Test Directory

Microarray Analysis, Product of Conception

Chromosomal microarray (CMA) is capable of detecting aneuploidies, deletions and duplications below the resolution of chromosome analysis (karyotyping), as well as long continuous regions of homozygosity.

A limited G Band chromosome analysis is also included in the study to detect balanced structural chromosome rearrangements.

The CytoScan HD Accel Assay is a qualitative assay intended for the postnatal, prenatal, and neoplastic detection of chromosomal copy number variants (CNV) in genomic DNA (gDNA) obtained from patients' fresh or frozen tissue biopsies, including bodily fluids (i.e. peripheral whole blood, bone marrow, lymph node, amniotic fluid, chorionic villus sampling, fetal tissue, tumor, saliva, buccal, direct/cultured cells) referred for chromosomal testing based on clinical presentation. The CytoScan HD Accel Assay is indicated for the detection of CNVs associated with developmental delay and/or intellectual disability (DD/ID), congenital anomalies, dysmorphic features, neoplasia, and fetal anomalies.

Assay results are intended to be used in conjunction with other clinical and diagnostic findings, consistent with professional standards of practice including confirmation by alternative methods, parental evaluation, clinical genetic evaluation, and counseling as appropriate. Interpretation of assay results is intended to be performed only by healthcare professionals board certified in clinical cytogenetics or molecular genetics.

The assay is intended to be used on the CytoScan GeneChip System 3000 and analyzed by Chromosome Analysis Suite Software (ChAS Software).

This device is not intended to be used for standalone diagnostic purposes for testing or screening of postnatal, prenatal, or somatic genetic aberrations. The results should be interpreted in conjunction with standard cytogenetics and/or molecular analyses and in correlation with the patient's clinical presentation.

Specimen: Nonfixed -Chorionic Villus Sampling (CVS) or Product of Conception (POC)

Collection Container: Sterile container with transport medium (Kit is provided by the Cytogenetics Department)

Desired Specimen Size: 5x5mm tissue

Minimum Acceptable Specimen Size: 2x3mm tissue

Specimen should be aseptically collected and placed in a sterile collection container with transport medium.

Each specimen must be accompanied by a requisition form, script, electronic order or physician note.

• Transport to the laboratory at room temperature.
• Store specimen in a sterile collection container with transport medium at room temperature and deliver to lab within 24 hours.
• If specimen cannot be delivered within 24 hours, store in refrigerator. Do not freeze specimen.
• Specimens collected on the weekends must be refrigerated upon arrival at HNL Lab Medicine.

• Specimens arriving without any form of patient identification.
• Specimen is in a fixative.
• Specimen frozen.
• Necrotic tissue submitted.
• Specimen is contaminated.

Reference Range:

SNP microarray analysis is performed using the Cytoscan HD Accel platform, which uses 743,130 SNP probes and 2,029,441 copy number probes. These probes cover the genome at a mean probe spacing of 0.818kb and include probes in the pericentromeric and subtelomeric regions. This analysis will not detect all types of genetic alterations including but not limited to balanced structural chromosome rearrangements (i.e. translocations, insertions,or inversions); deletions, duplications, or mosaicisms below the resolution of the CytoScan HD Accel analysis including mutations at the base pair genetic level. The microarray will detect DNA copy-number changes at a threshold >1Mb for deletions, >2Mb for duplications, and low level mosaicism 10%. Copy number variations (CNV) reported as common findings in the general population, not associated with known clinically relevant genes, or not located within a region previously reported as having diagnostic or prognostic significance are interpreted as not clinically relevant and may not be reported in this analysis. CNV are significantly detected at a resolution of >20kb spanning no less than 25 contiguous markers for losses of genomic DNA unless the copy number variant is classified as benign, does not include coding genes, or is located within the intron of a gene and >50kb spanning no less than 50 contiguous markers for gains of genomic DNA within the clinically significant gene regions represented in this CytoScan HD microarray platform. Mosaic copy number <10% may not be reliably detected and detection sensitivity is affected by the size of the CNV. Loss or absence of heterozygosity (LOH/AOH) is reliably detectable at a resolution of >3Mb. Contiguous region of homozygosity on a single chromosome of >20Mb interstitially or >10Mb telomerically is suggestive of uniparental disomy (UPD) though this threshold may vary depending upon the location of the ROH and the overall percentage of ROH that is detected. ROHs comprising 2.5% or greater of the covered genome will be reported and it is strongly recommended that UPD follow-up testing be performed. Contiguous regions of homozygosity of >8Mb on multiple chromosomes suggests Identical By Descent (IBD) alleles which has potential increased risk for recessive disorders.

This analysis will not detect all types of genetic alterations including but not limited to balanced structural chromosome rearrangements (i.e. translocations, insertions, or inversions); deletions, duplications, or mosaicisms below the resolution of the CytoScan HD analysis including mutations at the base pair genetic level.

• Product of Conception, Microarray
• SNP Microarray, Product of Conception
• CMA
• POC
• Microarray
• Prenatal

SNP/CGH microarray analysis is performed using the Applied Biosystems Cytoscan HD Accel platform, which uses 743,130 SNP probes and 2,029,441 copy number probes. These probes cover the genome at a mean probe spacing of 0.818kb and include probes in the pericentromeric and subtelomeric regions. The microarray will detect DNA copy-number changes at a threshold >1Mb for deletions, >2Mb for duplications and low level mosaicism 10%. This analysis will not detect all types of genetic alterations including, but not limited to, balanced structural chromosome rearrangements (i.e. translocations, insertions, or inversions); deletions, duplications, or mosaicisms below the resolution of the Cytoscan HD Accel analysis including mutations at the base pair genetic level.

A 10 cell limited G Band chromosome analysis is also included to detect balanced structural chromosome rearrangements.