A case with a de novo chromosome 8.9 Mb 11pter duplication and 6.4 Mb 11qter deletion derived from a father with a normal karyotype

Objectives – To determine the cause of marked hypotonia and neonatal encephalopathy, mild anemia and thrombocytopenia, and nonspecific facial dysmorphism in a neonate after extensive neurological and biochemical evaluations, and karyotyping failed to establish the etiology. Methods – Whole exome sequencing (WES), single-nucleotide polymorphisms chromosomal microarray (SNPs CMA), and fluorescence in-situ hybridization (FISH) analysis were performed in the patient and the parents. Results – WES did not show a candidate gene/diagnosis. Trio-CMA and FISH confirmed a de novo 8.9 Mb duplication of 11p15.4p15.5 and a 6.4 Mb deletion of 11q24.3q25 in the child, and that the duplicated 11p was of paternal origin, based on the SNPs analysis. On long-term follow-up, encephalopathy improved gradually, thrombocytopenia resolved, facial puffiness persisted, and developmental delay remained. The present patient represents the first case of de novo 11p duplication with 11q deletion and severe neonatal encephalopathy. The de novo chromosomal rearrangement could still have resulted from nonallelic homologous recombination, triggered by low-copy repeats (LCRs) at distal 11p and 11q during paternal meiosis, despite the lower LCR density. Alternatively, it may represent a random event, as it does not involve the recurrent deletion/duplication typically observed in regions with dense LCRs.