NIPBL rearrangements in Cornelia de Lange syndrome: evidence for replicative mechanism and genotype–phenotype correlation

Abstract

Purpose Cornelia de Lange syndrome (CdLS) is a multisystem congenital anomaly disorder characterized by mental retardation, limb abnormalities, distinctive facial features, and hirsutism. Mutations in three genes involved in sister chromatid cohesion, NIPBL, SMC1A, and SMC3, account for ~55% of CdLS cases. The molecular etiology of a significant fraction of CdLS cases remains unknown. We hypothesized that large genomic rearrangements of cohesin complex subunit genes may play a role in the molecular etiology of this disorder. Methods Custom high-resolution oligonucleotide array comparative genomic hybridization analyses interrogating candidate cohesin genes and breakpoint junction sequencing of identified genomic variants were performed. Results Of the 162 patients with CdLS, for whom mutations in known CdLS genes were previously negative by sequencing, deletions containing NIPBL exons were observed in 7 subjects (~5%). Breakpoint sequences in five patients implicated microhomology-mediated replicative mechanisms—such as serial replication slippage and fork stalling and template switching/microhomology-mediated break-induced replication—as a potential predominant contributor to these copy number variations. Most deletions are predicted to result in haploinsuflciency due to heterozygous loss-of-function mutations; such mutations may result in a more severe CdLS phenotype. Conclusion Our findings suggest a potential clinical utility to testing for copy number variations involving NIPBL when clinically diagnosed CdLS cases are mutation-negative by DNA-sequencing studies.

Exonic duplication CNV of NDRG1 associated with autosomal-recessive HMSN-Lom/CMT4D

“…Experiments were performed according to the manufacturer’s protocol and previously described methods. 8 …”

Human CLP1 Mutations Alter tRNA Biogenesis, Affecting Both Peripheral and Central Nervous System Function

“…To confirm the mutation detected by exome sequencing and to perform segregation analysis, standard PCR was carried out as previously described (Pehlivan et al, 2012) by using CLPF1: 5`-AGAGCTGACCCGAAACAAGA-3` and CLPR1: 5`-CCAGCTGAGAAAATGCAGTG-3` primers. Amplification products were electrophoresed on 0.8% agarose gels.…”

Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes

“…Up to 60% of CdLS cases harbor mutations in NIPBL, which encodes a regulatory protein loading the cohesin complex onto the sister chromatids. Copy number variants (CNVs) in the NIPBL locus are found in approximately 5% of NIPBL point mutation-negative CdLS cases, while mosaic mutations in NIPBL are reported to account for an additional 23% (7)(8)(9)(10). SMC1A and SMC3 are core structural components of the cohesin complex.…”