Journal article

Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection

Mark J Cowley, Yu-Chi Liu, Karen L Oliver, Gemma Carvill, Candace T Myers, Velimir Gayevskiy, Martin Delatycki, Danique RM Vlaskamp, Ying Zhu, Heather Mefford, Michael F Buckley, Melanie Bahlo, Ingrid E Scheffer, Marcel E Dinger, Tony Roscioli

HUMAN MUTATION | WILEY | Published : 2019

Abstract

Rapid advances in genomic technologies have facilitated the identification pathogenic variants causing human disease. We report siblings with developmental and epileptic encephalopathy due to a novel, shared heterozygous pathogenic 13 bp duplication in SYNGAP1 (c.435_447dup, p.(L150Vfs*6)) that was identified by whole genome sequencing (WGS). The pathogenic variant had escaped earlier detection via two methodologies: whole exome sequencing and high-depth targeted sequencing. Both technologies had produced reads carrying the variant, however, they were either not aligned due to the size of the insertion or aligned to multiple major histocompatibility complex (MHC) regions in the hg19 referenc..

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Grants

Awarded by Cancer Institute NSW


Awarded by NHMRC


Awarded by NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE


Funding Acknowledgements

W.G.S. was funded by the Kinghorn Foundation. M.J.C. was supported by Cancer Institute NSW (3/ECF/1-46) and an NSW Health Early-Mid Career Fellowship. M.B. was supported by NHMRC Program grant (ID: 1054618) and NHMRC Senior Research Fellowship (ID: 1102971). I.E.S. is supported by NHMRC Program grant (1091593, 2016-2020) and Senior Practitioner Fellowship (1104831, 2016-2020). T.R. was supported through a project grant from the NHMRC (ID: AU/1/BA51117)