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SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay
Guylaine D'Amours1,2,3, Mathieu Langlois4, Géraldine Mathonnet5
1Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. g.damours@umontreal.ca.
BMC Medical Genomics
|December 26, 2014
Summary
Single nucleotide polymorphism (SNP) arrays enhance diagnostic yield for intellectual disability (ID) and congenital anomalies by detecting copy number variations (CNVs) and loss of heterozygosity (LOH). This improves diagnosis rates for rare genetic disorders.
Area of Science:
- Genetics
- Molecular Biology
- Clinical Diagnostics
Background:
- Molecular karyotyping is the primary genetic test for unexplained intellectual disability (ID) and multiple congenital anomalies (MCA), identifying pathogenic copy number variations (CNVs) in 10-14% of cases.
- High-resolution single nucleotide polymorphism (SNP) arrays offer combined molecular karyotyping and SNP genotyping, detecting both CNVs and loss of heterozygosity (LOH).
- The clinical utility of LOH detection for diagnosing ID/MCA remains under investigation.
Purpose of the Study:
- To evaluate the diagnostic yield of high-resolution SNP arrays in children with unexplained ID and/or MCA.
- To assess the capability of SNP arrays in detecting pathogenic CNVs and informative LOHs.
- To compare the performance of SNP arrays with existing array-based comparative genomic hybridization (aCGH) platforms.
Main Methods:
- Twenty-one children with unexplained ID, with or without congenital malformations, were analyzed.
- High-resolution SNP array analysis was performed on four different platforms using DNA from patients and their parents.
- Results were compared to those obtained from a moderate-resolution aCGH platform.
Main Results:
- Pathogenic CNVs were identified in three patients, with all arrays successfully detecting them.
- Informative LOHs, indicative of potential recessive disorders, were found in four children, including two siblings.
- Homozygous mutations within identified LOH regions were confirmed in three patients, increasing the overall diagnostic yield from 14.3% to 28.6%.
Conclusions:
- SNP arrays are clinically valuable for diagnosing children with ID, effectively detecting pathogenic CNVs and identifying informative LOHs.
- The detection of LOHs by SNP arrays facilitates the diagnosis of recessive genetic disorders.
- Implementation of SNP arrays in clinical laboratories presents certain challenges that require consideration.
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