Targeted rapid microarray with backbone (CGH and SNP)

Test #:

111

Turnaround Time:

2-4 days

Specimen Requirements:

Specimens should be shipped at room temperature in a leak-proof, rigid container with overnight delivery. To discuss minimum acceptable specimens for prenatal patients or for sample types not listed, please contact Allele Diagnostics.

  • Amniotic fluid: 15-20 mL whole fluid
  • Chorionic villus sampling (CVS): 5-10 mg tissue in sterile media or saline
  • Cultured Cells: 2 x T-25 flasks (70% confluent)
  • DNA1,2: 5 μg
  • Products of conception (POC): 15-20 mg in sterile media or saline
CPT Codes:

81229 x1, 88233 x1 (POC), 88235 x1 (amnio/CVS)

Ordering Requirements:
Clinical Utility:
  • Abnormal cell-free fetal DNA test.
  • Abnormal fetal ultrasound.
  • Abnormal maternal serum screen.
  • Any patient undergoing invasive prenatal testing.
  • Diagnosis of trisomies in addition to microdeletions/duplications for rapid results.
  • Fetal loss or stillbirth.
  • Parental concern/anxiety.
  • Previous pregnancy with aneuploidy.
Test Description:

Test is performed using array CGH with SNP analysis. The platform utilizes a less dense backbone compared to Allele Diagnostics test #110, reducing the likelihood of unclear results.

In general, microarray is useful for detecting most large and small structural chromosome abnormalities and copy neutral AOH with rapid results. FISH visualization is routinely performed following an abnormal microarray result and reported independently from the microarray. Karyotype should be performed in conjunction with microarray if detection of balanced abnormalities is desired.

The CGH portion of this microarray can identify numeric chromosomal abnormalities as well as unbalanced structural abnormalities. The microarray is designed to target pericentromeric regions, subtelomeric regions, and regions associated with copy number abnormalities. In addition, a less dense backbone provides coverage throughout the whole genome. Abnormalities larger than approximately 40 kb in targeted regions and 400 kb in backbone regions can be identified. Test results will be reported as: 1) clinically significant, 2) abnormality identified with unclear clinical significance, or 3) normal (no clinically significant or unclear abnormalities identified). Copy number changes that are unlikely to have clinical relevance at the time of report will be noted in the report.

The SNP component of this microarray will detect long continuous stretches of homozygosity (or absence of heterozygosity, AOH) as well as triploidy. AOH can be indicative of uniparental disomy (UPD) if within a chromosome, or an increased risk of a recessive disorder if identified across multiple chromosomes. Note that for some regions of the genome, AOH of 8-10 Mb may be within normal limits and will not be reported. There are a small number of chromosome regions which are associated with imprinting or UPD disorders. AOH of 5 Mb or more will be reported for regions that have previously been associated with imprinting conditions. The SNP component of this assay also has the ability to determine an overall level of homozygosity throughout the genome of 5% or more. If identified, this will be reported as it may be reflective of identity by descent and an increased risk for recessive disorders. Clinical correlation is required to properly assess a potential for relatedness. In addition, this assay cannot determine whether the alteration is paternal, maternal or de novo in origin. Additional UPD or molecular testing may be required.

References:
  • American College of Obstetricians and Gynecologists Committee on Genetics. Committee Opinion No. 581: The use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol, 122(6):1374-1377 (2013). PubMed: 24264715
  • American College of Obstetricians and Gynecologists. Practice Bulletin No. 162 Summary: Prenatal Diagnostics Testing for Genetic Disorders. Obstet Gynecol, 127(5):976-978 (2016). PubMed: 27101119
  • Fiorentino F et al., Chromosomal microarray analysis as a first-line test in pregnancies with a priori low risk for the detection of submicroscopic chromosomal abnormalities. Euro J Hum Genet. 21(7):725-30 (2013). PubMed: 23211699
Footnotes:
  1. If submitting a specimen that cannot be cultured, a secondary specimen may be recommended for follow-up by FISH visualization (at no extra charge).
  2. Allele Diagnostics accepts DNA samples prepared by other laboratories for microarray testing. To provide clinicians with optimal results, we recommend using the Qiagen Gentra Puregene extraction kit. If upon receipt the DNA is found to be suboptimal, our staff will contact the clinician to discuss testing options.
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