Genome-wide detection of tandem repeats, TREs, and rare TREs

JW Jia Wen
BT Brett Trost
WE Worrawat Engchuan
MH Matthew Halvorsen
LP Linda M. Pallotto
AM Aleksandra Mitina
NA NaEshia Ancalade
MF Martilias Farrell
IB Ian Backstrom
KG Keyi Guo
GP Giovanna Pellecchia
BT Bhooma Thiruvahindrapuram
PG Paola Giusti-Rodriguez
JR Jonathan David Rosen
YL Yun Li
HW Hyejung Won
PM Patrik K. E. Magnusson
UG Ulf Gyllensten
AB Anne S. Bassett
CH Christina M. Hultman
PS Patrick F. Sullivan
RY Ryan K. C. Yuen
JS Jin P. Szatkiewicz
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We used ExpansionHunter Denovo (EHdn) [28], an efficient catalog-free method for genome-wide tandem repeat detection from short-read WGS data. We applied the density-based spatial clustering of applications with noise (DBSCAN) algorithm to identify TREs whose lengths were outliers compared with other members of the cohort [16, 29]. We defined rare TREs as TREs that were found in less than 0.1% of the 1000GP population controls. All genomic coordinates are given in NCBI Build 38/UCSC hg38. A detailed description of the detection methods is provided in Supplementary Methods.

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