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
DOI: 10.1002/humu.23699
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 Health and Medical Research Council of Australia
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)