Test Code: 4835

Chromosomal SNP Microarray: Products of conception – Prenatal testing
Test Code: 4835
Turnaround time: 2 to 3 weeks

CONDITION DESCRIPTION

At least 50% of first trimester miscarriages are caused by a chromosomal imbalance.  The CEN4GEN chromosomal SNP microarray analysis of uncultured products of conception (POC) samples increases the likelihood of detecting clinically significant genetic imbalances as compared to conventional G-banded analysis. Since this CEN4GEN test uses DNA extracted from uncultured cells, rather than cultured cells, tissue culture failure is avoided. Microarray testing detects smaller imbalances than conventional G-banded analysis, especially since POC samples often have poor chromosome morphology. This test detects triploidy, trisomy, monosomy, and chromosome deletions and duplications. This test is a cost effective method to detect chromosomal imbalances, which is important to determine the recurrence risk for future pregnancies.

Reference:
Schaeffer et al. (2004) Am J Hum Genet; 74:1168-1174.

INDICATIONS

  • warranted for the evaluation of any spontaneous pregnancy loss and can provide a diagnosis and recurrence risk for future pregnancies.

METHODOLOGY

DNA isolated from the products of conception sample is hybridized to an array containing oligonucleotide and SNP probes across the genome to detect copy number imbalances and regions of homozygosity.

This test consists of 2.6 million markers (including 750,000 SNPs) which allows for the detection of both copy number variation (CNV) and large stretches [>10 Megabases (Mb)] of absence of heterozygosity (AOH), which can result from uniparental disomy (UPD) or common parental descent. The design is based on recommendations from the International Standards for Cytogenomic Arrays (ISCA) Consortium (Baldwin et al. (2008) Genet Med; 10(6):415-429).

DETECTION

Deletions and duplications of 400 kilobases (kb) or greater are detected and will be reported. Smaller deletions or duplications in regions of known microdeletion/microduplication syndromes or in clinically relevant genes will also be reported.

This test is designed to detect whole and partial chromosome UPD, long stretches of absence of heterozygosity (AOH) greater than 3 Mb, and AOH in clinically relevant regions.  In addition, this test can also detect triploidy, a common cause of miscarriages. Possible UPD will be reported when a chromosome has at least one homozygous regions >10 Mb. Homozygosity due to apparent common descent will be reported when >5% of the autosomal genome is present in long stretches of AOH. These regions of AOH will be specified to consider recessive risk alleles.

This test will not detect balanced translocations, balanced inversions, imbalances smaller than the resolution of this array, point mutations, or low level mosaicism (usually less than 25%).

SPECIMEN REQUIREMENTS

Type: Maternal specimen
Maternal cell contamination studies are warranted to rule out the possibility of maternal cells in female products of conception.  Submit a 5cc maternal whole blood sample in an EDTA tube, or 20 to 60 ug of maternal DNA, together with only 1 specimen type of products of conception below.
 
Type: Chorionic Villi
Specimen Requirements:
5 to 10 ug of DNA in TE buffer.

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample overnight at room temperature for receipt at CEN4GEN within 24 hours of collection.

Type: Fetal Tissue Biopsy
Specimen Requirements:
5 to 10 ug of DNA in TE buffer.

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample overnight at room temperature for receipt at CEN4GEN within 24 hours of collection.