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Clearseq inherited disease panel

Manufactured by Agilent Technologies
Sourced in United States

The ClearSeq Inherited Disease Panel is a next-generation sequencing (NGS) panel that enables comprehensive analysis of genes associated with a wide range of inherited diseases. The panel targets regions of interest across multiple genes, allowing for efficient and cost-effective genetic testing.

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4 protocols using clearseq inherited disease panel

1

Genetic Analysis of Neuromuscular Disorders

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Through multidisciplinary interactions between the Neuropediatric and Genetics departments we included DNA of two affected siblings for genetic analysis, using NGS approach accordingly to the novel French national recommendations (Krahn et al., 2019).
This family gave informed consent, according to the Declaration of Helsinki, for molecular diagnosis of all four individuals explored (the two asymptomatic parents and two affected siblings). We also obtained consent for medical publication (including pictures of the siblings).
Genetic analysis consisted in clinical exome sequencing using the ClearSeq Inherited Disease Panel (Agilent technologies, CA, USA) on an Ion Proton platform (ThermoFisher Scientific, CA, USA). Sequencing data interpretation was initially focused on 44 genes associated with neuromuscular disorders (Supporting Information) (Kaplan & Hamroun, 2013), before extending analysis to other lists of genes following the novel French national recommendations (Krahn et al., 2019).
NGS findings were systematically confirmed, as well as variant familial segregation analysis performed by targeted Sanger sequencing on a 3500XL Genetic Analyzer® (ThermoFisher Scientific).
For the sequence variant nomenclature, we followed the Human Genome Variation Society (HGVS) recommendations and used the GLE1 transcript reference NM_001003722.1.
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2

Genomic DNA Extraction and Sequencing

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Genomic DNA was extracted from peripheral blood using the DNeasy Blood and Tissue Kit (QIAGEN) according to the manufacturer’s instructions. Samples were analyzed either by panel-based sequencing of known retinopathy-associated genes or by clinical exome sequencing using the ClearSeq Inherited Disease panel (Agilent). Libraries were sequenced on a NextSeq 500 sequencing platform (Illumina inc., San Diego, CA, USA) in collaboration with the NGS Core at the Telethon Institute of Genetics and Medicine (TIGEM).
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3

Targeted NGS for Retinopathy Gene Analysis

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Samples were analyzed either by panel-based analysis of known retinopathy genes or by clinical exome sequencing. One sample underwent whole-exome sequencing. Genomic DNA was extracted from peripheral blood using the DNeasy Blood and Tissue Kit (QIAGEN) according to standard protocols. Targeted NGS analysis was performed using the RETplex targeted sequencing panel as previously described [30 (link)]. Clinical exome and whole-exome sequencing libraries were prepared using the ClearSeq Inherited Disease Panel (Agilent Technologies, Santa Clara, CA, USA) and the SureSelect Human All Exon V7 (Agilent Technologies, Santa Clara, CA, USA), respectively. Targeted regions were enriched using the SureSelectQXT Target Enrichment system (Agilent Technologies, Santa Clara, CA, USA). Libraries were run on a NextSeq500 sequencing platform (Illumina inc., San Diego, CA, USA). Sequencing data were analyzed using a previously described pipeline [43 (link)].
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4

Genetic Enrichment for Inherited Disorders

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Gene enrichment during library preparation was performed using the commercial ClearSeq Inherited Disease Panel (Agilent Technologies). This panel has a 10.5 Mb capture capacity and targets the coding exons and splicing regions of 2,742 genes involved in inherited disorders. The panel includes 199 RD‐related genes, in accordance with the Retinal Information Network (RETNET; https://sph.uth.edu/retnet/home.htm) and the Online Mendelian Inheritance in Man (OMIM) catalog (https://www.omim.org/ ) at the time of the study (accessed on September 2018). One hundred and four of these genes have been implicated exclusively in non‐syndromic RDs, 23 are associated with both syndromic and non‐syndromic forms of RDs, and 72 are involved only in syndromic RDs (Table S1).
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