Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis

Yiran Guo; Ivan Prokudin; Cong Yu; Jinlong Liang; Yi Xie; Maree Flaherty; Lifeng Tian; Stephanie Crofts; Fengxiang Wang; James Snyder; Craig Donaldson; Nada Abdel-Magid; Lyam Vazquez; Brendan Keating; Hakon Hakonarson; Jun Wang; Robyn V. Jamieson

doi:10.3109/13816810.2014.886269

Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis

Yiran Guo, Ivan Prokudin, Cong Yu, Jinlong Liang, Yi Xie, Maree Flaherty, Lifeng Tian, Stephanie Crofts, Fengxiang Wang, James Snyder, Craig Donaldson, Nada Abdel-Magid, Lyam Vazquez, Brendan Keating, Hakon Hakonarson, Jun Wang, Robyn V. Jamieson^*

^*Corresponding author af dette arbejde

Genomforskning og Molekylær Biomedicin

9 Citationer (Scopus)

Abstract

Background: Leber congenital amaurosis (LCA) is a severe form of retinal dystrophy with marked underlying genetic heterogeneity. Until recently, allele-specific assays and Sanger sequencing of targeted segments were the only available approaches for attempted genetic diagnosis in this condition. A broader next-generation sequencing (NGS) strategy, such as whole exome sequencing, provides an improved molecular genetic diagnostic capacity for patients with these conditions.Materials and Methods: In a child with LCA, an allele-specific assay analyzing 135 known LCA-causing variations, followed by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and SnpEff to annotate the variants.Results: No disease-causing variants were found using the allele-specific or targeted segment Sanger sequencing assays. Analysis of variants in the exome sequence data revealed a novel homozygous nonsense mutation (c.1081C > T, p.Arg361) in TULP1, a gene with roles in photoreceptor function where mutations were previously shown to cause LCA and retinitis pigmentosa. The identified homozygous variant was the top candidate using both bioinformatic pipelines.Conclusions: This study highlights the value of the broad sequencing strategy of exome sequencing for disease gene identification in LCA, over other existing methods. NGS is particularly beneficial in LCA where there are a large number of causative disease genes, few distinguishing clinical features for precise candidate disease gene selection, and few mutation hotspots in any of the known disease genes.

Originalsprog	Engelsk
Tidsskrift	Ophthalmic Genetics
Vol/bind	36
Udgave nummer	4
Sider (fra-til)	333-338
Antal sider	6
ISSN	1381-6810
DOI	https://doi.org/10.3109/13816810.2014.886269
Status	Udgivet - 2015

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10.3109/13816810.2014.886269

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Guo, Y., Prokudin, I., Yu, C., Liang, J., Xie, Y., Flaherty, M., Tian, L., Crofts, S., Wang, F., Snyder, J., Donaldson, C., Abdel-Magid, N., Vazquez, L., Keating, B., Hakonarson, H., Wang, J., & Jamieson, R. V. (2015). Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis. Ophthalmic Genetics, 36(4), 333-338. https://doi.org/10.3109/13816810.2014.886269

Guo, Y, Prokudin, I, Yu, C, Liang, J, Xie, Y, Flaherty, M, Tian, L, Crofts, S, Wang, F, Snyder, J, Donaldson, C, Abdel-Magid, N, Vazquez, L, Keating, B, Hakonarson, H, Wang, J & Jamieson, RV 2015, 'Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis', Ophthalmic Genetics, bind 36, nr. 4, s. 333-338. https://doi.org/10.3109/13816810.2014.886269

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title = "Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis",

abstract = "Background: Leber congenital amaurosis (LCA) is a severe form of retinal dystrophy with marked underlying genetic heterogeneity. Until recently, allele-specific assays and Sanger sequencing of targeted segments were the only available approaches for attempted genetic diagnosis in this condition. A broader next-generation sequencing (NGS) strategy, such as whole exome sequencing, provides an improved molecular genetic diagnostic capacity for patients with these conditions.Materials and Methods: In a child with LCA, an allele-specific assay analyzing 135 known LCA-causing variations, followed by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and SnpEff to annotate the variants.Results: No disease-causing variants were found using the allele-specific or targeted segment Sanger sequencing assays. Analysis of variants in the exome sequence data revealed a novel homozygous nonsense mutation (c.1081C > T, p.Arg361) in TULP1, a gene with roles in photoreceptor function where mutations were previously shown to cause LCA and retinitis pigmentosa. The identified homozygous variant was the top candidate using both bioinformatic pipelines.Conclusions: This study highlights the value of the broad sequencing strategy of exome sequencing for disease gene identification in LCA, over other existing methods. NGS is particularly beneficial in LCA where there are a large number of causative disease genes, few distinguishing clinical features for precise candidate disease gene selection, and few mutation hotspots in any of the known disease genes.",

keywords = "Leber congenital amaurosis, retinitis pigmentosa, TULP1, whole exome sequencing",

author = "Yiran Guo and Ivan Prokudin and Cong Yu and Jinlong Liang and Yi Xie and Maree Flaherty and Lifeng Tian and Stephanie Crofts and Fengxiang Wang and James Snyder and Craig Donaldson and Nada Abdel-Magid and Lyam Vazquez and Brendan Keating and Hakon Hakonarson and Jun Wang and Jamieson, {Robyn V.}",

year = "2015",

doi = "10.3109/13816810.2014.886269",

language = "English",

volume = "36",

pages = "333--338",

journal = "Ophthalmic Genetics",

issn = "1381-6810",

publisher = "Taylor & Francis",

number = "4",

}

TY - JOUR

T1 - Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis

AU - Guo, Yiran

AU - Prokudin, Ivan

AU - Yu, Cong

AU - Liang, Jinlong

AU - Xie, Yi

AU - Flaherty, Maree

AU - Tian, Lifeng

AU - Crofts, Stephanie

AU - Wang, Fengxiang

AU - Snyder, James

AU - Donaldson, Craig

AU - Abdel-Magid, Nada

AU - Vazquez, Lyam

AU - Keating, Brendan

AU - Hakonarson, Hakon

AU - Wang, Jun

AU - Jamieson, Robyn V.

PY - 2015

Y1 - 2015

N2 - Background: Leber congenital amaurosis (LCA) is a severe form of retinal dystrophy with marked underlying genetic heterogeneity. Until recently, allele-specific assays and Sanger sequencing of targeted segments were the only available approaches for attempted genetic diagnosis in this condition. A broader next-generation sequencing (NGS) strategy, such as whole exome sequencing, provides an improved molecular genetic diagnostic capacity for patients with these conditions.Materials and Methods: In a child with LCA, an allele-specific assay analyzing 135 known LCA-causing variations, followed by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and SnpEff to annotate the variants.Results: No disease-causing variants were found using the allele-specific or targeted segment Sanger sequencing assays. Analysis of variants in the exome sequence data revealed a novel homozygous nonsense mutation (c.1081C > T, p.Arg361) in TULP1, a gene with roles in photoreceptor function where mutations were previously shown to cause LCA and retinitis pigmentosa. The identified homozygous variant was the top candidate using both bioinformatic pipelines.Conclusions: This study highlights the value of the broad sequencing strategy of exome sequencing for disease gene identification in LCA, over other existing methods. NGS is particularly beneficial in LCA where there are a large number of causative disease genes, few distinguishing clinical features for precise candidate disease gene selection, and few mutation hotspots in any of the known disease genes.

AB - Background: Leber congenital amaurosis (LCA) is a severe form of retinal dystrophy with marked underlying genetic heterogeneity. Until recently, allele-specific assays and Sanger sequencing of targeted segments were the only available approaches for attempted genetic diagnosis in this condition. A broader next-generation sequencing (NGS) strategy, such as whole exome sequencing, provides an improved molecular genetic diagnostic capacity for patients with these conditions.Materials and Methods: In a child with LCA, an allele-specific assay analyzing 135 known LCA-causing variations, followed by targeted segment sequencing of 61 regions in 14 causative genes was performed. Subsequently, exome sequencing was undertaken in the proband, unaffected consanguineous parents and two unaffected siblings. Bioinformatic analysis used two independent pipelines, BWA-GATK and SOAP, followed by Annovar and SnpEff to annotate the variants.Results: No disease-causing variants were found using the allele-specific or targeted segment Sanger sequencing assays. Analysis of variants in the exome sequence data revealed a novel homozygous nonsense mutation (c.1081C > T, p.Arg361) in TULP1, a gene with roles in photoreceptor function where mutations were previously shown to cause LCA and retinitis pigmentosa. The identified homozygous variant was the top candidate using both bioinformatic pipelines.Conclusions: This study highlights the value of the broad sequencing strategy of exome sequencing for disease gene identification in LCA, over other existing methods. NGS is particularly beneficial in LCA where there are a large number of causative disease genes, few distinguishing clinical features for precise candidate disease gene selection, and few mutation hotspots in any of the known disease genes.

KW - Leber congenital amaurosis

KW - retinitis pigmentosa

KW - TULP1

KW - whole exome sequencing

U2 - 10.3109/13816810.2014.886269

DO - 10.3109/13816810.2014.886269

M3 - Journal article

C2 - 24547928

AN - SCOPUS:84951909062

SN - 1381-6810

VL - 36

SP - 333

EP - 338

JO - Ophthalmic Genetics

JF - Ophthalmic Genetics

IS - 4

ER -

Advantage of whole exome sequencing over allele-specific and targeted segment sequencing in detection of novel TULP1 mutation in leber congenital amaurosis

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