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Chen D. Ethical frameworks of informed consent in the age of pediatric precision medicine. CAMBRIDGE PRISMS. PRECISION MEDICINE 2024; 2:e6. [PMID: 38774589 PMCID: PMC11106543 DOI: 10.1017/pcm.2024.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024]
Abstract
Precision medicine is an emergent medical paradigm that uses information technology to inform the use of targeted therapies and treatments. One of the first steps of precision medicine involves acquiring the patient's informed consent to protect their rights to autonomous medical decision-making. In pediatrics, there exists mixed recommendations and guidelines of consent-related practices designed to safeguard pediatric patient interests while protecting their autonomy. Here, we provide a high-level, clinical primer of (1) ethical informed consent frameworks widely used in clinical practice and (2) promising modern adaptations to improve informed consent practices in pediatric precision medicine. Given the rapid scientific advances and adoption of precision medicine, we highlight the dual need to both consider the clinical implementation of consent in pediatric precision medicine workflows as well as build rapport with pediatric patients and their substitute decision-makers working alongside interdisciplinary health teams.
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Affiliation(s)
- David Chen
- Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
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Zampoli M, Sykes J, Verstraete J, Cheng SY, Morrow B, Pepper MS, Stewart C, Zar HJ, Stephenson AL. Global disparities in cystic fibrosis outcomes prior to CFTR modulators: A CF registries cohort study in South Africa and Canada. J Cyst Fibros 2024; 23:334-340. [PMID: 37704465 DOI: 10.1016/j.jcf.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/01/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Outcomes of cystic fibrosis (CF) differ between low-middle income and high-income countries, but comparative data are lacking. We compared South African (SA) and Canadian CF outcomes to explore what disparities existed prior to access of CFTR modulators in Canada. METHODS A cross-sectional study of SA and Canadian CF registries data for period 1 January to 31 December 2018. CF registry data were harmonised between countries to compare lung function and nutrition outcomes. Poor nutrition was defined as BMIz-score < -1 in children and < 18.5 kg/m2 in adults. Standardised mean difference (SMD) >10 was considered significant. RESULTS After excluding Canadians on CFTR modulators and lung transplant recipients, data on 4049 Canadian and 446 SA people was analysed. Compared to Canada, people in SA were younger (median age 15.8 years vs. 24.1 years: SMD 52) with fewer males (47.8% vs 54.2%; SMD 12.5) and White (70.9% vs. 93.3%; SMD 61.3). Class I-III CFTR mutation frequency was similar in SA (n = 384, 86.1%) and Canada (n = 3426, 84.9%). After adjusting for age, gender, diagnosis age, genotype, P.aeruginosa infection and pulmonary treatments, FEV1pp was 8.9% lower (95% CI 6.3% to 11.4%) and poor nutrition 1.7-fold more common (OR 1.70; 95% CI 1.19-2.41) in SA compared to Canada. CONCLUSION Lung function and nutrition was significantly lower in SA compared to Canada. Global disparities in CF outcomes between high and low-middle income countries are likely to widen as CFTR modulators are rapidly scaled up in only high-income countries.
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Affiliation(s)
- Marco Zampoli
- Department of Paediatrics and Child Health, University of Cape Town, South Africa; South African MRC Unit for Child and Adolescent Health, University of Cape Town, South Africa.
| | - Jenna Sykes
- Department of Respirology, Adult Cystic Fibrosis Program, St. Michael's Hospital, University of Toronto, Toronto, Canada
| | - Janine Verstraete
- Department of Paediatrics and Child Health, University of Cape Town, South Africa
| | | | - Brenda Morrow
- Department of Paediatrics and Child Health, University of Cape Town, South Africa
| | - Michael S Pepper
- Department of Immunology, Institute for Cellular and Molecular Medicine, SAMRC Extramural Unit for Stem Cell Research and Therapy, University of Pretoria, South Africa
| | - Cheryl Stewart
- Department of Basic Medical Sciences, The University of the West Indies, Mona, Jamaica
| | - Heather J Zar
- Department of Paediatrics and Child Health, University of Cape Town, South Africa; South African MRC Unit for Child and Adolescent Health, University of Cape Town, South Africa
| | - Anne L Stephenson
- Department of Respirology, Adult Cystic Fibrosis Program, St. Michael's Hospital, University of Toronto, Toronto, Canada
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Cystic fibrosis in low and middle-income countries (LMIC): A view from four different regions of the world. Paediatr Respir Rev 2021; 38:37-44. [PMID: 32826173 DOI: 10.1016/j.prrv.2020.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/23/2023]
Abstract
Cystic fibrosis (CF) has been shown to affect people all over the world. While life expectancy for people with CF has increased substantially, CF is still associated with death in infants and young children in many regions, particularly in low and middle-income countries (LMIC). These countries face significant challenges to promote CF diagnosis and improvements to CF care due to financial constraints and a significant burden of other diseases. In this review, we describe the status of CF diagnosis and care in different LMIC settings, from four different parts of the world (Brazil, South Africa, Israel and India). We highlight challenges and opportunities for CF practitioners in LMIC to improve CF care and outcomes. While early CF diagnosis is the key to optimising outcomes, newborn screening may not be feasible for countries with lower CF incidence and higher birth rates, such as India or South Africa. CF therapies and care in LMIC need to be adapted to available resources of these countries. Collaboration initiatives of the global CF community with LMIC may improve CF care in these countries. Most individuals with CF in LMIC are not benefiting from CFTR modulator treatments due to the prohibitive cost of these drugs.
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Next-Generation Sequencing for Molecular Diagnosis of Cystic Fibrosis in a Brazilian Cohort. DISEASE MARKERS 2021; 2021:9812074. [PMID: 33613790 PMCID: PMC7878085 DOI: 10.1155/2021/9812074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/23/2020] [Accepted: 01/27/2021] [Indexed: 12/05/2022]
Abstract
Cystic fibrosis (CF), an autosomal recessive genetic disease, is recognized as one of the most prevalent diseases in Caucasian populations. Epidemiological data show that the incidence of CF varies between countries and ethnic groups in the same region. CF occurs due to pathogenic variants in the gene encoding cystic fibrosis transmembrane conductance regulator (CFTR), located on chromosome 7q31.2. To date, more than 2,000 variants have been registered in the CFTR database. The study of these variants leads to the diagnosis and the possibility of a specific treatment for each patient through precision medicine. In this study, complete screening of CFTR was performed through next-generation sequencing (NGS) to gain insight into the variants circulating in the population of Rio de Janeiro and to provide patient access to treatment through genotype-specific therapies. Samples from 93 patients with an inconclusive molecular diagnosis were subjected to full-length screening of CFTR using an Illumina NGS HiSeq platform. Among these patients, 46 had two pathogenic variants, whereas 12 had only one CFTR variant. Twenty-four variants were not part of our routine screening. Of these 24 variants, V938Gfs∗37 had not been described in the CF databases previously. This research achieved a molecular diagnosis of the patients with CF and identification of possible molecular candidates for genotype-specific treatments.
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da Silva Filho LVRF, Maróstica PJC, Athanazio RA, Reis FJC, Damaceno N, Paes AT, Hira AY, Schlesinger D, Kok F, Amaral MD. Extensive CFTR sequencing through NGS in Brazilian individuals with cystic fibrosis: unravelling regional discrepancies in the country. J Cyst Fibros 2020; 20:473-484. [PMID: 32819855 DOI: 10.1016/j.jcf.2020.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The Brazilian population has a tri-hybrid composition with a high degree of ethnic admixture. We hypothesized that Brazilian individuals with CF from different Brazilian regions have a specific distribution of CFTR variants. METHODS Individuals with CF with data available in the Patient Registry and without an established genotype were submitted to CFTR sequencing by Next Generation Sequencing (NGS) methodology, and results were anonymously incorporated to the Registry Database. Genotyping results were expressed as 'positive', 'inconclusive' or 'negative'. Logistic regression models were performed to investigate the association between demographic/clinical variables and genotyping results. Mediation analysis was conducted to estimate direct and indirect effects of Brazilian region on a binary positive genotyping response. RESULTS In October 2017, data from 4,654 individuals with CF were available, and 3,104(66.7%) of them had a genotyping result. A total of 236 variants (114 new variants) were identified, with F508del identified in 46% of the alleles tested. Genotyping revealed 2,002(64.5%) individuals positive, 757(24.4%) inconclusive and 345(11.1%) negative. Distribution of genotype categories was markedly different across Brazilian Regions, with greater proportions of negative individuals in the North (45%) and Northeast (26%) regions. Newborn screening (CF-NBS) and age at diagnosis were identified as mediators of the effect of Brazilian region on a positive genotyping result. CONCLUSIONS This large initiative of CFTR genotyping showed significant regional discrepancies in Brazil, probably related to socio-economic conditions, lack of adequate CF-NBS and poor access to reliable sweat testing. These results may be useful to indicate Regions where CF care demands more attention.
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Affiliation(s)
- Luiz Vicente Ribeiro Ferreira da Silva Filho
- Pediatric Pulmonology Unit, Instituto da Criança do Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil; Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil.
| | - Paulo José Cauduro Maróstica
- Pediatric Pulmonology Department, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rodrigo Abensur Athanazio
- Pulmonary Division - Heart Institute (InCor) - Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Francisco José Caldeira Reis
- Pediatric Pulmonology Department, Hospital Infantil João Paulo II - Rede FHEMIG, Belo Horizonte, Minas Gerais, Brazil
| | - Neiva Damaceno
- Pediatric Pumonology Department, Santa Casa de São Paulo, São Paulo, São Paulo, Brazil
| | - Angela Tavares Paes
- Faculdade Israelita de Ciências da Saúde Albert Einstein (FICSAE), São Paulo, São Paulo, Brazil
| | - Adilson Yuuji Hira
- Laboratório de Sistemas Integráveis (LSI), Escola Politécnica da USP, São Paulo, São Paulo, Brazil
| | | | | | - Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal
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Cystic Fibrosis: A Simple and Customized Strategy for Genetic Screening Able to Detect Over 90% of Identified Mutated Alleles in Brazilian Newborns. Mol Diagn Ther 2020; 24:315-325. [PMID: 32185651 DOI: 10.1007/s40291-020-00456-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION The incorporation of molecular genetic testing into cystic fibrosis (CF) screening programs increases the specificity of the diagnostic strategy and has the potential to decrease the rate of false- positive results. In this sense, our objective was to develop a genotyping assay that could detect 25 pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with high sensitivity and that could be incorporated into the routine of newborn screening, complementing the current existing protocol used in our public health institution. METHODS A mini-sequencing assay was standardized using single-base extension in a previously genotyped control sample. This strategy was validated in a Brazilian cohort of CF patients by Sanger sequencing. RESULTS The inclusion of the 25 variants in the current newborn screening program increased the identification rates of two alleles from 33 to 52.43% in CF patients. This new approach was able to detect a total of 37 variants, which represents 93.01% of all mutated alleles described in the last CF Brazilian Register. CONCLUSIONS Mini-sequencing for the simultaneous detection of 25 CFTR gene variants improves the screening of Brazilian newborns and decreases the number of inconclusive cases. This method uses minimal hands-on time and is suited for rapid screening, which reduces sample processing costs.
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Martínez-Hernández A, Larrosa J, Barajas-Olmos F, García-Ortíz H, Mendoza-Caamal EC, Contreras-Cubas C, Mirzaeicheshmeh E, Lezana JL, Orozco L. Next-generation sequencing for identifying a novel/de novo pathogenic variant in a Mexican patient with cystic fibrosis: a case report. BMC Med Genomics 2019; 12:68. [PMID: 31118044 PMCID: PMC6532186 DOI: 10.1186/s12920-019-0528-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 05/13/2019] [Indexed: 01/18/2023] Open
Abstract
Background Mexico is among the countries showing the highest heterogeneity of CFTR variants. However, no de novo variants have previously been reported in Mexican patients with cystic fibrosis (CF). Case presentation Here, we report the first case of a novel/de novo variant in a Mexican patient with CF. Our patient was an 8-year-old male who had exhibited the clinical onset of CF at one month of age, with steatorrhea, malabsorption, poor weight gain, anemia, and recurrent respiratory tract infections. Complete sequencing of the CFTR gene by next generation sequencing (NGS) revealed two different variants in trans, including the previously reported CF-causing variant c.3266G > A (p.Trp1089*, W1089*), that was inherited from the mother, and the novel/de novo CFTR variant c.1762G > T (p.Glu588*). Conclusion Our results demonstrate the efficiency of targeted NGS for making a rapid and precise diagnosis in patients with clinically suspected CF. This method can enable the provision of accurate genetic counselling, and improve our understanding of the molecular basis of genetic diseases.
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Affiliation(s)
- Angélica Martínez-Hernández
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Julieta Larrosa
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica, SS, CDMX, Mexico y Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, CDMX, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Humberto García-Ortíz
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | | | - Cecilia Contreras-Cubas
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - Elaheh Mirzaeicheshmeh
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico
| | - José Luis Lezana
- Clinica de Fibrosis Quística y Laboratorio de Fisiologia Pulmonar Hospital Infantil de México Federico Gómez. Asociación Mexicana de Fibrosis Quística, A. C, CDMX, Mexico City, Mexico
| | - Lorena Orozco
- Laboratorio de Inmunogenómica y enfermedades metabólicas, Instituto Nacional de Medicina Genómica,SS, Periférico Sur No. 4809, Arenal Tepepan,Tlalpan, 14610. CDMX, Mexico City, Mexico.
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Novel, rare and common pathogenic variants in the CFTR gene screened by high-throughput sequencing technology and predicted by in silico tools. Sci Rep 2019; 9:6234. [PMID: 30996306 PMCID: PMC6470152 DOI: 10.1038/s41598-019-42404-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is caused by ~300 pathogenic CFTR variants. The heterogeneity of which, challenges molecular diagnosis and precision medicine approaches in CF. Our objective was to identify CFTR variants through high-throughput sequencing (HTS) and to predict the pathogenicity of novel variants through in 8 silico tools. Two guidelines were followed to deduce the pathogenicity. A total of 169 CF patients had genomic DNA submitted to a Targeted Gene Sequencing and we identified 63 variants (three patients had three variants). The most frequent alleles were: F508del (n = 192), G542* (n = 26), N1303K (n = 11), R1162* and R334W (n = 9). The screened variants were classified as follows: 41 - pathogenic variants [classified as (I) n = 23, (II) n = 6, (III) n = 1, (IV) n = 6, (IV/V) n = 1 and (VI) n = 4]; 14 - variants of uncertain significance; and seven novel variants. To the novel variants we suggested the classification of 6b-16 exon duplication, G646* and 3557delA as Class I. There was concordance among the predictors as likely pathogenic for L935Q, cDNA.5808T>A and I1427I. Also, Y325F presented two discordant results among the predictors. HTS and in silico analysis can identify pathogenic CFTR variants and will open the door to integration of precision medicine into routine clinical practice in the near future.
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