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Harness the power of copy number variant detection with Chromosomal Microarray Analysis

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As one of the first laboratories to offer CMA testing, Baylor Genetics has performed over 100,000 CMA tests.

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.

As one of the first laboratories to offer CMA testing, Baylor Genetics has performed over 100,000 CMA tests.

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.

Postnatal CMA

Test Code
Turnaround Time

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
Turnaround Time

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.

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.

TARGETED 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

Turnaround Time (days)

7-10

7-10

7-10

7-10

21

CULTURED

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.

Take the first step with CMA Test

PRODUCT OVERVIEW
Requisitions
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 (infant <2 years).

For clarification or follow-up of CMA results, sodium heparin (green top) tubes are highly recommended. Send 3-5cc (adults/children) and 1-2cc (infant<2 years).

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.
Consent Form
Online Order
Medical Necessity Forms
Request Test Kit

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.

More questions? Please contact us by calling 1.800.411.4363.

Carlos A. Bacino
Carlos A. Bacino
MD
Medical Director, Cytogenetics
Janice Smith
Janice Smith
PhD
Sr. Clinical Director, Cytogenetics
Weimin Bi
Weimin Bi
PhD
Division Director, Cytogenetics
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. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. 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. Mechanisms for Complex Chromosomal Insertions. 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. Genome-wide copy number analysis on DNA from fetal cells isolated from the blood of pregnant women. 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. 4p16.3 microdeletions and microduplications detected by chromosomal microarray analysis: New insights into mechanisms and critical regions. 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. (2016) Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells. 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. Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing. Prenat Diagn. 2016 Sep 12. PubMed: 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. Triploidy mosaicism (45,X/68,XX) in an infant presenting with failure to thrive. 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.   Fibrochondrogenesis results from mutations in the COL11A1 type XI collagen gene.  Am J Hum Genet. 87:708-712, 2010. PMID: 21035103