Molecular characterization of CPS1 deletions by array CGH

Abstract

CPSI deficiency usually results in severe hyperammonemia presenting in the first days of life warranting prompt diagnosis. Most CPS1 defects are non-recurrent, private mutations, including point mutation, small insertions and deletions. In this study, we report the detection of large deletions varying from 1.4 kb to >130 kb in the CPS1 gene of 4 unrelated patients by targeted array CGH. These results underscore the importance of analysis of large deletions when only one mutation or no mutations are identified in cases where CPSI deficiency is strongly indicated.

Improvement of diagnostic yield in carbamoylphosphate synthetase 1 (CPS1) molecular genetic investigation by RNA sequencing

“…As reported before, 11 distribution of CPS1 mutations shows predominance of the catalytic domains (116 of 172 mutations): the bicarbonate phosphorylation domain (exons [13][14][15][16][17][18][19][20] was affected by 61 mutations and the carbamate phosphorylation domain (exons 25-34) by 55 mutations ( Figure 2).…”

“…More than 230 CPS1 mutations are currently reported . Molecular genetic investigation for CPS1D can use different methods: exon per exon sequencing (direct Sanger sequencing), next generation sequencing (NGS) as part of a (often custom‐made) gene panel or whole exome or whole genome sequencing with or without the analysis of copy number variation (CNV), and RNA analysis …”

“…[7][8][9][10][11][12][13][14][15] Molecular genetic investigation for CPS1D can use different methods: exon per exon sequencing (direct Sanger sequencing), next generation sequencing (NGS) as part of a (often custom-made) gene panel or whole exome or whole genome sequencing with or without the analysis of copy number variation (CNV), and RNA analysis. [16][17][18] While automated sequencing applying NGS became more widely available in recent years and showed improved detection rates if compared to direct Sanger sequencing, 19 our laboratory performed in most cases RNA analysis for the confirmation of CPS1D. 6,16 Source of RNA can be liver tissue but also skin fibroblasts 17 or, hereby improving the turn-around time, peripheral lymphocytes that were stimulated with phytohemagglutinin hereby applying a straightforward and less invasive protocol.…”

Novel Neonatal Variants of the Carbamoyl Phosphate Synthetase 1 Deficiency: Two Case Reports and Review of Literature

“…Of the variants, 81 (30.7%) were predicted to cause protein truncation, including 22 nonsense, 31 small deletions, 16 small insertions, 4 small indels, 6 splicing site changes, and 2 large deletions. Our reviewing data further clarified that most CPS1 variants (≥90%) were “private” with non-recurrence, and the few recurrent mutations tended to occur at CpG dinucleotides, which made the diagnosis more complicated ( Supplementary Tables S1 to S4 ) (Hoshide et al, 1993; Finckh et al, 1998; Summar et al, 1998; Ihara et al, 1999; Aoshima et al, 2001a; Aoshima et al, 2001b; Rapp et al, 2001; Wakutani et al, 2001; Häberle et al, 2003; Eeds et al, 2006; Kurokawa et al, 2007; Khayat, 2009; Ono et al, 2009; Pekkala et al, 2010; Häberle et al, 2011; Wang et al, 2011; Funghini et al, 2012; Kretz et al, 2012; Diez-Fernandez et al, 2014; Ali et al, 2016; Choi et al, 2017; Rokicki et al, 2017; Yang et al, 2017; Chen et al, 2018; Zhang et al, 2018).…”

Mutation analysis of urea cycle disorders

“…To detect copy number variations, two well established techniques are used. The method of CGH array [103,104] is able to detect copy number variations by measuring the fluorescence ratio between a reference and a sample, while the method of multiplex ligation-dependent probe amplification (MLPA) is able to detect genomic deletions and insertions of single nucleotides up to one or more entire exons.…”