Overcoming challenges for the unambiguous detection of copy number variations is essential to broaden our understanding of the role of genomic variants in the clinical phenotype. With the improvement ...of software and databases, whole-exome sequencing quickly can become an excellent strategy in the routine diagnosis of patients with a developmental delay and/or multiple congenital malformations. However, even after a detailed analysis of pathogenic single-nucleotide variants and indels in known disease genes, using whole-exome sequencing, some patients with suspected syndromic conditions are left without a conclusive diagnosis. These negative results could be the result of different factors including nongenetic etiologies, lack of knowledge about the genes that cause different disease phenotypes, or, in some cases, a deletion or duplication of genomic information not routinely detectable by whole-exome sequencing variant calling. Although copy number variant detection is possible using whole-exome sequencing data, such analysis presents significant challenges and cannot yet be used to replace chromosomal arrays for identification of deletions or duplications.
Background
Bloom syndrome (BS) is a rare autosomal recessive chromosome instability disorder. The main clinical manifestations are growth deficiency, telangiectasic facial erythema, immunodeficiency, ...and increased risk to develop neoplasias at early age. Cytogenetic test for sister chromatid exchanges (SCEs) is used as a diagnostic marker for BS. In addition, most patients also present mutations in the BLM gene, related to defects in the DNA repair mechanism. However, the molecular mechanism behind the pathogenicity of BS is still not completely understood.
Methods
We describe two patients confirmed with BS by SCE and molecular analysis. Also, we performed the gene expression profile by the RNA‐seq methodology in mRNA transcripts for differential gene expression analysis using as a biological condition for comparison BS versus health controls.
Results
We detected 216 differentially expressed genes related to immunological pathways such as positive regulation and activation of B cells, immune effector process and absence of difference of DNA repair genes expression. In addition; we also observed differentially expressed genes associated with apoptosis control, such as BCL2L1, CASP7, CDKN1A, E2F2, ITPR, CD274, TNFAIP6, TNFRSF25, TNFRSF13C, and TNFRSF17.
Conclusion
Our results suggest that the combination of altered expression of genes involved in signaling pathways of immune response and apoptosis control may contribute directly to the main characteristics observed in BS, such as recurrent infections, growth failure, and high risk of cancer. Transcriptome studies of other instability syndromes could allow a more accurate analysis of the relevant gene interactions associated with the destabilization of the genome. This is a first description of the profile of differential gene expression related to immunological aspects detected in patients with BS by RNA‐seq.
We investigate two patients with Bloom´s syndrome that presented immunological deficiency that was confirm by differential gene expression analysis by RNA‐seq using Illumina platform. The analysis showed an unexpected highly complex transcriptional profile with downregulated differentially expressed genes associated to activation and regulation of immune pathways and absence of difference of DNA repair genes. This is a first description of the profile of differential gene expression related to immunological aspects detected in patients with SB by RNA‐seq.
The most prevalent structural variations in the human genome are copy number variations (CNVs), which appear predominantly in the subtelomeric regions. Variable sizes of 4p/4q CNVs have been ...associated with several different psychiatric findings and developmental disability (DD). We analyzed 105 patients with congenital anomalies (CA) and developmental and/or intellectual disabilities (DD/ID) using MLPA subtelomeric specific kits (P036 /P070) and 4 of them using microarrays. We found abnormal subtelomeric CNVs in 15 patients (14.3%), including 8 patients with subtelomeric deletions at 4p/4q (53.3%). Additional genomic changes were observed at 1p36, 2q37.3, 5p15.3, 5q35.3, 8p23.3, 13q11, 14q32.3, 15q11.2, and Xq28/Yq12. This indicates the prevalence of independent deletions at 4p/4q, involving PIGG, TRIML2, and FRG1. Furthermore, we identified 15 genes with changes in copy number that contribute to neurological development and/or function, among them CRMP1, SORCS2, SLC25A4, and HELT. Our results highlight the association of genes with changes in copy number at 4p and 4q subtelomeric regions and the DD phenotype. Cytogenomic characterization of additional cases with distal deletions should help clarifying the role of subtelomeric CNVs in neurological diseases.
Genomic rearrangements encompass deletions, duplications, inversions, insertions and translocations and may be the cause of several genetic diseases. One of the most frequent mechanisms that generate ...these rearrangements is the Non-Allelic Homologous Recombination (NAHR). They are caused by a misalignment between regions of high level of similarity, like Low Copy Repeats (LCRs) and Alu sequences. We aimed to sequence the breakpoint of a patient with a single deletion on chromosome 22q13.2 in order to understand the genomic structure of the region involved as well as elucidate the mechanism behind this rearrangement. Investigating breakpoints are of the utmost importance in the understanding the influence of the genomic architecture in clinical assays. We flanked the breakpoint detected by array and then we captured the regions using Illumina Nextera Rapid Capture Custom to sequence with Illumina MiSeq. We found a chimeric read on Chr22:41,026,090, setting a 624,688 bp deletion on Chr22:41,026,112-41,650,780 (hg19). This deletion merges the intronic region of MKL1 and RANGAP1 genes, on two different Alu sequences (AluSx and AluY, respectively). The sequence of the breakpoint reveals that Alu elements are an important characteristic of the human genome on generating rearrangements.
•We investigated the breakpoint on chromosome 22q13.2 in order to understand the genomic structure of the region involved as well as elucidate the mechanism behind this rearrangement.•Our results showed that the breakpoint is inserted in two different Alu regions and the absence of micro-homology inside the breakpoint, lead us to consider NAHR mechanism driven by Alu. It is the first time that a fusion between MKL1 and RANGAP1 genes are sequenced.•Delineate breakpoints is important to understanding the influence of the genomic architecture in clinical assays.
PDF
