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Prenatal Cytogenomic Studies

Chromosome Analysis

Prenatal chromosome analysis is appropriate for indications of advanced maternal age, abnormal ultrasound findings, abnormal screening results, multiple fetal losses, or a suspected chromosomal cause of fetal loss/abnormalities. Chromosome analysis provides detection of numerical and structural abnormalities for the fetus and balanced chromosomal rearrangements in the family.

Amniotic fluid (AF): Supply 15-25 ml of amniotic fluid in sterile 15 ml conical tubes. Please provide gestational age. Average turnaround time is 10-14 days.

Chorionic villus (CVS): Supply 15-40 mg of villi in RPMI media along with gestational age. Average turnaround time is 7-10 days.

Products of conception (POC): The ideal sample would include both chorionic villus and fetal tissue. Place sample in sterile mammalian culture medium i.e. RPMI or HEPES (if not available, contact lab for transport medium – do not immerse in saline or formalin). Please provide gestational age. Average turnaround time is 14-28 days.

NOTE: These studies involve culturing of living cells; therefore, turnaround times given represent average times, which are subject to multiple variables.

Chromosome analysis CPT codes:
Amniotic Fluid: 88235, 88269, 88291
Chorionic Villus: 88235, 88267, 88291
Products of Conception: 88233, 88262, 88291
Note: additional codes may be used for extended analyses (rule out mosaicism 88263; additional karyotypes 88280; additional cell counts 88285)

FISH Tests

Fluorescence in Situ Hybridization (FISH) testing extends routine cytogenetic banding methods by resolving ambiguous diagnoses and providing another tool to diagnose submicroscopic and cryptic abnormalities. FISH is a relatively simple, fast, and reliable procedure. FISH testing can be performed independently or concurrently with other cytogenetics studies.

Applications of FISH in prenatal studies can include rapid detection of aneuploidies on directly prepared cells, or detection of recurrent constitutional microdeletion/microduplication syndromes from cultured cells. Average turnaround time for aneuploidy FISH is 1-3 days; microdeletion/microduplication FISH is 7-14 days.

NOTE: These studies may involve culturing of living cells; therefore, turnaround times given represent average times, which are subject to multiple variables.

FISH CPT codes:
FISH analysis may include 88230-88239, 88271-88275 and 88291. Contact lab for specific codes based on specimen type and exact testing being performed.

Microarray Analysis

Array comparative genomic hybridization (aCGH, CGH+SNP array) and OncoScan Microarray Assay (OMA, SNP array) analyses have been used for prenatal cases with suspected fetal anomalies, as reflex testing for POCs with normal chromosome results, and as a salvage procedure for POCs with cell culture failure.

Microarray test is performed on DNA extracted from cultured amniotic fluid or direct villi/fetal tissue samples. POC microarray is also available on DNA extracted from FFPE tissue. CVS microarray turnaround time is 7-14 days; AF microarray turnaround time is 14-21 days; Reflex POC microarray turnaround time is 14-21 days after chromosome results.

NOTE: Microarray turnaround time assumes insurance prior authorization/approval is in place.

Microarray CPT codes:
aCGH 180K (CGH+SNP Array) (most AF/CVS): 81228
aCGH 400K (CGH+SNP Array) (upon request): 81229
OMA (SNP array) (all POCs): 81228


Li P, Pomianowski P, DiMaio MS, Florio JR, Rossi MR, Xiang B, Xu F, Yang H, Geng Q, Xie J, Mahoney MJ. Genomic characterization of prenatally detected chromosomal structural abnormalities using oligonucleotide array comparative genomic hybridization. Am J Med Genet A. 2011 Jul;155A(7):1605-15.

Zhou Q, Wu SY, Amato K, DiAdamo A, Li P. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples. J Genet Genomics. 2016 Mar 20;43(3):121-31.

Chai H, DiAdamo A, Grommisch B, Boyle J, Amato K, Wang D, Wen J, Li P. Integrated FISH, Karyotyping and aCGH Analyses for Effective Prenatal Diagnosis of Common Aneuploidies and Other Cytogenomic Abnormalities. Med Sci (Basel). 2019 Jan 23;7(2):16.

Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H. A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings. Front Genet. 2019 Nov 20;10:1162.

Xie X, Tan W, Li F, Carrano E, Ramirez P, DiAdamo A, Grommisch B, Amato K, Chai H, Wen J, Li P. Diagnostic cytogenetic testing following positive noninvasive prenatal screening results of sex chromosome abnormalities: Report of five cases and systematic review of evidence. Mol Genet Genomic Med. 2020 Jul;8(7):e1297.

Wen J, Grommisch B, DiAdamo A, Chai H, Ng SME, Hui P, Bale A, Mak W, Wang G, Li P. Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues. Mol Cytogenet. 2021 Apr 2;14(1):21.