Baylor Genetics
Harness the power of copy number variant detection with Chromosomal Microarray Analysis
Chromosomal Microarray Analysis provides comprehensive genetic testing for the most common chromosomal conditions as well as a large number of severe genetic conditions not detected by traditional chromosome analysis.
Chromosomal Microarray Analysis (CMA) test examines chromosomes in detail to help detect genetic conditions that cause significant disabilities. Baylor Genetics evaluates the entire human genome for regions that contain too many or too few copies of genetic material.
When we receive your patient’s sample, it is analyzed against a control to determine differences in copy number variations (deletions or duplications). The location and type of change will often determine the cause of your patient’s health condition.
CMA may be considered for individuals with unexplained intellectual disability, developmental delay, autism spectrum disorder, or multiple congenital anomalies.
References
Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 2011;13:680–5; Manning M, Hudgins L. Array; based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med. 2010;12:742–5; Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86:749–64.
Patient Case: Chromosomal Microarray Analysis
Compound Heterozygous Deletions Lead to Dual Diagnoses
Postnatal CMA
Test Code
8665
Turnaround Time
14 Calendar Days
CMA-HR + SNP SCREEN (Comprehensive)
- High-resolution (HR) copy number analysis + SNPs for detection of absence of heterozygosity (AOH) & uniparental disomy (UPD).
- When an SNV is detected in only one allele, this test may detect potential copy number changes in an autosomal recessive disease gene.
- Custom In-house Design: Baylor Genetics’ 400K Agilent array provides enhanced coverage for more than 5,000 genes associated with autosomal dominant, autosomal recessive X-linked disorders, and best candidate disease genes.
Benefits
- Maximum sensitivity for detection of gains and losses
- Exon-by-exon coverage of over 5,000 clinically significant genes
- Probe coverage averaging 30kb across the entire genome
-
60,000 SNP probes used for the detection of AOH associated with UPD or consanguinity
Limitations
- AOH less than 10 Mb in size will not be reported
- The uniparental heterodisomy detection rate is not currently known for this assay
Test Code
8655
Turnaround Time
14 Calendar Days
CMA-HR
- High-resolution (HR) copy number analysis
- Custom Baylor design – 180K Agilent
Benefits
-
High sensitivity for detection of gains and losses
-
Exon-by-exon coverage of over 1,700 genes
-
Tiling coverage of the mitochondrial genome
-
Probe coverage averaging 30kb across the entire genome
Limitations
- Does not detect AOH, UPD, or consanguinity
- Does not have the highest level of exon-by-exon coverage available
Prenatal CMA
Prenatal CMA compares specific regions of an unborn baby’s DNA to that of a normal genome.
The discovery of a genetic change may provide vital information to help manage your patient’s pregnancy and prepare for their baby after delivery. If the ultrasound detects an abnormality, the CMA test might help to determine the cause.
Prenatal CMA should be considered for fetuses with abnormal findings on imaging methodologies, NIPT, or serum screening. It should also be considered for advanced maternal age or further characterization of a previously identified chromosomal abnormality.
The American College of Obstetricians and Gynecologists (ACOG) and the Society for Maternal-Fetal Medicine (SMFM) recommend CMA for prenatal diagnosis in cases with abnormal ultrasound findings.
References
ACOG Practice Bulletin No. 163: Screening for Fetal Aneuploidy. American Obstetricians and Gynecologists. Obstet Gynecol. 2016; 127(5):e12337; Hay SB, Sahoo T, Travis MK, Hovanes K, Dzidic N, Doherty C, Strecker MN. ACOG and SMFM guidelines for prenatal diagnosis: Is karyotyping really sufficient? Prenat Diagn. 2018 Feb;38(3):184-189. doi: 10.1002/pd.5212. Epub 2018 Feb 6. PMID: 29315677; PMCID: PMC5900922.
Harness the power of copy number variant detection with CMA
Expanded CMA
The expanded prenatal array offers exon-by-exon coverage of over 1,700 clinically relevant genes as well as SNP probes across the entire genome. It is recommended for providers and patients who want the highest level of detection possible.
Expanded CMA + Limited Chromosome Analysis
The combination of the expanded CMA and limited karyotype analysis provides a more comprehensive way to obtain the highest level of CMA information as well as detection of any balanced chromosomal rearrangements, triploidy, tetraploidy, and mosaicism diagnosed by cytogenetic analysis.
Target CMA
The targeted prenatal array contains 180,000 oligonucleotides for copy number analysis and SNP probes targeted for chromosomes 6, 7, 11, 14, 15, and 20 for detection of uniparental disomy (UPD). Comparable to the array in the National Institute of Child Health and Human Development (NICHD) trial, this prenatal array is ideal for providers and patients who want detection of all well-characterized deletion/duplication syndromes.
Targeted CMA + Limited Chromosome Analysis
The combination of the targeted CMA and limited karyotype analysis provides a more comprehensive and cost-effective way to obtain targeted CMA information as well as detection of any balanced chromosomal rearrangements, triploidy, tetraploidy, and mosaicism diagnosed by cytogenetic analysis.
Expanded CMA |
Expanded CMA + Limited Chromosome Analysis |
Targeted CMA |
Targeted CMA + Limited Chromosome Analysis |
Product of Conception CMA |
|
|---|---|---|---|---|---|
TEST CODE Amniotic Fluid (AF) |
8670 |
8675 |
8656 |
8673 |
NA |
TEST CODE Chorionic Villi Sampling (CVS) |
8671 |
8676 |
8657 |
8672 |
NA |
TEST CODE Tissue / Cord Blood |
NA |
NA |
NA |
NA |
8639 |
TEST CODE Cord Blood (for ongoing pregnancy) |
8665 |
NA |
NA |
NA |
NA |
DIRECT |
Yes |
Yes |
Yes |
Yes |
Yes |
Turnaround Time (days) |
7–10 |
7–10 |
7–10 |
7–10 |
21 |
CULTURED |
Yes |
Yes |
Yes |
Yes |
Yes |
Turnaround Time (days) |
21–28 |
21–28 |
21–28 |
21–28 |
21 |
Prenatal Specimen Requirements
Please call 1.800.411.4363 to discuss prenatal sample requirements with a genetic counselor. For detailed specimen requirements, please visit: www.baylorgenetics.com/cma
Are Parental Samples Necessary?
While not mandatory, if received, we use the maternal samples to check for maternal cell contamination and parental samples to clarify variants of unknown significance.
Detection of Clinically Relevant Monogenic Copy-Number Variants by a Comprehensive Genome-Wide Microarray with Exonic Coverage
Chau MHK, Anderson SA, Song R, Cooper L, Ward PA, Yuan B, Shaw C, Stankiewicz P, Cheung SW, Vossaert L, Wang Y, Owen NM, Smith J, Bacino CA, Schulze KV, Bi W. Clin Chem. 2025 Jan 3;71(1):141-154. doi: 10.1093/clinchem/hvae188. PMID: 39749505.
Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA
Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM. Nat Med. 2019 Mar;25(3):439-447. doi: 10.1038/s41591-018-0334-x. PMID: 30692697.
Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development
Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SW, Wu L, Yu F. Hum Mutat. 2017 Jun;38(6):669-677. PMID: 28247551
Mechanisms for Complex Chromosomal Insertions
Gu S, Szafranski P, Akdemir ZC, Yuan B, Cooper ML, Magriñá MA, Bacino CA, Lalani SR, Breman AM, Smith JL, Patel A, Song RH, Bi W, Cheung SW, Carvalho CM, Stankiewicz P, Lupski JR. PLoS Genet. 2016 Nov 23;12(11):e1006446. PMID: 27880765
Genome-wide copy number analysis on DNA from fetal cells isolated from the blood of pregnant women
Kølvraa S, Singh R, Normand EA, Qdaisat S, Van denVeyver IB, Jackson L, Hatt L, Schelde P, Uldbjerg N, Vestergaard EM, Zhao L, Chen R, Shaw CA, Breman AM, Beaudet AL. Prenat Diagn. 2016 Oct 19. PMID: 27761919
4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions
Bi W, Cheung SW, Breman AM, Bacino CA. Am J Med Genet A. 2016 Oct;170(10):2540-50. PMID: 27287194
Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells
Normand E, Qdaisat S, Bi W, Shaw C, Van den Veyver I, Beaudet A, Breman A. Prenat Diagn. 2016 Sep;36(9):823-30. PMID: 27368744
Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing
Amy M. Breman, Jennifer C. Chow, Lance U’Ren, Elizabeth A. Normand, Sadeem Qdaisat, Li Zhao, David M. Henke, Rui Chen, Chad A. Shaw, Laird Jackson, Yaping Yang, Liesbeth Vossaert, Rachel H.V. Needham, Daniel Campton, Jeffrey L. Werbin, Ron C. Seubert, Ignatia B. Van den Veyver, Jackie L. Stilwell, Eric P. Kaldjian, Arthur L. Beaudet. Prenat Diagn. 2016 Sep 12. PMID: 27616633
Triploidy mosaicism (45,X/68,XX) in an infant presenting with failure to thrive
Posey J, Mohrbacher N, Smith JL, Patel A, Potocki L, Breman AM. Am J Med Genet A. 2015 Nov 14. PMID: 26566716
Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene
Tompson SW, Bacino CA, Safina NP, Bober MB, Proud VK, Funari T, Wangler MF, Nevarez L, Ala-Kokko L, Wilcox WR, Eyre DR, Krakow D, Cohn DH. Am J Hum Genet. 87:708-712, 2010. PMID: 21035103
CMA Test Resources
Specimen Requirements
SAMPLE TYPE |
REQUIREMENTS |
SHIPPING CONDITIONS |
|---|---|---|
 Blood in EDTA |
Draw blood in an EDTA (purple-top) tube(s) and send 3–5cc (adults/children) and 2–3cc (infants
For clarification or follow-up of CMA results, sodium heparin (green-top) tubes are highly recommended. Send 3–5cc (adults/children) and 1–2cc (infants
| Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. |
 Extracted DNA |
Send at least 20μg of purified DNA (minimal concentration of 50ng/μg; A260/A280 of ~1.7–2.0). |
Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. |
 Skin Fibroblasts |
Send 1–2 T25 flasks at approximately 80% confluency. |
Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. |
 Buccal Swab |
Collect with ORAcollect•Dx (OCD-100) self-collection kit (provided by Baylor Genetics with instructions). We highly recommend the sample be collected by a healthcare professional. |
Ship at room temperature in an insulated container by overnight courier. Do not heat or freeze. |
How It Works
Order appropriate testing for your patient.
The patient’s sample is collected.
The patient’s sample is sent to Baylor Genetics.
Results are sent to the physician.
Discuss the results with the patient.