Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent

Adda Villanueva, Pooja Biswas, Kameron Kishaba, John Suk, Keerti Tadimeti, Pongali B. Raghavendra, Karine Nadeau, Bruno Lamontagne, Lambert Busque, Steve Geoffroy, Ian Mongrain, Géraldine Asselin, Sylvie Provost, Marie Pierre Dubé, Eric Nudleman, Radha Ayyagari

    Research output: Contribution to journalArticle

    Abstract

    Purpose: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. Methods: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. Results: Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. Conclusions: Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.

    Original languageEnglish
    Pages (from-to)1-7
    Number of pages7
    JournalOphthalmic Genetics
    DOIs
    Publication statusPublished - 25-09-2018

    Fingerprint

    Retinal Degeneration
    Pedigree
    Mexico
    Mutation
    Genes
    Color Vision
    Visual Field Tests
    Photography
    Visual Acuity
    Exons
    Phenotype
    DNA
    Population

    All Science Journal Classification (ASJC) codes

    • Pediatrics, Perinatology, and Child Health
    • Ophthalmology
    • Genetics(clinical)

    Cite this

    Villanueva, A., Biswas, P., Kishaba, K., Suk, J., Tadimeti, K., Raghavendra, P. B., ... Ayyagari, R. (2018). Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. Ophthalmic Genetics, 1-7. https://doi.org/10.1080/13816810.2017.1373830
    Villanueva, Adda ; Biswas, Pooja ; Kishaba, Kameron ; Suk, John ; Tadimeti, Keerti ; Raghavendra, Pongali B. ; Nadeau, Karine ; Lamontagne, Bruno ; Busque, Lambert ; Geoffroy, Steve ; Mongrain, Ian ; Asselin, Géraldine ; Provost, Sylvie ; Dubé, Marie Pierre ; Nudleman, Eric ; Ayyagari, Radha. / Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. In: Ophthalmic Genetics. 2018 ; pp. 1-7.
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    abstract = "Purpose: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. Methods: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. Results: Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. Conclusions: Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.",
    author = "Adda Villanueva and Pooja Biswas and Kameron Kishaba and John Suk and Keerti Tadimeti and Raghavendra, {Pongali B.} and Karine Nadeau and Bruno Lamontagne and Lambert Busque and Steve Geoffroy and Ian Mongrain and G{\'e}raldine Asselin and Sylvie Provost and Dub{\'e}, {Marie Pierre} and Eric Nudleman and Radha Ayyagari",
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    Villanueva, A, Biswas, P, Kishaba, K, Suk, J, Tadimeti, K, Raghavendra, PB, Nadeau, K, Lamontagne, B, Busque, L, Geoffroy, S, Mongrain, I, Asselin, G, Provost, S, Dubé, MP, Nudleman, E & Ayyagari, R 2018, 'Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent', Ophthalmic Genetics, pp. 1-7. https://doi.org/10.1080/13816810.2017.1373830

    Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. / Villanueva, Adda; Biswas, Pooja; Kishaba, Kameron; Suk, John; Tadimeti, Keerti; Raghavendra, Pongali B.; Nadeau, Karine; Lamontagne, Bruno; Busque, Lambert; Geoffroy, Steve; Mongrain, Ian; Asselin, Géraldine; Provost, Sylvie; Dubé, Marie Pierre; Nudleman, Eric; Ayyagari, Radha.

    In: Ophthalmic Genetics, 25.09.2018, p. 1-7.

    Research output: Contribution to journalArticle

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    T1 - Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent

    AU - Villanueva, Adda

    AU - Biswas, Pooja

    AU - Kishaba, Kameron

    AU - Suk, John

    AU - Tadimeti, Keerti

    AU - Raghavendra, Pongali B.

    AU - Nadeau, Karine

    AU - Lamontagne, Bruno

    AU - Busque, Lambert

    AU - Geoffroy, Steve

    AU - Mongrain, Ian

    AU - Asselin, Géraldine

    AU - Provost, Sylvie

    AU - Dubé, Marie Pierre

    AU - Nudleman, Eric

    AU - Ayyagari, Radha

    PY - 2018/9/25

    Y1 - 2018/9/25

    N2 - Purpose: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. Methods: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. Results: Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. Conclusions: Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.

    AB - Purpose: To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. Methods: A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. Results: Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. Conclusions: Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.

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