Lab Med Online.  2023 Jul;13(3):141-153. 10.47429/lmo.2023.13.3.141.

Practical Guidelines for Chromosomal Microarray Analysis for Constitutional Abnormalities: Part I, General and Prenatal

Affiliations
  • 1GC Genome Yongin, Korea
  • 2GC Labs Yongin, Korea
  • 3Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
  • 4Department of Laboratory Medicine, , Yonsei University College of Medicine, Seoul, Korea
  • 5Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Korea

Abstract

Chromosomal microarray (CMA) testing can enhance the quality of clinical care for congenital abnormalities, including prenatal diagnosis. Laboratories require a comprehensive understanding of the strengths, weaknesses, and purposes of CMA testing. They should also have appropriate plans, guidelines, and documented records for platform validation and quality control at all stages of testing. Performing prenatal CMA testing necessitates understanding the features of prenatal specimens, devising a verification process, reporting results, and providing genetic counseling. This guideline aims to establish standard test protocols for conducting CMA tests, ensuring accurate results, and aiding in diagnosing and treating patients.

Keyword

Congenital abnormalities; DNA copy number variations; Microarray analysis; Prenatal diagnosis

Reference

1. Gardner RJM, Sutherland GR, editors. Chromosome abnormalities and genetic counseling. 4th ed. Oxford, England: Oxford University Press;2011.
2. Zneimer SM. Cytogenetic abnormalities: Chromosomal, FISH and microarray-based clinical reporting and interpretation of result. 1st ed. Hoboken, NJ: John Wiley & Sons, Inc.;2014.
3. Ministry of Health and Welfare. 2019; Partial amendment of details on the application criteria and methods of medical care benefits. Notification no. 2019 - 166, Jul. 29, 2019. https://www.mohw.go.kr/react/modules/viewHtmlConv.jsp?BOARD_ID=5900&CONT_SEQ=350329&FILE_SEQ=269612. Updated on Jul 2019.
4. Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, et al. 2010; Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 86:749–64. DOI: 10.1016/j.ajhg.2010.04.006. PMID: 20466091. PMCID: PMC2869000.
5. Manning M, Hudgins L. 2010; Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med. 12:742–5. DOI: 10.1097/GIM.0b013e3181f8baad. PMID: 20962661. PMCID: PMC3111046.
6. Cooley LD, Lebo M, Li MM, Slovak ML, Wolff DJ. 2013; American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. Genet Med. 15:484–94. DOI: 10.1038/gim.2013.49. PMID: 23619274.
7. South ST, Lee C, Lamb AN, Higgins AW, Kearney HM. 2013; ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 15:901–9. DOI: 10.1038/gim.2013.129. PMID: 24071793.
8. Kearney HM, South ST, Wolff DJ, Lamb A, Hamosh A, Rao KW. 2011; American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med. 13:676–9. DOI: 10.1097/GIM.0b013e31822272ac. PMID: 21681105.
9. Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST. 2011; American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 13:680–5. DOI: 10.1097/GIM.0b013e3182217a3a. PMID: 21681106.
10. Brothman AR, Dolan MM, Goodman BK, Park JP, Persons DL, Saxe DF, et al. 2011; College of American Pathologists/American College of Medical Genetics proficiency testing for constitutional cytogenomic microarray analysis. Genet Med. 13:765–9. DOI: 10.1097/GIM.0b013e31821d3165. PMID: 21633292.
11. Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, et al. 2020; Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). Genet Med. 22:245–57. DOI: 10.1038/s41436-019-0686-8. PMID: 31690835. PMCID: PMC7313390.
12. Shao L, Akkari Y, Cooley LD, Miller DT, Seifert BA, Wolff DJ, et al. 2021; Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 23:1818–29. DOI: 10.1038/s41436-021-01214-w. PMID: 34131312.
13. Korean Society of Medical Genetics and Genomics. 2021. Guidelines for clinical practice of postnatal chromosomal microarray analysis. (https://www.guideline.or.kr/guide/view.php?number=1125&cate=A).
14. Cherry AM, Akkari YM, Barr KM, Kearney HM, Rose NC, South ST, et al. 2017; Diagnostic cytogenetic testing following positive noninvasive prenatal screening results: a clinical laboratory practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med. 19:845–50. DOI: 10.1038/gim.2017.91. PMID: 28726804.
15. Canadian College of Mmedical Geneticists Cytogenetics Committee. CCMG Guidelines for Genomic Microarray Testing. https://www.ccmg-ccgm.org/wp-content/uploads/2022/04/CCMG_Guidelines_for_Genomic_Microarray_Testing_FINAL.pdf. Updated on Jan 2016.
16. Armour CM, Dougan SD, Brock JA, Chari R, Chodirker BN, DeBie I, et al. 2018; Practice guideline: joint CCMG-SOGC recommendations for the use of chromosomal microarray analysis for prenatal diagnosis and assessment of fetal loss in Canada. J Med Genet. 55:215–21. DOI: 10.1136/jmedgenet-2017-105013. PMID: 29496978. PMCID: PMC5869456.
17. Committee on Genetics and the Society for Maternal-Fetal Medicine. 2016; Committee Opinion No.682: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology. Obstet Gynecol. 128:e262–8. DOI: 10.1097/AOG.0000000000001817. PMID: 27875474.
18. Clinical and Laboratory Standards Institute. Genomic copy number microarrays for constitutional genetic and oncology applications. 1st ed. CLSI guideline MM21. Wayne, PA: Clinical and Laboratory Standards Institute;2015.
19. Silva M, de Leeuw N, Mann K, Schuring-Blom H, Morgan S, Giardino D, et al. 2019; European guidelines for constitutional cytogenomic analysis. Eur J Hum Genet. 27:1–16. DOI: 10.1038/s41431-018-0244-x. PMID: 30275486. PMCID: PMC6303289.
20. Gill K, Sasaki J, Jayakar P, Sosa L, Welch E. 2021; Chromosomal microarray detects genetic risks of neurodevelopmental disorders in newborns with congenital heart disease. Cardiol Young. 31:1275–82. DOI: 10.1017/S1047951121000202. PMID: 33536103.
21. Cho SY, Ki CS, Jang JH, Sohn YB, Park SW, Kim SH, et al. Familial Xp22. 33-Xp22.12 deletion delineated by chromosomal microarray analysis causes proportionate short stature. Am J Med Genet A. 2012; 158A:1462–6. DOI: 10.1002/ajmg.a.35357. PMID: 22581654.
22. Masri A, Gimelli S, Hamamy H, Sloan-Béna F. Microarray delineation of familial chromosomal imbalance with deletion 5q35 and duplication 10q25 in a child showing multiple anomalies and dysmorphism. Am J Med Genet A. 2014; 164A:1254–61. DOI: 10.1002/ajmg.a.36412. PMID: 24478242.
23. Kohannim O, Peredo J, Dipple KM, Quintero-Rivera F. 2011; Clinical findings associated with a de novo partial trisomy 10p11.22p15.3 and monosomy 7p22.3 detected by chromosomal microarray analysis. Case Rep Genet. 2011:131768. DOI: 10.1155/2011/131768. PMID: 23074670. PMCID: PMC3447257.
24. Pinto IP, Minasi LB, da Cruz AS, de Melo AV, da Cruz e Cunha DM, Pereira RR, et al. 2014; A non-syndromic intellectual disability associated with a de novo microdeletion at 7q and 18p, microduplication at Xp, and 18q partial trisomy detected using chromosomal microarray analysis approach. Mol Cytogenet. 7:44. DOI: 10.1186/1755-8166-7-44. PMID: 25028595. PMCID: PMC4099144.
25. Sismani C, Kitsiou-Tzeli S, Ioannides M, Christodoulou C, Anastasiadou V, Stylianidou G, et al. 2008; Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype. Mol Cytogenet. 1:15. DOI: 10.1186/1755-8166-1-15. PMID: 18644119. PMCID: PMC2516517.
26. Korean Institute of Genetic Testing Evaluation. Korean Institute of Genetic Testing Evaluation inspection checklist for cytogenetic tests. In: Korean Institute of Genetic Testing Evaluation. 2022.
27. The Korean Society for Laboratory Medicine/Laboratory Medicine Foundation. Good laboratory inspection checklist: cytogenetic tests. In:The Korean Society for Laboratory Medicine/Laboratory Medicine Foundation. 2022.
28. Wapner RJ, Martin CL, Levy B, Ballif BC, Eng CM, Zachary JM, et al. 2012; Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 367:2175–84. DOI: 10.1056/NEJMoa1203382. PMID: 23215555. PMCID: PMC3549418.
29. Dugoff L, Norton ME, Kuller JA. 2016; The use of chromosomal microarray for prenatal diagnosis. Am J Obstet Gynecol. 215:B2–9. DOI: 10.1016/j.ajog.2016.07.016. PMID: 27427470.
30. Group of consensus of the use of chromosomal microarray analysis in prenatal diagnosis. 2014; Consensus of the use of chromosomal microarray analysis in prenatal diagnosis. Zhonghua Fu Chan Ke Za Zhi. 49:570–2.
31. Gu S, Jernegan M, Van den Veyver IB, Peacock S, Smith J, Breman A. 2018; Chromosomal microarray analysis on uncultured chorionic villus sampling can be complicated by confined placental mosaicism for aneuploidy and microdeletions. Prenat Diagn. 38:858–65. DOI: 10.1002/pd.5342. PMID: 30094853.
32. Hsu LY, Kaffe S, Jenkins EC, Alonso L, Benn PA, David K, et al. 1992; Proposed guidelines for diagnosis of chromosome mosaicism in amniocytes based on data derived from chromosome mosaicism and pseudomosaicism studies. Prenat Diagn. 12:555–73. DOI: 10.1002/pd.1970120702. PMID: 1508847.
33. Schreck RR, Falik-Borenstein Z, Hirata G. 1990; Chromosomal mosaicism in chorionic villus sampling. Clin Perinatol. 17:867–88. DOI: 10.1016/S0095-5108(18)30550-5. PMID: 2286032.
Full Text Links
  • LMO
Actions
Cited
CITED
export Copy
Close
Share
  • Twitter
  • Facebook
Similar articles
Copyright © 2024 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: koreamed@kamje.or.kr