Array‐based MLPA to detect recurrent copy number variations in patients with idiopathic mental retardation

Abstract

Microdeletions, either subtelomeric or interstitial, are responsible for the mental handicap in approximately 10-20% of all patients. Currently, Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used to detect these small aberrations in a routine fashion. Although cost-effective, the throughput is low and the degree of multiplexing is limited to maximally 40-50 probes. Therefore, we developed an array-based MLPA method, with probes identified by unique tag sequences, allowing the simultaneous analysis of 180 probes in a single experiment thereby covering all known mental retardation loci with at least two probes. We screened 120 patients with idiopathic mental retardation. In this group we detected 6 aberrations giving a detection rate of 5%, consistent with similar studies. In addition we tested 293 patients with mental retardation who were negative for fragile X syndrome and commercially available subtelomeric MLPA. We found seven causative rearrangements in this group (detection rate of 2.4%) thereby illustrating the value of including probes for interstitial microdeletion syndromes and additional probes in the telomeric regions in targeted screening sets for mental retardation. Array-based MLPA may thus be a good candidate to develop probe sets that rapidly detect copy number changes of disease associated loci in the human genome. This method may become a valuable tool in a routine diagnostic setting as it is a fast, user-friendly and relatively low-cost technique providing straightforward results requiring only 125 ng of genomic DNA.

CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability

“…Without further research options, a large amount of patients remains genetically undiagnosed. In the past decades, many causative genes were identified, using (combinations of) different molecular techniques [4,[6][7][8][9][10][11], including linkage analysis and Sanger sequencing of candidate genes [4,12,13]. With the introduction of next-generation sequencing techniques, detection of causative genes within large linkage areas has become more feasible [1,2,[14][15][16][17][18].…”

Multiplex ligation-dependent probe amplification workflow for the detection of submicroscopic chromosomal abnormalities in patients with developmental delay/intellectual disability

“…High-resolution G-banded karyotyping and fluorescence in situ hybridization (FISH) studies using probes targeted to the subtelomeres and/or known microdeletion loci were considered the gold standard for detecting cytogenetic aberrations [2,3]. The development and availability of multiplex ligation-dependent probe amplification (MLPA) and array based comparative genomic hybridization (arrayCGH) techniques for the accurate assessment of copy number changes at multiple loci has provided a better approach for subtelomere and microdeletions testing in routine settings [4,5]. The next-generation sequencing techniques (NGS) which includes whole genome sequencing (WGS) or whole exome sequencing (WES), that may detect single-nucleotide changes through the whole genome are now increasingly applied in clinical diagnostics [6,7].…”

Subtelomeric 6.7 Mb trisomy 10p and 5.6 Mb monosomy 21q detected by FISH and array‐CGH in three related patients

“…Cryptic unbalanced subtelomeric chromosomal aberrations have been recognized as a significant cause of intellectual disability and multiple congenital anomalies. Numerous studies have shown that subtelomeric aberrations are responsible for 5–10% of moderate/severe and 1% of mild intellectual disability [Rossi et al, 2001; Anderlid et al, 2002; Koolen et al, 2004; Madrigal et al, 2010; Rooms et al, 2010]. Human subtelomeric regions contain gene‐rich segments, unbalanced rearrangements of which result in variable phenotypes.…”