Genetic Diagnostic Workflow for Chromatinopathies

Genetic analyses were performed for diagnostic purposes and no further authorization was required from the Ethical Committee. Informed consents for genetic testing and the publication of significant results were obtained.
The patient underwent firstly array-CGH (comparative genomic hybridization) analysis with the commercial Agilent 2 × 244 kit (following manufacturer’s instructions, using the ADM-2 algorithm for data analysis with Agilent CytoGenomics software) (Agilent Technologies, Santa Clara, CA, USA), with normal results.
A NGS (Next Generation Sequencing) multigene panel to screen 70 genes responsible for chromatinopathies was subsequently performed with a customised HaloPlex Target Enrichment NGS panel (Agilent Technologies, Santa Clara, CA, USA Agilent Technologies) [11 (link)]. Potentially pathogenic variants were confirmed with PCR amplification and Sanger sequencing. DNA from parents was analysed to assess inheritance.
The significance of candidate variants was classified according to the American College of Medical Genetics and Genomics criteria [12 (link)] using InterVar (http://wintervar.wglab.org/), Varsome (https://varsome.com/), CAVA and PMut prediction (http://mmb.pcb.ub.es/PMut/) tools. Sequence variants were described according to the Human Genome Variation Society nomenclature guidelines (https://varnomen.hgvs.org/).

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Bigoni S., Marangi G., Frangella S., Panfili A., Ognibene D., Squeo G.M., Merla G, & Zollino M. (2020). Clinical Genetics Can Solve the Pitfalls of Genome-Wide Investigations: Lesson from Mismapping a Loss-of-Function Variant in KANSL1. Genes, 11(10), 1177.

Publication 2020

Agilent CytoGenomics software

Cava Comparative genomic hybridization Diagnostic Genes Genetic Hgvs Human genome Inheritance Parents Pathogenic Patient Sequence variants

Corresponding Organization : Istituti di Ricovero e Cura a Carattere Scientifico

Other organizations : Arcispedale Sant'Anna, University of Ferrara, Casa Sollievo della Sofferenza

Top 5 similar protocols

Variable analysis

independent variables

Array-CGH (comparative genomic hybridization) analysis with the commercial Agilent 2 × 244 kit
NGS (Next Generation Sequencing) multigene panel to screen 70 genes responsible for chromatinopathies with a customised HaloPlex Target Enrichment NGS panel

dependent variables

Genetic analyses performed for diagnostic purposes

control variables

Manufacturer's instructions for array-CGH analysis
ADM-2 algorithm for data analysis with Agilent CytoGenomics software
PCR amplification and Sanger sequencing to confirm potentially pathogenic variants
Analysis of DNA from parents to assess inheritance of variants

positive controls

None specified

negative controls

None specified

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