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Onoja BA, Oguzie JU, George UE, Asoh KE, Ajayi P, Omofaye TF, Igeleke IO, Eromon P, Harouna S, Parker E, Adeniji AJ, Happi CT. Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria. Emerg Microbes Infect 2024; 13:2307511. [PMID: 38240324 PMCID: PMC10829817 DOI: 10.1080/22221751.2024.2307511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.
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Affiliation(s)
- Bernard Anyebe Onoja
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Judith Uche Oguzie
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem Etop George
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kaego Emmanuel Asoh
- Department of Medical Laboratory Science, College of Medicine, University of Ibadan, Ibadan, State Nigeria
| | - Philip Ajayi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | | | - Philomena Eromon
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Soumare Harouna
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
| | - Edyth Parker
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Christian T. Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- African Center of Excellence for Genomics of Infectious Diseases, Redeemer’s University, Ede, Osun State, Nigeria
- Department of Immunology and Infectious Diseases, Harvard T H Chan School of Public Health, Boston, MA, USA
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Gutierrez AM, Robinson JO, Smith HS, Desrosiers LR, Scollon SR, Canfield I, Hsu RL, Schneider NM, Parsons DW, Plon SE, Allen-Rhoades W, Majumder MA, Malek J, McGuire AL. Genomic sequencing research in pediatric cancer care: Decision-making, attitudes, and perceived utility among adolescents and young adults and their parents. Genet Med 2024:101168. [PMID: 38767058 DOI: 10.1016/j.gim.2024.101168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024] Open
Abstract
PURPOSE Professional guidelines recommend engaging adolescents and young adults (AYAs) in medical decision-making (DM), including whether to undergo genomic sequencing (GS). We explored DM around GS and attitudes after return of GS results among a diverse group of AYAs with cancer and their parents. METHODS We surveyed AYAs with cancer (n=75) and their parents (n=52) six months after receiving GS results through the Texas KidsCanSeq Study. We analyzed AYAs' DM role in GS research enrollment and their satisfaction with that role. We compared AYAs' and parents' self-reported understanding of, attitudes toward, and perceived utility of the AYAs' GS results. RESULTS Most AYAs reported equally sharing DM with their parents (55%) or leading DM (36%) about GS research. Compared to their cancer care DM role, 56% of AYAs reported the same level of involvement in GS research DM while 32% were more involved and 13% were less involved (p=0.011). AYAs were satisfied (99%) with their DM role regarding GS study participation. AYAs and parents had similar self-reported understanding of, attitudes toward, and perceived utility of the GS results. CONCLUSION Our results support engaging AYAs in DM about GS research and provide insights into AYAs' DM preferences and positive attitudes toward GS.
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Affiliation(s)
- Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX.
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Hadley S Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX; Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Lauren R Desrosiers
- Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Sarah R Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Isabel Canfield
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Rebecca L Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | | | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Cancer Center, Texas Children's Hospital, Houston, TX
| | | | - Mary A Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
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Vieira JIG, Braga LG, Chud TCS, Ferreira PH, Guimarães SEF, Martins MF, do Carmo Panetto JC, Machado MA, Silva DBDS, Bonafé CM, Magalhães AFB, da Silva MVGB, Verardo LL. Resequencing of Brazilian locally adapted cattle breeds revealed variants in candidate genes and transcription factors for meat fatty acid profile. J Anim Breed Genet 2024. [PMID: 38686591 DOI: 10.1111/jbg.12869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.
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Affiliation(s)
| | - Larissa Graciano Braga
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Lucas Lima Verardo
- Universidade Federal dos Vales Do Jequitinhonha e Mucuri, Diamantina, Minas Gerais, Brazil
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Smith HS, Rubanovich CK, Robinson JO, Levchenko AN, Classen SA, Malek J, Biesecker B, Brothers KB, Wilfond BS, Rini C, Knight SJ, McGuire AL, Bloss CS. Measuring perceived utility of genomic sequencing: Development and validation of the GENEtic Utility (GENE-U) scale for pediatric diagnostic testing. Genet Med 2024:101146. [PMID: 38676451 DOI: 10.1016/j.gim.2024.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
INTRODUCTION Measuring effects of genomic sequencing (GS) on patients and families is critical for translational research. We aimed to develop and validate an instrument to assess parents' perceived utility of pediatric diagnostic GS. METHODS Informed by a five-domain conceptual model, the study comprised five steps: (1) item writing, (2) cognitive testing, (3) pilot testing and item reduction, (4) psychometric testing, and (5) evaluation of construct validity. Parents of pediatric patients who had received results of clinically indicated GS participated in structured cognitive interviews and two rounds of surveys. After eliminating items based on theory and quantitative performance, we conducted an exploratory factor analysis and calculated Pearson correlations with related instruments. RESULTS We derived the 21-item Pediatric Diagnostic version of the GENEtic Utility (GENE-U) scale, which has a two-factor structure that includes an Informational Utility subscale (16 items, α = 0.91) and an Emotional Utility subscale (5 items, α = 0.71). Scores can be summed to calculate a Total scale score (α = 0.87). The Informational Utility subscale was strongly associated with empowerment and personal utility of GS, and the Emotional Utility subscale was moderately associated with psychosocial impact and depression and anxiety. DISCUSSION The Pediatric Diagnostic GENE-U scale demonstrated good psychometric performance in this initial evaluation and could be a useful tool for translational genomics researchers, warranting additional validation.
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Affiliation(s)
- Hadley Stevens Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School, Boston, MA; Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX.
| | - Caryn Kseniya Rubanovich
- San Diego State University/University of California San Diego Joint Doctoral Program in Clinical Psychology, San Diego, CA
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Ariel N Levchenko
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Sarah A Classen
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | | | - Kyle B Brothers
- Norton Children's Research Institute affiliated with the University of Louisville School of Medicine, Louisville, KY
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics and Palliative Care, Seattle Children's Research Institute and Hospital, Seattle, WA; Division of Bioethics and Palliative Care, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Sara J Knight
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Cinnamon S Bloss
- Herbert Wertheim School of Public Health, University of California San Diego, San Diego, CA
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Di L, Gu C, Salman S, Li Y. The complete genomic sequencing of a Klebsiella pneumoniae isolated from a patient suffering from urinary tract infection. Microbiol Resour Announc 2024; 13:e0125423. [PMID: 38509050 PMCID: PMC11008213 DOI: 10.1128/mra.01254-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/24/2024] [Indexed: 03/22/2024] Open
Abstract
The present study examines the genomic sequence of Klebsiella pneumoniae strain ACESH02121hy, which possesses a genome size of 5,281,767 bp. The strain was obtained from a patient's urine sample presenting symptoms associated with urinary tract infection.
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Affiliation(s)
- Lingfang Di
- Department of Clinical Laboratory, Tongxiang First People's Hospital, Tongxiang, Zhejiang, China
| | - Chunyan Gu
- Department of Hematology, Tongxiang First People's Hospital, Tongxiang, Zhejiang, China
| | - Sayyed Salman
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yafei Li
- Department of Clinical Laboratory, Tongxiang First People's Hospital, Tongxiang, Zhejiang, China
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Velarde CA, Hurtado U, Cardona Rios AF, Ortiz C, Betancur I. Genomic epidemiology of SARS-CoV-2 δ sublineages of the second wave of 2021 in Antioquia, Colombia. Biomedica 2024; 44:54-66. [PMID: 38648352 DOI: 10.7705/biomedica.6862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 02/09/2024] [Indexed: 04/25/2024]
Abstract
Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, ɣ, β, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation. Objective. To characterize the genetic diversity of the different SARS-CoV-2 δ sublineages in Antioquia and to describe its prevalence. Materials and methods. We collected sociodemographic information from 2,675 samples, and obtained 1,115 genomes from the GISAID database between July 12th, 2021, and January 18th, 2022. From the analyzed genomes, 515 were selected because of their high coverage values (>90%) to perform phylogenetic analysis and to infer allele frequencies of mutations of interest. Results. We characterized 24 sublineages. The most prevalent was AY.25. Mutations of interest as L452R, P681R, and P681H were identified in this sublineage, comprising a frequency close to 0.99. Conclusions. This study identified that the AY.25 sublineage has a transmission advantage compared to the other δ sublineages. This attribute may be related to the presence of the L452R and P681R mutations associated in other studies with higher evasion of the immune system and less efficacy of drugs against SARS-CoV-2.
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Affiliation(s)
- Cristian Arbey Velarde
- Laboratorio Departamental de Salud Pública de Antioquia, Secretaría Seccional de Salud y Protección Social de Antioquia, Medellín, Colombia
| | - Uriel Hurtado
- Corporación para Investigaciones Biológicas, Medellín, Colombia
| | | | - Celeny Ortiz
- Dirección de Salud Colectiva, Secretaria de Salud de Antioquia, Secretaría Seccional de Salud de Antioquia, Medellín, Colombia
| | - Idabely Betancur
- Laboratorio Departamental de Salud Pública de Antioquia, Secretaría Seccional de Salud y Protección Social de Antioquia, Medellín, Colombia
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Wilkinson H, McDonald J, McCarthy HS, Perry J, Wright K, Hulme C, Cool P. Using nanopore sequencing to identify bacterial infection in joint replacements: a preliminary study. Brief Funct Genomics 2024:elae008. [PMID: 38555497 DOI: 10.1093/bfgp/elae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
This project investigates if third-generation genomic sequencing can be used to identify the species of bacteria causing prosthetic joint infections (PJIs) at the time of revision surgery. Samples of prosthetic fluid were taken during revision surgery from patients with known PJIs. Samples from revision surgeries from non-infected patients acted as negative controls. Genomic sequencing was performed using the MinION device and the rapid sequencing kit from Oxford Nanopore Technologies. Bioinformatic analysis pipelines to identify bacteria included Basic Local Alignment Search Tool, Kraken2 and MinION Detection Software, and the results were compared with standard of care microbiological cultures. Furthermore, there was an attempt to predict antibiotic resistance using computational tools including ResFinder, AMRFinderPlus and Comprehensive Antibiotic Resistance Database. Bacteria identified using microbiological cultures were successfully identified using bioinformatic analysis pipelines. Nanopore sequencing and genomic classification could be completed in the time it takes to perform joint revision surgery (2-3 h). Genomic sequencing in this study was not able to predict antibiotic resistance in this time frame, this is thought to be due to a short-read length and low read depth. It can be concluded that genomic sequencing can be useful to identify bacterial species in infected joint replacements. However, further work is required to investigate if it can be used to predict antibiotic resistance within clinically relevant timeframes.
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Affiliation(s)
- Hollie Wilkinson
- Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
| | | | - Helen S McCarthy
- Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
| | - Jade Perry
- Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
| | - Karina Wright
- Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
| | - Charlotte Hulme
- Centre for Regenerative Medicine, School of Pharmacy and Bioengineering, Keele University, Keele, UK
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
- School of Medicine, Keele University, Keele, UK
| | - Paul Cool
- Oswestry Keele Orthopaedic Research Group (OsKOR), The Robert Jones and Agnes Hunt Orthopaedic Hospital Foundation Trust, Oswestry, UK
- School of Medicine, Keele University, Keele, UK
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Cornelis C, Tibben A, Brilstra E, Bolt I, van Summeren M, Knoers N, Bredenoord AL. Hope, but never expect? Comparing parents' pre- and post-disclosure attitudes toward return of results from diagnostic exome sequencing for their child. Mol Genet Genomic Med 2024; 12:e2341. [PMID: 38366804 PMCID: PMC10958177 DOI: 10.1002/mgg3.2341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Counseling for whole-exome sequencing (WES) could benefit from aligning parents' pre- and post-disclosure attitudes. A few studies have qualitatively compared parents' pre- and post-disclosure attitudes toward receiving WES results for their child in a diagnostic setting. This study explored these attitudes in the context of children with a developmental delay. METHODS Semi-structured interviews were conducted with parents (n = 27) of 16 children undergoing diagnostic WES in trio-analysis, both before and after receiving results. RESULTS Three key insights emerged. First, the distinction between hoping and expecting was relevant for shaping parents' experiences with receiving results related to the primary indication. Second, parents of young children whose development of autonomous capacities was uncertain sometimes found themselves in a situation resembling a Catch-22 when confronted with decisions about unsolicited findings (UFs): an important reason for consenting to WES was to gain a better picture of how the child might develop, but in order to make responsible choices about UFs, some ideas of their child's development is needed. Third, default opt-ins and opt-outs helped parents fathom new kinds of considerations for accepting or declining UFs in different categories, thereby aiding decision-making. CONCLUSION Results from this study are relevant for counseling and policy development.
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Affiliation(s)
- Candice Cornelis
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Medical Humanities, Julius CenterUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Aad Tibben
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Eva Brilstra
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Ineke Bolt
- Department of Medical Ethics, Philosophy and History of MedicineErasmus Medical CenterRotterdamThe Netherlands
| | - Marieke van Summeren
- Department of General PediatricsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine Knoers
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Centre GroningenGroningenThe Netherlands
| | - Annelien L. Bredenoord
- Department of Medical Humanities, Julius CenterUniversity Medical Center UtrechtUtrechtThe Netherlands
- Erasmus School of PhilosophyErasmus University RotterdamRotterdamThe Netherlands
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Bautista-Cruz A, Aquino-Bolaños T, Hernández-Canseco J, Quiñones-Aguilar EE. Cellulolytic Aerobic Bacteria Isolated from Agricultural and Forest Soils: An Overview. Biology (Basel) 2024; 13:102. [PMID: 38392320 PMCID: PMC10886624 DOI: 10.3390/biology13020102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
This review provides insights into cellulolytic bacteria present in global forest and agricultural soils over a period of 11 years. It delves into the study of soil-dwelling cellulolytic bacteria and the enzymes they produce, cellulases, which are crucial in both soil formation and the carbon cycle. Forests and agricultural activities are significant contributors to the production of lignocellulosic biomass. Forest ecosystems, which are key carbon sinks, contain 20-30% cellulose in their leaf litter. Concurrently, the agricultural sector generates approximately 998 million tons of lignocellulosic waste annually. Predominant genera include Bacillus, Pseudomonas, Stenotrophomonas, and Streptomyces in forests and Bacillus, Streptomyces, Pseudomonas, and Arthrobacter in agricultural soils. Selection of cellulolytic bacteria is based on their hydrolysis ability, using artificial cellulose media and dyes like Congo red or iodine for detection. Some studies also measure cellulolytic activity in vitro. Notably, bacterial cellulose hydrolysis capability may not align with their cellulolytic enzyme production. Enzymes such as GH1, GH3, GH5, GH6, GH8, GH9, GH10, GH12, GH26, GH44, GH45, GH48, GH51, GH74, GH124, and GH148 are crucial, particularly GH48 for crystalline cellulose degradation. Conversely, bacteria with GH5 and GH9 often fail to degrade crystalline cellulose. Accurate identification of cellulolytic bacteria necessitates comprehensive genomic analysis, supplemented by additional proteomic and transcriptomic techniques. Cellulases, known for degrading cellulose, are also significant in healthcare, food, textiles, bio-washing, bleaching, paper production, ink removal, and biotechnology, emphasizing the importance of discovering novel cellulolytic strains in soil.
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Affiliation(s)
- Angélica Bautista-Cruz
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Teodulfo Aquino-Bolaños
- Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Jessie Hernández-Canseco
- Doctoral Programme in Conservation and Use of Natural Resources, Instituto Politécnico Nacional, CIIDIR-Oaxaca, Hornos 1003, Santa Cruz Xoxocotlán 71230, Oaxaca, Mexico
| | - Evangelina Esmeralda Quiñones-Aguilar
- Laboratorio de Fitopatología de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C. Camino Arenero 1227, El Bajío del Arenal, Zapopan 45019, Jalisco, Mexico
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10
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Aekka A, Weisman AG, Papadakis J, Yerkes E, Baker J, Keswani M, Weinstein J, Finlayson C. Clinical utility of early rapid genome sequencing in the evaluation of patients with differences of sex development. Am J Med Genet A 2024; 194:351-357. [PMID: 37789729 DOI: 10.1002/ajmg.a.63377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/05/2023]
Abstract
Establishing an early and accurate genetic diagnosis among patients with differences of sex development (DSD) is crucial in guiding the complex medical and psychosocial care they require. Genetic testing routinely utilized in clinical practice for this population is predicated upon physical exam findings and biochemical and endocrine profiling. This approach, however, is inefficient and unstandardized. Many patients with DSD, particularly those with 46,XY DSD, never receive a molecular genetic diagnosis. Rapid genome sequencing (rGS) is gaining momentum as a first-tier diagnostic instrument in the evaluation of patients with DSD given its ability to provide greater diagnostic yield and timely results. We present the case of a patient with nonbinary genitalia and systemic findings for whom rGS identified a novel variant of the WT1 gene and resulted in a molecular diagnosis within two weeks of life. This timeframe of diagnosis for syndromic DSD is largely unprecedented at our institution. Rapid GS expedited mobilization of a multidisciplinary medical team; enabled early understanding of clinical trajectory; informed planning of medical and surgical interventions; and guided individualized psychosocial support provided to the family. This case highlights the potential of early rGS in transforming the evaluation and care of patients with DSD.
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Affiliation(s)
- Apoorva Aekka
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Allison Goetsch Weisman
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jaclyn Papadakis
- Department of Psychiatry and Behavioral Health, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Elizabeth Yerkes
- Division of Urology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Baker
- Division of Genetics, Genomics, and Metabolism, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mahima Keswani
- Division of Nephrology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joanna Weinstein
- Division of Hematology, Oncology, Neuro-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Courtney Finlayson
- Division of Endocrinology, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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11
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Lynch F, Best S, Gaff C, Downie L, Archibald AD, Gyngell C, Goranitis I, Peters R, Savulescu J, Lunke S, Stark Z, Vears DF. Australian Public Perspectives on Genomic Newborn Screening: Risks, Benefits, and Preferences for Implementation. Int J Neonatal Screen 2024; 10:6. [PMID: 38248635 PMCID: PMC10801595 DOI: 10.3390/ijns10010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Recent dramatic reductions in the timeframe in which genomic sequencing can deliver results means its application in time-sensitive screening programs such as newborn screening (NBS) is becoming a reality. As genomic NBS (gNBS) programs are developed around the world, there is an increasing need to address the ethical and social issues that such initiatives raise. This study therefore aimed to explore the Australian public's perspectives and values regarding key gNBS characteristics and preferences for service delivery. We recruited English-speaking members of the Australian public over 18 years of age via social media; 75 people aged 23-72 participated in 1 of 15 focus groups. Participants were generally supportive of introducing genomic sequencing into newborn screening, with several stating that the adoption of such revolutionary and beneficial technology was a moral obligation. Participants consistently highlighted receiving an early diagnosis as the leading benefit, which was frequently linked to the potential for early treatment and intervention, or access to other forms of assistance, such as peer support. Informing parents about the test during pregnancy was considered important. This study provides insights into the Australian public's views and preferences to inform the delivery of a gNBS program in the Australian context.
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Affiliation(s)
- Fiona Lynch
- Biomedical Ethics Research Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (F.L.); (C.G.); (J.S.)
- Melbourne Law School, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephanie Best
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Melbourne, VIC 3052, Australia;
- Australian Genomics, Melbourne, VIC 3052, Australia; (I.G.); (Z.S.)
- Department of Health Services Research, Peter MacCallum Cancer Centre, Melbourne, VIC 3052, Australia
| | - Clara Gaff
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (C.G.); (L.D.); (A.D.A.)
- Melbourne Genomics, Melbourne, VIC 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Lilian Downie
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (C.G.); (L.D.); (A.D.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Alison D. Archibald
- Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (C.G.); (L.D.); (A.D.A.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (F.L.); (C.G.); (J.S.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Ilias Goranitis
- Australian Genomics, Melbourne, VIC 3052, Australia; (I.G.); (Z.S.)
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3052, Australia;
| | - Riccarda Peters
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3052, Australia;
| | - Julian Savulescu
- Biomedical Ethics Research Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (F.L.); (C.G.); (J.S.)
- Melbourne Law School, The University of Melbourne, Melbourne, VIC 3052, Australia
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
- Department of Pathology, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Zornitza Stark
- Australian Genomics, Melbourne, VIC 3052, Australia; (I.G.); (Z.S.)
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia;
| | - Danya F. Vears
- Biomedical Ethics Research Group, Murdoch Children’s Research Institute, Parkville, VIC 3052, Australia; (F.L.); (C.G.); (J.S.)
- Melbourne Law School, The University of Melbourne, Melbourne, VIC 3052, Australia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3052, Australia
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, KU Leuven, 3000 Leuven, Belgium
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12
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Shinn LM, Mansharamani A, Baer DJ, Novotny JA, Charron CS, Khan NA, Zhu R, Holscher HD. Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials. J Nutr 2024; 154:271-283. [PMID: 37949114 DOI: 10.1016/j.tjnut.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/11/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus revealing the potential of using metagenomic data for developing objective biomarkers of food intake. OBJECTIVES As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine-learning approach to identify fecal KEGG (Kyoto encyclopedia of genes and genomes) Orthology (KO) categories as biomarkers that accurately classify food intake. METHODS Data were aggregated from 5 controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. Deoxyribonucleic acid from preintervention and postintervention fecal samples underwent shotgun genomic sequencing. After preprocessing, sequences were aligned and functionally annotated with Double Index AlignMent Of Next-generation sequencing Data v2.0.11.149 and MEtaGenome ANalyzer v6.12.2, respectively. After the count normalization, the log of the fold change ratio for resulting KOs between pre- and postintervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine-learning models examining potential biomarkers in both single-food and multi-food models. RESULTS We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups using a random forest model to classify food intake into each food group's respective treatment and control arms, respectively. The mixed-food random forest achieved 81% accuracy. CONCLUSIONS Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.
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Affiliation(s)
- Leila M Shinn
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Aditya Mansharamani
- Department of Computer Science, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David J Baer
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Janet A Novotny
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Craig S Charron
- USDA, Agricultural Research Service, Beltsville Human Nutrition Research Center, Beltsville, MD, United States
| | - Naiman A Khan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States; Department of Kinesiology and Community Health, University of Illinois, Urbana, IL, United States
| | - Ruoqing Zhu
- Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, United States; National Center for Supercomputing Applications, University of Illinois, Urbana, IL, United States.
| | - Hannah D Holscher
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States; Department of Kinesiology and Community Health, University of Illinois, Urbana, IL, United States; National Center for Supercomputing Applications, University of Illinois, Urbana, IL, United States; Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL, United States.
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13
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Plante MM, Kimbrough EO, Agarwal AK, Jiang L, Bourgeois K, Stamper GC, Stewart MW, Tun HW. Hyperviscosity Syndrome Induced Bilateral Visual and Auditory Impairment in Therapy Resistant Waldenström Macroglobulinemia with MYD88 and CXCR4 Mutations. J Blood Med 2023; 14:639-648. [PMID: 38116327 PMCID: PMC10729678 DOI: 10.2147/jbm.s424072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Hyperviscosity syndrome (HVS) is an emergent complication of Waldenström macroglobulinemia (WM) characterized by visual, neurologic, and rarely auditory impairment. We report a 69-year-old female with MYD88 and CXCR4-mutant WM who developed HVS resulting in bilateral blindness and deafness associated with neurologic manifestations including confusion, severe generalized weakness, and imbalance. Ophthalmologic evaluation revealed bilateral central retinal vein occlusion (CRVO), diffuse retinal hemorrhages, macular edema, and serous macular detachments (SMD). Magnetic resonance imaging of the brain showed bleeding in the inner ears. Management was challenging as her WM was resistant to systemic therapies including bendamustine + rituximab (BR) and rituximab + bortezomib + dexamethasone (RVD). Bruton's tyrosine kinase inhibitors could not be used initially due to ongoing lower gastrointestinal bleeding. She required five total sessions of plasma exchange and was finally initiated on zanubrutinib, achieving a partial response. She also received intravitreal bevacizumab with rapid resolution of the retinal hemorrhages but with little improvement of the SMD. She had partial restoration of her hearing in the right ear and only slight improvement in her bilateral visual deficits. The management of HVS in frail, elderly patients with therapy-resistant WM can be challenging. In these cases, plasma exchange is required until an effective systemic therapy can be safely instituted. Genomic profiling is important in the management of WM as it can predict treatment resistance and guide therapeutic decisions.
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Affiliation(s)
- Marie M Plante
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, USA
| | | | - Amit K Agarwal
- Department of Radiology, Mayo Clinic, Jacksonville, FL, USA
| | - Liuyan Jiang
- Department of Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - Kirk Bourgeois
- Department of Pathology, Mayo Clinic, Jacksonville, FL, USA
| | - Greta C Stamper
- Department of Otolaryngology and Audiology, Mayo Clinic, Jacksonville, FL, USA
| | | | - Han W Tun
- Division of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA
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Abstract
PURPOSE OF REVIEW There are thousands of different clinical genetic tests currently available. Genetic testing and its applications continue to change rapidly for multiple reasons. These reasons include technological advances, accruing evidence about the impact and effects of testing, and many complex financial and regulatory factors. RECENT FINDINGS This article considers a number of key issues and axes related to the current and future state of clinical genetic testing, including targeted versus broad testing, simple/Mendelian versus polygenic and multifactorial testing models, genetic testing for individuals with high suspicion of genetic conditions versus ascertainment through population screening, the rise of artificial intelligence in multiple aspects of the genetic testing process, and how developments such as rapid genetic testing and the growing availability of new therapies for genetic conditions may affect the field. SUMMARY Genetic testing is expanding and evolving, including into new clinical applications. Developments in the field of genetics will likely result in genetic testing becoming increasingly in the purview of a very broad range of clinicians, including general paediatricians as well as paediatric subspecialists.
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Affiliation(s)
- Benjamin D. Solomon
- Medical Genetics Branch, National Human Genome Research Institute, United States of America
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15
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Mandrell BN, Blake AK, Sharp KMH, Gattuso JS, McGee RB, Harrison L, Ouma A, Caples M, Johnson LM, Nichols KE. Parental Understanding of Their Child's Germline Genomic Testing: Intent of Disclosure to Their Child and Family. J Pers Med 2023; 13:1656. [PMID: 38138883 PMCID: PMC10744428 DOI: 10.3390/jpm13121656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Genomic testing is becoming increasingly common in the care of pediatric patients with cancer. Parental understanding of germline results and their intent and timing of results disclosure to their child and family may have significant implications on the family unit. The purpose of this study was to examine parental understanding of germline genomic results and plans for disclosure to their child and other relatives. Semi-structured interviews were conducted with 64 parents of children with cancer, approximately eight weeks after parents had received their child's results. Parents of children with negative results (n = 20), positive results (n = 15), or variants of uncertain significance (n = 29), were interviewed. Fifty-three parents (83%) correctly identified their child's results as negative, uncertain, or positive. Most parents had disclosed results to family members; however, only 11 parents (17%) acknowledged discussing results with their child. Most parents delayed disclosure due to the young age of their child at the time of testing. In summary, most parents appropriately described their child's germline genomic results, yet few discussed the results with their child due to age. Families should be followed with supportive counseling to assist parents in the timing and content of result disclosure to their children.
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Affiliation(s)
- Belinda N. Mandrell
- Division of Nursing Research, Department of Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.S.G.); (M.C.)
| | - Alise K. Blake
- Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.K.B.); (R.B.M.); (L.H.); (A.O.); (K.E.N.)
| | | | - Jami S. Gattuso
- Division of Nursing Research, Department of Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.S.G.); (M.C.)
| | - Rose B. McGee
- Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.K.B.); (R.B.M.); (L.H.); (A.O.); (K.E.N.)
| | - Lynn Harrison
- Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.K.B.); (R.B.M.); (L.H.); (A.O.); (K.E.N.)
| | - Annastasia Ouma
- Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.K.B.); (R.B.M.); (L.H.); (A.O.); (K.E.N.)
| | - Mary Caples
- Division of Nursing Research, Department of Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (J.S.G.); (M.C.)
| | - Liza-Marie Johnson
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA;
| | - Kim E. Nichols
- Division of Cancer Predisposition, Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (A.K.B.); (R.B.M.); (L.H.); (A.O.); (K.E.N.)
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16
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Paolino J, Dimitrov B, Winger BA, Sandoval-Perez A, Rangarajan AV, Ocasio-Martinez N, Tsai HK, Li Y, Robichaud AL, Khalid D, Hatton C, Gillani R, Polonen P, Dilig A, Gotti G, Kavanagh J, Adhav AA, Gow S, Tsai J, Li YD, Ebert BL, Van Allen EM, Bledsoe J, Kim AS, Tasian SK, Cooper SL, Cooper TM, Hijiya N, Sulis ML, Shukla NN, Magee JA, Mullighan CG, Burke MJ, Luskin MR, Mar BG, Jacobson MP, Harris MH, Stegmaier K, Place AE, Pikman Y. Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res 2023; 29:4613-4626. [PMID: 37725576 PMCID: PMC10872648 DOI: 10.1158/1078-0432.ccr-22-2562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/22/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. EXPERIMENTAL DESIGN We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia. RESULTS Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL. CONCLUSIONS Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Boris Dimitrov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | | | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Julia Kavanagh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Asmani A. Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sean Gow
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jonathan Tsai
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Yen Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jacob Bledsoe
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Sarah K. Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, and Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stacy L. Cooper
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Todd M. Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA
| | - Nobuko Hijiya
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, NY
| | - Maria Luisa Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav N. Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey A. Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, MO
| | | | - Michael J. Burke
- Medical College of Wisconsin, Children’s Hospital of Wisconsin, Milwaukee, WI
| | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
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Li J, Zhang D, Luo C, Li B, Zhang G. In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting. Environ Sci Technol 2023; 57:17087-17098. [PMID: 37823365 DOI: 10.1021/acs.est.3c04247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of 13C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.
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Affiliation(s)
- Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Dayi Zhang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130012, China
- College of New Energy and Environment, Jilin University, Changchun 130021, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bei Li
- State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, 130033 Changchun, China
- HOOKE Instruments Ltd., 130033 Changchun, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
- CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
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18
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Lutgring JD, Kent AG, Bowers JR, Jasso-Selles DE, Albrecht V, Stevens VA, Pfeiffer A, Barnes R, Engelthaler DM, Johnson JK, Gargis AS, Rasheed JK, Limbago BM, Elkins CA, Karlsson M, Halpin AL. Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators. Microb Genom 2023; 9. [PMID: 37987646 DOI: 10.1099/mgen.0.001119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community.
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Affiliation(s)
- Joseph D Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Daniel E Jasso-Selles
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Riley Barnes
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amy S Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of Science, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Smith HS, Bonkowski ES, Hickingbotham MR, Pereira S, May T, Guerrini CJ. Clinically Indicated Genomic Sequencing of Children in Foster Care: Legal and Ethical Issues. J Pediatr 2023; 262:113612. [PMID: 37468037 PMCID: PMC10792112 DOI: 10.1016/j.jpeds.2023.113612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/21/2023]
Abstract
There are approximately 400 000 children in foster care in the US, approximately one-half of whom have chronic health problems and approximately 10% of whom have complex healthcare needs. Given the increasing relevance of genomic sequencing to guide clinical care for children with rare, chronic, and undiagnosed conditions, it may be an important component of diagnostic evaluation for children in foster care. Clinically indicated genomic sequencing may provide information that has health implications for children in foster care, as well as for their biological parents and other relatives. Whether and how genomic sequencing results impact legal decision making and family court outcomes is not yet well-understood. We describe scenarios that highlight legal, ethical, and policy issues surrounding genomic sequencing for children in foster care using 3 cases adapted from real-world events. Together, these cases highlight important yet underexplored issues that arise when genomic information has legal relevance in family court and ethical implications for child and family well-being. As genomic sequencing becomes more routine for the general pediatric population, additional research is needed to better understand its impacts on children and other stakeholders within the foster care system.
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Affiliation(s)
- Hadley Stevens Smith
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA.
| | - Emily S Bonkowski
- St. Jude Children's Research Hospital, Memphis, TN; University of Washington Institute for Public Health Genetics, Seattle, WA
| | - Madison R Hickingbotham
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Thomas May
- Department of Medical Education and Clinical Sciences, Washington State University, Pullman, WA
| | - Christi J Guerrini
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
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20
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Gutierrez AM, Robinson JO, Raesz-Martinez R, Canfield I, Majumder MA, Scollon S, Desrosiers LR, Hsu RL, Allen-Rhoades W, Parsons DW, Plon SE, McGuire AL, Malek J. Views of Adolescents and Young Adults with Cancer and Their Oncologists Toward Patients' Participation in Genomic Research. J Adolesc Young Adult Oncol 2023; 12:773-781. [PMID: 36595372 PMCID: PMC10611971 DOI: 10.1089/jayao.2022.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Purpose: With increased use of genomic testing in cancer research and clinical care, it is important to understand the perspectives and decision-making preferences of adolescents and young adults (AYAs) with cancer and their treating oncologists. Methods: We conducted an interview substudy of the BASIC3 Study, which enrolled newly diagnosed cancer patients <18 years of age with assent. Of 32 young adults (YAs) with cancer who reached the age of majority (AOM; 18 years) while on study, 12 were successfully approached and all consented to study continuation at AOM. Of those, seven completed an interview. Patients' oncologists, who enrolled and participated in return of clinical genomic results, were also interviewed (n = 12). Interviews were transcribed, deidentified, and analyzed using thematic analysis. Results: YAs cited the possibility of helping others and advancing science as major reasons for their assent to initial study enrollment and their willingness to consent at AOM. YAs thought obtaining informed consent from research participants for study continuation at AOM was a good idea in case they changed their minds or wanted to make their own decisions, and to keep them aware of study activities. There was diversity in what YAs understood and learned from genomic testing: some recalled specific findings, while some remembered minimal information about their results. Oncologists varied in their assessment of adolescents' engagement with the study and understanding of their results. Conclusion: Given the different ways AYAs engage with genomic information, careful assessment of AYAs' diverse communication and decision-making preferences is needed to tailor interactions accordingly.
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Affiliation(s)
- Amanda M. Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O. Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robin Raesz-Martinez
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel Canfield
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Mary A. Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Sarah Scollon
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Lauren R. Desrosiers
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Rebecca L. Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Wendy Allen-Rhoades
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - D. Williams Parsons
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Sharon E. Plon
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Janet Malek
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
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21
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Lajmi A, Glinka F, Privman E. Optimizing ddRAD sequencing for population genomic studies with ddgRADer. Mol Ecol Resour 2023. [PMID: 37732396 DOI: 10.1111/1755-0998.13870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023]
Abstract
Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.
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Affiliation(s)
- Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Felix Glinka
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
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22
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Guo B, Knerr S, Kauffman TL, Mittendorf KF, Keast E, Gilmore MJ, Feigelson HS, Lynch FL, Muessig KR, Okuyama S, Zepp JM, Veenstra DL, Hsu L, Phipps AI, Lindström S, Leo MC, Goddard KAB, Wilfond BS, Devine B. Risk management actions following genetic testing in the Cancer Health Assessments Reaching Many (CHARM) Study: A prospective cohort study. Cancer Med 2023; 12:19112-19125. [PMID: 37644850 PMCID: PMC10557878 DOI: 10.1002/cam4.6485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Genetic testing can identify cancer risk early, enabling prevention and early detection. We describe use of risk management interventions following genetic testing in the Cancer Health Assessment Reaching Many (CHARM) study. CHARM assessed risk and provided genetic testing to low income, low literacy, and other underserved populations that historically face barriers to accessing cancer genetic services. METHODS CHARM was implemented in Kaiser Permanente Northwest (KPNW) and Denver Health (DH) between 2018 and 2020. We identified post-testing screening (mammography, breast MRI, colonoscopy) and surgical (mastectomy, oophorectomy) procedures using electronic health records. We examined utilization in participants who did and did not receive actionable risk management recommendations from study genetic counselors following national guidelines. RESULTS CHARM participants were followed for an average of 15.4 months (range: 0.4-27.8 months) after results disclosure. Less than 2% (11/680) received actionable risk management recommendations (i.e., could be completed in the initial years following testing) based on their test result. Among those who received actionable recommendations, risk management utilization was moderate (54.5%, 6/11 completed any procedure) and varied by procedure (mammogram: 0/3; MRI: 2/4; colonoscopy: 4/5; mastectomy: 1/5; oophorectomy: 0/3). Cancer screening and surgery procedures were rare in participants without actionable recommendations. CONCLUSION Though the number of participants who received actionable risk management recommendations was small, our results suggest that implementing CHARM's risk assessment and testing model increased access to evidence-based genetic services and provided opportunities for patients to engage in recommended preventive care, without encouraging risk management overuse.
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Affiliation(s)
- Boya Guo
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Sarah Knerr
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kathleen F. Mittendorf
- Vanderbilt‐Ingram Cancer CenterVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Erin Keast
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Marian J. Gilmore
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | | | - Frances L. Lynch
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Kristin R. Muessig
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Sonia Okuyama
- Division of Oncology, Denver Health and Hospital AuthorityDenverColoradoUSA
| | - Jamilyn M. Zepp
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - David L. Veenstra
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
| | - Li Hsu
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Amanda I. Phipps
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Sara Lindström
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Michael C. Leo
- Center for Health Research, Kaiser Permanente NorthwestPortlandOregonUSA
| | - Katrina A. B. Goddard
- Department of Translational and Applied GenomicsCenter for Health ResearchPortlandOregonUSA
| | - Benjamin S. Wilfond
- Treuman Katz Center for Pediatric BioethicsSeattle Children's Research InstituteSeattleWashingtonUSA
- Department of Pediatrics, Division of Bioethics and Palliative CareUniversity of WashingtonSeattleWashingtonUSA
| | - Beth Devine
- School of Public HealthUniversity of WashingtonSeattleWashingtonUSA
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, School of PharmacyUniversity of WashingtonSeattleWashingtonUSA
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23
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Meng W, Chen S, Huang L, Yang J, Zhang W, Zhong Z, Zhou Z, Liu H, Fu H, He T, Peng G. Isolation, characterization, and pathogenicity assessment of Corynebacterium pseudotuberculosis biovar equi strains from alpacas ( Vicugna pacos) in China. Front Microbiol 2023; 14:1206187. [PMID: 37465023 PMCID: PMC10350510 DOI: 10.3389/fmicb.2023.1206187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 06/15/2023] [Indexed: 07/20/2023] Open
Abstract
Corynebacterium pseudotuberculosis is a zoonotic pathogen that causes lymphadenitis in humans, livestock, and wildlife. In this study, C. pseudotuberculosis biovar equi strains were isolated from three alpacas. Antibiotic susceptibility tests and pathogenicity tests were also conducted. Moreover, one strain was sequenced using DNBSEQ and Oxford Nanopore technology. The three strains exhibited resistance to aztreonam, fosfomycin, and nitrofurantoin. The median lethal doses (LD50) of strains G1, S2 and BA3 in experimentally infected mice was 1.66 × 105 CFU, 3.78 × 105 CFU and 3.78 × 105 CFU, respectively. The sequencing of strain G1 resulted in the assembly of a chromosomal scaffold comprising 2,379,166 bp with a G + C content of 52.06%. Genome analysis of strain G1 revealed the presence of 48 virulence genes and 5 antibiotic resistance genes (ARGs). Comparative genomic analysis demonstrates a high degree of genetic similarity among C. pseudotuberculosis strains, in contrast to other Corynebacterium species, with a clear delineation between strains belonging to the two biovars (ovis and equi). The data of the present study contribute to a better understanding of the properties of C. pseudotuberculosis biovar equi strains and the potential risk they pose to alpacas and other livestock, as well as the necessity of ongoing surveillance and monitoring of infectious diseases in animals.
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Affiliation(s)
- Wanyu Meng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shanyu Chen
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Huang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinpeng Yang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenqing Zhang
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhijun Zhong
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ziyao Zhou
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haifeng Liu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hualin Fu
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tingmei He
- Sichuan Wolong National Natural Reserve Administration, Wenchuan, Sichuan, China
| | - Guangneng Peng
- The Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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24
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Vears DF, Savulescu J, Christodoulou J, Wall M, Newson AJ. Are We Ready for Whole Population Genomic Sequencing of Asymptomatic Newborns? Pharmgenomics Pers Med 2023; 16:681-691. [PMID: 37415831 PMCID: PMC10321326 DOI: 10.2147/pgpm.s376083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
The introduction of genomic sequencing technologies into routine newborn screening programs in some form is not only inevitable but also already occurring in some settings. The question is therefore not "if" but "when and how" genomic newborn screening (GNBS) should be implemented. In April 2022, the Centre for Ethics of Paediatric Genomics held a one-day symposium exploring ethical issues relating to the use of genomic sequencing in a range of clinical settings. This review article synthesises the panel discussion and presents both the potential benefits of wide-scale implementation of genomic newborn screening, as well as its practical and ethical issues, including obtaining appropriate consent, and health system implications. A more in-depth understanding of the barriers associated with implementing genomic newborn screening is critical to the success of GNBS programs, both from a practical perspective and also in order to maintain public trust in an important public health initiative.
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Affiliation(s)
- Danya F Vears
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Julian Savulescu
- Chen Su Lan Centennial Professor in Medical Ethics, Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Visiting Professorial Fellow in Biomedical Ethics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Distinguished Visiting Professor in Law, Melbourne University, Carlton, Victoria, Australia
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK
| | - John Christodoulou
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Service, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Ainsley J Newson
- Faculty of Medicine & Health, Sydney School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
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25
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Casauria S, Lewis S, Lynch F, Saffery R. Australian parental perceptions of genomic newborn screening for non-communicable diseases. Front Genet 2023; 14:1209762. [PMID: 37434950 PMCID: PMC10330815 DOI: 10.3389/fgene.2023.1209762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/15/2023] [Indexed: 07/13/2023] Open
Abstract
Background: Newborn bloodspot screening (NBS) programs have improved neonatal healthcare since the 1960s. Genomic sequencing now offers potential to generate polygenic risk score (PRS) that could be incorporated into NBS programs, shifting the focus from treatment to prevention of future noncommunicable disease (NCD). However, Australian parents' knowledge and attitudes regarding PRS for NBS is currently unknown. Methods: Parents with at least one Australian-born child under 18 years were invited via social media platforms to complete an online questionnaire aimed at examining parents' knowledge of NCDs, PRS, and precision medicine, their opinions on receiving PRS for their child, and considerations of early-intervention strategies to prevent the onset of disease. Results: Of 126 participants, 90.5% had heard the term "non-communicable disease or chronic condition," but only 31.8% and 34.4% were aware of the terms "polygenic risk score" and "precision medicine" respectively. A large proportion of participants said they would consider screening their newborn to receive a PRS for allergies (77.9%), asthma (81.0%), cancer (64.8%), cardiovascular disease (65.7%), mental illness (56.7%), obesity (49.5%), and type 2 diabetes (66.7%). Additionally, participants would primarily consider diet and exercise as interventions for specific NCDs. Discussion: The results from this study will inform future policy for genomic NBS, including expected rate of uptake and interventions that parents would consider employing to prevent the onset of disease.
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Affiliation(s)
- Sarah Casauria
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Sharon Lewis
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Fiona Lynch
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Richard Saffery
- Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
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26
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Daly R, Hetherington K, Hazell E, Wadling BR, Tyrrell V, Tucker KM, Marshall GM, Ziegler DS, Lau LMS, Trahair TN, O'Brien TA, Collins K, Gifford AJ, Haber M, Pinese M, Malkin D, Cowley MJ, Karpelowsky J, Drew D, Jacobs C, Wakefield CE. Precision Medicine Is Changing the Roles of Healthcare Professionals, Scientists, and Research Staff: Learnings from a Childhood Cancer Precision Medicine Trial. J Pers Med 2023; 13:1033. [PMID: 37511646 PMCID: PMC10381580 DOI: 10.3390/jpm13071033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Precision medicine programs aim to utilize novel technologies to identify personalized treatments for children with cancer. Delivering these programs requires interdisciplinary efforts, yet the many groups involved are understudied. This study explored the experiences of a broad range of professionals delivering Australia's first precision medicine trial for children with poor-prognosis cancer: the PRecISion Medicine for Children with Cancer (PRISM) national clinical trial of the Zero Childhood Cancer Program. We conducted semi-structured interviews with 85 PRISM professionals from eight professional groups, including oncologists, surgeons, clinical research associates, scientists, genetic professionals, pathologists, animal care technicians, and nurses. We analyzed interviews thematically. Professionals shared that precision medicine can add complexity to their role and result in less certain outcomes for families. Although many participants described experiencing a greater emotional impact from their work, most expressed very positive views about the impact of precision medicine on their profession and its future potential. Most reported navigating precision medicine without formal training. Each group described unique challenges involved in adapting to precision medicine in their profession. Addressing training gaps and meeting the specific needs of many professional groups involved in precision medicine will be essential to ensure the successful implementation of standard care.
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Affiliation(s)
- Rebecca Daly
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Kate Hetherington
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Emily Hazell
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bethany R Wadling
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Vanessa Tyrrell
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Katherine M Tucker
- Hereditary Cancer Centre, Department of Medical Oncology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
- Prince of Wales Clinical School, UNSW Sydney, Randwick, NSW 2031, Australia
| | - Glenn M Marshall
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - David S Ziegler
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Loretta M S Lau
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Toby N Trahair
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Tracey A O'Brien
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Kiri Collins
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Andrew J Gifford
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Michelle Haber
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Mark Pinese
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Mark J Cowley
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children's Cancer Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute, Darlinghurst, NSW 2010, Australia
| | - Jonathan Karpelowsky
- Department of Paediatric Surgery, Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Children's Cancer Research Unit, Kids Research Institute, Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Division of Child and Adolescent Health, University of Sydney, Sydney, NSW 2145, Australia
| | - Donna Drew
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Chris Jacobs
- Graduate School of Health, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Claire E Wakefield
- Discipline of Pediatrics and Child Health, School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2031, Australia
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Hessey S, Fessas P, Zaccaria S, Jamal-Hanjani M, Swanton C. Insights into the metastatic cascade through research autopsies. Trends Cancer 2023; 9:490-502. [PMID: 37059687 DOI: 10.1016/j.trecan.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 04/16/2023]
Abstract
Metastasis is a complex process and the leading cause of cancer-related death globally. Recent studies have demonstrated that genomic sequencing data from paired primary and metastatic tumours can be used to trace the evolutionary origins of cells responsible for metastasis. This approach has yielded new insights into the genomic alterations that engender metastatic potential, and the mechanisms by which cancer spreads. Given that the reliability of these approaches is contingent upon how representative the samples are of primary and metastatic tumour heterogeneity, we review insights from studies that have reconstructed the evolution of metastasis within the context of their cohorts and designs. We discuss the role of research autopsies in achieving the comprehensive sampling necessary to advance the current understanding of metastasis.
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Affiliation(s)
- Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Petros Fessas
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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28
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Cantelmi MC, Merola C, Averaimo D, Chiaverini A, Cito F, Cocco A, Di Teodoro G, De Angelis ME, Di Bernardo D, Auzino D, Petrini A. Identification of the Novel Streptococcus equi subsp. zooepidemicus Sequence Type 525 in Donkeys of Abruzzo Region, Italy. Pathogens 2023; 12:750. [PMID: 37375440 PMCID: PMC10305129 DOI: 10.3390/pathogens12060750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Streptococcus equi sub. zooepidemicus (SEZ) is described as a commensal bacterium of several animal species, including humans. Growing evidence supports the potential role of SEZ in the onset and progression of severe clinical manifestations of diseases in horses and other animals. In the present communication, we describe the diagnostic procedure applied to characterize the streptococcal infections caused by a novel SEZ sequence type (ST525) in donkeys raised on a farm in Abruzzo, Italy. The diagnostic process began with anamnesis and anatomopathological analysis, which revealed a severe bacterial suppurative bronchopneumonia associated with systemic vascular damage and haemorrhages. Then, SEZ infection was confirmed by applying an integrative diagnostic strategy that included standard bacterial isolation techniques, analytical tools for bacteria identification (MALDI-TOF MS), and molecular analysis (qPCR). Furthermore, the application of the whole-genome sequencing approach helped us to identify the bacterial strains and the virulence factors involved in animal diseases. The novel SEZ-ST525 was identified in two cases of the disease. This new sequence type was isolated from the lung, liver, and spleen in Case 1, and from retropharyngeal lymph nodes in Case 2. Moreover, the presence of the virulence gene mf2, a virulence factor carried by prophages in Streptococcus pyogenes, was also found for the first time in an SEZ strain. The results of the present study highlight the need to apply an integrated diagnostic approach for the identification and tracking of pathogenic strains of SEZ, shedding new light on the re-evaluation of these bacteria as a causative agent of disease in animals and humans.
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Affiliation(s)
- Maria Chiara Cantelmi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Carmine Merola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Daniela Averaimo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Francesca Cito
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Antonio Cocco
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Maria Elisabetta De Angelis
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | | | - Davide Auzino
- Freelance Veterinary Practitioner, 65019 Pescara, Italy; (D.D.B.); (D.A.)
| | - Antonio Petrini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
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Zhang J, Jiang R, Hong X, Wu H, Han X, Wu W. Metastatic insulinoma: exploration from clinicopathological signatures and genetic characteristics. Front Oncol 2023; 13:1109330. [PMID: 37251916 PMCID: PMC10213277 DOI: 10.3389/fonc.2023.1109330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Background Insulinoma is a rare type of pancreatic neuroendocrine tumor with low incidence and low-malignant features. While very few insulinomas present with malignant behaviours, such as lymph node and liver metastasis, only a few studies have focused on this field owing to the limitation of samples. Existing evidence suggests that metastatic insulinoma largely derive from non-functional pancreatic neuroendocrine tumor. However, we found a portion of metastatic insulinomas may derive from non-metastatic insulinomas and explored their clinicopathological signatures and genetic characteristics. Methods Four metastatic insulinoma patients with synchronous liver metastasis or lymph node metastasis at the Peking Union Medical College Hospital between October 2016 and December 2018 were enrolled, and whole exon and genome sequencing were performed on fresh frozen tissues and peripheral blood samples. Clinicopathological information and genomic sequencing results were collected and matched to explore the characteristics of the metastatic insulinomas. Results These four metastatic insulinoma patients underwent surgery or interventional therapy, and their blood glucose levels immediately increased and maintained within standard range after treatment. For these four patients, the proinsulin/insulin molar ratio <1 and primary tumors were all present as PDX1+, ARX-, and insulin+, which were similar to non-metastatic insulinomas. However, the liver metastasis showed PDX1+ and ARX+, insulin+. Meanwhile, genomic sequencing data showed no recurrently mutations and typical CNV patterns. However, one patient harboured the YY1 T372R mutation, a recurrently mutated gene in non-metastatic insulinomas. Conclusions A portion of metastatic insulinomas were largely derived from non-metastatic insulinomas in hormone secretion and ARX/PDX1 expression patterns. Meanwhile, the accumulation of ARX expression may be involved in the progression of metastatic insulinomas.
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Affiliation(s)
- Jingcheng Zhang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Rui Jiang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xiafei Hong
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Xianlin Han
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Wenming Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
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Arkell K, Gyngell C, Stark Z, Vears DF. Rapid Genomic Testing in Intensive Care: Health Professionals' Perspectives on Ethical Challenges. Children (Basel) 2023; 10:children10050824. [PMID: 37238372 DOI: 10.3390/children10050824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
Ultra-rapid genomic sequencing (urGS) is increasingly used in neonatal and pediatric intensive care settings (NICU/PICU), demonstrating high diagnostic and clinical utility. This study aimed to explore the perspectives of healthcare professionals (HPs) and the challenges raised by urGS, particularly when making treatment decisions. Four focus groups and two interviews were conducted with HPs who had experience using urGS in NICU/PICU. Inductive content analysis was used to analyze the data. Nineteen HPs participated overall (eight clinical geneticists, nine genetic counselors, and two intensivists). One challenging area of practice identified by HPs was setting realistic expectations for outcomes of urGS among HPs and families. HPs reported modifying pre-test counseling to include life-limiting diagnoses as a possible test outcome and felt concerned about the timing of the test and its impact on parent-child bonding. UrGS results of uncertain prognostic significance posed considerable challenges. Moral distress arose when families and HPs were misaligned regarding treatment goals following the urGS diagnosis. We identified areas of practice that remain ethically challenging for HPs using urGS in the NICU/PICU. HPs experiences of using urGS in the NICU/PICU could inform specialized training in withdrawal of treatment decision making for the genomics workforce.
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Affiliation(s)
- Katie Arkell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Melbourne Law School, The University of Melbourne, Carlton, VIC 3053, Australia
| | - Zornitza Stark
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Australian Genomics, Parkville, VIC 3052, Australia
| | - Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
- Melbourne Law School, The University of Melbourne, Carlton, VIC 3053, Australia
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Jones A. Molecular identification and mapping of mixed root samples to species and individuals. New Phytol 2023; 238:924-925. [PMID: 36906881 DOI: 10.1111/nph.18817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Andy Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, Panamá
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32
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de Souza Andrade A, Freitas EF, de Castro Barbosa E, Guimarães N, de Melo Iani FC, da Costa AVB, Bernardes AFL, Adelino TER, Ataide ACZ, Gregianini TS, Nunes JD, Stringari LL, Riediger IN, Fernandes SB, de Jesus R, Fonseca V, Caldas S. Potential use of high-resolution melting analyses for SARS-CoV-2 genomic surveillance. J Virol Methods 2023; 317:114742. [PMID: 37116586 PMCID: PMC10132831 DOI: 10.1016/j.jviromet.2023.114742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 04/30/2023]
Abstract
The pandemic caused by COVID-19 and the emergence of new variants of SARS-CoV-2 have generated clinical and epidemiological impacts on a global scale. The use of strategies for monitoring viral circulation and identifying mutations in genomic regions involved in host interaction are important measures to mitigate viral dissemination and reduce its likely complications on population health. In this context, the objective of this work was to explore the potential of high-resolution melting (HRM) analysis combined with one-step real-time reverse transcription PCR in a closed-tube system, as a fast and convenient method of screening for SARS-CoV-2 mutations with possible implications on host-pathogen interactions. The HRM analyses allowed the distinction of the Gamma, Zeta, Alpha, Delta, and Omicron variants against the predecessors (B.1.1.28, B.1.1.33) of occurrence in Brazil. It is concluded that the molecular tool standardized here has the potential to optimize the genomic surveillance of SARS-CoV-2, and could be adapted for genomic surveillance of other pathogens, due to its ability to detect, prior to sequencing, samples suggestive of new variants, selecting them more assertively and earlier for whole genome sequencing when compared to random screening.
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Affiliation(s)
- Adriana de Souza Andrade
- Serviço de Pesquisa em Doenças Infecciosas, Divisão de Ciência e Inovação, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Eduarda Fernandes Freitas
- Serviço de Pesquisa em Doenças Infecciosas, Divisão de Ciência e Inovação, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Emerson de Castro Barbosa
- Serviço de Pesquisa em Doenças Infecciosas, Divisão de Ciência e Inovação, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Natália Guimarães
- Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Felipe Campos de Melo Iani
- Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alana Vitor Barbosa da Costa
- Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - André Felipe Leal Bernardes
- Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Talita Emile Ribeiro Adelino
- Serviço de Virologia e Riquetsioses, Divisão de Epidemiologia e Controle de Doenças, Laboratório Central do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Ana Caroline Zampiroli Ataide
- Serviço de Pesquisa em Doenças Infecciosas, Divisão de Ciência e Inovação, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil
| | - Tatiana Schäffer Gregianini
- Laboratório de Influenza e outros Vírus Respiratórios, Laboratório de Biologia Molecular de Dengue, Febre Amarela, Zika e Chikungunya, Seção de Virologia. Laboratório Central do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jônathas Dias Nunes
- Laboratório Central Noel Nutels. Laboratório Central do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lorenzzo L Stringari
- Laboratório Central de Saúde Pública do Estado do Espírito Santo, Secretaria de Estado de Saúde do Espírito Santo, Vitória, ES, Brazil; Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Irina Nastassja Riediger
- Divisão dos Laboratórios de Epidemiologia e Controle de Doenças, Laboratório Central do Estado do Paraná, São José dos Pinhais, PR, Brazil
| | | | - Ronaldo de Jesus
- Coordenação-Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília, Distrito Federal, Brazil; Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | - Sérgio Caldas
- Serviço de Pesquisa em Doenças Infecciosas, Divisão de Ciência e Inovação, Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil.
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33
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Smith HS, Bonkowski ES, Hickingbotham MR, Deloge RB, Pereira S. Framing the Family: A Qualitative Exploration of Factors That Shape Family-Level Experience of Pediatric Genomic Sequencing. Children (Basel) 2023; 10:774. [PMID: 37238322 PMCID: PMC10217651 DOI: 10.3390/children10050774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023]
Abstract
Families of children with rare and undiagnosed conditions face many psychosocial and logistical challenges that may affect their approach to decisions about their child's care and their family's well-being. As genomic sequencing (GS) is increasingly incorporated into pediatric diagnostic workups, assessing the family-level characteristics that shape the experience of pediatric GS is crucial to understanding how families approach decision-making about the test and how they incorporate the results into their family life. We conducted semi-structured interviews with parents and other primary caregivers of pediatric patients who were evaluated for a suspected genetic condition and who were recommended to have GS (n = 20) or who had recently completed GS (n = 21). We analyzed qualitative data using multiple rounds of thematic analysis. We organized our thematic findings into three domains of factors that influence the family-level experience of GS: (1) family structure and dynamics; (2) parental identity, relationships, and philosophies; and (3) social and cultural differences. Participants conceptualized their child's family in various ways, ranging from nuclear biological family to support networks made up of friends and communities. Our findings can inform the design and interpretation of preference research to advance family-level value assessment of GS as well as genetic counseling for families.
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Affiliation(s)
- Hadley Stevens Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emily S. Bonkowski
- Institute for Public Health Genetics, University of Washington School of Public Health, Seattle, WA 98195, USA
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Madison R. Hickingbotham
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Raymond Belanger Deloge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
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Turco GM, Gupta A, Monteleone P, Kelly KM, Klein RD, Wiltsie L, Barth M. An institutional review of genomic sequencing in pediatric solid tumors. Pediatr Blood Cancer 2023; 70:e30324. [PMID: 37017066 DOI: 10.1002/pbc.30324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Although tumor genomic profiling has aided the advancement of targeted genetic therapy, its clinical integration remains a challenge in pediatric cancers due to lower mutation frequency and less available targeted drugs. There have been multiple novel studies examining molecular sequencing in pediatrics; however, many of these studies primarily utilized large-scale, genome-wide screening applications that limit applicable use due to the availability of testing. This study examined the institutional use of a targeted, clinically available approach to tumor genomic sequencing. METHODS A retrospective chart review was performed on pediatric patients with solid tumors who were managed at Roswell Park Comprehensive Cancer Center and underwent molecular testing of their tumor biopsy via OmniSeq from August 2016 to July 2021. Results were reviewed for mutations considered to be "actionable" by targeted therapy. Patients with actionable mutations were further examined to evaluate treatment course, receival of targeted therapy, and clinical outcomes. RESULTS We identified 64 pediatric patients consisting of 20 (31%) with CNS tumors and 44 (69%) with non-CNS tumors, ranging in age from 9 months to 21 years. Thirty-five total actionable mutations were identified amongst 27 patients (42%). Of these 27, 12 patients (44%) received at least 1 targeted drug against a respective actionable mutation, of which 6 patients (50%) achieved clinical benefit to therapy, including 1 complete response. CONCLUSIONS The use of a clinically focused and readily available targeted molecular sequencing panel identified actionable mutations at a comparable rate to the large-scale, less readily available sequencing panels utilized in other studies. Half of our patients who received targeted therapy achieved a complete response or clinical benefit from therapy. Although targeted therapy has a role in pediatric cancer treatment, many newer drugs require further research on their safety and efficacy.
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Affiliation(s)
- George M Turco
- Pediatric Hematology/Oncology Fellow, Duke University, Durham, North Carolina, USA
| | - Ajay Gupta
- Division of Pediatric Hematology/Oncology, Roswell Park Oishei Children's Cancer and Blood Disorders Program, Buffalo, New York, USA
| | - Philip Monteleone
- Division of Pediatric Hematology/Oncology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Kara M Kelly
- Division of Pediatric Hematology/Oncology, Roswell Park Oishei Children's Cancer and Blood Disorders Program, Buffalo, New York, USA
| | | | - Laura Wiltsie
- Division of Pediatric Hematology/Oncology, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Matthew Barth
- Division of Pediatric Hematology/Oncology, Roswell Park Oishei Children's Cancer and Blood Disorders Program, Buffalo, New York, USA
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35
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Campigotto A, Chris A, Orkin J, Lau L, Marshall C, Bitnun A, Buchan SA, MacDonald L, Thampi N, McCready J, Juni P, Parekh RS, Science M. Utility of SARS-CoV-2 Genomic Sequencing for Understanding Transmission and School Outbreaks. Pediatr Infect Dis J 2023; 42:324-331. [PMID: 36795555 PMCID: PMC9990487 DOI: 10.1097/inf.0000000000003834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2022] [Indexed: 02/17/2023]
Abstract
OBJECTIVE An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period. STUDY DESIGN School outbreaks were identified for sequencing by local public health units based on multiple cases without known epidemiological links. Cases of SARS-CoV-2 from students and staff from 4 school outbreaks in Ontario underwent WGS and phylogenetic analysis. The epidemiological clinical cohort data and genomic cluster data are described to help further characterize these outbreaks. RESULTS A total of 132 positive SARS-CoV-2 cases among students and staff from 4 school outbreaks were identified with 65 (49%) of cases able to be sequenced with high-quality genomic data. The 4 school outbreaks consisted of 53, 37, 21 and 21 positive cases; within each outbreak there were between 8 and 28 different clinical cohorts identified. Among the sequenced cases, between 3 and 7 genetic clusters, defined as different strains, were identified in each outbreak. We found genetically different viruses within several clinical cohorts. CONCLUSIONS WGS, together with public health investigation, is a useful tool to investigate SARS-CoV-2 transmission within schools. Its early use has the potential to better understand when transmission may have occurred, can aid in evaluating how well mitigation interventions are working and has the potential to reduce unnecessary school closures when multiple genetic clusters are identified.
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Affiliation(s)
- Aaron Campigotto
- From the Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children
- Department of Laboratory Medicine and Pathobiology, University of Toronto
| | | | | | - Lynette Lau
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine
| | - Christian Marshall
- Department of Laboratory Medicine and Pathobiology, University of Toronto
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine
| | - Ari Bitnun
- Department of Paediatrics
- Division of Infectious Diseases, The Hospital for Sick Children
| | - Sarah A Buchan
- Public Health Ontario
- Dalla Lana School of Public Health, University of Toronto
| | | | - Nisha Thampi
- Department of Paediatrics, Children’s Hospital of Eastern Ontario
| | - Janine McCready
- Division of Infectious Diseases, Department of Medicine, Michael Garron Hospital
| | - Peter Juni
- St. Michael’s Hospital, Applied Health Research Centre, Li Ka Shing Knowledge Institute, University of Toronto
| | - Rulan S Parekh
- Department of Medicine, Women’s College Hospital, Toronto, ON, Canada
| | - Michelle Science
- Division of Infectious Diseases, The Hospital for Sick Children
- Public Health Ontario
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36
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Brown RB. Biases in COVID-19 Case and Death Definitions: Potential Causes and Consequences. Disaster Med Public Health Prep 2022; 17:e313. [PMID: 36503702 PMCID: PMC9947039 DOI: 10.1017/dmp.2022.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This paper investigates three controversies involving potential causes and consequences of information bias in case and death definitions during the coronavirus disease (COVID-19) pandemic. First, evidence suggests China's surveillance data were biased and misinterpreted by the World Health Organization (WHO), prompting the WHO to advise nations to copy China's lockdowns. China appeared to use narrow diagnostic definitions that undercounted cases and deaths. Second, novel genomic data disseminated during the pandemic without adequate guidance from rigorous epidemiologic studies biased infection control policies in many countries. A novel genomic sequence of a virus is insufficient to declare new cases of a novel disease. Third, media reports of COVID-19 surveillance data in many nations appeared to be biased. Broadened surveillance definitions captured additional information, but unadjusted surveillance data disseminated to the public are not true cases and deaths. Recommendations include clarification of the proper use of diagnostic and surveillance case and death definitions to avoid information bias.
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Affiliation(s)
- Ronald B. Brown
- School of Public Health Sciences, University of Waterloo, Waterloo, ON, Canada
- Corresponding author: Ronald B. Brown,
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37
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Jiang XF, Zhang BM, Du FQ, Guo JN, Wang D, Li YE, Deng SH, Cui BB, Liu YL. Exploring biomarkers for prognosis and neoadjuvant chemosensitivity in rectal cancer: Multi-omics and ctDNA sequencing collaboration. Front Immunol 2022; 13:1013828. [PMID: 36569844 PMCID: PMC9780298 DOI: 10.3389/fimmu.2022.1013828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction This study aimed to identified the key genes and sequencing metrics for predicting prognosis and efficacy of neoadjuvant chemotherapy (nCT) in rectal cancer (RC) based on genomic DNA sequencing in samples with different origin and multi-omics association database. Methods We collected 16 RC patients and obtained DNA sequencing data from cancer tissues and plasma cell-free DNA before and after nCT. Various gene variations were analyzed, including single nucleotide variants (SNV), copy number variation (CNV), tumor mutation burden (TMB), copy number instability (CNI) and mutant-allele tumor heterogeneity (MATH). We also identified genes by which CNV level can differentiate the response to nCT. The Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database were used to further evaluate the specific role of therapeutic relevant genes and screen out the key genes in multi-omics levels. After the intersection of the screened genes from differential expression analysis, survival analysis and principal components analysis dimensionality reduction cluster analysis, the key genes were finally identified. Results The genes CNV level of principal component genes in baseline blood and cancer tissues could significantly distinguish the two groups of patients. The CNV of HSP90AA1, EGFR, SRC, MTOR, etc. were relatively gained in the better group compared with the poor group in baseline blood. The CNI and TMB was significantly different between the two groups. The increased expression of HSP90AA1, EGFR, and SRC was associated with increased sensitivity to multiple chemotherapeutic drugs. The nCT predictive score obtained by therapeutic relevant genes could be a potential prognostic indicator, and the combination with TMB could further refine prognostic prediction for patients. After a series of analysis in multi-omics association database, EGFR and HSP90AA1 with significant differences in multiple aspects were identified as the key predictive genes related to prognosis and the sensitivity of nCT. Discussion This work revealed that effective combined application and analysis in multi-omics data are critical to search for predictive biomarkers. The key genes EGFR and HSP90AA1 could serve as an effective biomarker to predict prognose and neoadjuvant chemosensitivity.
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Affiliation(s)
- Xiu-Feng Jiang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bo-Miao Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Fen-Qi Du
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jun-Nan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dan Wang
- Department of Neurology, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, China
| | - Yi-En Li
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shen-Hui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
| | - Yan-Long Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China,*Correspondence: Bin-Bin Cui, ; Yan-Long Liu,
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38
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Zhang J, Shen J, Cong Q, Martin G, Grishin NV. Genomic analysis reveals a new genus of Firetip skippers (Lepidoptera: Hesperiidae: Pyrrhopyginae). Trop Lepid Res 2022; 32:73-78. [PMID: 36386254 PMCID: PMC9648695 DOI: 10.5281/zenodo.7246139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We obtained whole genome shotgun sequence reads for a number of Firetip skippers (subfamily Pyrrhopyginae), including all known species from the genera Yanguna Watson, 1893 and Gunayan Mielke, 2002 and representative species of Pyrrhopyge Hübner, [1819]. Phylogenetic analysis of their protein-coding regions unexpectedly revealed that Yanguna tetricus Bell, 1931 was not monophyletic with the other species of Yanguna (type species Pyrrhopyga spatiosa Hewitson, 1870). Instead, Y. tetricus formed a phylogenetic lineage as ancient as other three genera in its clade (Pyrrhopyge, Yanguna and Gunayan) that rapidly diversified from their ancestor. Therefore a new genus, Guyanna Grishin, gen. n. (type species Yanguna tetricus), is proposed for this lineage. The specimen that we sequenced was the Y. tetricus holotype in the Natural History Museum, London, leaving no doubt that we are dealing with this species. Genomic sequencing and comparison of specimens from museum collections offers a powerful strategy to reveal unforeseen phylogenetic relationships, and sequencing of primary types ensures that the conclusions are accurate in terms of nomenclature.
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Affiliation(s)
- Jing Zhang
- 1. Departments of Biophysics, Biochemistry
| | | | - Qian Cong
- 2. Eugene McDermott Center For Human Growth & Development, University of Texas Southwestern Medical Center
| | - Geoff Martin
- 3. Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Nick V Grishin
- 1. Departments of Biophysics, Biochemistry
- 4. Howard Hughes Medical Institute and 5323 Harry Hines Blvd, Dallas, TX, USA 75390-9050
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39
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Gordon LG, Elliott TM, Bennett C, Hollway G, Waddell N, Vadlamudi L. Early cost-utility analysis of genetically guided therapy for patients with drug-resistant epilepsy. Epilepsia 2022; 63:3111-3121. [PMID: 36082520 DOI: 10.1111/epi.17408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Existing gene panels were developed to understand the etiology of epilepsy, and further benefits will arise from an effective pharmacogenomics panel for personalizing therapy and achieving seizure control. Our study assessed the cost-effectiveness of a pharmacogenomics panel for patients with drug-resistant epilepsy, compared with usual care. METHODS A cost-utility analysis was employed using a discrete event simulation model. The microsimulation model aggregated the costs and benefits of genetically guided treatment versus usual care for 5000 simulated patients. The 10-year model combined data from various sources including genomic databases on prevalence of variants, population-level pharmaceutical claims on antiseizure medications, published long-term therapy retention rates, patient-level cost data, and systematic reviews. Incremental cost per quality-adjusted life-year (QALY) gained was computed. Deterministic and probabilistic sensitivity analyses were undertaken to address uncertainty in model parameters. RESULTS The mean cost of the genetically guided treatment option was AU$98 199 compared with AU$95 386 for usual care. Corresponding mean QALYs were 4.67 compared with 4.28 for genetically guided and usual care strategies, respectively. The incremental cost per QALY gained was AU$7381. In probabilistic sensitivity analyses, the incremental cost per QALY gained was AU$6321 (95% uncertainty interval = AU$3604-AU$9621), with a 100% likelihood of being cost-effective in the Australian health care system. The most influential drivers of the findings were the monthly health care costs associated with reduced seizures, costs when seizures continued, and the quality-of-life estimates under genetically guided and usual care strategies. SIGNIFICANCE This early economic evaluation of a pharmacogenomics panel to guide treatment for drug-resistant epilepsy could potentially be cost-effective in the Australian health care system. Clinical trial evidence is necessary to confirm these findings.
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Affiliation(s)
- Louisa G Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Nursing and Cancer and Palliative Care Outcomes Centre, Queensland University of Technology, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Thomas M Elliott
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Carmen Bennett
- University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Georgina Hollway
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,genomiQa, Brisbane, Queensland, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,genomiQa, Brisbane, Queensland, Australia
| | - Lata Vadlamudi
- University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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40
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Cao M, Notini L, Ayres S, Vears DF. Australian healthcare professionals' perspectives on the ethical and practical issues associated with genomic newborn screening. J Genet Couns 2022; 32:376-386. [PMID: 36245433 DOI: 10.1002/jgc4.1645] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/20/2022] [Accepted: 09/24/2022] [Indexed: 11/08/2022]
Abstract
Newborn bloodspot screening (NBS) is a successful public health initiative that seeks to identify serious, treatable medical conditions. The increasing use of genomic sequencing (GS) in a wide range of medical settings has reignited the discussion on whether GS can and should be integrated into NBS. Yet, the perspectives of healthcare professionals (HCPs) in Australia on the ethical and practical issues associated with the implementation of genomic newborn screening (GNBS) are underexplored. To address this, we conducted semi-structured interviews with 16 Australian HCPs with clinical or policy experience in NBS and/or GS to explore their perspectives on the ethical, social, and practical issues raised by integrating GS into NBS. Interviews were analyzed using inductive content analysis. When asked whether GS should be incorporated into NBS, HCPs did not feel it was currently appropriate but there was a strong consensus it may be implemented within the next decade. However, HCPs had differing perspectives on what conditions should be included and how to best handle the volume of data generated from GNBS. Our findings have important implications for determining at what point and how genomics can be integrated into NBS. The differing views expressed amongst HCPs suggest that further research is needed to explore the reasons behind this. Importantly, our participants highlighted a potential role for genetic counselors in the implementation of GNBS on a larger scale by developing educational resources to facilitate obtaining informed consent and return of results.
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Affiliation(s)
- Michelle Cao
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Lauren Notini
- Melbourne Law School, University of Melbourne, Carlton, Melbourne, Australia.,Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Samantha Ayres
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Danya F Vears
- Melbourne Law School, University of Melbourne, Carlton, Melbourne, Australia.,Biomedical Ethics Research Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
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41
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Safiee AWM, Mohd Ali MR, Zoqratt MZHM, Siew TH, Chuan CW, Huey LL, Fauzi MH, Besari AM, Yean Yean C, Ismail N. Putative Pathogenic Genes of Leptospira interrogans and Leptospira weilii Isolated from Patients with Acute Febrile Illness. Trop Med Infect Dis 2022; 7:tropicalmed7100284. [PMID: 36288025 PMCID: PMC9610858 DOI: 10.3390/tropicalmed7100284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Leptospirosis is an important worldwide tropical disease caused by pathogenic Leptospira spp. The determination of virulence genes is important, as it influences patients' clinical manifestations and clinical outcomes. This case report focused on detecting the pathogenic genes of Leptospira in association with the clinical manifestations of patients at the Hospital Universiti Sains Malaysia, Malaysia, who presented with acute febrile illness. Two cases were found and, to the best of our knowledge, these were the first two cases in Malaysia in which patients presented with febrile illness were associated with successful Leptospira isolation from clinical samples. Both clinical isolates were identified by 16S rRNA sequencing as Leptospira weilii and Leptospira interrogans, respectively, and they were classified as pathogenic Leptospira by the presence of different pathogenic genes, based on a polymerase chain reaction (PCR) amplification of targeted genes. This report emphasizes that different infecting Leptospira species and the presence of different virulence factors cause a slight difference in clinical manifestations and laboratory findings of leptospirosis. Genomic sequencing and annotation revealed the detection of classical leptospiral virulence factor genes that were otherwise missed using PCR for detection of Leptospira weilii genome B208.
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Affiliation(s)
- Amira Wahida Mohamad Safiee
- Microbiology Transfusion Unit, Department of Transfusion Medicine, Hospital Queen Elizabeth II, Lorong Bersatu Off Jalan Damai, Kota Kinabalu 88300, Sabah, Malaysia
| | - Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research, National Institutes of Health (NIH) Complex, Setia Alam, Shah Alam 40170, Selangor, Malaysia
| | | | - Tan Hock Siew
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Selangor, Malaysia
| | - Chua Wei Chuan
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Lee Lih Huey
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Mohd Hashairi Fauzi
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Emergency Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Alwi Muhd Besari
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Medicine, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nabilah Ismail
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Correspondence:
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42
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Maljkovic Berry I, Conte MA. Intrahost SARS-CoV-2 k-mer Identification Method (iSKIM) for Rapid Detection of Mutations of Concern Reveals Emergence of Global Mutation Patterns. Viruses 2022; 14:2128. [PMID: 36298683 PMCID: PMC9609618 DOI: 10.3390/v14102128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022] Open
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Montgomery Blair High School, Silver Spring, MD 20901, USA
| | - Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Christian K. Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Matthew A. Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
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43
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Thommana A, Shakya M, Gandhi J, Fung CK, Chain PSG, Berry IM, Conte MA. Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns. bioRxiv 2022:2022.08.16.504117. [PMID: 36032969 PMCID: PMC9413717 DOI: 10.1101/2022.08.16.504117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite unprecedented global sequencing and surveillance of SARS-CoV-2, timely identification of the emergence and spread of novel variants of concern (VoCs) remains a challenge. Several million raw genome sequencing runs are now publicly available. We sought to survey these datasets for intrahost variation to study emerging mutations of concern. We developed iSKIM ("intrahost SARS-CoV-2 k-mer identification method") to relatively quickly and efficiently screen the many SARS-CoV-2 datasets to identify intrahost mutations belonging to lineages of concern. Certain mutations surged in frequency as intrahost minor variants just prior to, or while lineages of concern arose. The Spike N501Y change common to several VoCs was found as a minor variant in 834 samples as early as October 2020. This coincides with the timing of the first detected samples with this mutation in the Alpha/B.1.1.7 and Beta/B.1.351 lineages. Using iSKIM, we also found that Spike L452R was detected as an intrahost minor variant as early as September 2020, prior to the observed rise of the Epsilon/B.1.429/B.1.427 lineages in late 2020. iSKIM rapidly screens for mutations of interest in raw data, prior to genome assembly, and can be used to detect increases in intrahost variants, potentially providing an early indication of novel variant spread.
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Affiliation(s)
- Ashley Thommana
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Montgomery Blair High School, Silver Spring, MD, USA
| | - Migun Shakya
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Jaykumar Gandhi
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Christian K Fung
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Patrick S G Chain
- Los Alamos National Laboratory, Biosecurity and Public Health Group, Bioscience Division, Los Alamos, NM, USA
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew A Conte
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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44
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Minear MA, Phillips MN, Kau A, Parisi MA. Newborn screening research sponsored by the NIH: From diagnostic paradigms to precision therapeutics. Am J Med Genet C Semin Med Genet 2022; 190:138-152. [PMID: 36102292 PMCID: PMC10328555 DOI: 10.1002/ajmg.c.31997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/21/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Newborn screening (NBS) is a successful public health initiative that effectively identifies pre-symptomatic neonates so that treatment can be initiated before the onset of irreversible morbidity and mortality. Legislation passed in 2008 has supported a system of state screening programs, educational resources, and an evidence-based review process to add conditions to a recommended universal newborn screening panel (RUSP). The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, has promoted NBS research to advance legislative goals by supporting research that will uncover fundamental mechanisms of disease, develop treatments for NBS disorders, and promote pilot studies to test implementation of new conditions. NICHD's partnerships with other federal agencies have contributed to activities that support nominations of new conditions to the RUSP. The NIH's Newborn Sequencing In Genomic Medicine and Public Health (NSIGHT) initiative funded research projects that considered how genomic sequencing could be integrated into NBS and its ethical ramifications. Recently, the workshop, "Gene Targeted Therapies: Early Diagnosis and Equitable Delivery," has explored the possibility of expanding NBS to include genetic diagnosis and precision, gene-based therapies. Although hurdles remain to realize such a vision, broad engagement of multiple stakeholders is essential to advance genomic medicine within NBS.
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Affiliation(s)
- Mollie A. Minear
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Megan N. Phillips
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Present address: Allen Institute for Brain Science, Seattle, WA, USA
| | - Alice Kau
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Melissa A. Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
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Frontiers Production Office. Erratum: Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka. Front Microbiol 2022; 13:898684. [PMID: 35479638 PMCID: PMC9038216 DOI: 10.3389/fmicb.2022.898684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2021.722838.].
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Nelson KN, Talarico S, Poonja S, McDaniel CJ, Cilnis M, Chang AH, Raz K, Noboa WS, Cowan L, Shaw T, Posey J, Silk BJ. Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission. Front Public Health 2022; 9:790544. [PMID: 35096744 PMCID: PMC8793027 DOI: 10.3389/fpubh.2021.790544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters. Existence of few genomic differences between Mtb isolates might indicate TB cases are the result of recent transmission. However, the variable and sometimes long duration of latent infection, combined with uncertainty in the Mtb mutation rate during latency, can complicate interpretation of WGS results. To estimate the association between infection duration and single nucleotide polymorphism (SNP) accumulation in the Mtb genome, we first analyzed pairwise SNP differences among TB cases from Los Angeles County, California, with strong epidemiologic links. We found that SNP distance alone was insufficient for concluding that cases are linked through recent transmission. Second, we describe a well-characterized cluster of TB cases in California to illustrate the role of genomic data in conclusions regarding recent transmission. Longer presumed latent periods were inconsistently associated with larger SNP differences. Our analyses suggest that WGS alone cannot be used to definitively determine that a case is attributable to recent transmission. Methods for integrating clinical, epidemiologic, and genomic data can guide conclusions regarding the likelihood of recent transmission, providing local public health practitioners with better tools for monitoring and investigating TB transmission.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Sarah Talarico
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Shameer Poonja
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Clinton J McDaniel
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Martin Cilnis
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Alicia H Chang
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Kala Raz
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Wendy S Noboa
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Lauren Cowan
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tambi Shaw
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
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Armstrong B, Christensen KD, Genetti CA, Parad RB, Robinson JO, Blout Zawatsky CL, Zettler B, Beggs AH, Holm IA, Green RC, McGuire AL, Smith HS, Pereira S. Parental Attitudes Toward Standard Newborn Screening and Newborn Genomic Sequencing: Findings From the BabySeq Study. Front Genet 2022; 13:867371. [PMID: 35571041 PMCID: PMC9091188 DOI: 10.3389/fgene.2022.867371] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/31/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: With increasing utility and decreasing cost of genomic sequencing, augmentation of standard newborn screening (NBS) programs with newborn genomic sequencing (nGS) has been proposed. Before nGS can be integrated into newborn screening, parents' perspectives must be better understood. Objective: Using data from surveys administered to parents of healthy newborns who were enrolled in the BabySeq Project, a randomized clinical trial of nGS alongside NBS, this paper reports parents' attitudes regarding population-based NBS and nGS assessed 3 months after results disclosure. Methods: Parental attitudes regarding whether all newborns should receive, and whether informed consent should be required for, NBS and nGS, as well as whether nGS should be mandated were assessed using 5-point scales from strongly disagree (=1) to strongly agree (=5). Parents' interest in receiving types of results from nGS was assessed on a 5-point scale from not at all interested (=1) to very interested (=5). Survey responses were analyzed using Fisher's exact tests, paired t-tests, and repeated measures ANOVA. Results: At 3 months post-disclosure, 248 parents of 174 healthy newborns submitted a survey. Support for every newborn receiving standard NBS (mean 4.67) was higher than that for every newborn receiving nGS (mean 3.60; p < 0.001). Support for required informed consent for NBS (mean 3.44) was lower than that for nGS (mean 4.27, p < 0.001). Parents' attitudes toward NBS and nGS were not significantly associated with self-reported political orientation. If hypothetically receiving nGS outside of the BabySeq Project, most parents reported being very interested in receiving information on their baby's risk of developing a disease in childhood that can be prevented, treated, or cured (86.8%) and their risk of developing a disease during adulthood that can be prevented, treated, or cured (84.6%). Discussion: Parents' opinions are crucial to inform design and delivery of public health programs, as the success of the program hinges on parents' trust and participation. To accommodate parents' preferences without affecting the current high participation rates in NBS, an optional add-on consent to nGS in addition to NBS may be a feasible approach. Trial Registration ClinicalTrials.gov Identifier: NCT02422511.
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Affiliation(s)
- Brittan Armstrong
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Kurt D. Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
| | - Richard B. Parad
- Harvard Medical School, Boston, MA, United States
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jill Oliver Robinson
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Carrie L. Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Medical and Population Genetics, The Broad Institute, Cambridge, MA, United States
- Ariadne Labs, Boston, MA, United States
- The MGH Institute of Health Professions, Boston, MA, United States
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Alan H. Beggs
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Robert C. Green
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Ariadne Labs, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Amy L. McGuire
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Hadley Stevens Smith
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Stacey Pereira
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
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Fissel JA, Mestas J, Chen PY, Flores-Vazquez J, Truong TT, Bootwalla M, Maglinte DT, Gai X, Dien Bard J. Implementation of a Streamlined SARS-CoV-2 Whole-Genome Sequencing Assay for Expeditious Surveillance during the Emergence of the Omicron Variant. J Clin Microbiol 2022; 60:e0256921. [PMID: 35317603 DOI: 10.1128/jcm.02569-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Powell SN, Byfield G, Bennetone A, Frantz AM, Harrison LK, James-Crook ER, Osborne H, Owens TH, Shaw JL, O’Daniel J, Milko LV. Parental Guidance Suggested: Engaging Parents as Partners in Research Studies of Genomic Screening for a Pediatric Population. Front Genet 2022; 13:867030. [PMID: 35401676 PMCID: PMC8990237 DOI: 10.3389/fgene.2022.867030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Recent advances in genomic sequencing and genomic medicine are reshaping the landscape of clinical care. As a screening modality, genetic sequencing has the potential to dramatically expand the clinical utility of newborn screening (NBS), though significant barriers remain regarding ethical, legal, and social implications (ELSI) and technical and evidentiary challenges. Stakeholder-informed implementation research is poised to grapple with many of these barriers, and parents are crucial stakeholders in this process. We describe the formation and activities of a Community Research Board (CRB) composed of parents with diverse backgrounds assembled to participate in an ongoing research partnership with genomic and public health researchers at the University of North Carolina. The mission of the CRB is to provide insight into parental perspectives regarding the prospect of adding genomic sequencing to NBS and collaboratively develop strategies to ensure its equitable uptake. We describe how these contributions can improve the accessibility of research and recruitment methods and promote trust and inclusivity within diverse communities to maximize the societal benefit of population genomic screening in healthy children.
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Affiliation(s)
- Sabrina N. Powell
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Grace Byfield
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Annabelle M. Frantz
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Langston K. Harrison
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | | | - Heather Osborne
- Community Research Board Member, Mooresville, NC, United States
| | | | | | - Julianne O’Daniel
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Laura V. Milko
- Program for Precision Medicine in Health Care, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Laura V. Milko,
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Lin J, Duchêne D, Carøe C, Smith O, Ciucani MM, Niemann J, Richmond D, Greenwood AD, MacPhee R, Zhang G, Gopalakrishnan S, Gilbert MTP. Probing the genomic limits of de-extinction in the Christmas Island rat. Curr Biol 2022:S0960-9822(22)00249-4. [PMID: 35271794 DOI: 10.1016/j.cub.2022.02.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022]
Abstract
Three principal methods are under discussion as possible pathways to “true” de-extinction; i.e., back-breeding, cloning, and genetic engineering.1,2 Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.3, 4, 5 We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species. Evolutionary divergence limits the completeness of extinct species genomes The extinct Christmas Island rat was re-sequenced to ca. 60× coverage Nevertheless, 4.85% of the Norway brown rat genome remains absent after mapping Absences are not random; immune response and olfaction are excessively affected
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