Dataset Information

Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases.

ABSTRACT: The purpose of this study was to develop a flexible, cost-efficient, next-generation sequencing (NGS) protocol for genetic testing. Long-range polymerase chain reaction (PCR) amplicons of up to 20 kb in size were designed to amplify entire genomic regions for a panel (n = 35) of inherited retinal disease (IRD)-associated loci. Amplicons were pooled and sequenced by NGS. The analysis was applied to 227 probands diagnosed with IRD: (A) 108 previously molecularly diagnosed, (B) 94 without previous genetic testing, and (C) 25 undiagnosed after whole-exome sequencing (WES). The method was validated with 100% sensitivity on cohort A. Long-range PCR-based sequencing revealed likely causative variant(s) in 51% and 24% of proband from cohorts B and C, respectively. Breakpoints of 3 copy number variants (CNVs) could be characterized. Long-range PCR libraries spike-in extended coverage of WES. Read phasing confirmed compound heterozygosity in 5 probands. The proposed sequencing protocol provided deep coverage of the entire gene, including intronic and promoter regions. Our method can be used (i) as a first-tier assay to reduce genetic testing costs, (ii) to elucidate missing heritability cases, (iii) to characterize breakpoints of CNVs at nucleotide resolution, (iv) to extend WES data to non-coding regions by spiking-in long-range PCR libraries, and (v) to help with phasing of candidate variants.

SUBMITTER: Maggi J

PROVIDER: S-EPMC7913364 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases.

Maggi Jordi J Koller Samuel S Bähr Luzy L Feil Silke S Kivrak Pfiffner Fatma F Hanson James V M JVM Maspoli Alessandro A Gerth-Kahlert Christina C Berger Wolfgang W

International journal of molecular sciences 20210203 4

The purpose of this study was to develop a flexible, cost-efficient, next-generation sequencing (NGS) protocol for genetic testing. Long-range polymerase chain reaction (PCR) amplicons of up to 20 kb in size were designed to amplify entire genomic regions for a panel (<i>n</i> = 35) of inherited retinal disease (IRD)-associated loci. Amplicons were pooled and sequenced by NGS. The analysis was applied to 227 probands diagnosed with IRD: (A) 108 previously molecularly diagnosed, (B) 94 without pr ...[more]

PMID: 33546218

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Dataset Information

Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases.

Publications

Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases.

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