Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability

Abstract

BackgroundThe etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read massive parallel sequencing approaches do not allow the detection of larger tandem repeat expansions, we hypothesized that such expansions could be a hidden cause of X-linked intellectual disability.MethodsWe selectively captured over 1800 tandem repeats on the X chromosome and characterized them by long read single molecule sequencing in 3 families with idiopathic X-linked intellectual disability.ResultsIn male DNA samples, full tandem repeat length sequences were obtained for 88–93% of the targets and up to 99.6% of the repeats with a moderate guanine-cytosine content. Read length and analysis pipeline allow to detect cases of > 900 bp tandem repeat expansion. In one family, one repeat expansion co-occurs with down-regulation of the neighboring MIR222 gene. This gene has previously been implicated in intellectual disability and is apparently linked to FMR1 and NEFH overexpression associated with neurological disorders.ConclusionsThis study demonstrates the power of single molecule sequencing to measure tandem repeat lengths and detect expansions, and suggests that tandem repeat mutations may be a hidden cause of X-linked intellectual disability.Electronic supplementary materialThe online version of this article (10.1186/s12920-018-0446-7) contains supplementary material, which is available to authorized users.

DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms

“…However, emerging long-read sequencing (LRS) technologies, typified by PacBio single-molecule and real-time (SMRT) sequencing, offer complementary strengths to those of the SRS methods and are well suited to determine expanded tract length and variation in repeat numbers [ 76 ]. Applied to Fragile-X diagnosis, LRS technology enabled researchers to completely sequence expanded full mutation FMR1 alleles, with up to 750 CGG repeats, which translates to >2 kb of 100% CGG-repeat DNA [ 77 , 78 ]. In DM1 patients, LRS sequencing detected de novo repeat interruptions at the DMPK locus, associated with the reduced somatic instability of the repeat expansion [ 79 ].…”

“…In addition, a genome-wide DNA methylation assay has been successfully applied to the molecular diagnosis of genetically unresolved cases, uncovering new hypervariable trinucleotide repeat loci [ 72 , 83 ]. Collectively, emerging Next-Generation Sequencing (NGS) technologies offer efficient strategies in the characterization of expandable regions that are difficult to assess with NGS short-read approaches and, thus, we believe that novel hypermethylated expansion disorders could be identified in the future [ 72 , 76 , 78 ]. Fascinatingly, these new technologies could lead a new field of studies to trace DNA methylation in repeat ancestors by comparing ancient and modern human genomes and highlighting epigenetic differences at disease repeat loci.…”

Bioinformatics Analysis Revealed Novel 3′UTR Variants Associated with Intellectual Disability

“…Genes including SHROOM3, FCER1A, DLEC1, and PSAPL1 are shown to be targeted by miR-145; genes ROBO2, CHAF1B, P2RY22, XRRA1, GPX8, P2RY2, and NSG1 are targeted by miR-183 [33]. Genes ARMCX2, NEFH, and FMR1 are shown to be targeted by miR-222 [37]. The gene MECP2, which is related to IDs such as Rett Syndrome can be targeted by miR-302c, miR-483-5p, miR-130a, and miR-200a.…”

“…Though there are several widely accepted miRNA targeting databases available, in order to obtain ID-related miRNA-mRNA pairings, we collected known and predicted pairs of miRNA and target genes from published literatures. After extensive research about known miRNA and mRNA targeting relationships, we obtained a list of miRNA-mRNA pairs from nine published literatures [24,[32][33][34][35][36][37]. The list of miRNA-mRNA pairs selected for this study is reported in Table S1.…”