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  1. Article ; Online: Reply.

    Mustafi, Debarshi / Sawyer, Charles / Huang, Laura C

    Ophthalmology. Retina

    2024  Volume 8, Issue 3, Page(s) e7–e8

    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Letter
    ISSN 2468-6530
    ISSN (online) 2468-6530
    DOI 10.1016/j.oret.2023.11.020
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  2. Article ; Online: Immunology of Retinitis Pigmentosa and Gene Therapy-Associated Uveitis.

    Yang, Paul / Mustafi, Debarshi / Pepple, Kathryn L

    Cold Spring Harbor perspectives in medicine

    2024  Volume 14, Issue 1

    Abstract: The underlying immune state of inherited retinal degenerations (IRDs) and retinitis pigmentosa (RP) has been an emerging area of interest, wherein the consequences have never been greater given the widespread recognition of gene therapy-associated ... ...

    Abstract The underlying immune state of inherited retinal degenerations (IRDs) and retinitis pigmentosa (RP) has been an emerging area of interest, wherein the consequences have never been greater given the widespread recognition of gene therapy-associated uveitis (GTU) in gene therapy clinical trials. Whereas some evidence suggests that the adaptive immune system may play a role, the majority of studies indicate that the innate immune system is likely the primary driver of neuroinflammation in RP. During retinal degeneration, discrete mechanisms activate resident microglia and promote infiltrating macrophages that can either be protective or detrimental to photoreceptor cell death. This persistent stimulation of innate immunity, overlaid by the introduction of viral antigens as part of gene therapy, has the potential to trigger a complex microglia/macrophage-driven proinflammatory state. A better understanding of the immune pathophysiology in IRD and GTU will be necessary to improve the success of developing novel treatments for IRDs.
    MeSH term(s) Humans ; Retinitis Pigmentosa/genetics ; Retinitis Pigmentosa/therapy ; Retinal Degeneration ; Macrophages ; Genetic Therapy ; Uveitis/genetics ; Uveitis/therapy
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2157-1422
    ISSN (online) 2157-1422
    DOI 10.1101/cshperspect.a041305
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Unilateral peripheral vascular retinal disease associated with a developmental arcade vessel anomaly in adult-onset Coats' disease.

    Mustafi, Debarshi / Stacey, Andrew W

    American journal of ophthalmology case reports

    2022  Volume 25, Page(s) 101408

    Language English
    Publishing date 2022-02-09
    Publishing country United States
    Document type Journal Article
    ISSN 2451-9936
    ISSN (online) 2451-9936
    DOI 10.1016/j.ajoc.2022.101408
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  4. Article ; Online: Re: Yahya et al.: Late-onset autosomal dominant macular degeneration caused by deletion of the CRX gene (Ophthalmology. 2023;130:68-76).

    Mustafi, Debarshi / Chao, Jennifer R

    Ophthalmology

    2022  Volume 130, Issue 3, Page(s) e9

    MeSH term(s) Humans ; Macular Degeneration/genetics ; Phenotype ; Homeodomain Proteins/genetics
    Chemical Substances Homeodomain Proteins
    Language English
    Publishing date 2022-11-15
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 392083-5
    ISSN 1549-4713 ; 0161-6420
    ISSN (online) 1549-4713
    ISSN 0161-6420
    DOI 10.1016/j.ophtha.2022.10.014
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  5. Article ; Online: Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients.

    Nakamichi, Kenji / Van Gelder, Russell N / Chao, Jennifer R / Mustafi, Debarshi

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 8535

    Abstract: Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, ...

    Abstract Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autosomal recessive IRDs, one or no disease-causing variants are identified. Furthermore, chromosomal maps cannot be reconstructed for allelic variant discovery with short-reads. Long-read genome sequencing can provide complete coverage of disease loci and a targeted approach can focus sequencing bandwidth to a genomic region of interest to provide increased depth and haplotype reconstruction to uncover cases of missing heritability. We demonstrate that targeted adaptive long-read sequencing on the Oxford Nanopore Technologies (ONT) platform of the USH2A gene from three probands in a family with the most common cause of the syndromic IRD, Usher Syndrome, resulted in greater than 12-fold target gene sequencing enrichment on average. This focused depth of sequencing allowed for haplotype reconstruction and phased variant identification. We further show that variants obtained from the haplotype-aware genotyping pipeline can be heuristically ranked to focus on potential pathogenic candidates without a priori knowledge of the disease-causing variants. Moreover, consideration of the variants unique to targeted long-read sequencing that are not covered by short-read technology demonstrated higher precision and F1 scores for variant discovery by long-read sequencing. This work establishes that targeted adaptive long-read sequencing can generate targeted, chromosome-phased data sets for identification of coding and non-coding disease-causing alleles in IRDs and can be applicable to other Mendelian diseases.
    MeSH term(s) Humans ; Pedigree ; Retinal Degeneration/genetics ; Usher Syndromes/genetics ; Sequence Analysis, DNA/methods ; Alleles ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2023-05-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-35791-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Targeted long-read sequencing allows for rapid identification of pathogenic disease-causing variants in retinoblastoma.

    Nakamichi, Kenji / Stacey, Andrew / Mustafi, Debarshi

    Ophthalmic genetics

    2022  Volume 43, Issue 6, Page(s) 762–770

    Abstract: Background: Identification of disease-causing variants of the retinoblastoma gene (RB1), the predominant cause of retinoblastoma, is challenging. Targeted long-read genome sequencing offers a novel approach to resolve the diverse range of pathogenic ... ...

    Abstract Background: Identification of disease-causing variants of the retinoblastoma gene (RB1), the predominant cause of retinoblastoma, is challenging. Targeted long-read genome sequencing offers a novel approach to resolve the diverse range of pathogenic variants in RB1 and provides haplotype information rapidly.
    Materials and methods: Genomic DNA was isolated from a venipuncture blood draw of a retinoblastoma patient. Whole genome sequencing (WGS) was carried out using the short-read Ilumina platform. WGS and targeted sequencing of RB1 was accomplished using the long-read Oxford Nanopore Technologies (ONT) platform. Deep-learning frameworks allowed haplotagging, variant calling, and variant annotation of both short- and long-read data.
    Results: Targeted long-read sequencing of the RB1 gene allowed for enhanced depth of read coverage for discovery of rare variants and haplotype analysis. A duplication leading to a frameshift and early termination in RB1 was identified as the most deleterious variant by all sequencing methods, with long-read technology providing additional information of methylation signal and haplotype information. More importantly, there was greater than 98% concordance of RB1 variants identified between short-read and targeted long-read sequencing modalities.
    Conclusions: Targeted long-read technology allows for focused sequencing effort for variant discovery. Application of this for the first time in a retinoblastoma patient allowed haplotagged variant identification and demonstrated excellent concordance with benchmark short-read sequencing. The added benefit of targeted long-read sequencing to resolve disease-causing genomic variation in RB1 rapidly from a blood draw will provide a more definitive diagnosis of heritable RB and guide management decisions for patients and their families.
    MeSH term(s) Humans ; Retinoblastoma/diagnosis ; Retinoblastoma/genetics ; Retinoblastoma/pathology ; Genes, Retinoblastoma/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Retinal Neoplasms/pathology
    Language English
    Publishing date 2022-11-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1199279-7
    ISSN 1744-5094 ; 0167-6784 ; 1381-6810
    ISSN (online) 1744-5094
    ISSN 0167-6784 ; 1381-6810
    DOI 10.1080/13816810.2022.2141797
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  7. Article ; Online: Successful Treatment Response of a Juxtapapillary Retinal Capillary Hemangioblastoma Due to von Hippel-Lindau Syndrome with Belzutifan in a Pediatric Patient.

    Mustafi, Debarshi / Huang, Johnson / Ting, Michelle A / Waligorski, Natalie / Stacey, Andrew W / Huang, Laura C

    Retina (Philadelphia, Pa.)

    2023  Volume 44, Issue 5, Page(s) e31–e33

    MeSH term(s) Humans ; von Hippel-Lindau Disease/complications ; von Hippel-Lindau Disease/diagnosis ; von Hippel-Lindau Disease/drug therapy ; Retinal Neoplasms/drug therapy ; Retinal Neoplasms/diagnosis ; Hemangioblastoma/drug therapy ; Hemangioblastoma/diagnosis ; Fluorescein Angiography ; Female ; Male ; Child
    Language English
    Publishing date 2023-12-15
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 603192-4
    ISSN 1539-2864 ; 0275-004X
    ISSN (online) 1539-2864
    ISSN 0275-004X
    DOI 10.1097/IAE.0000000000003973
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  8. Article ; Online: Diagnostic Role of Oral Fluorescein Angiography in Pediatric Ambulatory Clinics.

    Sawyer, Charles / Huang, Laura C / Vincent, Jennifer / Cabrera, Michelle T / Herlihy, Erin / Mustafi, Debarshi

    Ophthalmology. Retina

    2023  Volume 8, Issue 2, Page(s) 204–206

    Abstract: Oral ingestion of fluorescein can be done in ambulatory pediatric clinics. We show that oral ultra-widefield fluorescein angiography is a non-invasive approach to rapidly diagnose and manage a diverse set of pediatric retinal vascular diseases. ...

    Abstract Oral ingestion of fluorescein can be done in ambulatory pediatric clinics. We show that oral ultra-widefield fluorescein angiography is a non-invasive approach to rapidly diagnose and manage a diverse set of pediatric retinal vascular diseases.
    MeSH term(s) Humans ; Fluorescein Angiography/methods ; Child ; Retinal Diseases/diagnosis ; Fluorescein/administration & dosage ; Fundus Oculi ; Male ; Female ; Adolescent ; Retinal Vessels/diagnostic imaging ; Child, Preschool ; Ambulatory Care Facilities ; Administration, Oral
    Chemical Substances Fluorescein (TPY09G7XIR)
    Language English
    Publishing date 2023-10-29
    Publishing country United States
    Document type Journal Article
    ISSN 2468-6530
    ISSN (online) 2468-6530
    DOI 10.1016/j.oret.2023.10.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The Current State of Genetic Testing Platforms for Inherited Retinal Diseases.

    Mustafi, Debarshi / Hisama, Fuki M / Huey, Jennifer / Chao, Jennifer R

    Ophthalmology. Retina

    2022  Volume 6, Issue 8, Page(s) 702–710

    Abstract: Purpose: To evaluate genetic testing platforms used to aid in the diagnosis of inherited retinal degenerations (IRDs).: Design: Evaluation of diagnostic tests and technologies.: Subjects: Targeted genetic panel testing for IRDs.: Methods: Data ... ...

    Abstract Purpose: To evaluate genetic testing platforms used to aid in the diagnosis of inherited retinal degenerations (IRDs).
    Design: Evaluation of diagnostic tests and technologies.
    Subjects: Targeted genetic panel testing for IRDs.
    Methods: Data collected regarding targeted genetic panel testing for IRDs offered by different laboratories were investigated for the inclusion of coding and noncoding variants in disease genes. Both large IRD panels and smaller, more focused, disease-specific panels were included in the analysis.
    Main outcome measures: Number of disease genes tested as well as the commonality and uniqueness across testing platforms in both coding and noncoding variants of disease.
    Results: Across the 3 IRD panel tests investigated, 409 unique genes are represented, of which 269 genes are tested by all 3 panels. The top 20 genes known to cause over 70% of all IRDs are represented in the 269 common genes tested by all 3 panels. In addition, 138 noncoding variants in 50 unique genes are assayed across the 3 platforms. Focused, disease-specific panels exhibit significant variability across the 5 testing platforms that were studied.
    Conclusions: Ordering genetic testing for IRDs is not straightforward, as evidenced by the multitude of panels available to providers. It is important that there is coverage of both coding and noncoding regions in IRD genes to offer diagnoses in these patients. This paper details the diversity of testing platforms currently available to clinicians and provides a thorough explanation of the genes tested in the different IRD panels. In a time of increased importance of the clinical genetic testing of patients with IRDs, knowledge of the proper test to order is paramount.
    MeSH term(s) Genetic Testing ; Humans ; Mutation ; Retina ; Retinal Degeneration
    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2468-6530
    ISSN (online) 2468-6530
    DOI 10.1016/j.oret.2022.03.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: HUMAN CELLULAR MODELS FOR RETINAL DISEASE: From Induced Pluripotent Stem Cells to Organoids.

    Mustafi, Debarshi / Bharathan, Sumitha P / Calderon, Rosanna / Nagiel, Aaron

    Retina (Philadelphia, Pa.)

    2022  Volume 42, Issue 10, Page(s) 1829–1835

    Abstract: Purpose: To provide a concise review of induced pluripotent stem cells (iPSCs) and retinal organoids as models for human retinal diseases and their role in gene discovery and treatment of inherited retinal diseases (IRDs).: Methods: A PubMed ... ...

    Abstract Purpose: To provide a concise review of induced pluripotent stem cells (iPSCs) and retinal organoids as models for human retinal diseases and their role in gene discovery and treatment of inherited retinal diseases (IRDs).
    Methods: A PubMed literature review was performed for models of human retinal disease, including animal models and human pluripotent stem cell-derived models.
    Results: There is a growing body of research on retinal disease using human pluripotent stem cells. This is a significant change from just a decade ago when most research was performed on animal models. The advent of induced pluripotent stem cells has permitted not only the generation of two-dimensional human cell cultures such as RPE but also more recently the generation of three-dimensional retinal organoids that better reflect the multicellular laminar architecture of the human retina.
    Conclusion: Modern stem cell techniques are improving our ability to model human retinal disease in vitro, especially with the use of patient-derived induced pluripotent stem cells. In the future, a personalized approach may be used in which the individual's unique genotype can be modeled in two-dimensional culture or three-dimensional organoids and then rescued with an optimized therapy before treating the patient.
    MeSH term(s) Animals ; Cell Differentiation ; Humans ; Induced Pluripotent Stem Cells ; Organoids ; Pluripotent Stem Cells ; Retinal Diseases/therapy
    Language English
    Publishing date 2022-07-20
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 603192-4
    ISSN 1539-2864 ; 0275-004X
    ISSN (online) 1539-2864
    ISSN 0275-004X
    DOI 10.1097/IAE.0000000000003571
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