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Article ; Online: Sexual violence as a precipitator of chronic pain in young adults with sickle cell disease.

Chopra, Maya / Byrd, Jeannie / Wuichet, Kristin / DeBaun, Michael R

2022 Volume 6, Issue 16, Page(s) 4831–4833

MeSH term(s)	Anemia, Sickle Cell/complications ; Chronic Pain/etiology ; Humans ; Sex Offenses ; Young Adult
Language	English
Publishing date	2022-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2022007600
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Article ; Online: Expansion of the Genotypic and Phenotypic Spectrum of

Cordova, Ineke / Blesson, Alyssa / Savatt, Juliann M / Sveden, Abigail / Mahida, Sonal / Hazlett, Heather / Rooney Riggs, Erin / Chopra, Maya

Genes

2024 Volume 15, Issue 4

Abstract: ... ...

Abstract	Pathogenic
MeSH term(s)	Humans ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/pathology ; Phenotype ; Male ; Histone-Lysine N-Methyltransferase/genetics ; Female ; Child ; Genotype ; DNA-Binding Proteins/genetics ; Intellectual Disability/genetics ; Intellectual Disability/pathology ; Transcription Factors/genetics ; Child, Preschool ; Autism Spectrum Disorder/genetics ; Autism Spectrum Disorder/pathology ; Mutation ; Adolescent
Chemical Substances	Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; ASH1L protein, human (EC 2.1.1.43) ; DNA-Binding Proteins ; Transcription Factors
Language	English
Publishing date	2024-03-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review ; Research Support, N.I.H., Extramural ; Case Reports
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes15040423
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Article ; Online: Clinical utility of a genetic diagnosis in individuals with cerebral palsy and related motor disorders.

Santana Almansa, Alexandra / Gable, Dustin L / Frazier, Zoë / Sveden, Abigail / Quinlan, Aisling / Chopra, Maya / Lewis, Sara A / Kruer, Michael / Poduri, Annapurna / Srivastava, Siddharth

Annals of clinical and translational neurology

2024 Volume 11, Issue 2, Page(s) 251–262

Abstract: Objective: Evaluation of the clinical utility of a genetic diagnosis in CP remains limited. We aimed to characterize the clinical utility of a genetic diagnosis by exome sequencing (ES) in patients with CP and related motor disorders.: Methods: We ... ...

Abstract	Objective: Evaluation of the clinical utility of a genetic diagnosis in CP remains limited. We aimed to characterize the clinical utility of a genetic diagnosis by exome sequencing (ES) in patients with CP and related motor disorders. Methods: We enrolled participants with CP and "CP masquerading" conditions in an institutional ES initiative. In those with genetic diagnoses who had clinical visits to discuss results, we retrospectively reviewed medical charts, evaluating recommendations based on the genetic diagnosis pertaining to medication intervention, surveillance initiation, variant-specific testing, and patient education. Results: We included 30 individuals with a molecular diagnosis and clinical follow-up. Nearly all (28 out of 30) had clinical impact resulting from the genetic diagnosis. Medication interventions included recommendation of mitochondrial multivitamin supplementation (6.67%, n = 2), ketogenic diet (3.33%, n = 1), and fasting avoidance (3.33%, n = 1). Surveillance-related actions included recommendations for investigating systemic complications (40%, n = 12); referral to new specialists to screen for systemic manifestations (33%, n = 10); continued follow-up with established specialists to focus on specific manifestations (16.67%, n = 5); referral to clinical genetics (16.67%, n = 5) to oversee surveillance recommendations. Variant-specific actions included carrier testing (10%, n = 3) and testing of potentially affected relatives (3.33%, n = 1). Patient education-specific actions included referral to experts in the genetic disorder (30%, n = 9); and counseling about possible changes in prognosis, including recognition of disease progression and early mortality (36.67%, n = 11). Interpretation: This study highlights the clinical utility of a genetic diagnosis for CP and "CP masquerading" conditions, evident by medication interventions, surveillance impact, family member testing, and patient education, including possible prognostic changes.
MeSH term(s)	Humans ; Cerebral Palsy ; Motor Disorders ; Retrospective Studies ; Cognition ; Diet, Ketogenic
Language	English
Publishing date	2024-01-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2740696-9
ISSN	2328-9503 ; 2328-9503
ISSN (online)	2328-9503
ISSN	2328-9503
DOI	10.1002/acn3.51942
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Article ; Online: Molecular Diagnostic Yield of Exome Sequencing and Chromosomal Microarray in Cerebral Palsy: A Systematic Review and Meta-analysis.

Srivastava, Siddharth / Lewis, Sara A / Cohen, Julie S / Zhang, Bo / Aravamuthan, Bhooma R / Chopra, Maya / Sahin, Mustafa / Kruer, Michael C / Poduri, Annapurna

JAMA neurology

2022 Volume 79, Issue 12, Page(s) 1287–1295

Abstract: Importance: There are many known acquired risk factors for cerebral palsy (CP), but in some cases, CP is evident without risk factors (cryptogenic CP). Early CP cohort studies report a wide range of diagnostic yields for sequence variants assessed by ... ...

Abstract	Importance: There are many known acquired risk factors for cerebral palsy (CP), but in some cases, CP is evident without risk factors (cryptogenic CP). Early CP cohort studies report a wide range of diagnostic yields for sequence variants assessed by exome sequencing (ES) and copy number variants (CNVs) assessed by chromosomal microarray (CMA). Objective: To synthesize the emerging CP genetics literature and address the question of what percentage of individuals with CP have a genetic disorder via ES and CMA. Data sources: Searched articles were indexed by PubMed with relevant queries pertaining to CP and ES/CMA (query date, March 15, 2022). Study selection: Inclusion criteria were as follows: primary research study, case series with 10 or more nonrelated individuals, CP diagnosis, and ES and/or CMA data used for genetic evaluation. Nonblinded review was performed. Data extraction and synthesis: Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines were used for assessing data quality and validity. Data were extracted by a single observer. Main outcomes and measures: A separate meta-analysis was performed for each modality (ES, CMA). The primary outcome was proportion/molecular diagnostic yield (number of patients with a discovered genetic disorder divided by the total number of patients in the cohort), evaluated via meta-analysis of single proportions using random-effects logistic regression. A subgroup meta-analysis was conducted, using risk factor classification as a subgroup. A forest plot was used to display diagnostic yields of individual studies. Results: In the meta-analysis of ES yield in CP, the overall diagnostic yield of ES among the cohorts (15 study cohorts comprising 2419 individuals from 11 articles) was 23% (95% CI, 15%-34%). The diagnostic yield across cryptogenic CP cohorts was 35% (95% CI, 27%-45%), compared with 7% (95% CI, 4%-12%) across cohorts with known risk factors (noncryptogenic CP). In the meta-analysis of CMA yield in CP, the diagnostic yield of CMA among the cohorts (5 study cohorts comprising 294 individuals from 5 articles) was 5% (95% CI, 2%-12%). Conclusions and relevance: Results of this systematic review and meta-analysis suggest that for individuals with cryptogenic CP, ES followed by CMA to identify molecular disorders may be warranted.
MeSH term(s)	Humans ; Pathology, Molecular ; Cerebral Palsy/diagnosis ; Cerebral Palsy/genetics ; Microarray Analysis/methods ; Exome Sequencing ; DNA Copy Number Variations/genetics
Language	English
Publishing date	2022-10-24
Publishing country	United States
Document type	Meta-Analysis ; Systematic Review ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2702023-X
ISSN	2168-6157 ; 2168-6149
ISSN (online)	2168-6157
ISSN	2168-6149
DOI	10.1001/jamaneurol.2022.3549
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Article: GENE TARGET: A framework for evaluating Mendelian neurodevelopmental disorders for gene therapy.

Chopra, Maya / Modi, Meera E / Dies, Kira A / Chamberlin, Nancy L / Buttermore, Elizabeth D / Brewster, Stephanie Jo / Prock, Lisa / Sahin, Mustafa

Molecular therapy. Methods & clinical development

2022 Volume 27, Page(s) 32–46

Abstract: Interest in gene-based therapies for neurodevelopmental disorders is increasing exponentially, driven by the rise in recognition of underlying genetic etiology, progress in genomic technology, and recent proof of concept in several disorders. The current ...

Abstract	Interest in gene-based therapies for neurodevelopmental disorders is increasing exponentially, driven by the rise in recognition of underlying genetic etiology, progress in genomic technology, and recent proof of concept in several disorders. The current prioritization of one genetic disorder over another for development of therapies is driven by competing interests of pharmaceutical companies, advocacy groups, and academic scientists. Although these are all valid perspectives, a consolidated framework will facilitate more efficient and rational gene therapy development. Here we outline features of Mendelian neurodevelopmental disorders that warrant consideration when determining suitability for gene therapy. These features fit into four broad domains: genetics, preclinical validation, clinical considerations, and ethics. We propose a simple mnemonic, GENE TARGET, to remember these features and illustrate how they could be scored using a preliminary scoring rubric. In this suggested rubric, for a given disorder, scores for each feature may be added up to a composite GENE TARGET suitability (GTS) score. In addition to proposing a systematic method to evaluate and compare disorders, our framework helps identify gaps in the translational pipeline for a given disorder, which can inform prioritization of future research efforts.
Language	English
Publishing date	2022-08-29
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2872938-9
ISSN	2329-0501 ; 2329-0501
ISSN (online)	2329-0501
ISSN	2329-0501
DOI	10.1016/j.omtm.2022.08.007
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Article ; Online: The Brain Gene Registry: a data snapshot.

Baldridge, Dustin / Kaster, Levi / Sancimino, Catherine / Srivastava, Siddharth / Molholm, Sophie / Gupta, Aditi / Oh, Inez / Lanzotti, Virginia / Grewal, Daleep / Riggs, Erin Rooney / Savatt, Juliann M / Hauck, Rachel / Sveden, Abigail / Constantino, John N / Piven, Joseph / Gurnett, Christina A / Chopra, Maya / Hazlett, Heather / Payne, Philip R O

Journal of neurodevelopmental disorders

2024 Volume 16, Issue 1, Page(s) 17

Abstract: Monogenic disorders account for a large proportion of population-attributable risk for neurodevelopmental disabilities. However, the data necessary to infer a causal relationship between a given genetic variant and a particular neurodevelopmental ... ...

Abstract	Monogenic disorders account for a large proportion of population-attributable risk for neurodevelopmental disabilities. However, the data necessary to infer a causal relationship between a given genetic variant and a particular neurodevelopmental disorder is often lacking. Recognizing this scientific roadblock, 13 Intellectual and Developmental Disabilities Research Centers (IDDRCs) formed a consortium to create the Brain Gene Registry (BGR), a repository pairing clinical genetic data with phenotypic data from participants with variants in putative brain genes. Phenotypic profiles are assembled from the electronic health record (EHR) and a battery of remotely administered standardized assessments collectively referred to as the Rapid Neurobehavioral Assessment Protocol (RNAP), which include cognitive, neurologic, and neuropsychiatric assessments, as well as assessments for attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). Co-enrollment of BGR participants in the Clinical Genome Resource's (ClinGen's) GenomeConnect enables display of variant information in ClinVar. The BGR currently contains data on 479 participants who are 55% male, 6% Asian, 6% Black or African American, 76% white, and 12% Hispanic/Latine. Over 200 genes are represented in the BGR, with 12 or more participants harboring variants in each of these genes: CACNA1A, DNMT3A, SLC6A1, SETD5, and MYT1L. More than 30% of variants are de novo and 43% are classified as variants of uncertain significance (VUSs). Mean standard scores on cognitive or developmental screens are below average for the BGR cohort. EHR data reveal developmental delay as the earliest and most common diagnosis in this sample, followed by speech and language disorders, ASD, and ADHD. BGR data has already been used to accelerate gene-disease validity curation of 36 genes evaluated by ClinGen's BGR Intellectual Disability (ID)-Autism (ASD) Gene Curation Expert Panel. In summary, the BGR is a resource for use by stakeholders interested in advancing translational research for brain genes and continues to recruit participants with clinically reported variants to establish a rich and well-characterized national resource to promote research on neurodevelopmental disorders.
MeSH term(s)	Humans ; Male ; Female ; Autism Spectrum Disorder/genetics ; Autistic Disorder ; Neurodevelopmental Disorders ; Intellectual Disability ; Brain ; Registries ; Methyltransferases
Chemical Substances	SETD5 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2024-04-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2487174-6
ISSN	1866-1955 ; 1866-1955
ISSN (online)	1866-1955
ISSN	1866-1955
DOI	10.1186/s11689-024-09530-3
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Article ; Online: Toward representative genomic research: the children's rare disease cohorts experience.

Frazier, Zoë J / Brown, Eurnestine / Rockowitz, Shira / Lee, Ted / Zhang, Bo / Sveden, Abigail / Chamberlin, Nancy L / Dies, Kira A / Poduri, Annapurna / Sliz, Piotr / Chopra, Maya

Therapeutic advances in rare disease

2023 Volume 4, Page(s) 26330040231181406

Abstract: Background: Due to racial, cultural, and linguistic marginalization, some populations experience disproportionate barriers to genetic testing in both clinical and research settings. It is difficult to track such disparities due to non-inclusive self- ... ...

Abstract	Background: Due to racial, cultural, and linguistic marginalization, some populations experience disproportionate barriers to genetic testing in both clinical and research settings. It is difficult to track such disparities due to non-inclusive self-reported race and ethnicity categories within the electronic health record (EHR). Inclusion and access for all populations is critical to achieve health equity and to capture the full spectrum of rare genetic disease. Objective: We aimed to create revised race and ethnicity categories. Additionally, we identified racial and ethnic under-representation amongst three cohorts: (1) the general Boston Children's Hospital patient population (general BCH), (2) the BCH patient population that underwent clinical genomic testing (clinical sequencing), and (3) Children's Rare Disease Cohort (CRDC) research initiative participants. Design and methods: Race and ethnicity data were collected from the EHRs of the general BCH, clinical sequencing, and CRDC cohorts. We constructed a single comprehensive set of race and ethnicity categories. EHR-based race and ethnicity variables were mapped within each cohort to the revised categories. Then, the numbers of patients within each revised race and ethnicity category were compared across cohorts. Results: There was a significantly lower percentage of Black or African American/African, non-Hispanic/non-Latine individuals in the CRDC cohort compared with the general BCH cohort, but there was no statistically significant difference between the CRDC and the clinical sequencing cohorts. There was a significantly lower percentage of multi-racial, Hispanic/Latine individuals in the CRDC cohort than the clinical sequencing cohort. White, non-Hispanic/non-Latine individuals were over-represented in the CRDC compared to the two other groups. Conclusion: We highlight underrepresentation of certain racial and ethnic populations in sequencing cohorts compared to the general hospital population. We propose a range of measures to address these disparities, to strive for equitable future precision medicine-based clinical care and for the benefit of the whole rare disease community.
Language	English
Publishing date	2023-08-22
Publishing country	England
Document type	Journal Article
ISSN	2633-0040
ISSN (online)	2633-0040
DOI	10.1177/26330040231181406
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Article ; Online: Sex Differences in Coronary Arterial Calcification in Symptomatic Patients.

Kim, Beom Soo / Chan, Nicholas / Hsu, Greg / Makaryus, Amgad N / Chopra, Maya / Cohen, Stuart L / Makaryus, John N

The American journal of cardiology

2021 Volume 149, Page(s) 16–20

Abstract: Despite the increasing use of Coronary Artery Calcium (CAC) scoring for cardiovascular risk stratification in asymptomatic patients, the gender differences in CAC among symptomatic patients have not been well evaluated. We analyzed patients presenting to ...

Abstract	Despite the increasing use of Coronary Artery Calcium (CAC) scoring for cardiovascular risk stratification in asymptomatic patients, the gender differences in CAC among symptomatic patients have not been well evaluated. We analyzed patients presenting to the emergency department (ED) with chest pain suggesting possible coronary artery disease (CAD) who received coronary computed tomography angiography (CCTA). Ordinal logistic regression was used to determine the odds ratio for the association of traditional cardiovascular risk factors and CAC. Patients with a CAC score ≥ 100 were followed for cardiovascular events or changes in medical management. Our cohort included 542 individuals (263 male, 279 female). Ordinal logistic regression model showed that among traditional cardiovascular risk factors, male sex had the highest odds ratio (OR) of 3.04 (p < 0.001, 95% CI [2.01, 4.59]) for the presence of CAC. Also, males had more diffuse distribution of coronary atherosclerosis (p=0.01). Subgroup analysis revealed that obesity was a bigger risk factor in male patients (OR 2.16), while smoking showed the greatest effect (OR 4.27) on CAC in women. Of patients who had CAC > 100 with an average follow-up of 346 days, there was an increase in both aspirin and statin use, yet significant sex differences were observed especially in patients with non-obstructive lesions on CCTA. Among male patients with non-obstructive lesions, 68.2% were on aspirin and 86.4% were on statin therapy after the CCTA compared to 27.3% and 45.5% respectively in their female counterparts. In conclusion, sex not only is the most powerful predictor for higher CAC among traditional cardiovascular risk factors in symptomatic patients but also influences the contribution of various traditional risk factors to elevated CAC. Furthermore, the discovery of CAD led to the initiation of medical therapy in male patients more frequently than in female patients, even after adjusting for the degree of luminal stenosis detected on coronary CT angiography.
MeSH term(s)	Adult ; Aspirin/therapeutic use ; Chest Pain/physiopathology ; Cohort Studies ; Computed Tomography Angiography ; Coronary Angiography ; Coronary Artery Disease/diagnostic imaging ; Coronary Artery Disease/epidemiology ; Coronary Artery Disease/physiopathology ; Coronary Stenosis/diagnostic imaging ; Coronary Stenosis/epidemiology ; Coronary Stenosis/physiopathology ; Female ; Heart Disease Risk Factors ; Humans ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/therapeutic use ; Logistic Models ; Male ; Middle Aged ; Obesity/epidemiology ; Platelet Aggregation Inhibitors/therapeutic use ; Retrospective Studies ; Sex Factors ; Smoking/epidemiology ; Vascular Calcification/diagnostic imaging ; Vascular Calcification/epidemiology ; Vascular Calcification/physiopathology
Chemical Substances	Hydroxymethylglutaryl-CoA Reductase Inhibitors ; Platelet Aggregation Inhibitors ; Aspirin (R16CO5Y76E)
Language	English
Publishing date	2021-03-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	80014-4
ISSN	1879-1913 ; 0002-9149
ISSN (online)	1879-1913
ISSN	0002-9149
DOI	10.1016/j.amjcard.2021.03.025
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Article: Clinical actionability of genetic findings in cerebral palsy.

Lewis, Sara A / Chopra, Maya / Cohen, Julie S / Bain, Jennifer / Aravamuthan, Bhooma / Carmel, Jason B / Fahey, Michael C / Segel, Reeval / Wintle, Richard F / Zech, Michael / May, Halie / Haque, Nahla / Fehlings, Darcy / Srivastava, Siddharth / Kruer, Michael C

medRxiv : the preprint server for health sciences

2023

Abstract: Background and objectives: Single gene mutations are increasingly recognized as causes of cerebral palsy (CP) phenotypes, yet there is currently no standardized framework for measuring their clinical impact. We evaluated Pathogenic/Likely Pathogenic (P/ ... ...

Abstract	Background and objectives: Single gene mutations are increasingly recognized as causes of cerebral palsy (CP) phenotypes, yet there is currently no standardized framework for measuring their clinical impact. We evaluated Pathogenic/Likely Pathogenic (P/LP) variants identified in individuals with CP to determine how frequently genetic testing results would prompt changes in care. Methods: We analyzed published P/LP variants in OMIM genes identified in clinical (n = 1,345 individuals) or research (n = 496) cohorts using exome sequencing of CP patients. We established a working group of clinical and research geneticists, developmental pediatricians, genetic counselors, and neurologists and performed a systematic review of existing literature for evidence of clinical management approaches linked to genetic disorders. Scoring rubrics were adapted, and a modified Delphi approach was used to build consensus and establish the anticipated impact on patient care. Overall Results: We found 140/1,841 (8%) of individuals in published CP cohorts had a genetic diagnosis classified as Discussion: Our findings indicate that actionable genetic findings occur in 8% of individuals referred for genetic testing with CP. Evaluation of potential
Language	English
Publishing date	2023-09-11
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.08.23295195
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Article ; Online: Creating an automated contemporaneous cohort in sickle cell anemia to predict survival after disease-modifying therapy.

Cronin, Robert M / Wuichet, Kristin / Ghafuri, Djamila L / Hodges, Brock / Chopra, Maya / He, Jing / Niu, Xinnan / Kassim, Adetola A / Wilkerson, Karina / Rodeghier, Mark / DeBaun, Michael R

Blood advances

2022 Volume 7, Issue 15, Page(s) 3775–3782

Abstract: The Food and Drug Administration requires contemporaneous controls to compare clinical outcomes for participants receiving experimental gene therapy or gene editing clinical trials. However, developing a contemporaneous cohort of rare diseases requires ... ...

Abstract	The Food and Drug Administration requires contemporaneous controls to compare clinical outcomes for participants receiving experimental gene therapy or gene editing clinical trials. However, developing a contemporaneous cohort of rare diseases requires multiple person-hours. In a single referral center for sickle cell disease, we tested the hypothesis that we could create an automated contemporaneous cohort of children and adults with sickle cell anemia (SCA) to predict mortality. Data were obtained between 1 January 2004 and 30 April 2021. We identified 419 individuals with SCA with consistent medical care defined as followed continuously for >0.5 years with no visit gaps >3.0 years. The median age was 10.2 years (IQR, 1-24 years), with a median follow-up of 7.4 years (IQR, 3.6-13.5 years) and 47 deaths. A total of 98% (274 of 277) of the children remained alive at 18 years of age, and 34.3% (94 of 274) of those children were followed into adulthood. For adults, the median age of survival was 49.3 years. Treatment groups were mutually exclusive and in a hierarchical order: hematopoietic stem cell transplant (n = 22)>regular blood transfusion for at least 2 years (n = 56)>hydroxyurea for at least 1 year (n = 243)>no disease-modifying therapy (n = 98). Compared to those receiving no disease-modifying treatment, those treated with hydroxyurea therapy had a significantly lower hazard of mortality (hazard ratio = 0.38; P = 0.016), but no statistical difference for those receiving regular blood transfusions compared to no disease-modifying therapy (hazard ratio = 0.71; P = 0.440). An automated contemporaneous SCA cohort can be generated to estimate mortality in children and adults with SCA.
MeSH term(s)	United States ; Child ; Adult ; Humans ; Middle Aged ; Hydroxyurea/therapeutic use ; Antisickling Agents/therapeutic use ; Stroke/drug therapy ; Anemia, Sickle Cell/complications ; Anemia, Sickle Cell/therapy ; Blood Transfusion
Chemical Substances	Hydroxyurea (X6Q56QN5QC) ; Antisickling Agents
Language	English
Publishing date	2022-11-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2022008692
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