Integrated genome and transcriptome analyses solves about one third of the patients with rare developmental disorders and negative first-line molecular investigations

• Published in: European journal of human genetics : EJHG 2020, Vol.28 (Suppl 1), p.65-66
• Main Authors: Vitobello, A., Mau-Them, F. T., Bruel, A. L., Duffourd, Y., Tisserant, E., Callier, P., Moutton, S., Nambot, S., Lehalle, D., Jean-Marcais, N., Delanne, J., Racine, C., Thevenon, J., Poe, C., Jouan, T., Chevarin, M., Willems, M., Coubes, C., Genevieve, D., Houcinat, N., Masurel-Paulet, A., Mosca-Boidron, A., Sorlin, A., Isidor, Bertrand, Heide, S., Afenjar, A., Rodriguez, D., Mignot, C., Heron, D., Vincent, M., Charles, P., Odent, S., Dubourg, C., Faudet, A., Keren, B., Cogné, Benjamin, Boland, Anne, Olaso, Robert, Philippe, C., Deleuze, Jean-François, Faivre, L., Thauvin-Robinet, C.
• Format: Article
• Language: English
• Subjects: Biochemistry, Molecular Biology; Genetics; Genomics; Life Sciences
• ISSN: 1018-4813; 1476-5438

Exome sequencing (ES) represents the first-tier diagnostic test in patients presenting with syndromic developmental delay with suspected monogenic etiology. Yet, about 50% of these patients remain unsolved, arguing the interest to extend the genetic investigations beyond the protein-coding genome and to integrate multi-omics approaches. We launched a multi-centric pilot study gathering 53 unsolved patients, after trio ES and array-CGH results, presenting with heterogeneous mild to severe syndromic intellectual disabilities. We performed genome sequencing (GS) combined with transcriptome analysis, highlighting a molecular cause in 32% of the cohort (18/53 patients). GS identified 7 causative structural variants, including 1 deletion, 2 balanced inversions, 1 balanced translocation and 3 complex variants. The molecular readouts of such variants were all validated and furtherly investigated by RNAseq. One deep intronic SNV causing the activation of a cryptic exon, changing the open reading frame of the transcript, was detected by RNAseq. Two frameshift-causing indels were identified in protein-coding regions not captured by ES. Three variants were identified in genes not yet known as disease-causing at the time of the ES analysis. Finally, genotype-phenotype correlation could establish 3 additional diagnoses not identified during the ES analysis. In addition, we detected 2 complex structural variants of unknown significance, not resolvable by short-read GS, as well as new candidate genes identified through RNA-seq differential expression analysis. Overall, GS and RNAseq analyses allowed the identification of the molecular mechanisms underlying 1/3 of previously unsolved patients, and additional candidate variants requiring further investigation (3rd-generation sequencing, 3C techniques) to demonstrate their causality.