De novo 9q gain in an infant with tetralogy of Fallot with absent pulmonary valve: Patient report and review of congenital heart disease in 9q duplication syndrome

Abstract

Genomic disruptions, altered epigenetic mechanisms, and environmental factors contribute to the heterogeneity of congenital heart defects (CHD). In recent years, chromosomal microarray analysis (CMA) has led to the identification of numerous copy number variations (CNV) in patients with CHD. Genes disrupted by and within these CNVs thus represent excellent candidate genes for CHD. Microduplications of 9q (9q+) have been described in patients with CHD, however, the critical gene locus remains undetermined. Here we discuss an infant with tetralogy of Fallot with absent pulmonary valve, fetal hydrops, and a 3.76 Mb de novo contiguous gain of 9q34.2-q34.3 detected by CMA, and confirmed by karyotype and FISH studies. This duplicated interval disrupted RXRA (retinoid X receptor alpha; OMIM #180245) at intron 1. We also review CHD findings among previously reported patients with 9q (9q+) duplication syndrome. This is the first report implicating RXRA in CHD with 9q duplication, providing additional data in understanding the genetic etiology of tetralogy of Fallot, CHD, and disorders linked to 9q microduplication syndrome. This report also highlights the significance of CMA in the clinical diagnosis and genetic counseling of patients and families with complex CHD.

Keywords: RXRA; retinoid X receptor alpha; tetralogy of Fallot with absent pulmonary valve.

FIG. 1.

Postmortem MRI demonstrating cardiomegaly, enlarged right pulmonary artery (black arrow), atelectasis especially of left lung, and abdominal ascites.

FIG. 2.

Cytogenomic studies in our patient with 9q34.2-q34.3 gains. A: CMA (Affymetrix ChAS Browser) detected contiguous copy number gains; 9q34.2q34.3(137,259,675–139,328,332) x4 (2.1 Mb; 5’ breakpoint at intron 1 of RXRA and gains of exons 2–10; 3’ breakpoint at intron 3 of INPP5E and gains of exons 1–3), 9q34.3(139,328,793–140,018,897) x3 (690 Kb; no gene disruption), 9q34.3(140,018,931–141,020,389) x4 (1.0 Mb; no gene disruption); allele peaks (AP) (0.5, 0, –0.5); weighted log ratio (WLR) (0.5, 0, –0.5); smooth signal (SS) (1–4); oligo and SNP probes (dark and light green). The nearest normal marker is 4.4 Kb from 5’ of gain at intron 1 of RXRA. B and C: Post-CMA karyotype result supported the copy number gains on 9qter (magnified in C). D and E: FISH studies using RP11–644H13 BAC Clone (185 Kb) for 9q34.3 locus; [hg19] chr9:140,535,102–140,719,726) and 9q21-specific control probe revealed enhanced 9q34.3 signal in metaphase (D) and interphase (E) cells; and at least five 9q34.3 signals in interphase nuclei (E).

FIG. 3.

Patients #1–48 with 9q+ detected by karyotype analysis or CMA. Each line represents the extent of 9q+ and corresponds to the patient #, and in parentheses, the ratio of the number of patients with CHD of the total number of patients with the same interval. Breakpoints within 9q21.2-qter end in solid circles, and those outside of 9q21.2-qter end in arrows. While 19/20 patients with only 9q34.3+ do not exhibit CHD (green horizontal dotted interval), patients with 9q34.2 have CHD (red horizontal dotted interval). Patients 1, 2, 11 (no CHD) do not overlap with our patient’s interval. Based on these findings, we suggest that RXRA at 9q34.2 (vertical red dotted lines) may be a critical locus for 9q+-associated CHD. Box: Disruptions in patient #27 (no CHD); and patient #33 at intron 2 of NOTCH1 (with TOF).

FIG. 4.

The genomics and epigenomics landscape of RXRA showing: (A) CpG islands (CGIs) distributed across the gene; (B) the RXRA locus including introns and exons 1–10 and the disruptions (lightning bolt) at introns 1 (our patient; #28) and 7 (patient #27); (C) H3K27Ac marks for predicted active regulatory regions; (D) repeat elements including SINEs (Alu, MIR) (red), LINEs (orange), DNA transposons (blue), long terminal repeats (green), simple repeats (brown). E–I: Each square compares fetal (top) and adult left ventricle (bottom): (E) different intensity peaks (asterisk) in DNase hypersensitivity sites in fetal and adult left ventricle; (F) RNAseq profile; (G) H3K4 methylation; (H) H3K9 methylation; (I) H3K27 methylation.