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SNP Array for Tissue and POC

Item Value
Available Stat? No
Test code SNPAT
Performed by Medical Genomics - Cytogenetics (Microarray)
Method 850K SNP Array
Collection Instructions Insurance pre-authorization required for outpatients

Only collect samples Monday - Friday and avoid holidays if possible.

Label tube with type of tissue being submitted

Transport sample at room temperature as soon as possible to lab. If transport is delayed refrigerate sample.

For UCSF Samples (from remote sites) Click here for sample collection instructions

For NON-UCSF Samples Click here for Requisition form & Account set-up instructions. Note we only do institutional billing.
Container type Sterile centrifuge tube with transport media provided by lab, Hanks balanced salt solution or RPMI with antibiotics
Amount to Collect 1 cc (Cubic centimeter) or 20 mg tissue
Sample type Tissue or POC
Preferred volume 1 cc3 (Cubic centimeter) or 20 mg tissue
Min. Volume 0.3 cc3 (Cubic centimeter) or 15 mg tissue
UCSF Rejection Criteria Leaking, contaminated, frozen or mislabeled tube(s)
Processing notes Refrigerate samples DO NOT CENTRIFUGE OR FREEZE. Transport asap to China Basin Cytogenetics

For questions, contact the microarray laboratory at 514-8964
Normal range
Synonyms SNP array amniocentesis; SNP array CVS; SNP array chorionic villus sample; ACGHT; Array CGH Tissue or Products of Conception
Stability 48 hours at Room temperature
Turn around times 7-10 days
Additional information Method
High density single-nucleotide polymorphism (SNP) oligo BeadChip arrays are used for the assay. Genomic DNA from the prenatal sample is amplified, fragmented, and hybridized to synthetic oligonucleotides covalently deposited on the BeadChip array. A single base-pair extension reaction with nucleotides conjugated to different fluorophores is carried out. Analysis with an imaging system reveals the presence of a major or minor allele at a given SNP, while total fluorescence intensity at a given SNP reflects copy number of that locus.

The Illumina CytoSNP 850k BeadChip contains 850,000 SNP probes distributed across the genome, with average resolution of 18 Kb. This array targets 3,262 genes of clinical significance, as defined by the International Collaboration for Clinical Genomics and Cancer Cytogenetics Microarray Consortium, with resolution averaging 10 Kb in these genes. Overall, these SNP probes cover known disease- or syndrome-related loci, subtelomeric regions, pericentromeric regions, and sex chromosomes. Both copy number and B-allele frequency at a given locus are used to guide clinical interpretation.

Classification of copy number variants (CNVs), ROH, and total genome ploidy is performed primarily using BlueFuse Multi Software.

Accuracy
The Accuracy of detecting clinically significant unbalanced changes by the SNP array is 100%.

Detection of aneuploidy and triploidy: 15 aneuploidy and 2 triploidy prenatal samples detected by conventional chromosome analysis performed in our laboratory were all precisely detected by the SNP array.

Detection of CNVs: 44 prenatal samples, including 15 with CNVs and 29 with normal findings reported by an external reference laboratory were all precisely confirmed by the SNP array.

Detection of ROH: 1 prenatal sample and 1 blood sample with known ROH were both confirmed by the SNP array.

There were no discrepant results within the capabilities of the SNP array technology in comparison of the samples between the SNP array findings and that of the reference lab/alternative methods (such as karyotyping and DNA methylation test).


Limitations
Genomic aberrations that may not be detected by SNP array assay include:
- Balanced rearrangement (i.e. balanced translocation, insertion or inversion) and tetraploidy resulted from endoduplication.
- Low level (<30%) mosaicism for unbalanced rearrangements and aneuploidy
- Nucleotide sequence changes (i.e. point mutation or small insertion/deletion below the level of detection or cut-off thresholds)
Imbalances of regions not represented on the array
- Genomic changes in mixed samples (i.e. prenatal samples with maternal cell contamination)

The lab will charge a tissue culture setup fees (TCAFCV) if SNP microarray is ordered without chromosomes studies

The lab will charge a tissue culture setup fees (TCPOC) if SNP microarray is ordered without chromosome studies
CPT coding 81229, 88233

Not: Additional charges for MCC studies when necessary, culture set-up fees may apply
LDT or Mod FDA? Yes
Last Updated 8/18/2015 12:32:16 PM
Entry Number 1613
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