Journal article

Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data

Rick M Tankard, Mark E Bennett, Peter Degorski, Martin B Delatycki, Paul J Lockhart, Melanie Bahlo

American Journal of Human Genetics | CELL PRESS | Published : 2018

Abstract

Repeat expansions cause more than 30 inherited disorders, predominantly neurogenetic. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single-gene or small-panel PCR-based methods can help to identify the precise genetic cause, but they can be slow and costly and often yield no result. Researchers are increasingly performing genomic analysis via whole-exome and whole-genome sequencing (WES and WGS) to diagnose genetic disorders. However, until recently, analysis protocols could not identify repeat expansions in these datasets. We developed exSTRa (expanded short tandem repeat algorithm), a method that uses either WES or WGS to identify repeat ex..

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Grants

Awarded by Australian National Health and Medical Research Council (NHMRC) Career Development Award Level 2


Awarded by NHMRC


Awarded by NHMRC Senior Research Fellowship


Funding Acknowledgements

We would like to thank Egor Dolzhenko and Michael Eberle (Illumina), who produced the STR specification files for Expansion-Hunter and who facilitated access to the dataset EGA00001003562 from the European Genome-Phenome Archive. We thank Leslie Burnett, Ben Lundie, Katie Ayres, and Andrew Sinclair for granting access to control datasets. We also thank Kate Pope and Greta Gillies for assistance with recruitment and sample preparation. R.M.T. was supported by an Australian Postgraduate Award and funding from the Edith Moffat fund. P.J.L. was supported by the Australian National Health and Medical Research Council (NHMRC) Career Development Award Level 2 (GNT1032364). M.B. was supported by an NHMRC Program Grant (GNT1054618) and an NHMRC Senior Research Fellowship (GNT1102971). This work was supported by the Victorian Government's Operational Infrastructure Support Program and the NHMRC Independent Research Institute Infrastructure Support Scheme (IRIISS).