Background Balanced chromosomal rearrangements associated with abnormal phenotype are rare events, but may be challenging for genetic counselling, since molecular characterisation of breakpoints is not performed routinely. We used next-generation sequencing to characterise breakpoints of balanced chromosomal rearrangements at the molecular level in patients with intellectual disability and/or congenital anomalies.
Methods Breakpoints were characterised by a paired-end low depth whole genome sequencing (WGS) strategy and validated by Sanger sequencing. Expression study of disrupted and neighbouring genes was performed by RT-qPCR from blood or lymphoblastoid cell line RNA.
Results Among the 55 patients included (41 reciprocal translocations, 4 inversions, 2 insertions and 8 complex chromosomal rearrangements), we were able to detect 89% of chromosomal rearrangements (49/55). Molecular signatures at the breakpoints suggested that DNA breaks arose randomly and that there was no major influence of repeated elements. Non-homologous end-joining appeared as the main mechanism of repair (55% of rearrangements). A diagnosis could be established in 22/49 patients (44.8%), 15 by gene disruption (KANSL1, FOXP1, SPRED1, TLK2, MBD5, DMD, AUTS2, MEIS2, MEF2C, NRXN1, NFIX, SYNGAP1, GHR, ZMIZ1) and 7 by position effect (DLX5, MEF2C, BCL11B, SATB2, ZMIZ1). In addition, 16 new candidate genes were identified. Systematic gene expression studies further supported these results. We also showed the contribution of topologically associated domain maps to WGS data interpretation.
Conclusion Paired-end WGS is a valid strategy and may be used for structural variation characterisation in a clinical setting.
- whole genome sequencing
- chromosomal rearrangements
- intellectual disability
- position effect
- structural variation
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Contributors CS-B conceived the project, designed and coordinated the research, interpreted the data and wrote the paper. AA, FA, JA, SB, YC, PC, M-PC, CC, AC, FDem, FDev, MD-F, CD, SD-G, LF, A-MG, MH, BI, GJ-H, DL, AL, ML, GL, JL, AM-P, CMig, CMis, FM-P, SM, CP-R, SO, VP-F, LP, NP, MP, M-FP, FP, AP, MR, MasR, CS, MT, SV, AV, SW and PE provided patients phenotyping, collected clinical samples and enrolled the cohort. PC, BD, J-MD, BG, SJ, VK, CLC, JL, VM, MM-D, GN, JP, CR, VS, JP, RT, AT, A-CT, DS assisted design of the work and data interpretation. FD, NC, JM, LP conducted the experiments, analysed the data and contributed to the interpretation. P-AR-F, CB conducted bioinformatics analyses.
Funding This study was supported by the French Ministry of Health (DGOS) and the French National Agency for Research (ANR) (PRTS 2013 grant to CS-B, n° PRTSN1300001N).
Competing interests None declared.
Ethics approval This study was approved by the local ethics committee (CPP Lyon Sud-Est 06/04/2014).
Provenance and peer review Not commissioned; externally peer reviewed.
Data sharing statement The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.
Patient consent for publication Obtained.