2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-Evaluating Technical and Analytical Validity of the Illumina Infinium Global Diversity Array with Cytogenetics (GDACyto) for Clinical Testing

Evaluating Technical and Analytical Validity of the Illumina Infinium Global Diversity Array with Cytogenetics (GDACyto) for Clinical Testing

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The document discusses the validation study of the Illumina Global Diversity Array Cyto Array (GDA+Cyto) for clinical cytogenetics testing. The study aimed to assess the analytical performance of the GDA+Cyto array and compare it with the Agilent SurePrint G3 Human ISCA 180k array.<br /><br />The study found that the GDA+Cyto array had a higher resolution and required a lower DNA input compared to the Agilent array. The cost per sample was also lower for the GDA+Cyto array.<br /><br />Precision and reproducibility assessment was conducted using technical triplicates on different positions of array slides. Data quality variability was evaluated, and the results showed minimal variation associated with array positions.<br /><br />Analytical validation was performed on a panel of "normals" using the GDA+Cyto array. The accuracy, sensitivity, and specificity of copy number variation (CNV) detection were assessed, and the GDA+Cyto array demonstrated high concordance with clinically reported CNVs.<br /><br />Future directions for the study include experimental validation of CNVs detected by the GDA+Cyto array using quantitative polymerase chain reaction (qPCR) and complete clinical validation on additional samples. The study also aims to refine data processing parameters and expand the analysis for different tissue types in prenatal and oncology testing.<br /><br />The study acknowledges the technical assistance and support from Illumina and Bionano Genomics. Training funding support for one of the authors is provided by the Stanford-Natera Clinical Laboratory Genetics and Genomics Fellowship Award.<br /><br />Overall, the study validates the analytical performance of the Illumina GDA+Cyto array for clinical cytogenetics testing and presents future directions for further validation and improvement of the testing method.

Asset Subtitle

Presenting Author - Shih Yu Cindy Yang, PhD; Co-Author - Jason Erdmann, BSc; Co-Author - Leena Borkar, BSc; Co-Author - Elizabeth M. Spiteri, Phd;

Meta Tag

array CGH

Bioinformatics

Chromosomal Abnormalities

Clinical Applications of Molecular Cytogenetics

Clinical Cytogenetics

Cytogenetics

Genetic Testing

Genomic Methodologies

Methodology

Microarray

Molecular Cytogenetics

Variant Detection

Co-Author Jason Erdmann, BSc

Co-Author Leena Borkar, BSc

Co-Author Elizabeth M. Spiteri, Phd

Presenting Author Shih Yu Cindy Yang, PhD

Keywords

Illumina Global Diversity Array Cyto Array

GDA+Cyto array

clinical cytogenetics testing

Agilent SurePrint G3 Human ISCA 180k array

resolution

DNA input

cost per sample

precision

reproducibility assessment

data quality variability