Exome Sequencing of Tumor and Constitutional DNA

For cases E4051 and E6526 we sequenced both tumor (peripheral blood leucocyte) and constitutional (cultured T-cell) DNA. T-cells were isolated from anticoagulated peripheral blood using CD3 MicroBeads and cultured using a T-cell Activation/Expansion kit (Miltenyi Biotec, Bisley, UK). Samples were prepared for exome sequencing using the Agilent SureSelect kit (Agilent Technologies, Palo Alto, CA, USA) (Human All Exon 50 Mb) and then sequenced on an Illumina HiSeq 2000 (Illumina, Great Abington, UK) at the Wellcome Trust Centre for Human Genetics, Oxford, UK. Exome sequencing of ULSAM1182, ULSAM1242 and ULSAM1356 (peripheral blood leukocyte DNA only) was performed by SciLifeLab (Stockholm, Sweden). Sequence data from all five samples were analyzed using a custom bioinformatic pipeline as previously described.18 (link)

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Chase A., Pellagatti A., Singh S., Score J., Tapper W.J., Lin F., Hoade Y., Bryant C., Trim N., Yip B.H., Zoi K., Rasi C., Forsberg L.A., Dumanski J.P., Boultwood J, & Cross N.C. (2018). PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age related clonal hematopoiesis and myeloid neoplasia. Leukemia.

Publication 2018

T-cell Activation/Expansion kit HiSeq 2000

Blood Cultured cell Exon Human Microbeads Peripheral blood leukocyte T cell Tumor

Corresponding Organization :

Other organizations : University of Southampton, University of Oxford, Salisbury NHS Foundation Trust, Wessex Regional Genetics Laboratory, Salisbury District Hospital, Academy of Athens, Science for Life Laboratory, Uppsala University

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Variable analysis

independent variables

Tissue type (tumor vs. constitutional)
Exome sequencing platform (Illumina HiSeq 2000 vs. SciLifeLab)

dependent variables

Exome sequencing data

control variables

CD3 MicroBeads for T-cell isolation
T-cell Activation/Expansion kit for T-cell culture
Agilent SureSelect kit for exome library preparation

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

Annotations

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