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Postnatal Cytogenomic Studies

Chromosome Analysis

Chromosome analysis is indicated for patients with suspected chromosomal abnormalities, family history of a chromosome abnormality, primary or secondary amenorrhea, couples experiencing multiple pregnancy losses or infertility, etc. Supply blood in sodium heparin vacutainer (green top) – 3-5 ml total should be sufficient to perform all requested cytogenetics testing. Average turnaround time for routine chromosome analysis is 3-14 days.

Cytogenetic analysis from skin biopsies is indicated for suspicion of mosaicism and cases such as Pallister-Killian syndrome. Ideal sample is a sterile punch biopsy including some dermal tissue. Place sample in sterile mammalian culture medium (if not available, contact lab for transport medium – do not immerse in saline). Average turnaround time is 2-4 weeks.

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:
Peripheral/fetal/cord blood: 88230, 88262, 88291
Fibroblast: 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 for constitutional abnormalities include detection of origin of marker chromosomes, delineation of subtle rearrangements with the use of subtelomeric FISH probes, and confirmation of common microdeletion/duplication syndromes. Average turnaround time for routine FISH analysis is 3-14 days.

FISH tests for common microdeletion/duplication syndrome:
  • Wolf-Hirschhorn syndrome (4p-)
  • Cri-du-Chat syndrome (5p del)
  • Saethre-Chotzen syndrome (7p21.1 del)
  • Williams-Beuren syndrome (7q11.23 del)
  • Pallister-Killian syndrome (12p++)
  • Prader-Willi and Angelman syndromes (15q11.2 del)
  • Smith-Magenis syndrome (17p11.2 del)
  • Charcot-Marie-Tooth (17p12+)
  • Hereditary neuropathy with lability to pressure palsies (HNPP, 17p12 del)
  • Miller-Diecker/Lissencephaly (17p13 del)
  • Cat-eye syndrome (22q11.2++)
  • DiGeorge/Velocardiofacial/CATCH 22 (22q11.2 del)
  • Phelan McDermid syndrome (22q13.3 del)
  • STS/Steroid sulfatase/Ichthyosis and Kallman syndromes (Xp22.3 del)
  • SRY, Sex reversal (Yp11.2+/-)
  • XIST, X inactivation (Xq13)
NOTE: These studies 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.

Chromosome Microarray Analysis

Chromosomal microarray analysis (CMA) has been recommended as the first-tier genetic evaluation for pediatric patients with multiple congenital anomalies (MCA), dysmorphic features, failure to thrive (FTT), unexplained developmental delay (DD), intellectual disability (ID) and autism spectrum disorders (ASD). Array comparative genomic hybridization with single nucleotide polymorphism (aCGH+SNP) analysis is used to examine the entire genome for pathogenic copy number variant (pCNVs, deletions and duplications), as well as copy neutral regions of homozygosity (ROH) that may be clinically significant. Average turnaround time for aCGH is 10-21 days.

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

Microarray CPT codes:
Genomic Microarray 180K (aCGH+SNP): 81228
Genomic Microarray 400K (aCGH+SNP): 81229


Xiang B, Li A, Valentin D, Nowak NJ, Zhao H, Li P. Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay. Am J Med Genet A. 2008 Aug 1;146A(15):1942-54.

Xiang B, Zhu H, Shen Y, Miller DT, Lu K, Hu X, Andersson HC, Narumanchi TM, Wang Y, Martinez JE, Wu BL, Li P, Li MM, Chen TJ, Fan YS. Genome-wide oligonucleotide array comparative genomic hybridization for etiological diagnosis of mental retardation: a multicenter experience of 1499 clinical cases. J Mol Diagn. 2010 Mar;12(2):204-12.

Wei Y, Xu F, Li P. Technology-driven and evidence-based genomic analysis for integrated pediatric and prenatal genetics evaluation. J Genet Genomics. 2013 Jan 20;40(1):1-14.

Wen J, Comerford K, Xu Z, Wu W, Amato K, Grommisch B, DiAdamo A, Xu F, Chai H, Li P. Analytical validation and chromosomal distribution of regions of homozygosity by oligonucleotide array comparative genomic hybridization from normal prenatal and postnatal case series. Mol Cytogenet. 2019 Mar 6;12:12.

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.