologies have shown remarkable promise for improving health trajectories. The Human Genome Project has catalyzed the integration of genomic tools into clinical practice, such as disease risk assessment, prenatal testing and reproductive genomics, cancer diagnostics and prognostication, and therapeutic decision making. Despite the promise of genomic technologies, their full potential remains untapped without including individuals of diverse ancestries and integrating social determinants of health (SDOHs). The NHGRI launched the 2020 Strategic Vision with ten bold predictions by 2030, including "individuals from ancestrally diverse backgrounds will benefit equitably from advances in human genomics." Meeting this goal requires a holistic approach that brings together genomic advancements with careful consideration to healthcare access as well as SDOHs to ensure that translation of genetics research is inclusive, affordable, and accessible and ultimately narrows rather than widens health disparities. With this prediction in mind, this review delves into the two paramount applications of genetic testing-reproductive genomics and precision oncology. When discussing these applications of genomic advancements, we evaluate current accessibility limitations, highlight challenges in achieving representativeness, and propose paths forward to realize the ultimate goal of their equitable applications.
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Affiliation(s)
- Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Yixuan He
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yue Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Reproductive Medicine Center, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - David C Qian
- Department of Thoracic Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathryn J Gray
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Robert Winn
- Virginia Commonwealth University Massey Cancer Center, Richmond, VA, USA
| | - Alicia R Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
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13
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da Silva Rosa SC, Barzegar Behrooz A, Guedes S, Vitorino R, Ghavami S. Prioritization of genes for translation: a computational approach. Expert Rev Proteomics 2024; 21:125-147. [PMID: 38563427 DOI: 10.1080/14789450.2024.2337004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 02/21/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Gene identification for genetic diseases is critical for the development of new diagnostic approaches and personalized treatment options. Prioritization of gene translation is an important consideration in the molecular biology field, allowing researchers to focus on the most promising candidates for further investigation. AREAS COVERED In this paper, we discussed different approaches to prioritize genes for translation, including the use of computational tools and machine learning algorithms, as well as experimental techniques such as knockdown and overexpression studies. We also explored the potential biases and limitations of these approaches and proposed strategies to improve the accuracy and reliability of gene prioritization methods. Although numerous computational methods have been developed for this purpose, there is a need for computational methods that incorporate tissue-specific information to enable more accurate prioritization of candidate genes. Such methods should provide tissue-specific predictions, insights into underlying disease mechanisms, and more accurate prioritization of genes. EXPERT OPINION Using advanced computational tools and machine learning algorithms to prioritize genes, we can identify potential targets for therapeutic intervention of complex diseases. This represents an up-and-coming method for drug development and personalized medicine.
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Affiliation(s)
- Simone C da Silva Rosa
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
| | - Amir Barzegar Behrooz
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sofia Guedes
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- LAQV/REQUIMTE, Department of Chemistry, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, Aveiro, Portugal
- UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Canada
- Faculty of Medicine in Zabrze, Academia of Silesia, Katowice, Poland
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, Canada
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14
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Danek BP, Makarious MB, Dadu A, Vitale D, Lee PS, Singleton AB, Nalls MA, Sun J, Faghri F. Federated learning for multi-omics: A performance evaluation in Parkinson's disease. PATTERNS (NEW YORK, N.Y.) 2024; 5:100945. [PMID: 38487808 PMCID: PMC10935499 DOI: 10.1016/j.patter.2024.100945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/29/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024]
Abstract
While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated learning (FL) represents an opportunity to enable collaborative curation of such datasets among participating institutions. We compare the simulated performance of several models trained using FL against classically trained ML models on the task of multi-omics Parkinson's disease prediction. We find that FL model performance tracks centrally trained ML models, where the most performant FL model achieves an AUC-PR of 0.876 ± 0.009, 0.014 ± 0.003 less than its centrally trained variation. We also determine that the dispersion of samples within a federation plays a meaningful role in model performance. Our study implements several open-source FL frameworks and aims to highlight some of the challenges and opportunities when applying these collaborative methods in multi-omics studies.
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Affiliation(s)
- Benjamin P. Danek
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- DataTecnica, Washington, DC 20037, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Anant Dadu
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- DataTecnica, Washington, DC 20037, USA
| | - Dan Vitale
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- DataTecnica, Washington, DC 20037, USA
| | - Paul Suhwan Lee
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew B. Singleton
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mike A. Nalls
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- DataTecnica, Washington, DC 20037, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jimeng Sun
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
| | - Faraz Faghri
- Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
- DataTecnica, Washington, DC 20037, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Blee AM, Gallagher K, Kim HS, Kim M, Kharat S, Troll C, D’Souza A, Park J, Neufer P, Schärer O, Chazin W. XPA tumor variant leads to defects in NER that sensitize cells to cisplatin. NAR Cancer 2024; 6:zcae013. [PMID: 38500596 PMCID: PMC10946055 DOI: 10.1093/narcan/zcae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Nucleotide excision repair (NER) reduces efficacy of treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of the NER genes Excision Repair Cross Complementation Group 1 and 2 (ERCC1 and ERCC2) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair. In this study, we report in-depth analyses of a subset of the predicted variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to improve variant effect prediction. Broadly, these findings suggest XPA tumor variants should be considered when predicting chemotherapy response.
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Affiliation(s)
- Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Suhas S Kharat
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Christina R Troll
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Areetha D’Souza
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jiyoung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - P Drew Neufer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Orlando D Schärer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
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16
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Lappalainen T, Li YI, Ramachandran S, Gusev A. Genetic and molecular architecture of complex traits. Cell 2024; 187:1059-1075. [PMID: 38428388 DOI: 10.1016/j.cell.2024.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/20/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024]
Abstract
Human genetics has emerged as one of the most dynamic areas of biology, with a broadening societal impact. In this review, we discuss recent achievements, ongoing efforts, and future challenges in the field. Advances in technology, statistical methods, and the growing scale of research efforts have all provided many insights into the processes that have given rise to the current patterns of genetic variation. Vast maps of genetic associations with human traits and diseases have allowed characterization of their genetic architecture. Finally, studies of molecular and cellular effects of genetic variants have provided insights into biological processes underlying disease. Many outstanding questions remain, but the field is well poised for groundbreaking discoveries as it increases the use of genetic data to understand both the history of our species and its applications to improve human health.
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Affiliation(s)
- Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Yang I Li
- Section of Genetic Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Sohini Ramachandran
- Ecology, Evolution and Organismal Biology, Center for Computational Molecular Biology, and the Data Science Institute, Brown University, Providence, RI 029129, USA
| | - Alexander Gusev
- Harvard Medical School and Dana-Farber Cancer Institute, Boston, MA, USA
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17
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Oladayo AM, Odukoya O, Sule V, Molobe I, Busch T, Akodu B, Adeyemo WL, Gowans LJJ, Eshete M, Alade A, Awotoye W, Adeyemo AA, Mossey PA, Prince AER, Murray JC, Butali A. Perceptions and beliefs of community gatekeepers about genomic risk information in African cleft research. BMC Public Health 2024; 24:507. [PMID: 38365612 PMCID: PMC10873930 DOI: 10.1186/s12889-024-17987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND A fundamental ethical issue in African genomics research is how socio-cultural factors impact perspectives, acceptance, and utility of genomic information, especially in stigmatizing conditions like orofacial clefts (OFCs). Previous research has shown that gatekeepers (e.g., religious, political, family or community leaders) wield considerable influence on the decision-making capabilities of their members, including health issues. Thus, their perspectives can inform the design of engagement strategies and increase exposure to the benefits of genomics testing/research. This is especially important for Africans underrepresented in genomic research. Our study aims to investigate the perspectives of gatekeepers concerning genomic risk information (GRI) in the presence of OFCs in a sub-Saharan African cohort. METHODS Twenty-five focus group discussions (FGDs) consisting of 214 gatekeepers (religious, community, ethnic leaders, and traditional birth attendants) in Lagos, Nigeria, explored the opinions of participants on genomic risk information (GRI), OFC experience, and the possibility of involvement in collaborative decision-making in Lagos, Nigeria. Transcripts generated from audio recordings were coded and analyzed in NVivo using thematic analysis. RESULTS Three main themes-knowledge, beliefs, and willingness to act-emerged from exploring the perspective of gatekeepers about GRI in this group. We observed mixed opinions regarding the acceptance of GRI. Many participants believed their role is to guide and support members when they receive results; this is based on the level of trust their members have in them. However, participants felt they would need to be trained by medical experts to do this. Also, religious and cultural beliefs were crucial to determining participants' understanding of OFCs and the acceptance and utilization of GRI. CONCLUSIONS Incorporating cultural sensitivity into public engagement could help develop appropriate strategies to manage conflicting ideologies surrounding genomic information in African communities. This will allow for more widespread access to the advances in genomics research in underrepresented populations. We also recommend a synergistic relationship between community health specialists/scientists, and community leaders, including spiritual providers to better understand and utilize GRI.
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Affiliation(s)
- Abimbola M Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA.
| | - Oluwakemi Odukoya
- Department of Community Health and Primary Care, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Ikenna Molobe
- Department of Community Health and Primary Care, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Tamara Busch
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Babatunde Akodu
- Department of Community Health and Primary Care, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Lord J J Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- School of Medicine, Department of Surgery, Addis Ababa University, Addis Ababa, Ethiopia
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | | | - Peter A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | | | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA.
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18
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Danek B, Makarious MB, Dadu A, Vitale D, Lee PS, Nalls MA, Sun J, Faghri F. Federated Learning for multi-omics: a performance evaluation in Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.04.560604. [PMID: 37986893 PMCID: PMC10659429 DOI: 10.1101/2023.10.04.560604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
While machine learning (ML) research has recently grown more in popularity, its application in the omics domain is constrained by access to sufficiently large, high-quality datasets needed to train ML models. Federated Learning (FL) represents an opportunity to enable collaborative curation of such datasets among participating institutions. We compare the simulated performance of several models trained using FL against classically trained ML models on the task of multi-omics Parkinson's Disease prediction. We find that FL model performance tracks centrally trained ML models, where the most performant FL model achieves an AUC-PR of 0.876 ± 0.009, 0.014 ± 0.003 less than its centrally trained variation. We also determine that the dispersion of samples within a federation plays a meaningful role in model performance. Our study implements several open source FL frameworks and aims to highlight some of the challenges and opportunities when applying these collaborative methods in multi-omics studies.
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Affiliation(s)
- Benjamin Danek
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- DataTecnica, Washington, DC, 20037, USA
| | - Mary B. Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
| | - Anant Dadu
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- DataTecnica, Washington, DC, 20037, USA
| | - Dan Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- DataTecnica, Washington, DC, 20037, USA
| | - Paul Suhwan Lee
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- DataTecnica, Washington, DC, 20037, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jimeng Sun
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, 61820, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
- DataTecnica, Washington, DC, 20037, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
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19
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Chappell E, Arbour L, Laksman Z. The Inclusion of Underrepresented Populations in Cardiovascular Genetics and Epidemiology. J Cardiovasc Dev Dis 2024; 11:56. [PMID: 38392270 PMCID: PMC10888590 DOI: 10.3390/jcdd11020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
Novel genetic risk markers have helped us to advance the field of cardiovascular epidemiology and refine our current understanding and risk stratification paradigms. The discovery and analysis of variants can help us to tailor prognostication and management. However, populations underrepresented in cardiovascular epidemiology and cardiogenetics research may experience inequities in care if prediction tools are not applicable to them clinically. Therefore, the purpose of this article is to outline the barriers that underrepresented populations can face in participating in genetics research, to describe the current efforts to diversify cardiogenetics research, and to outline strategies that researchers in cardiovascular epidemiology can implement to include underrepresented populations. Mistrust, a lack of diverse research teams, the improper use of sensitive biodata, and the constraints of genetic analyses are all barriers for including diverse populations in genetics studies. The current work is beginning to address the paucity of ethnically diverse genetics research and has already begun to shed light on the potential benefits of including underrepresented and diverse populations. Reducing barriers for individuals, utilizing community-driven research processes, adopting novel recruitment strategies, and pushing for organizational support for diverse genetics research are key steps that clinicians and researchers can take to develop equitable risk stratification tools and improve patient care.
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Affiliation(s)
- Elias Chappell
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Zachary Laksman
- Department of Medicine and the School of Biomedical Engineering, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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20
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Morris JA, Sun JS, Sanjana NE. Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis. Trends Genet 2024; 40:118-133. [PMID: 37989654 PMCID: PMC10872607 DOI: 10.1016/j.tig.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/23/2023]
Abstract
Programmable genome-engineering technologies, such as CRISPR (clustered regularly interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens that capitalize on this programmability, have transformed biomedical science. These screens connect genes and noncoding genome elements to disease-relevant phenotypes, but until recently have been limited to individual phenotypes such as growth or fluorescent reporters of gene expression. By pairing massively parallel screens with high-dimensional profiling of single-cell types/states, we can now measure how individual genetic perturbations or combinations of perturbations impact the cellular transcriptome, proteome, and epigenome. We review technologies that pair CRISPR screens with single-cell multiomics and the unique opportunities afforded by extending pooled screens using deep multimodal phenotyping.
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Affiliation(s)
- John A Morris
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Jennifer S Sun
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA.
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21
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Mersha TB. From Mendel to multi-omics: shifting paradigms. Eur J Hum Genet 2024; 32:139-142. [PMID: 37468578 PMCID: PMC10853174 DOI: 10.1038/s41431-023-01420-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/24/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Affiliation(s)
- Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
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22
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Casillan A, Florido ME, Galarza-Cornejo J, Bakken S, Lynch JA, Chung WK, Mittendorf KF, Berner ES, Connolly JJ, Weng C, Holm IA, Khan A, Kiryluk K, Limdi NA, Petukhova L, Sabatello M, Wynn J. Participant-guided development of bilingual genomic educational infographics for Electronic Medical Records and Genomics Phase IV study. J Am Med Inform Assoc 2024; 31:306-316. [PMID: 37860921 PMCID: PMC10797276 DOI: 10.1093/jamia/ocad207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 09/11/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVE Developing targeted, culturally competent educational materials is critical for participant understanding of engagement in a large genomic study that uses computational pipelines to produce genome-informed risk assessments. MATERIALS AND METHODS Guided by the Smerecnik framework that theorizes understanding of multifactorial genetic disease through 3 knowledge types, we developed English and Spanish infographics for individuals enrolled in the Electronic Medical Records and Genomics Network. Infographics were developed to explain concepts in lay language and visualizations. We conducted iterative sessions using a modified "think-aloud" process with 10 participants (6 English, 4 Spanish-speaking) to explore comprehension of and attitudes towards the infographics. RESULTS We found that all but one participant had "awareness knowledge" of genetic disease risk factors upon viewing the infographics. Many participants had difficulty with "how-to" knowledge of applying genetic risk factors to specific monogenic and polygenic risks. Participant attitudes towards the iteratively-refined infographics indicated that design saturation was reached. DISCUSSION There were several elements that contributed to the participants' comprehension (or misunderstanding) of the infographics. Visualization and iconography techniques best resonated with those who could draw on prior experiences or knowledge and were absent in those without. Limited graphicacy interfered with the understanding of absolute and relative risks when presented in graph format. Notably, narrative and storytelling theory that informed the creation of a vignette infographic was most accessible to all participants. CONCLUSION Engagement with the intended audience who can identify strengths and points for improvement of the intervention is necessary to the development of effective infographics.
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Affiliation(s)
- Aimiel Casillan
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, United States
| | - Jamie Galarza-Cornejo
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Suzanne Bakken
- Department of Nursing Scholarship and Research, School of Nursing, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - John A Lynch
- Department of Communication, School of Communication, Film, and Media Studies, University of Cincinnati, Cincinnati, OH 45221, United States
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Eta S Berner
- Department of Health Services Administration, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - John J Connolly
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, MA 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, United States
| | - Atlas Khan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, United States
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, United States
| | - Lynn Petukhova
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, NY 10032, United States
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Maya Sabatello
- Department of Medicine, Center for Precision Medicine and Genomics, Columbia University Irving Medical Center, New York, NY 10032, United States
- Department of Medical Humanities and Ethics, Division of Ethics, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Julia Wynn
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, United States
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, United States
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23
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Bentz M, Saperstein A, Fullerton SM, Shim JK, Lee SSJ. Conflating race and ancestry: Tracing decision points about population descriptors over the precision medicine research life course. HGG ADVANCES 2024; 5:100243. [PMID: 37771152 PMCID: PMC10585473 DOI: 10.1016/j.xhgg.2023.100243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Responding to calls for human genomics to shift away from the use of race, genomic investigators are coalescing around the possibility of using genetic ancestry. This shift has renewed questions about the use of social and genetic concepts of difference in precision medicine research (PMR). Drawing from qualitative data on five PMR projects, we illustrate negotiations within and between research teams as genomic investigators deliberate on the relevance of race and genetic ancestry for different analyses and contexts. We highlight how concepts of both social and genetic difference are embedded within and travel through research practices, and identify multiple points across the research life course at which conceptual slippage and conflation between race and genetic ancestry occur. We argue that moving beyond race will require PMR investigators to confront the entrenched ways in which race is built into research practices and biomedical infrastructures.
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Affiliation(s)
- Michael Bentz
- Division of Ethics, Department of Medical Humanities and Ethics, Vagelos College of Physicians & Surgeons, Columbia University, 630 West 168th Street, PH 1525, New York, NY 10032, USA.
| | - Aliya Saperstein
- Department of Sociology, Stanford University, 450 Jane Stanford Way, Building 120, Room 160, Stanford, CA 94305-2047, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Box 357120, Seattle, WA 98195-7120, USA
| | - Janet K Shim
- Department of Social & Behavioral Sciences, University of California, San Francisco, 490 Illinois Street, Floor 12, Box 0612, San Francisco, CA 94143-0612, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Vagelos College of Physicians & Surgeons, Columbia University, 630 West 168th Street, PH 1525, New York, NY 10032, USA.
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24
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Sen SK, Green ED, Hutter CM, Craven M, Ideker T, Di Francesco V. Opportunities for basic, clinical, and bioethics research at the intersection of machine learning and genomics. CELL GENOMICS 2024; 4:100466. [PMID: 38190108 PMCID: PMC10794834 DOI: 10.1016/j.xgen.2023.100466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 07/14/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024]
Abstract
The data-intensive fields of genomics and machine learning (ML) are in an early stage of convergence. Genomics researchers increasingly seek to harness the power of ML methods to extract knowledge from their data; conversely, ML scientists recognize that genomics offers a wealth of large, complex, and well-annotated datasets that can be used as a substrate for developing biologically relevant algorithms and applications. The National Human Genome Research Institute (NHGRI) inquired with researchers working in these two fields to identify common challenges and receive recommendations to better support genomic research efforts using ML approaches. Those included increasing the amount and variety of training datasets by integrating genomic with multiomics, context-specific (e.g., by cell type), and social determinants of health datasets; reducing the inherent biases of training datasets; prioritizing transparency and interpretability of ML methods; and developing privacy-preserving technologies for research participants' data.
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Affiliation(s)
- Shurjo K Sen
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carolyn M Hutter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Craven
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53792, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Valentina Di Francesco
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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25
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Garrison SM, Webster EE, Good R. Advancing Diversity in Behavior Genetics: Strategies for Incorporating Undergraduates into Student-Driven Research. Behav Genet 2024; 54:4-23. [PMID: 38252380 DOI: 10.1007/s10519-023-10172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Undergraduate research experiences are crucial for fostering the next generation of behavior genetics researchers. However, incorporating undergraduates into research can be challenging for faculty mentors. In this article, we provide strategies for successfully integrating undergraduates into behavior genetics research based on our experiences mentoring undergraduates in our lab. These strategies include: (1) Practicing reflexivity, specifically an ongoing self-examination and critical self-awareness of personal biases, beliefs, and practices; (2) Implementing an Inclusion, Diversity, Equity, and Access (IDEA) centered approach; (3) empowering students through clear expectations; (4) Providing focused training and mentorship; (5) Aligning research projects with student interests; (6) Assigning meaningful tasks; and (7) Facilitating professional development opportunities. By following these strategies, faculty mentors can cultivate a supportive and inclusive research environment that empowers undergraduates for successful careers in behavior genetics research.
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Affiliation(s)
- S Mason Garrison
- Department of Psychology, Wake Forest University, Winston-Salem, USA.
| | - Emma E Webster
- Department of Psychology, Wake Forest University, Winston-Salem, USA
- Department of Psychology, Emory University, Atlanta, USA
| | - Rachel Good
- Department of Psychology, Wake Forest University, Winston-Salem, USA
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26
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George SHL, Medina-Rivera A, Idaghdour Y, Lappalainen T, Gallego Romero I. Increasing diversity of functional genetics studies to advance biological discovery and human health. Am J Hum Genet 2023; 110:1996-2002. [PMID: 37995684 PMCID: PMC10716434 DOI: 10.1016/j.ajhg.2023.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.
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Affiliation(s)
- Sophia H L George
- Department of Obstetrics, Gynecology and Reproductive Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA; Sylvester Comprehensive Cancer Center, Miami, FL, USA.
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre El Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE; Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Tuuli Lappalainen
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; New York Genome Center, New York, NY, USA.
| | - Irene Gallego Romero
- Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, VIC, Australia; Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Tartu, Estonia
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27
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Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep 2023; 42:113233. [PMID: 38510311 PMCID: PMC10954246 DOI: 10.1016/j.celrep.2023.113233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no-MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.
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Affiliation(s)
- Rebecca H. Gellman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolé cules Biologiques, INRAE, CNRS, Aix-Marseille Université, Marseille, France
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K. Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
| | - Erica D. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
- Lead contact
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28
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David SP, Dunnenberger HM, Choi S, DePersia A, Ilbawi N, Ward C, Wake DT, Khandekar JD, Shannon Y, Hughes K, Miller N, Mangold KA, Sabatini LM, Helseth DL, Xu J, Sanders A, Kaul KL, Hulick PJ. Personalized medicine in a community health system: the NorthShore experience. Front Genet 2023; 14:1308738. [PMID: 38090148 PMCID: PMC10713750 DOI: 10.3389/fgene.2023.1308738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Genomic and personalized medicine implementation efforts have largely centered on specialty care in tertiary health systems. There are few examples of fully integrated care systems that span the healthcare continuum. In 2014, NorthShore University HealthSystem launched the Center for Personalized Medicine to catalyze the delivery of personalized medicine. Successful implementation required the development of a scalable family history collection tool, the Genetic and Wellness Assessment (GWA) and Breast Health Assessment (BHA) tools; integrated pharmacogenomics programming; educational programming; electronic medical record integration; and robust clinical decision support tools. To date, more than 225,000 patients have been screened for increased hereditary conditions, such as cancer risk, through these tools in primary care. More than 35,000 patients completed clinical genetic testing following GWA or BHA completion. An innovative program trained more than 100 primary care providers in genomic medicine, activated with clinical decision support and access to patient genetic counseling services and digital healthcare tools. The development of a novel bioinformatics platform (FLYPE) enabled the incorporation of genomics data into electronic medical records. To date, over 4,000 patients have been identified to have a pathogenic or likely pathogenic variant in a gene with medical management implications. Over 33,000 patients have clinical pharmacogenomics data incorporated into the electronic health record supported by clinical decision support tools. This manuscript describes the evolution, strategy, and successful multispecialty partnerships aligned with health system leadership that enabled the implementation of a comprehensive personalized medicine program with measurable patient outcomes through a genomics-enabled learning health system model that utilizes implementation science frameworks.
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Affiliation(s)
- Sean P. David
- Department of Family Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Family Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Outcomes Research Network, NorthShore University HealthSystem, Evanston, IL, United States
| | - Henry M. Dunnenberger
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Sarah Choi
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Allison DePersia
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Outcomes Research Network, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Nadim Ilbawi
- Department of Family Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Family Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Christopher Ward
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Dyson T. Wake
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Janardan D. Khandekar
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Kellogg Cancer Center, NorthShore University HealthSystem, Evanston, IL, United States
| | - Yvette Shannon
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Kristen Hughes
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Nicholas Miller
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Kathy A. Mangold
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Linda M. Sabatini
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Donald L. Helseth
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Jianfeng Xu
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
| | - Alan Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL, United States
- Departments of Psychiatry and Behavioral Neuroscience, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
| | - Karen L. Kaul
- Outcomes Research Network, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Pathology, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
- Department of Pathology, NorthShore University HealthSystem, Evanston, IL, United States
| | - Peter J. Hulick
- Mark R. Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Outcomes Research Network, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, United States
- Department of Medicine, University of Chicago Pritzker School of Medicine, Chicago, IL, United States
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29
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Feng C, Wang J, Chu X. Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes. J Mol Cell Biol 2023; 15:mjad042. [PMID: 37365687 PMCID: PMC10782906 DOI: 10.1093/jmcb/mjad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/22/2023] [Accepted: 06/25/2023] [Indexed: 06/28/2023] Open
Abstract
The organized three-dimensional chromosome architecture in the cell nucleus provides scaffolding for precise regulation of gene expression. When the cell changes its identity in the cell-fate decision-making process, extensive rearrangements of chromosome structures occur accompanied by large-scale adaptations of gene expression, underscoring the importance of chromosome dynamics in shaping genome function. Over the last two decades, rapid development of experimental methods has provided unprecedented data to characterize the hierarchical structures and dynamic properties of chromosomes. In parallel, these enormous data offer valuable opportunities for developing quantitative computational models. Here, we review a variety of large-scale polymer models developed to investigate the structures and dynamics of chromosomes. Different from the underlying modeling strategies, these approaches can be classified into data-driven ('top-down') and physics-based ('bottom-up') categories. We discuss their contributions to offering valuable insights into the relationships among the structures, dynamics, and functions of chromosomes and propose the perspective of developing data integration approaches from different experimental technologies and multidisciplinary theoretical/simulation methods combined with different modeling strategies.
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Affiliation(s)
- Cibo Feng
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Green e Materials Laboratory, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- College of Physics, Jilin University, Changchun 130012, China
| | - Jin Wang
- Department of Chemistry and Physics, The State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Xiakun Chu
- Advanced Materials Thrust, Function Hub, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Green e Materials Laboratory, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR 999077, China
- Guangzhou Municipal Key Laboratory of Materials Informatics, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou 511400, China
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30
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Symecko H, Schnoll R, Beidas RS, Bekelman JE, Blumenthal D, Bauer AM, Gabriel P, Boisseau L, Doucette A, Powers J, Cappadocia J, McKenna DB, Richardville R, Cuff L, Offer R, Clement EG, Buttenheim AM, Asch DA, Rendle KA, Shelton RC, Fayanju OM, Wileyto EP, Plag M, Ware S, Shulman LN, Nathanson KL, Domchek SM. Protocol to evaluate sequential electronic health record-based strategies to increase genetic testing for breast and ovarian cancer risk across diverse patient populations in gynecology practices. Implement Sci 2023; 18:57. [PMID: 37932730 PMCID: PMC10629034 DOI: 10.1186/s13012-023-01308-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Germline genetic testing is recommended by the National Comprehensive Cancer Network (NCCN) for individuals including, but not limited to, those with a personal history of ovarian cancer, young-onset (< 50 years) breast cancer, and a family history of ovarian cancer or male breast cancer. Genetic testing is underused overall, and rates are consistently lower among Black and Hispanic populations. Behavioral economics-informed implementation strategies, or nudges, directed towards patients and clinicians may increase the use of this evidence-based clinical practice. METHODS Patients meeting eligibility for germline genetic testing for breast and ovarian cancer will be identified using electronic phenotyping algorithms. A pragmatic cohort study will test three sequential strategies to promote genetic testing, two directed at patients and one directed at clinicians, deployed in the electronic health record (EHR) for patients in OB-GYN clinics across a diverse academic medical center. We will use rapid cycle approaches informed by relevant clinician and patient experiences, health equity, and behavioral economics to optimize and de-risk our strategies and methods before trial initiation. Step 1 will send patients messages through the health system patient portal. For non-responders, step 2 will reach out to patients via text message. For non-responders, Step 3 will contact patients' clinicians using a novel "pend and send" tool in the EHR. The primary implementation outcome is engagement with germline genetic testing for breast and ovarian cancer predisposition, defined as a scheduled genetic counseling appointment. Patient data collected through the EHR (e.g., race/ethnicity, geocoded address) will be examined as moderators of the impact of the strategies. DISCUSSION This study will be one of the first to sequentially examine the effects of patient- and clinician-directed strategies informed by behavioral economics on engagement with breast and ovarian cancer genetic testing. The pragmatic and sequential design will facilitate a large and diverse patient sample, allow for the assessment of incremental gains from different implementation strategies, and permit the assessment of moderators of strategy effectiveness. The findings may help determine the impact of low-cost, highly transportable implementation strategies that can be integrated into healthcare systems to improve the use of genomic medicine. TRIAL REGISTRATION ClinicalTrials.gov. NCT05721326. Registered February 10, 2023. https://www. CLINICALTRIALS gov/study/NCT05721326.
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Affiliation(s)
- Heather Symecko
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert Schnoll
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
- Center for Interdisciplinary Research On Nicotine Addiction, University of Pennsylvania, Philadelphia, PA, USA
| | - Rinad S Beidas
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Justin E Bekelman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Daniel Blumenthal
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Interdisciplinary Research On Nicotine Addiction, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna-Marika Bauer
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Interdisciplinary Research On Nicotine Addiction, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter Gabriel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Leland Boisseau
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Abigail Doucette
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Jacquelyn Powers
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Cappadocia
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Danielle B McKenna
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Richardville
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren Cuff
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Offer
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth G Clement
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alison M Buttenheim
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
- School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - David A Asch
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Katharine A Rendle
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Rachel C Shelton
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Oluwadamilola M Fayanju
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - E Paul Wileyto
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Interdisciplinary Research On Nicotine Addiction, University of Pennsylvania, Philadelphia, PA, USA
| | - Martina Plag
- Center for Healthcare Transformation and Innovation, Penn Medicine, Philadelphia, PA, USA
| | - Sue Ware
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center for Interdisciplinary Research On Nicotine Addiction, University of Pennsylvania, Philadelphia, PA, USA
| | - Lawrence N Shulman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Katherine L Nathanson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA
| | - Susan M Domchek
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Center for Cancer Care Innovation, Abramson Cancer Center, Penn Medicine, Philadelphia, PA, USA.
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31
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Gunter C, Green ED. To boldly go: Unpacking the NHGRI's bold predictions for human genomics by 2030. Am J Hum Genet 2023; 110:1829-1831. [PMID: 37922881 PMCID: PMC10663102 DOI: 10.1016/j.ajhg.2023.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023] Open
Abstract
The 2020 strategic vision for human genomics, written by the National Human Genome Research Institute (NHGRI), was punctuated by a set of provocatively audacious "bold predictions for human genomics by 2030." Starting here, these will be unpacked and discussed in an upcoming series in the American Journal of Human Genetics.
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Affiliation(s)
- Chris Gunter
- National Human Genome Research Institute, National Institutes of Health, 31 Center Dr., Bethesda, MD 20892-2152, USA.
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, 31 Center Dr., Bethesda, MD 20892-2152, USA
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32
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Middleton A, Costa A, Milne R, Patch C, Robarts L, Tomlin B, Danson M, Henriques S, Atutornu J, Aidid U, Boraschi D, Galloway C, Yazmir K, Pettit S, Harcourt T, Connolly A, Li A, Cala J, Lake S, Borra J, Parry V. The legacy of language: What we say, and what people hear, when we talk about genomics. HGG ADVANCES 2023; 4:100231. [PMID: 37869565 PMCID: PMC10589723 DOI: 10.1016/j.xhgg.2023.100231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023] Open
Abstract
The way we "talk" about genetics plays a vital role in whether public audiences feel at ease in having conversations about it. Our research explored whether there was any difference between "what we say" and "what people hear" when providing information about genetics to community groups who are known to be missing from genomics datasets. We conducted 16 focus groups with 100 members of the British public who had limited familiarity with genomics and self-identified as belonging to communities with Black African, Black Caribbean, and Pakistani ancestry as well as people of various ancestral heritage who came from disadvantaged socio-economic backgrounds. Participants were presented with spoken messages explaining genomics and their responses to these were analyzed. Results indicated that starting conversations that framed genomics through its potential benefits were met with cynicism and skepticism. Participants cited historical and present injustices as reasons for this as well as mistrust of private companies and the government. Instead, more productive conversations led with an acknowledgment that some people have questions-and valid concerns-about genomics, before introducing any of the details about the science. To diversify genomic datasets, we need to linguistically meet public audiences where they are at. Our research has demonstrated that everyday talk about genomics, used by researchers and clinicians alike, is received differently than it is likely intended. We may inadvertently be further disengaging the very audiences that diversity programs aim to reach.
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Affiliation(s)
- Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Alessia Costa
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Richard Milne
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Christine Patch
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Lauren Robarts
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ben Tomlin
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Mark Danson
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sasha Henriques
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Jerome Atutornu
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Ugbaad Aidid
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Daniela Boraschi
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Catherine Galloway
- Kavli Centre for Ethics, Science and the Public, Faculty of Education, University of Cambridge, 184 Hills Road, Cambridge CB4 8PQ, UK
| | - Keith Yazmir
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Sachi Pettit
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Tegan Harcourt
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Alannah Connolly
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Amanda Li
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Jacob Cala
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Shelby Lake
- Maslansky and Partners, 200 Varick Street, Suite 601, New York, NY 10014, USA
| | - Julian Borra
- The Thin Air Factory Ltd, 71-75 Shelton Street, London WC2H 9JQ, UK
| | - Vivienne Parry
- Genomics England, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, UK
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Skantharajah N, Baichoo S, Boughtwood TF, Casas-Silva E, Chandrasekharan S, Dave SM, Fakhro KA, Falcon de Vargas AB, Gayle SS, Gupta VK, Hendricks-Sturrup R, Hobb AE, Li S, Llamas B, Lopez-Correa C, Machirori M, Melendez-Zajgla J, Millner MA, Page AJ, Paglione LD, Raven-Adams MC, Smith L, Thomas EM, Kumuthini J, Corpas M. Equity, diversity, and inclusion at the Global Alliance for Genomics and Health. CELL GENOMICS 2023; 3:100386. [PMID: 37868041 PMCID: PMC10589617 DOI: 10.1016/j.xgen.2023.100386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
A lack of diversity in genomics for health continues to hinder equitable leadership and access to precision medicine approaches for underrepresented populations. To avoid perpetuating biases within the genomics workforce and genomic data collection practices, equity, diversity, and inclusion (EDI) must be addressed. This paper documents the journey taken by the Global Alliance for Genomics and Health (a genomics-based standard-setting and policy-framing organization) to create a more equitable, diverse, and inclusive environment for its standards and members. Initial steps include the creation of two groups: the Equity, Diversity, and Inclusion Advisory Group and the Regulatory and Ethics Diversity Group. Following a framework that we call "Reflected in our Teams, Reflected in our Standards," both groups address EDI at different stages in their policy development process.
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Affiliation(s)
- Neerjah Skantharajah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | | | | | - Sanjay M. Dave
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Khalid A. Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Aida B. Falcon de Vargas
- Hospital Vargas de Caracas, Vargas Medical School, Universidad Central de Venezuela, Caracas, Venezuela
- Hospital de Clínicas Caracas, Caracas, Venezuela
| | | | - Vivek K. Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Stephanie Li
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA, Australia
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA, Australia
| | | | - Mavis Machirori
- Ada Lovelace Institute, London, UK
- PEALS, Newcastle University, Newcastle Upon Tyne, UK
| | | | - Mareike A. Millner
- Maastricht University, Health Law and Governance Group, Maastricht, the Netherlands
| | - Angela J.H. Page
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Broad Institute, Cambridge, MA, USA
| | - Laura D. Paglione
- Spherical Cow Group, New York, NY, USA
- Laura Paglione LLC, New York, NY, USA
| | - Maili C. Raven-Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | - Lindsay Smith
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Ericka M. Thomas
- The All of Us Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Judit Kumuthini
- South African National Bioinformatics Institute, University of Western Cape, Cape Town, South Africa
| | - Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
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O'Neill MJ, Yang T, Laudeman J, Calandranis M, Solus J, Roden DM, Glazer AM. ParSE-seq: A Calibrated Multiplexed Assay to Facilitate the Clinical Classification of Putative Splice-altering Variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.04.23295019. [PMID: 37732247 PMCID: PMC10508793 DOI: 10.1101/2023.09.04.23295019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Background Interpreting the clinical significance of putative splice-altering variants outside 2-base pair canonical splice sites remains difficult without functional studies. Methods We developed Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed minigene-based assay, to test variant effects on RNA splicing quantified by high-throughput sequencing. We studied variants in SCN5A, an arrhythmia-associated gene which encodes the major cardiac voltage-gated sodium channel. We used the computational tool SpliceAI to prioritize exonic and intronic candidate splice variants, and ClinVar to select benign and pathogenic control variants. We generated a pool of 284 barcoded minigene plasmids, transfected them into Human Embryonic Kidney (HEK293) cells and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), sequenced the resulting pools of splicing products, and calibrated the assay to the American College of Medical Genetics and Genomics scheme. Variants were interpreted using the calibrated functional data, and experimental data were compared to SpliceAI predictions. We further studied some splice-altering missense variants by cDNA-based automated patch clamping (APC) in HEK cells and assessed splicing and sodium channel function in CRISPR-edited iPSC-CMs. Results ParSE-seq revealed the splicing effect of 224 SCN5A variants in iPSC-CMs and 244 variants in HEK293 cells. The scores between the cell types were highly correlated (R2=0.84). In iPSCs, the assay had concordant scores for 21/22 benign/likely benign and 24/25 pathogenic/likely pathogenic control variants from ClinVar. 43/112 exonic variants and 35/70 intronic variants with determinate scores disrupted splicing. 11 of 42 variants of uncertain significance were reclassified, and 29 of 34 variants with conflicting interpretations were reclassified using the functional data. SpliceAI computational predictions correlated well with experimental data (AUC = 0.96). We identified 20 unique SCN5A missense variants that disrupted splicing, and 2 clinically observed splice-altering missense variants of uncertain significance had normal function when tested with the cDNA-based APC assay. A splice-altering intronic variant detected by ParSE-seq, c.1891-5C>G, also disrupted splicing and sodium current when introduced into iPSC-CMs at the endogenous locus by CRISPR editing. Conclusions ParSE-seq is a calibrated, multiplexed, high-throughput assay to facilitate the classification of candidate splice-altering variants.
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Affiliation(s)
| | - Tao Yang
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Julie Laudeman
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Maria Calandranis
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Joseph Solus
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Dan M Roden
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M Glazer
- Vanderbilt Center for Arrhythmia Research and Therapeutics (VanCART), Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
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Krzyzanowski MC, Ives CL, Jones NL, Entwisle B, Fernandez A, Cullen TA, Darity WA, Fossett M, Remington PL, Taualii M, Wilkins CH, Pérez-Stable EJ, Rajapakse N, Breen N, Zhang X, Maiese DR, Hendershot TP, Mandal M, Hwang SY, Huggins W, Gridley L, Riley A, Ramos EM, Hamilton CM. The PhenX Toolkit: Measurement Protocols for Assessment of Social Determinants of Health. Am J Prev Med 2023; 65:534-542. [PMID: 36935055 PMCID: PMC10505248 DOI: 10.1016/j.amepre.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/21/2023]
Abstract
INTRODUCTION Social determinants are structures and conditions in the biological, physical, built, and social environments that affect health, social and physical functioning, health risk, quality of life, and health outcomes. The adoption of recommended, standard measurement protocols for social determinants of health will advance the science of minority health and health disparities research and provide standard social determinants of health protocols for inclusion in all studies with human participants. METHODS A PhenX (consensus measures for Phenotypes and eXposures) Working Group of social determinants of health experts was convened from October 2018 to May 2020 and followed a well-established consensus process to identify and recommend social determinants of health measurement protocols. The PhenX Toolkit contains data collection protocols suitable for inclusion in a wide range of research studies. The recommended social determinants of health protocols were shared with the broader scientific community to invite review and feedback before being added to the Toolkit. RESULTS Nineteen social determinants of health protocols were released in the PhenX Toolkit (https://www.phenxtoolkit.org) in May 2020 to provide measures at the individual and structural levels for built and natural environments, structural racism, economic resources, employment status, occupational health and safety, education, environmental exposures, food environment, health and health care, and sociocultural community context. CONCLUSIONS Promoting the adoption of well-established social determinants of health protocols can enable consistent data collection and facilitate comparing and combining studies, with the potential to increase their scientific impact.
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Affiliation(s)
- Michelle C Krzyzanowski
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Cataia L Ives
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Nancy L Jones
- National Institute on Minority Health and Health Disparities, NIH, Bethesda, Maryland.
| | - Barbara Entwisle
- Department of Sociology, College of Arts and Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alicia Fernandez
- Division of General Internal Medicine, Department of Medicine, University of California San Francisco, San Francisco, Carolina
| | | | - William A Darity
- Sanford School of Public Policy, Duke University, Durham, North Carolina
| | - Mark Fossett
- Department of Sociology, College of Arts & Sciences, Texas A&M University, College Station, Texas
| | - Patrick L Remington
- Department of Population Health Sciences, University of Wisconsin-Madison College of Medicine and Public Health, Madison, Wisconsin
| | - Maile Taualii
- Center for Integrated Health Care Research, Hawaii Permanente Medical Group, Honolulu, Hawaii
| | - Consuelo H Wilkins
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eliseo J Pérez-Stable
- National Institute on Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Nishadi Rajapakse
- Center for Translation Research & Implementation Science, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Nancy Breen
- National Institute on Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Xinzhi Zhang
- Center for Translation Research & Implementation Science, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Deborah R Maiese
- Division for Research Services, RTI International, Research Triangle Park, North Carolina
| | - Tabitha P Hendershot
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Meisha Mandal
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Stephen Y Hwang
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Wayne Huggins
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Lauren Gridley
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Amanda Riley
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
| | - Erin M Ramos
- National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Carol M Hamilton
- GenOmics, Bioinformatics, and Translation Research Center, RTI International, Research Triangle Park, North Carolina
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AlAbdi L, Maddirevula S, Shamseldin HE, Khouj E, Helaby R, Hamid H, Almulhim A, Hashem MO, Abdulwahab F, Abouyousef O, Alqahtani M, Altuwaijri N, Jaafar A, Alshidi T, Alzahrani F, Alkuraya FS. Diagnostic implications of pitfalls in causal variant identification based on 4577 molecularly characterized families. Nat Commun 2023; 14:5269. [PMID: 37644014 PMCID: PMC10465531 DOI: 10.1038/s41467-023-40909-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Despite large sequencing and data sharing efforts, previously characterized pathogenic variants only account for a fraction of Mendelian disease patients, which highlights the need for accurate identification and interpretation of novel variants. In a large Mendelian cohort of 4577 molecularly characterized families, numerous scenarios in which variant identification and interpretation can be challenging are encountered. We describe categories of challenges that cover the phenotype (e.g. novel allelic disorders), pedigree structure (e.g. imprinting disorders masquerading as autosomal recessive phenotypes), positional mapping (e.g. double recombination events abrogating candidate autozygous intervals), gene (e.g. novel gene-disease assertion) and variant (e.g. complex compound inheritance). Overall, we estimate a probability of 34.3% for encountering at least one of these challenges. Importantly, our data show that by only addressing non-sequencing-based challenges, around 71% increase in the diagnostic yield can be expected. Indeed, by applying these lessons to a cohort of 314 cases with negative clinical exome or genome reports, we could identify the likely causal variant in 54.5%. Our work highlights the need to have a thorough approach to undiagnosed diseases by considering a wide range of challenges rather than a narrow focus on sequencing technologies. It is hoped that by sharing this experience, the yield of undiagnosed disease programs globally can be improved.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Norah Altuwaijri
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia.
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37
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Kurzlechner LM, Kishnani S, Chowdhury S, Atkins SL, Moya-Mendez ME, Parker LE, Rosamilia MB, Tadros HJ, Pace LA, Patel V, Chahal CAA, Landstrom AP. DiscoVari: A Web-Based Precision Medicine Tool for Predicting Variant Pathogenicity in Cardiomyopathy- and Channelopathy-Associated Genes. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:317-327. [PMID: 37409478 PMCID: PMC10527712 DOI: 10.1161/circgen.122.003911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/30/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND With genetic testing advancements, the burden of incidentally identified cardiac disease-associated gene variants is rising. These variants may carry a risk of sudden cardiac death, highlighting the need for accurate diagnostic interpretation. We sought to identify pathogenic hotspots in sudden cardiac death-associated genes using amino acid-level signal-to-noise (S:N) analysis and develop a web-based precision medicine tool, DiscoVari, to improve variant evaluation. METHODS The minor allele frequency of putatively pathogenic variants was derived from cohort-based cardiomyopathy and channelopathy studies in the literature. We normalized disease-associated minor allele frequencies to rare variants in an ostensibly healthy population (Genome Aggregation Database) to calculate amino acid-level S:N. Amino acids with S:N above the gene-specific threshold were defined as hotspots. DiscoVari was built using JavaScript ES6 and using open-source JavaScript library ReactJS, web development framework Next.js, and JavaScript runtime NodeJS. We validated the ability of DiscoVari to identify pathogenic variants using variants from ClinVar and individuals clinically evaluated at the Duke University Hospitals with cardiac genetic testing. RESULTS We developed DiscoVari as an internet-based tool for S:N-based variant hotspots. Upon validation, a higher proportion of ClinVar likely pathogenic/pathogenic variants localized to DiscoVari hotspots (43.1%) than likely benign/benign variants (17.8%; P<0.0001). Further, 75.3% of ClinVar variants reclassified to likely pathogenic/pathogenic were in hotspots, compared with 41.3% of those reclassified as variants of uncertain significance (P<0.0001) and 23.4% of those reclassified as likely benign/benign (P<0.0001). Of the clinical cohort variants, 73.1% of likely pathogenic/pathogenic were in hotspots, compared with 0.0% of likely benign/benign (P<0.01). CONCLUSIONS DiscoVari reliably identifies disease-susceptible amino acid residues to evaluate variants by searching amino acid-specific S:N ratios.
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Affiliation(s)
| | - Sujata Kishnani
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Shawon Chowdhury
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Sage L. Atkins
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Lauren E. Parker
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | | | - Hanna J. Tadros
- Dept of Pediatrics, Section of Pediatric Cardiology, Baylor College of Medicine, Houston, TX
| | - Leslie A. Pace
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
| | - Viraj Patel
- North West Thames Regional Genetics Service, St Mark’s Hospital, London, United Kingdom
| | - C. Anwar A. Chahal
- Center for Inherited Cardiovascular Diseases, WellSpan Health, Lancaster, PA
- Barts Heart Centre, St Bartholomew’s Hospital, Barts Health NHS Trust, London, United Kingdom
- Cardiac Electrophysiology, Cardiovascular Division, Hospital of the Univ of Pennsylvania, Philadelphia, PA
- Dept of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Andrew P. Landstrom
- Dept of Pediatrics, Division of Pediatric Cardiology, Durham, NC
- Dept of Cell Biology, Duke Univ School of Medicine, Durham, NC
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38
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The Impact of Genomic Variation on Function (IGVF) Consortium. ARXIV 2023:arXiv:2307.13708v1. [PMID: 37547663 PMCID: PMC10402186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could reveal novel mechanisms of human biology and uncover the basis of genetic predispositions to diseases, thereby guiding the development of new diagnostics and therapeutics. Yet, understanding how genomic variation alters genome function to influence phenotype has proven challenging. To unlock these insights, we need a systematic and comprehensive catalog of genome function and the molecular and cellular effects of genomic variants. Toward this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations, and predictive modeling to investigate the relationships among genomic variation, genome function, and phenotypes. Through systematic comparisons and benchmarking of experimental and computational methods, we aim to create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how both coding and noncoding variants may connect through gene regulatory and protein interaction networks. These experimental data, computational predictions, and accompanying standards and pipelines will be integrated into an open resource that will catalyze community efforts to explore genome function and the impact of genetic variation on human biology and disease across populations.
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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40
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Löhr JM. The FIRST-Dx Study Takes Steps Toward Personalized Cancer Therapy. JAMA Netw Open 2023; 6:e2323298. [PMID: 37459105 DOI: 10.1001/jamanetworkopen.2023.23298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Affiliation(s)
- J-Matthias Löhr
- Karolinska Institutet and Karolinska Comprehensive Cancer Center, Stockholm, Sweden
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41
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Blee AM, Gallagher KS, Kim HS, Kim M, Troll CR, D'Souza A, Park J, Neufer PD, Schärer OD, Chazin WJ. XPA tumor variants lead to defects in NER that sensitize cells to cisplatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547124. [PMID: 37425789 PMCID: PMC10327148 DOI: 10.1101/2023.06.29.547124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Nucleotide excision repair (NER) neutralizes treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of either of the NER genes Excision Repair Cross Complementation Group 1 and 2 ( ERCC1 and ERCC2 ) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of such mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER scaffold protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair activity on a UV-damaged substrate. In this study, we report in-depth analyses of a subset of the predicted NER-deficient XPA variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation resulting from tumor missense mutation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to further improve variant effect prediction efforts. More broadly, these findings suggest XPA tumor variants should be considered when predicting patient response to Pt-based chemotherapy. Significance A destabilized, readily degraded tumor variant identified in the NER scaffold protein XPA sensitizes cells to cisplatin, suggesting that XPA variants can be used to predict response to chemotherapy.
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Dolan DD, Cho MK, Lee SSJ. Innovating for a Just and Equitable Future in Genomic and Precision Medicine Research. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2023; 23:1-4. [PMID: 37353052 PMCID: PMC10339710 DOI: 10.1080/15265161.2023.2215201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Affiliation(s)
- Deanne Dunbar Dolan
- Center for ELSI Resources and Analysis (CERA), Stanford University School of Medicine, Stanford, CA, USA
| | - Mildred K. Cho
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandra Soo-Jin Lee
- Division of Ethics, Department of Medical Humanities & Ethics, Columbia University, New York, NY, USA
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Hopkins CE, McCormick K, Brock T, Wood M, Ruggiero S, Mcbride K, Kim C, Lawson JA, Helbig I, Bainbridge MN. Clinical variants in Caenorhabditis elegans expressing human STXBP1 reveal a novel class of pathogenic variants and classify variants of uncertain significance. GENETICS IN MEDICINE OPEN 2023; 1:100823. [PMID: 38827422 PMCID: PMC11141691 DOI: 10.1016/j.gimo.2023.100823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Purpose Modeling disease variants in animals is useful for drug discovery, understanding disease pathology, and classifying variants of uncertain significance (VUS) as pathogenic or benign. Methods Using Clustered Regularly Interspaced Short Palindromic Repeats, we performed a Whole-gene Humanized Animal Model procedure to replace the coding sequence of the animal model's unc-18 ortholog with the coding sequence for the human STXBP1 gene. Next, we used Clustered Regularly Interspaced Short Palindromic Repeats to introduce precise point variants in the Whole-gene Humanized Animal Model-humanized STXBP1 locus from 3 clinical categories (benign, pathogenic, and VUS). Twenty-six phenotypic features extracted from video recordings were used to train machine learning classifiers on 25 pathogenic and 32 benign variants. Results Using multiple models, we were able to obtain a diagnostic sensitivity near 0.9. Twenty-three VUS were also interrogated and 8 of 23 (34.8%) were observed to be functionally abnormal. Interestingly, unsupervised clustering identified 2 distinct subsets of known pathogenic variants with distinct phenotypic features; both p.Tyr75Cys and p.Arg406Cys cluster away from other variants and show an increase in swim speed compared with hSTXBP1 worms. This leads to the hypothesis that the mechanism of disease for these 2 variants may differ from most STXBP1-mutated patients and may account for some of the clinical heterogeneity observed in the patient population. Conclusion We have demonstrated that automated analysis of a small animal system is an effective, scalable, and fast way to understand functional consequences of variants in STXBP1 and identify variant-specific intensities of aberrant activity suggesting a genotype-to-phenotype correlation is likely to occur in human clinical variations of STXBP1.
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Affiliation(s)
| | | | | | | | - Sarah Ruggiero
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA
- University of Pennsylvania, Neuroscience Program, Philadelphia, PA
| | | | | | | | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, PA
- University of Pennsylvania, Neuroscience Program, Philadelphia, PA
| | - Matthew N. Bainbridge
- Codified Genomics, LLC, Houston, TX
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
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Afiaz A, Ivanov AA, Chamberlin J, Hanauer D, Savonen CL, Goldman MJ, Morgan M, Reich M, Getka A, Holmes A, Pati S, Knight D, Boutros PC, Bakas S, Caporaso JG, Del Fiol G, Hochheiser H, Haas B, Schloss PD, Eddy JA, Albrecht J, Fedorov A, Waldron L, Hoffman AM, Bradshaw RL, Leek JT, Wright C. Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? ARXIV 2023:arXiv:2306.03255v1. [PMID: 37332562 PMCID: PMC10274942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Software is vital for the advancement of biology and medicine. Through analysis of usage and impact metrics of software, developers can help determine user and community engagement. These metrics can be used to justify additional funding, encourage additional use, and identify unanticipated use cases. Such analyses can help define improvement areas and assist with managing project resources. However, there are challenges associated with assessing usage and impact, many of which vary widely depending on the type of software being evaluated. These challenges involve issues of distorted, exaggerated, understated, or misleading metrics, as well as ethical and security concerns. More attention to the nuances, challenges, and considerations involved in capturing impact across the diverse spectrum of biological software is needed. Furthermore, some tools may be especially beneficial to a small audience, yet may not have comparatively compelling metrics of high usage. Although some principles are generally applicable, there is not a single perfect metric or approach to effectively evaluate a software tool's impact, as this depends on aspects unique to each tool, how it is used, and how one wishes to evaluate engagement. We propose more broadly applicable guidelines (such as infrastructure that supports the usage of software and the collection of metrics about usage), as well as strategies for various types of software and resources. We also highlight outstanding issues in the field regarding how communities measure or evaluate software impact. To gain a deeper understanding of the issues hindering software evaluations, as well as to determine what appears to be helpful, we performed a survey of participants involved with scientific software projects for the Informatics Technology for Cancer Research (ITCR) program funded by the National Cancer Institute (NCI). We also investigated software among this scientific community and others to assess how often infrastructure that supports such evaluations is implemented and how this impacts rates of papers describing usage of the software. We find that although developers recognize the utility of analyzing data related to the impact or usage of their software, they struggle to find the time or funding to support such analyses. We also find that infrastructure such as social media presence, more in-depth documentation, the presence of software health metrics, and clear information on how to contact developers seem to be associated with increased usage rates. Our findings can help scientific software developers make the most out of the evaluations of their software so that they can more fully benefit from such assessments.
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Affiliation(s)
- Awan Afiaz
- Department of Biostatistics, University of Washington, Seattle, WA
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Andrey A. Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Emory University, Atlanta, GA
| | - John Chamberlin
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - David Hanauer
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI
| | - Candace L. Savonen
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
| | | | - Martin Morgan
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | - Aaron Holmes
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA
- Institute for Precision Health, University of California, Los Angeles, CA
- Department of Human Genetics, University of California, Los Angeles, CA
- Department of Urology, University of California, Los Angeles, CA
| | | | - Dan Knight
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA
- Institute for Precision Health, University of California, Los Angeles, CA
- Department of Human Genetics, University of California, Los Angeles, CA
- Department of Urology, University of California, Los Angeles, CA
| | - Paul C. Boutros
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA
- Institute for Precision Health, University of California, Los Angeles, CA
- Department of Human Genetics, University of California, Los Angeles, CA
- Department of Urology, University of California, Los Angeles, CA
| | | | - J. Gregory Caporaso
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ
| | - Guilherme Del Fiol
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Harry Hochheiser
- Department of Biomedical Informatics, University of Pittsburgh,Pittsburgh, PA
| | - Brian Haas
- Methods Development Laboratory, Broad Institute, Cambridge, MA
| | - Patrick D. Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | | | | | - Andrey Fedorov
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Levi Waldron
- Department of Epidemiology and Biostatistics, City University of New York Graduate School of Public Health and Health Policy, New York, NY
| | - Ava M. Hoffman
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Richard L. Bradshaw
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Jeffrey T. Leek
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Carrie Wright
- Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA
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Fife JD, Cassa CA. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet 2023; 110:940-949. [PMID: 37236177 PMCID: PMC10257006 DOI: 10.1016/j.ajhg.2023.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
While pathogenic variants can significantly increase disease risk, it is still challenging to estimate the clinical impact of rare missense variants more generally. Even in genes such as BRCA2 or PALB2, large cohort studies find no significant association between breast cancer and rare missense variants collectively. Here, we introduce REGatta, a method to estimate clinical risk from variants in smaller segments of individual genes. We first define these regions by using the density of pathogenic diagnostic reports and then calculate the relative risk in each region by using over 200,000 exome sequences in the UK Biobank. We apply this method in 13 genes with established roles across several monogenic disorders. In genes with no significant difference at the gene level, this approach significantly separates disease risk for individuals with rare missense variants at higher or lower risk (BRCA2 regional model OR = 1.46 [1.12, 1.79], p = 0.0036 vs. BRCA2 gene model OR = 0.96 [0.85, 1.07] p = 0.4171). We find high concordance between these regional risk estimates and high-throughput functional assays of variant impact. We compare our method with existing methods and the use of protein domains (Pfam) as regions and find REGatta better identifies individuals at elevated or reduced risk. These regions provide useful priors and are potentially useful for improving risk assessment for genes associated with monogenic diseases.
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Affiliation(s)
- James D Fife
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
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Martschenko DO, Wand H, Young JL, Wojcik GL. Including multiracial individuals is crucial for race, ethnicity and ancestry frameworks in genetics and genomics. Nat Genet 2023; 55:895-900. [PMID: 37202500 DOI: 10.1038/s41588-023-01394-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Daphne O Martschenko
- Center for Biomedical Ethics, Department of Pediatrics, Stanford Medicine, Stanford, CA, USA
| | - Hannah Wand
- Department of Cardiology, Stanford Medicine, Stanford, CA, USA
| | - Jennifer L Young
- Center for Biomedical Ethics, Department of Pediatrics, Stanford Medicine, Stanford, CA, USA
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Lin WS. Translating Genetic Discovery into a Mechanistic Understanding of Pediatric Movement Disorders: Lessons from Genetic Dystonias and Related Disorders. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200018. [PMID: 37288166 PMCID: PMC10242408 DOI: 10.1002/ggn2.202200018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Indexed: 06/09/2023]
Abstract
The era of next-generation sequencing has increased the pace of gene discovery in the field of pediatric movement disorders. Following the identification of novel disease-causing genes, several studies have aimed to link the molecular and clinical aspects of these disorders. This perspective presents the developing stories of several childhood-onset movement disorders, including paroxysmal kinesigenic dyskinesia, myoclonus-dystonia syndrome, and other monogenic dystonias. These stories illustrate how gene discovery helps focus the research efforts of scientists trying to understand the mechanisms of disease. The genetic diagnosis of these clinical syndromes also helps clarify the associated phenotypic spectra and aids the search for additional disease-causing genes. Collectively, the findings of previous studies have led to increased recognition of the role of the cerebellum in the physiology and pathophysiology of motor control-a common theme in many pediatric movement disorders. To fully exploit the genetic information garnered in the clinical and research arenas, it is crucial that corresponding multi-omics analyses and functional studies also be performed at scale. Hopefully, these integrated efforts will provide us with a more comprehensive understanding of the genetic and neurobiological bases of movement disorders in childhood.
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Affiliation(s)
- Wei-Sheng Lin
- Department of Pediatrics Taipei Veterans General Hospital Taipei 11217 Taiwan
- School of Medicine National Yang Ming Chiao Tung University Taipei 112304 Taiwan
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48
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Khan SS, Post WS, Guo X, Tan J, Zhu F, Bos D, Sedaghati-Khayat B, van Rooij J, Aday A, Allen NB, Bos MM, Uitterlinden AG, Budoff MJ, Lloyd-Jones DM, Mosley JD, Rotter JI, Greenland P, Kavousi M. Coronary Artery Calcium Score and Polygenic Risk Score for the Prediction of Coronary Heart Disease Events. JAMA 2023; 329:1768-1777. [PMID: 37219552 PMCID: PMC10208141 DOI: 10.1001/jama.2023.7575] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
Importance Coronary artery calcium score and polygenic risk score have each separately been proposed as novel markers to identify risk of coronary heart disease (CHD), but no prior studies have directly compared these markers in the same cohorts. Objective To evaluate change in CHD risk prediction when a coronary artery calcium score, a polygenic risk score, or both are added to a traditional risk factor-based model. Design, Setting, and Participants Two observational population-based studies involving individuals aged 45 years through 79 years of European ancestry and free of clinical CHD at baseline: the Multi-Ethnic Study of Atherosclerosis (MESA) study involved 1991 participants at 6 US centers and the Rotterdam Study (RS) involved 1217 in Rotterdam, the Netherlands. Exposure Traditional risk factors were used to calculate CHD risk (eg, pooled cohort equations [PCEs]), computed tomography for the coronary artery calcium score, and genotyped samples for a validated polygenic risk score. Main Outcomes and Measures Model discrimination, calibration, and net reclassification improvement (at the recommended risk threshold of 7.5%) for prediction of incident CHD events were assessed. Results The median age was 61 years in MESA and 67 years in RS. Both log (coronary artery calcium+1) and polygenic risk score were significantly associated with 10-year risk of incident CHD (hazards ratio per SD, 2.60; 95% CI, 2.08-3.26 and 1.43; 95% CI, 1.20-1.71, respectively), in MESA. The C statistic for the coronary artery calcium score was 0.76 (95% CI, 0.71-0.79) and for the polygenic risk score, 0.69 (95% CI, 0.63-0.71). The change in the C statistic when each was added to the PCEs was 0.09 (95% CI, 0.06-0.13) for the coronary artery calcium score, 0.02 (95% CI, 0.00-0.04) for the polygenic risk score, and 0.10 (95% CI, 0.07-0.14) for both. Overall categorical net reclassification improvement was significant when the coronary artery calcium score (0.19; 95% CI, 0.06-0.28) but was not significant when the polygenic risk score (0.04; 95% CI, -0.05 to 0.10) was added to the PCEs. Calibration of the PCEs and models with coronary artery calcium and/or polygenic risk scores was adequate (all χ2<20). Subgroup analysis stratified by the median age demonstrated similar findings. Similar findings were observed for 10-year risk in RS and in longer-term follow-up in MESA (median, 16.0 years). Conclusions and Relevance In 2 cohorts of middle-aged to older adults from the US and the Netherlands, the coronary artery calcium score had better discrimination than the polygenic risk score for risk prediction of CHD. In addition, the coronary artery calcium score but not the polygenic risk score significantly improved risk discrimination and risk reclassification for CHD when added to traditional risk factors.
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Affiliation(s)
- Sadiya S. Khan
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Wendy S. Post
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Fang Zhu
- Department of Epidemiology Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Daniel Bos
- Department of Epidemiology Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Bahar Sedaghati-Khayat
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Aaron Aday
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Norrina B. Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maxime M. Bos
- Department of Epidemiology Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Matthew J. Budoff
- Department of Medicine, Lundquist Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Donald M. Lloyd-Jones
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jonathan D. Mosley
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Philip Greenland
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Senior Editor, JAMA
| | - Maryam Kavousi
- Department of Epidemiology Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Sperling K, Scherb H, Neitzel H. Population monitoring of trisomy 21: problems and approaches. Mol Cytogenet 2023; 16:6. [PMID: 37183244 PMCID: PMC10183086 DOI: 10.1186/s13039-023-00637-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/02/2023] [Indexed: 05/16/2023] Open
Abstract
Trisomy 21 (Down syndrome) is the most common autosomal aneuploidy among newborns. About 90% result from meiotic nondisjunction during oogenesis, which occurs around conception, when also the most profound epigenetic modifications take place. Thus, maternal meiosis is an error prone process with an extreme sensitivity to endogenous factors, as exemplified by maternal age. This contrasts with the missing acceptance of causal exogenous factors. The proof of an environmental agent is a great challenge, both with respect to ascertainment bias, determination of time and dosage of exposure, as well as registration of the relevant individual health data affecting the birth prevalence. Based on a few exemplary epidemiological studies the feasibility of trisomy 21 monitoring is illustrated. In the nearer future the methodical premises will be clearly improved, both due to the establishment of electronic health registers and to the introduction of non-invasive prenatal tests. Down syndrome is a sentinel phenotype, presumably also with regard to other congenital anomalies. Thus, monitoring of trisomy 21 offers new chances for risk avoidance and preventive measures, but also for basic research concerning identification of relevant genomic variants involved in chromosomal nondisjunction.
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Affiliation(s)
- Karl Sperling
- Institute of Medical and Human Genetics, Charité-Universitaetsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Hagen Scherb
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Heidemarie Neitzel
- Institute of Medical and Human Genetics, Charité-Universitaetsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
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50
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Lo RS, Cromie GA, Tang M, Teng K, Owens K, Sirr A, Kutz JN, Morizono H, Caldovic L, Ah Mew N, Gropman A, Dudley AM. The functional impact of 1,570 individual amino acid substitutions in human OTC. Am J Hum Genet 2023; 110:863-879. [PMID: 37146589 PMCID: PMC10183466 DOI: 10.1016/j.ajhg.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/30/2023] [Indexed: 05/07/2023] Open
Abstract
Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Individuals with neonatal onset appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma, and death, outcomes ameliorated by rapid diagnosis and treatment. Here, we develop a high-throughput functional assay for human OTC and individually measure the impact of 1,570 variants, 84% of all SNV-accessible missense mutations. Comparison to existing clinical significance calls, demonstrated that our assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. This functional stratification allowed us to identify score ranges corresponding to clinically relevant levels of impairment of OTC activity. Examining the results of our assay in the context of protein structure further allowed us to identify a 13 amino acid domain, the SMG loop, whose function appears to be required in human cells but not in yeast. Finally, inclusion of our data as PS3 evidence under the current ACMG guidelines, in a pilot reclassification of 34 variants with complete loss of activity, would change the classification of 22 from variants of unknown significance to clinically actionable likely pathogenic variants. These results illustrate how large-scale functional assays are especially powerful when applied to rare genetic diseases.
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Affiliation(s)
- Russell S Lo
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Michelle Tang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Kevin Teng
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Katherine Owens
- Pacific Northwest Research Institute, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Amy Sirr
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Hiroki Morizono
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Nicholas Ah Mew
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Andrea Gropman
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA; Department of Neurology, Division of Neurogenetics and Neurodevelopmental Disabilities, Children's National Hospital, Washington, DC, USA; Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
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