Abstract
Congenital heart defects (CHDs) are the most common birth defects in neonatal life. CHDs could be presented as isolated defects or associated with developmental delay (DD) and/or other congenital malformations. A small proportion of cardiac defects are caused by chromosomal abnormalities or single gene defects; however, in a large proportion of cases no genetic diagnosis could be achieved by clinical examination and conventional genetic analysis. The development of genome wide array-Comparative Genomic Hybridization technique (array-CGH) allowed for the detection of cryptic chromosomal imbalances and pathogenic copy number variants (CNVs) not detected by conventional techniques. We investigated 94 patients having CHDs associated with other malformations and/or DD. Clinical examination and Echocardiography was done to all patients to evaluate the type of CHD. To investigate for genome defects we applied high-density array-CGH 2 × 400K (41 patients) and CGH/SNP microarray 2 × 400K (Agilent) for 53 patients. Confirmation of results was done using Fluorescent in situ hybridization (FISH) or qPCR techniques in certain cases. Chromosomal abnormalities such as trisomy 18, 13, 21, microdeletions: del22q11.2, del7q11.23, del18 (p11.32; p11.21), tetrasomy 18p, trisomy 9p, del11q24-q25, add 15p, add(18)(q21.3), and der 9, 15 (q34.2; q11.2) were detected in 21/94 patients (22%) using both conventional cytogenetics methods and array-CGH technique. Cryptic chromosomal anomalies and pathogenic variants were detected in 15/73 (20.5%) cases. CNVs were observed in a large proportion of the studied samples (27/56) (48%). Clustering of variants was observed in chromosome 1p36, 1p21.1, 2q37, 3q29, 5p15, 7p22.3, 8p23, 11p15.5, 14q11.2, 15q11.2, 16p13.3, 16p11.2, 18p11, 21q22, and 22q11.2. CGH/SNP array could detect loss of heterozygosity (LOH) in different chromosomal loci in 10/25 patients. Array-CGH technique allowed for detection of cryptic chromosomal imbalances that could not be detected by conventional cytogenetics methods. CHDs associated with DD/congenital malformations presented with a relatively high rate of cryptic chromosomal abnormalities. Clustering of CNVs in certain genome loci needs further analysis to identify candidate genes that may provide clues for understanding the molecular pathway of cardiac development.
Similar content being viewed by others
References
Alabdulgader AA (2001) Congenital heart disease in 740 subjects: epidemiological aspects. Ann Trop Paediatr 21:111–118
Fida NM, Al-Aama J, Nichols W, Nichols W, Alqahtani M (2007) A prospective study of congenital malformations among live born neonates at a University Hospital in Western Saudi Arabia. Saudi Med J 28:1367–1373
Greer W, Sandridge AL, Al-Menieir M, Al Rowais A (2005) Geographical distribution of congenital heart defects in Saudi Arabia. Ann Saudi Med 25:63–69
Alqurashi M, El Mouzan M, Al Herbish A, Al Salloum A, Al Omer A (2007) Symptomatic congenital heart disease in the Saudi Children and Adolescents Project. Ann Saudi Med 27:442–444
Al-Mesned A, Al Akhfash AA, Sayed M (2012) Incidence of severe congenital heart disease at the province of Al-Qassim, Saudi Arabia. Congenit Heart Dis 7:277–282
Blue GM, Kirk EP, Sholler GF, Harvey RP, Winlaw DS (2012) Congenital heart disease: current knowledge about causes and inheritance. Med J Aust 197:155–159
Bittel DC, Yu S, Newkirk H, Kibiryeva N, Holt A 3rd, et al. (2009) Refining the 22q11.2 deletion breakpoints in DiGeorge syndrome by aCGH. Cytogenet Genome Res 124:113–120
Breckpot J, Thienpont B, Peeters H, de Ravel T, Singer A et al (2010) Array comparative genomic hybridization as a diagnostic tool for syndromic heart defects. J Pediatr 156:810–817, 817 e811–817 e814
Richards AA, Santos LJ, Nichols HA, Crider BP, Elder FF et al (2008) Cryptic chromosomal abnormalities identified in children with congenital heart disease. Pediatr Res 64:358–363
Becker SM, Al Halees Z, Molina C, Paterson RM (2001) Consanguinity and congenital heart disease in Saudi Arabia. Am J Med Genet 99:8–13
Kearney HM, Kearney JB, Conlin LK (2011) Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med 31:595–613, ix
VanGuilder HD, Vrana KE, Freeman WM (2008) Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques 44:619–626
Baker K, Sanchez-de-Toledo J, Munoz R, Orr R, Kiray S et al (2012) Critical congenital heart disease–utility of routine screening for chromosomal and other extracardiac malformations. Congenit Heart Dis 7:145–150
Hartman RJ, Rasmussen SA, Botto LD, Riehle-Colarusso T, Martin CL et al (2011) The contribution of chromosomal abnormalities to congenital heart defects: a population-based study. Pediatr Cardiol 32:1147–1157
Thienpont B, Breckpot J, Holvoet M, Vermeesch JR, Devriendt K (2007) A microduplication of CBP in a patient with mental retardation and a congenital heart defect. Am J Med Genet A 143A:2160–2164
De Gregori M, Ciccone R, Magini P, Pramparo T, Gimelli S et al (2007) Cryptic deletions are a common finding in “balanced” reciprocal and complex chromosome rearrangements: a study of 59 patients. J Med Genet 44:750–762
Baptista J, Mercer C, Prigmore E, Gribble SM, Carter NP et al (2008) Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. Am J Hum Genet 82:927–936
Campbell CL, Collins RT 2nd, Zarate YA (2014) Severe neonatal presentation of Kleefstra syndrome in a patient with hypoplastic left heart syndrome and 9q34.3 microdeletion. Birth Defects Res A 100:985–990
Cody JD, Ghidoni PD, DuPont BR, Hale DE, Hilsenbeck SG et al (1999) Congenital anomalies and anthropometry of 42 individuals with deletions of chromosome 18q. Am J Med Genet 85:455–462
Hale DE, Cody JD, Baillargeon J, Schaub R, Danney MM et al (2000) The spectrum of growth abnormalities in children with 18q deletions. J Clin Endocrinol Metab 85:4450–4454
Versacci P, Digilio MC, Sauer U, Dallapiccola B, Marino B (2005) Absent pulmonary valve with intact ventricular septum and patent ductus arteriosus: a specific cardiac phenotype associated with deletion 18q syndrome. Am J Med Genet Part A 138A:185–186
Cody JD, Sebold C, Heard P, Carter E, Soileau B et al (2015) Consequences of chromsome18q deletions. Am J Med Genet Part C 169:265–280
Turleau C (2008) Monosomy 18p. Orphanet J Rare Dis 3:4
Schmidt B, Udink ten Cate F, Weiss M, Koehler U (2012) Cardiac malformation of partial trisomy 7p/monosomy 18p and partial trisomy 18p/monosomy 7p in siblings as a result of reciprocal unbalanced malsegregation–and review of the literature. Eur J Pediatr 171:1047–1053
Kim EY, Kim YK, Kim MK, Jung JM, Jeon GW et al (2011) A case of de novo duplication of 15q24-q26.3. Korean J Pediatr 54:267–271
Zollino M, Tiziano F, Di Stefano C, Neri G (1999) Partial duplication of the long arm of chromosome 15: confirmation of a causative role in craniosynostosis and definition of a 15q25-qter trisomy syndrome. Am J Med Genet 87:391–394
Xu H, Xiao B, Ji X, Hu Q, Chen Y et al (2014) Nonmosaic tetrasomy 15q25.2 → qter identified with SNP microarray in a patient with characteristic facial appearance and review of the literature. Eur J Med Genet 57:329–333
Al Turki S, Manickaraj AK, Mercer CL, Gerety SS, Hitz MP et al (2014) Rare variants in NR2F2 cause congenital heart defects in humans. Am J Hum Genet 94:574–585
Soemedi R, Wilson IJ, Bentham J, Darlay R, Topf A et al (2012) Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. Am J Hum Genet 91:489–501
Serra-Juhe C, Rodriguez-Santiago B, Cusco I, Vendrell T, Camats N et al (2012) Contribution of rare copy number variants to isolated human malformations. PLoS ONE 7:e45530
Girirajan S, Rosenfeld JA, Cooper GM, Antonacci F, Siswara P et al (2010) A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet 42:203–209
Jansen FA, Blumenfeld YJ, Fisher A, Cobben JM, Odibo AO et al (2015) Array comparative genomic hybridization and fetal congenital heart defects: a systematic review and meta-analysis. Ultrasound Obstet Gynecol 45:27–35
Lu XY, Phung MT, Shaw CA, Pham K, Neil SE et al (2008) Genomic imbalances in neonates with birth defects: high detection rates by using chromosomal microarray analysis. Pediatrics 122:1310–1318
Acknowledgements
The authors would like to thank the King Abdulaziz City for Science and Technology (KACST), King Abdulaziz University, for funding this study as part of the project No. P-L-11-0556. We thank Assoc. Prof. M. Abu-Elmagd for helping in editing and improving the quality of the figures. We also thank all the patients and their families who participated in this study for donating their blood samples.
Funding
The study was part of a project funded by King Abdulaziz City for Science and Technology (KACST), KSA, Project No. (P-L-11-0556). The research team declares that the copyrights are reserved to the KACST and that all views, scientific findings, conclusions, and recommendations mentioned in the study represent the sole opinion of the research team and do not in any way reflect KACST views.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethics Approval
The work was part of the KACST large project (P-L-11-0556) approved by the CEGMR Ethical committee under the Code # 016-CEGMR-ETH. The Ethical committee License # at KACST: HA-02-J-003.
Informed Consent
An informed consent to participate in this study was obtained from patients, or their parents or legal guardians.
Rights and permissions
About this article
Cite this article
Hussein, I.R., Bader, R.S., Chaudhary, A.G. et al. Identification of De Novo and Rare Inherited Copy Number Variants in Children with Syndromic Congenital Heart Defects. Pediatr Cardiol 39, 924–940 (2018). https://doi.org/10.1007/s00246-018-1842-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00246-018-1842-7