High-resolution SNP arrays in mental retardation diagnostics: how much do we gain? View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-02

AUTHORS

Laura Bernardini, Viola Alesi, Sara Loddo, Antonio Novelli, Irene Bottillo, Agatino Battaglia, Maria Cristina Digilio, Giuseppe Zampino, Adam Ertel, Paolo Fortina, Saul Surrey, Bruno Dallapiccola

ABSTRACT

We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes approximately 900,000 SNP probes and 900,000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number 'neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as 'normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as 'normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms. More... »

PAGES

ejhg2009154

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ejhg.2009.154

DOI

http://dx.doi.org/10.1038/ejhg.2009.154

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1033905253

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19809473


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