Illumina HiSeqX whole genome sequence data on 58 samples including 54 with known HTT triplet repeat expansions (2 premutation and 52 full expansions)

Whole genome sequence (WGS) data was generated on 58 samples with validated repeat lengths for the CAG repeat associated with Huntington disease, These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and the repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001003512	This dataset includes bam files from 58 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the HTT repeat expansion. These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and aligned using bwa. Twelve of the samples used TruSeq Nano library preparation and 46 samples used TruSeq DNA PCR-free sample preparation.	HiSeq X Ten	58

Publications	Citations
Detection of long repeat expansions from PCR-free whole-genome sequence data. Dolzhenko E, van Vugt JJFA, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, Ajay SS, Rajan V, Lajoie BR, Johnson NH, Kingsbury Z, Humphray SJ, Schellevis RD, Brands WJ, Baker M, Rademakers R, Kooyman M, Tazelaar GHP, van Es MA, McLaughlin R, Sproviero W, Shatunov A, Jones A, Al Khleifat A, Pittman A, Morgan S, Hardiman O, Al-Chalabi A, Shaw C, Smith B, Neo EJ, Morrison K, Shaw PJ, Reeves C, Winterkorn L, Wexler NS, US–Venezuela Collaborative Research Group, Housman DE, Ng CW, Li AL, Taft RJ, van den Berg LH, Bentley DR, Veldink JH, Eberle MA. Genome Res 27: 2017 1895-1903	202

Publications

Citations

Detection of long repeat expansions from PCR-free whole-genome sequence data.
Dolzhenko E, van Vugt JJFA, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, Ajay SS, Rajan V, Lajoie BR, Johnson NH, Kingsbury Z, Humphray SJ, Schellevis RD, Brands WJ, Baker M, Rademakers R, Kooyman M, Tazelaar GHP, van Es MA, McLaughlin R, Sproviero W, Shatunov A, Jones A, Al Khleifat A, Pittman A, Morgan S, Hardiman O, Al-Chalabi A, Shaw C, Smith B, Neo EJ, Morrison K, Shaw PJ, Reeves C, Winterkorn L, Wexler NS, US–Venezuela Collaborative Research Group, Housman DE, Ng CW, Li AL, Taft RJ, van den Berg LH, Bentley DR, Veldink JH, Eberle MA. Genome Res 27: 2017 1895-1903

202