Microarrays: 180K Oligo Array and SNP Array

Ambry offers several microarray options for detection of DNA rearrangements, including the 180k Oligo Array and an enhanced option, the SNP Array.

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Ambry offers several microarray options for detection of DNA rearrangements, including the 180k Oligo Array and an enhanced option, the SNP Array.

Chromosomal microarray analysis (CMA) via array-based comparative genomic hybridization (aCGH) is a technique that allows for high resolution genome-wide detection of unbalanced structural and numerical chromosomal abnormalities,  such as copy number variants (CNVs). These imbalances may be an underlying cause of syndromic or non-syndromic developmental delay, intellectual disability, autism spectrum disorders, multiple congenital anomalies and numerous other genetic syndromes.

CMA offers superior resolution (100-300kb vs. 4-10Mb) and greater diagnostic yield (15-20% vs. 3%) over traditional karyotype analysis when testing individuals with unexplained developmental delay, intellectual disability, autism spectrum disorders, or multiple congenital anomalies 1. It has also become a cost-effective approach for testing individuals with other clinical indications and numerous genetic syndromes. 

Indications for Testing
The 180K Oligo Array or the SNP Array should be considered for all individuals with syndromic or non-syndromic conditions that may be caused by genomic imbalance.

Disease Name 
Autism Spectrum Disorder
Developmental Delay
Intellectual Disability
Multiple Congenital Anomalies
Disease Information 

180K Oligo Array: This option utilizes array CGH technology and is developed for high-resolution, genomic-wide screening of copy number variations (CNVs). Because of its superior resolution, the 180K Oligo Array frequently provides a relevant result for patients with an apparently normal karyotype. We have designed this array to detect aneuploidies, well-characterized microdeletion or microduplication syndromes, and subtelomeric or other unbalanced chromosomal DNA rearrangements. It may also be clinically useful to detect microdeletions/duplications in a specific gene(s) in patients negative for point mutations or small intragenic aberrations.

SNP Array: This option is the gold standard chromosomal microarray option that includes >2.6 million copy number probes and 750,000 single nucleotide probe (SNP) probes. This detects copy number and regions of homozygosity (ROH) that cover the entire genome at high density. This enhanced microarray option: 

  • Is designed to detect aneuploidies, known microdeletion and microduplication syndromes, including CNVs in the pericentromeric and subtelomeric regions
  • Also allows for the detection of ROH and uniparental disomy (UPD) to determine parent-of-origin effects
    • ROH may indicate consanguinity and raises the possibility of an autosomal recessive disorder with a causative gene in the ROH
    • UPD is relevant to conditions like transient neonatal diabetes mellitus, Beckwith-Wiedemann syndrome, Prader-Willi syndrome, Angelman syndrome, and Russell-Silver syndrome

Test Description 

180K Oligo Array: This option contains 180,000 oligonucleotide probes that cover the entire genome at a median probe spacing of 13kb (5kb on the X chromosome). There are also ~680 disease-causing genes with exon level resolution. Our 180 Oligo Array also includes probes for the pericentromeric and subtelomeric regions, with dense probe coverage spanning 10Mb at each subtelomere. This array detects all known microdeletion/duplication syndromes and most disorders detected by chromosomal analysis and FISH tests. Deletions of any size covering a known disease locus are reported as a COPY NUMBER LOSS and duplications of any size covering a known disease locus are reported as a COPY NUMBER GAIN. Deletions less than ~100kb and duplications less than ~300kb outside known disease loci are not reported. Typically, “Database of Genomic Variants”-documented deletion or duplication CNVs are not reported unless there is cause to believe the CNV may be correlated with the presenting phenotype.

SNP Array: This option contains >2.6 million copy number probes and 750,000 SNP probes used for genotyping and copy number analysis. These probes cover the entire genome at a median probe spacing of 1.1kb. Our SNP Array also includes probes for all genes, including genes located in the pericentromeric and subtelomeric regions, with dense probe coverage. Deletions of any size covering a known disease locus are reported as COPY NUMBER LOSS and duplications of any size covering a known disease locus are reported as a COPY NUMBER GAIN. Deletions less than ~100kb and duplications less than ~300kb outside known disease loci are not reported. Typically, “Database of Genomic Variants”-documented deletion or duplication CNVs are not reported unless there is cause to believe the CNV may be correlated with the presenting phenotype. Copy number neutral ROH/UPD regions greater than 10.0Mb in size are reported, though this threshold may vary depending on the location of the ROH/UPD region.

Parental Studies
Fluorescence in situ hybridization (FISH) may be available to the parents of a proband for which microarray results have revealed a copy number variant (CNV).  A sample from the proband and each parent will be needed for this testing (1-5ml in green top sodium heparin (NaHep) tube).  Ambry Genetics will provide complimentary parental FISH analysis for VUS identified on CMA under the following conditions:

  • The proband’s findings are a CNV of unknown significance
  • The rearrangement is large enough to perform FISH analysis (>0.5Mb for deletions and >2Mb for duplications)
  • Probes are commercially available for this region

Parental FISH analysis may be available for charge for pathogenic CNVs.  Please contact the laboratory to confirm availability and pricing.

Specimen Requirements 

Specimens: Blood, saliva, DNA (blood spot and prenatal samples not accepted)

Blood:
Container: Purple top EDTA tube (preferred) or yellow top citric acetate tube.
Amount:  3-5cc;
Minimum for newborns:  180K Oligo Array (0.5-1cc); SNP Array (1cc)

Storage: 2-8°C. Do not freeze.
Shipment: Room temperature for two-day delivery.
 
DNA:
Container: Sterile plastic tube.
Amount: 5 μg of DNA in TE (10mM Tris-Cl pH 8.0, 1mM EDTA); preferred 200 μl at ~100 ng/μl conc.

Quality: Please provide DNA OD 260:280 ratio (preferred 1.7-1.9) and send agarose picture with high molecular weight genomic DNA, if available.

Storage: -20°C.
Shipment: Frozen on dry ice (preferred) or ship on ice.

Saliva:
Container: Oragene Self Collection container.
Amount: 2 ml.
Storage: At room temperature in sterile bag.
Shipment: Room temperature for two-day delivery.
 

Turnaround Time 
Technique DAYS
180K Oligo Array 10-14
 SNP Array 14-21

 

Specialty 
References 
  1. Miller DT, et al., Am J Hum Genet., 2010.