Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies

  • Mohamed A. M. AliEmail author
  • Abdelrahman M. Hassan
  • Mosaab A. Saafan
  • Adel A. Abdelmagid
Original Article


Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.


Chromosomal microarray Loss of heterozygosity Developmental delay Dysmorphology Multiple congenital anomalies 


Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical Approval

All procedures performed in studies involving human participants were in accordance with the local ethical committee and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.

Informed Consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

10528_2019_9931_MOESM1_ESM.docx (18 kb)
Supplementary material 1 (DOCX 18 kb)
10528_2019_9931_MOESM2_ESM.docx (109 kb)
Supplementary material 2 (DOCX 108 kb)
10528_2019_9931_MOESM3_ESM.docx (68 kb)
Supplementary material 3 (DOCX 67 kb)


  1. Alkuraya FS (2010) Homozygosity mapping: one more tool in the clinical geneticist’s toolbox. Genet Med 12(4):236–239PubMedCrossRefGoogle Scholar
  2. Battaglia A, Doccini V, Bernardini L, Novelli A, Loddo S, Capalbo A, Filippi T, Carey JC (2013) Confirmation of chromosomal microarray as a first-tier clinical diagnostic test for individuals with developmental delay, intellectual disability, autism spectrum disorders and dysmorphic features. Eur J Paediatr Neurol 17(6):589–599PubMedCrossRefGoogle Scholar
  3. Bi W, Borgan C, Pursley AN, Hixson P, Shaw CA, Bacino CA, Lalani SR, Patel A, Stankiewicz P, Lupski JR, Beaudet AL, Cheung SW (2013) Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosome analysis in today’s genomic array era? Genet Med 15(6):450–457PubMedCrossRefGoogle Scholar
  4. Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, Li D, Amaral D, Brown N, Lockhart PJ, Scheffer IE, Alberti A, Shaw M, Pettinato R, Tervo R, de Leeuw N, Reijnders MR, Torchia BS, Peeters H, O’Roak BJ, Fichera M, Hehir-Kwa JY, Shendure J, Mefford HC, Haan E, Gécz J, de Vries BB, Romano C, Eichler EE (2014) Refining analyses of copy number variation identifies specific genes associated with developmental delay. Nat Genet 46(10):1063–1071PubMedPubMedCentralCrossRefGoogle Scholar
  5. Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif BC, Shaffer LG, Eichler EE (2011) A copy number variation morbidity map of developmental delay. Nat Genet 43(9):838–846PubMedPubMedCentralCrossRefGoogle Scholar
  6. Coulter ME, Miller DT, Harris DJ, Hawley P, Picker J, Roberts AE, Sobeih MM, Irons M (2011) Chromosomal microarray testing influences medical management. Genet Med 13(9):770–776PubMedCrossRefGoogle Scholar
  7. D’Arrigo S, Gavazzi F, Alfei E, Zuffardi O, Montomoli C, Corso B, Buzzi E, Sciacca FL, Bulgheroni S, Riva D, Pantaleoni C (2016) The diagnostic yield of array comparative genomic hybridization is high regardless of severity of intellectual disability/developmental delay in children. J Child Neurol 31(6):691–699PubMedCrossRefGoogle Scholar
  8. Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P, Itsara A, Vives L, Walsh T, McCarthy SE, Baker C, Mefford HC, Kidd JM, Browning SR, Browning BL, Dickel DE, Levy DL, Ballif BC, Platky K, Farber DM, Gowans GC, Wetherbee JJ, Asamoah A, Weaver DD, Mark PR, Dickerson J, Garg BP, Ellingwood SA, Smith R, Banks VC, Smith W, McDonald MT, Hoo JJ, French BN, Hudson C, Johnson JP, Ozmore JR, Moeschler JB, Surti U, Escobar LF, El-Khechen D, Gorski JL, Kussmann J, Salbert B, Lacassie Y, Biser A, McDonald-McGinn DM, Zackai EH, Deardorff MA, Shaikh TH, Haan E, Friend KL, Fichera M, Romano C, Gécz J, DeLisi LE, Sebat J, King MC, Shaffer LG, Eichler EE (2010) A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet 42(3):203–209PubMedPubMedCentralCrossRefGoogle Scholar
  9. Girirajan S, Rosenfeld JA, Coe BP, Parikh S, Friedman N, Goldstein A, Filipink RA, McConnell JS, Angle B, Meschino WS, Nezarati MM, Asamoah A, Jackson KE, Gowans GC, Martin JA, Carmany EP, Stockton DW, Schnur RE, Penney LS, Martin DM, Raskin S, Leppig K, Thiese H, Smith R, Aberg E, Niyazov DM, Escobar LF, El-Khechen D, Johnson KD, Lebel RR, Siefkas K, Ball S, Shur N, McGuire M, Brasington CK, Spence JE, Martin LS, Clericuzio C, Ballif BC, Shaffer LG, Eichler EE (2012) Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 367(14):1321–1331PubMedPubMedCentralCrossRefGoogle Scholar
  10. Hehir-Kwa JY, Pfundt R, Veltman JA (2015) Exome sequencing and whole genome sequencing for the detection of copy number variation. Expert Rev Mol Diagn 15(8):1023–1032PubMedCrossRefGoogle Scholar
  11. Henderson LB, Applegate CD, Wohler E, Sheridan MB, Hoover-Fong J, Batista DA (2014) The impact of chromosomal microarray on clinical management: a retrospective analysis. Genet Med 16(9):657–664PubMedCrossRefGoogle Scholar
  12. Hochstenbach R, van Binsbergen E, Engelen J, Nieuwint A, Polstra A, Poddighe P, Ruivenkamp C, Sikkema-Raddatz B, Smeets D, Poot M (2009) Array analysis and karyotyping: workflow consequences based on a retrospective study of 36,325 patients with idiopathic developmental delay in the Netherlands. Eur J Med Genet 52(4):161–169PubMedCrossRefGoogle Scholar
  13. Kaminsky EB, Kaul V, Paschall J, Church DM, Bunke B, Kunig D, Moreno-De-Luca D, Moreno-De-Luca A, Mulle JG, Warren ST, Richard G, Compton JG, Fuller AE, Gliem TJ, Huang S, Collinson MN, Beal SJ, Ackley T, Pickering DL, Golden DM, Aston E, Whitby H, Shetty S, Rossi MR, Rudd MK, South ST, Brothman AR, Sanger WG, Iyer RK, Crolla JA, Thorland EC, Aradhya S, Ledbetter DH, Martin CL (2011) An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities. Genet Med 13(9):777–784PubMedPubMedCentralCrossRefGoogle Scholar
  14. Kearney HM, Kearney JB, Conlin LK (2011a) Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med 31(4):595–613PubMedCrossRefGoogle Scholar
  15. Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST, Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee (2011b) American College of Medical Genetics Standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 13(7):680–685PubMedCrossRefGoogle Scholar
  16. Kharbanda M, Tolmie J, Joss S (2015) How to use… microarray comparative genomic hybridisation to investigate developmental disorders. Arch Dis Child Educ Pract Ed 100(1):24–29PubMedCrossRefGoogle Scholar
  17. Manning M, Hudgins L, Practice Professional, Committee Guidelines (2010) Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet Med 12(11):742–745PubMedPubMedCentralCrossRefGoogle Scholar
  18. Martin CL, Warburton D (2015) Detection of chromosomal aberrations in clinical practice: from karyotype to genome sequence. Annu Rev Genomics Hum Genet 16:309–326PubMedCrossRefGoogle Scholar
  19. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40(10):1166–1174PubMedCrossRefGoogle Scholar
  20. McGowan-Jordan J, Simons A, Schmid M (2016) ISCN 2016: an international system for human cytogenomic nomenclature (2016). In: McGowan-Jordan J, Simons A, Schmid M (eds) Reprint of: Cytogenetic and Genome Research, vol 149. Karger, Basel, pp 1–2Google Scholar
  21. 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 (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(5):749–764PubMedPubMedCentralCrossRefGoogle Scholar
  22. Palmer E, Speirs H, Taylor PJ, Mullan G, Turner G, Einfeld S, Tonge B, Mowat D (2014) Changing interpretation of chromosomal microarray over time in a community cohort with intellectual disability. Am J Med Genet A 164A(2):377–385PubMedCrossRefGoogle Scholar
  23. Papenhausen P, Schwartz S, Risheg H, Keitges E, Gadi I, Burnside RD, Jaswaney V, Pappas J, Pasion R, Friedman K, Tepperberg J (2011) UPD detection using homozygosity profiling with a SNP genotyping microarray. Am J Med Genet A 155A(4):757–768PubMedCrossRefGoogle Scholar
  24. Rauch A, Hoyer J, Guth S, Zweier C, Kraus C, Becker C, Zenker M, Hüffmeier U, Thiel C, Rüschendorf F, Nürnberg P, Reis A, Trautmann U (2006) Diagnostic yield of various genetic approaches in patients with unexplained developmental delay or mental retardation. Am J Med Genet A 140(19):2063–2074PubMedCrossRefGoogle Scholar
  25. Ravnan JB, Tepperberg JH, Papenhausen P, Lamb AN, Hedrick J, Eash D, Ledbetter DH, Martin CL (2006) Subtelomere FISH analysis of 11 688 cases: an evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J Med Genet 43(6):478–489PubMedCrossRefGoogle Scholar
  26. Rehder CW, David KL, Hirsch B, Toriello HV, Wilson CM, Kearney HM (2013) American College of Medical Genetics and Genomics: standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med 15(2):150–152PubMedCrossRefGoogle Scholar
  27. Reiff M, Bernhardt BA, Mulchandani S, Soucier D, Cornell D, Pyeritz RE, Spinner NB (2012) “What does it mean?”: uncertainties in understanding results of chromosomal microarray testing. Genet Med 14(2):250–258PubMedPubMedCentralCrossRefGoogle Scholar
  28. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, Laboratory Quality Assurance Committee ACMG (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17(5):405–424PubMedPubMedCentralCrossRefGoogle Scholar
  29. Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, Kearney HM, Ledbetter DH, South ST, Thorland EC, Martin CL (2012) Towards an evidence-based process for the clinical interpretation of copy number variation. Clin Genet 81(5):403–412PubMedCrossRefGoogle Scholar
  30. Riggs ER, Wain KE, Riethmaier D, Smith-Packard B, Faucett WA, Hoppman N, Thorland EC, Patel VC, Miller DT (2014) Chromosomal microarray impacts clinical management. Clin Genet 85(2):147–153PubMedCrossRefGoogle Scholar
  31. Roberts JL, Hovanes K, Dasouki M, Manzardo AM, Butler MG (2014) Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services. Gene 535(1):70–78PubMedCrossRefGoogle Scholar
  32. Sagoo GS, Butterworth AS, Sanderson S, Shaw-Smith C, Higgins JP, Burton H (2009) Array CGH in patients with learning disability (mental retardation) and congenital anomalies: updated systematic review and meta-analysis of 19 studies and 13,926 subjects. Genet Med 11(3):139–146PubMedCrossRefGoogle Scholar
  33. Schnekenberg RP, Németh AH (2014) Next-generation sequencing in childhood disorders. Arch Dis Child 99(3):284–290PubMedCrossRefGoogle Scholar
  34. Shaffer LG, Bejjani BA, Torchia B, Kirkpatrick S, Coppinger J, Ballif BC (2007) The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future. Am J Med Genet C Semin Med Genet 145C(4):335–345PubMedCrossRefGoogle Scholar
  35. Shevell M, Ashwal S, Donley D, Flint J, Gingold M, Hirtz D, Majnemer A, Noetzel M, Sheth RD, Quality Academy of Neurology; Practice Committee of the Child Neurology Society (2003) Practice parameter: evaluation of the child with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and The Practice Committee of the Child Neurology Society. Neurology 60(3):367–380PubMedCrossRefGoogle Scholar
  36. Shoukier M, Klein N, Auber B, Wickert J, Schröder J, Zoll B, Burfeind P, Bartels I, Alsat EA, Lingen M, Grzmil P, Schulze S, Keyser J, Weise D, Borchers M, Hobbiebrunken E, Röbl M, Gärtner J, Brockmann K, Zirn B (2013) Array CGH in patients with developmental delay or intellectual disability: are there phenotypic clues to pathogenic copy number variants? Clin Genet 83(1):53–65PubMedCrossRefGoogle Scholar
  37. Slavotinek AM (2008) Novel microdeletion syndromes detected by chromosome microarrays. Hum Genet 124(1):1–17PubMedCrossRefGoogle Scholar
  38. Smeets DF (2004) Historical prospective of human cytogenetics: from microscope to microarray. Clin Biochem 37(6):439–446PubMedCrossRefGoogle Scholar
  39. South ST, Lee C, Lamb AN, Higgins AW, Kearney HM, Working Group for the American College of Medical Genetics and Genomics Laboratory Quality Assurance Committee (2013) ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med 15(11):901–909PubMedCrossRefGoogle Scholar
  40. Srebniak MI, Diderich KE, Govaerts LC, Joosten M, Riedijk S, Galjaard RJ, Van Opstal D (2014) Types of array findings detectable in cytogenetic diagnosis: a proposal for a generic classification. Eur J Hum Genet 22(7):856–858PubMedCrossRefGoogle Scholar
  41. Turner DJ, Miretti M, Rajan D, Fiegler H, Carter NP, Blayney ML, Beck S, Hurles ME (2008) Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat Genet 40(1):90–95PubMedCrossRefGoogle Scholar
  42. Vallespín E, Palomares Bralo M, Mori MÁ, Martín R, García-Miñaúr S, Fernández L, de Torres ML, García-Santiago F, Mansilla E, Santos F, M-Montaño VE, Crespo MC, Martín S, Martínez-Glez V, Delicado A, Lapunzina P, Nevado J (2013) Customized high resolution CGH-array for clinical diagnosis reveals additional genomic imbalances in previous well-defined pathological samples. Am J Med Genet A 161A(8):1950–1960PubMedCrossRefGoogle Scholar
  43. van Ommen GJ (2005) Frequency of new copy number variation in humans. Nat Genet 37(4):333–334PubMedCrossRefGoogle Scholar
  44. Vulto-van Silfhout AT, Hehir-Kwa JY, van Bon BW, Schuurs-Hoeijmakers JH, Meader S, Hellebrekers CJ, Thoonen IJ, de Brouwer AP, Brunner HG, Webber C, Pfundt R, de Leeuw N, de Vries BB (2013) Clinical significance of de novo and inherited copy-number variation. Hum Mutat 34(12):1679–1687PubMedCrossRefGoogle Scholar
  45. Wang JC, Ross L, Mahon LW, Owen R, Hemmat M, Wang BT, El Naggar M, Kopita KA, Randolph LM, Chase JM, Matas Aguilera MJ, Siles JL, Church JA, Hauser N, Shen JJ, Jones MC, Wierenga KJ, Jiang Z, Haddadin M, Boyar FZ, Anguiano A, Strom CM, Sahoo T (2015) Regions of homozygosity identified by oligonucleotide SNP arrays: evaluating the incidence and clinical utility. Eur J Hum Genet 23(5):663–671PubMedCrossRefGoogle Scholar
  46. Watson CT, Marques-Bonet T, Sharp AJ, Mefford HC (2014) The genetics of microdeletion and microduplication syndromes: an update. Annu Rev Genomics Hum Genet 15:215–244PubMedPubMedCentralCrossRefGoogle Scholar
  47. Wincent J, Anderlid BM, Lagerberg M, Nordenskjöld M, Schoumans J (2011) High-resolution molecular karyotyping in patients with developmental delay and/or multiple congenital anomalies in a clinical setting. Clin Genet 79(2):147–157PubMedCrossRefGoogle Scholar
  48. Wiszniewska J, Bi W, Shaw C, Stankiewicz P, Kang SH, Pursley AN, Lalani S, Hixson P, Gambin T, Tsai CH, Bock HG, Descartes M, Probst FJ, Scaglia F, Beaudet AL, Lupski JR, Eng C, Cheung SW, Bacino C, Patel A (2014) Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing. Eur J Hum Genet 22(1):79–87PubMedCrossRefGoogle Scholar
  49. Zarrei M, MacDonald JR, Merico D, Scherer SW (2015) A copy number variation map of the human genome. Nat Rev Genet 16(3):172–183PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Mohamed A. M. Ali
    • 1
    Email author
  • Abdelrahman M. Hassan
    • 2
  • Mosaab A. Saafan
    • 3
  • Adel A. Abdelmagid
    • 3
  1. 1.Department of Biochemistry, Faculty of ScienceAin Shams UniversityCairoEgypt
  2. 2.Human Cytogenetics DepartmentNational Research CenterCairoEgypt
  3. 3.Cytogenetics UnitAl Borg Medical LaboratoriesJeddahKingdom of Saudi Arabia

Personalised recommendations