5-cell karyotype + microarray bundle (pediatric)

Test #:


Turnaround Time:

Microarray: 2-4 days. Karyotype: 7 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 neonatal patients or for sample types not listed, please contact Allele Diagnostics.

  • Peripheral blood: 3-5 mL EDTA + 3-5 mL NaHep
CPT Codes:

81229 x1, 88230 x1, 88261 x1, 88285 x01, 88291 x1

Ordering Requirements:
Clinical Utility:
  • Patients with multiple anomalies not specific to a well-delineated genetic syndrome.
  • Apparent nonsyndromic DD/ID.
  • Autism spectrum disorders.
  • Diagnosis of trisomies in addition to microdeletions/duplications for rapid results in a NICU setting.
Test Description:

Test is a combination of array CGH with SNP analysis and chromosome analysis by karyotype.

This bundle includes a limited karyotype study and rapid CGH and SNP microarray. The combination of these tests allows for identification of large and small chromosomal abnormalities as well as unbalanced and balanced structural abnormalities. FISH visualization is routinely performed following the detection of a copy number abnormality by microarray. Karyotype, microarray, and FISH tests are reported as each test is completed to provide each result as quickly as possible.


Karyotype can identify numeric chromosomal abnormalities, large unbalanced and balanced structural abnormalities. Abnormalities larger than approximately 5-10 Mb can be visualized. Karyotype is useful in conjunction with microarray to identify balanced abnormalities, such as translocations and inversions, that microarray is not designed to detect. This abbreviated blood karyotype study involves counting and analyzing 5 cells and karyotyping 3 cells. This karyotype study is not designed to rule out mosaicism, however, additional cells are evaluated as indicated if mosaicism is suspected.


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 20 kb in targeted regions and 80 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). 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.

  • Manning & Hudgins, Professional Practice and Guidelines Committee. Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med. 12(11):742-5 (2010). PubMed: 20962661
  • Miller et al., Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 86(5):749-64 (2010). PubMed: 20466091
  1. Multiplier used here is specific to the study performed. Standard karyotype with 5 cells analyzed will not use CPT code 88285, however, this code will be included x1 if additional cells are required to complete the study.