Whole-exome Sequencing of Fibroblasts and Leukocytes

Whole-exome sequencing was performed on DNA extracted from the fibroblasts of P1 and peripheral leukocytes from the parents and P2 and P3 of family A with the Sure Select All Exome V4 capture kit (Agilent) on a HiSeq2000 machine (Illumina). The statistics are provided in Table S1. BWA version 0.5.9 (Li and Durbin, 2009 (link)) and NARWHAL software (Brouwer et al., 2012 (link)) were used to align reads with the reference genome (hg19). Variants were called with GATK (version 1.2–29; McKenna et al., 2010 (link)) and SAMtools (version 0.1.13). Variants were annotated with ANNOVAR software (revision 511; Wang et al., 2010 (link)) and filtered with TIBCO Spotfire version 4.5 (Tables S1 and S2).

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Meuwissen M.E., Schot R., Buta S., Oudesluijs G., Tinschert S., Speer S.D., Li Z., van Unen L., Heijsman D., Goldmann T., Lequin M.H., Kros J.M., Stam W., Hermann M., Willemsen R., Brouwer R.W., Van IJcken W.F., Martin-Fernandez M., de Coo I., Dudink J., de Vries F.A., Bertoli Avella A., Prinz M., Crow Y.J., Verheijen F.W., Pellegrini S., Bogunovic D, & Mancini G.M. (2016). Human USP18 deficiency underlies type 1 interferonopathy leading to severe pseudo-TORCH syndrome. The Journal of Experimental Medicine, 213(7), 1163-1174.

Publication 2016

HiSeq2000 machine

Exome Fibroblasts Genome Leukocytes Narwhal Parents

Corresponding Organization : Child Health and Development Institute

Other organizations : University Hospital Carl Gustav Carus, Innsbruck Medical University, Institut Pasteur, Inserm, Centre National de la Recherche Scientifique, University of Freiburg, Université Paris Cité, University of Manchester, Institut des Maladies Génétiques Imagine, Manchester Academic Health Science Centre

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Variable analysis

independent variables

Whole-exome sequencing

dependent variables

Variants called with GATK and SAMtools

control variables

DNA extracted from fibroblasts of P1 and peripheral leukocytes from the parents and P2 and P3 of family A
Sure Select All Exome V4 capture kit (Agilent) used for sequencing
HiSeq2000 machine (Illumina) used for sequencing
BWA version 0.5.9 and NARWHAL software used for read alignment with reference genome (hg19)
ANNOVAR software used for variant annotation

Annotations

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