Microarrays: SNP+CGH Array and 180K Oligo Array
Ambry offers several microarray options for detection of DNA rearrangements, including the 180k Oligo Array and an enhanced option, the SNP+CGH Array.
PrintAmbry offers several microarray options for detection of DNA rearrangements, including the 180k Oligo Array and an enhanced option, the SNP+CGH Array.
Genomic imbalances are an underlying cause of syndromic or non-syndromic developmental delay, mental retardation, autism spectrum disorder, dysmorphic features, birth defects or other congenital anomalies and numerous genetic syndromes.
Routine karyotype analysis can detect some common chromosomal imbalances such as aneuploidies, but other genomic imbalances will be missed with a routine karyotype. Chromosomal aberrations have been seen in 3-8% of the population with developmental delay. 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.
Indications for Testing
The 180K Oligo Array or the SNP+CGH Array should be considered for all individuals with syndromic or non-syndromic conditions that may be caused by genomic imbalance.
180K Oligo Array: The 180K Oligo Array utilizes array CGH technology, which was developed for high-resolution, genomic-wide screening of copy number variations. Because of its superior resolution, the 180K Oligo Array can frequently provide a relevant result when the patient has an apparently normal karyotype. Ambry has designed this array to detect aneuploidies, well-characterized microdeletion or microduplication syndromes and subtelomeric or other unbalanced chromosomal DNA rearrangements. In addition, it may be clinically useful for the detection of microdeletions/duplications in a specific gene(s) in patients who are negative for point mutations or small intragenic aberrations.
SNP+CGH Array: The SNP+CGH Array is an enhanced test option that includes the addition of SNP probe coverage allowing for the detection of runs of homozygosity (also known as loss of heterozygosity, LOH) and uniparental disomy (UPD). Runs of homozygosity (ROH) represent identity by descent (IBD) where chromosomal segments are inherited from a common ancestor. UPD is associated with conditions such as Prader-Willi/Angelman syndrome and Beckwith-Weidemann syndrome where two copies of an imprinted parental chromosome (due to abnormal chromosome segregation) leads to complete silencing of genes within the locus.
180K Oligo Array : The180K Oligo Array (Agilent Technologies, Santa Clara, CA) contains 180,000 oligonucleotide probes that cover the entire genome at a median probe spacing of 13 kb and 5 kb on the X chromosome. In addition, there are ~680 disease causing genes with exon level resolution. The array also includes probes for the pericentromeric and subtelomeric regions with dense probe coverage spanning 10 Mb at each subtelomere. The 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 copy number variants (CNV) are not reported unless there is cause to believe the CNV may be correlated with the presenting phenotype.
SNP+CGH Array: The aCGH supplemented with single nucleotide polymorphism (SNP) probes contains ~300,000 CGH probes and ~100,000 SNP probes that cover the entire genome at a median probe spacing of 13 kb and 5 kb on the X chromosome. This assay can capture copy number changes as described with the 180K Oligo Array as well as copy neutral aberrations such as runs of homozygosity (ROH) and uniparental disomy (UPD). Copy number neutral ROH/UPD regions of any size covering known imprinted gene/loci are reported. ROH/UPD regions greater than 13.5 Mb in size are reported, though this threshold may vary depending on the location of the ROH/UPD region.1
Microarray Results and Parental Studies
Ambry Genetics will provide complimentary parental FISH analysis for microarray results of uncertain significance under the following conditions:
- The proband’s findings are a copy number variant (CNV) of uncertain significance
- The rearrangement is large enough to perform FISH analysis (>0.5Mb for deletions and >1Mb for duplications)
- Probes are commercially available for this region
Note: If alteration is thought to be causative (due to large size) or a known microdeletion or microduplication syndrome (such as 22q11.2) was observed in the proband, then parental/familial FISH analysis is available as a paid testing option. If the alteration is too small to perform a FISH assay (see parameters above), then parental/familial microarray analysis is available as a paid testing option.
Not applicable.
Specimens: Blood, saliva, DNA, (NO BLOOD SPOTS, NO PRENATAL)
Blood:
Container: Purple top EDTA tube (preferred) or yellow top citric acetate tube.
Amount: 3-5 cc;
Minimum for newborns: 180K Oligo Array (0.5-1cc); SNP+CGH 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.
For 180K Oligo Array:
FISH studies may be offered to the parents of a proband for which the microarray results have revealed of copy number variant (CNV) of uncertain significance. This can be done to determine whether the alteration was inherited or de novo. FISH probes are not always available for all regions for which a CNV is observed. The minimum size requirements for FISH on a CNV are >0.3 Mb for deletions and 1Mb for duplications. A sample from the proband and each parent of 1-5ml in a green top sodium heparin (NaHep) tube would be needed for this testing. Please call the lab and confirm that parental studies will be performed at no cost prior to submitting samples.
| Test Code | Technique |
|---|---|
| 3002 | 180K Oligo Array |
| 5480 | SNP+CGH Array |
| Technique | Days |
|---|---|
| 180K Oligo Array | 10-14 |
| SNP+CGH Array | 14-21 |
1. Papenhausen P et al. Am J Med Genet A. UPD detection using homozygosity profiling with a SNP genotyping microarray. 2011;155A(4):757-768. [PMID: 21594998]