Targeted Sequencing for Genetic Profiling

Samples from diagnostic and remission BM or PB underwent DNA extraction using the AllPrep Extraction Kit (Qiagen). The integrity of the samples was confirmed by visualization on a 0.8% agarose gel. All samples then underwent targeted exome capture sequencing, which included the entire coding region of KIT, as previously described.(31 (link)) Samples from relapse specimens underwent analysis of mutations of exon 8 and 17 using amplification by genomic PCR as previously described.(19 (link))

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Tarlock K., Alonzo T.A., Wang Y.C., Gerbing R.B., Ries R., Loken M.R., Pardo L., Hylkema T., Joaquin J., Sarukkai L., Raimondi S.C., Hirsch B., Sung L., Aplenc R., Bernstein I., Gamis A.S., Meshinchi S, & Pollard J.A. (2019). Functional Properties of KIT Mutations are Associated with Differential Clinical Outcomes and Response to Targeted Therapeutics in CBF Acute Myeloid Leukemia. Clinical cancer research : an official journal of the American Association for Cancer Research, 25(16), 5038-5048.

Publication 2019

AllPrep Extraction Kit

Agarose Diagnostic Exon Genomic Mutations Relapse

Corresponding Organization : University of Washington

Other organizations : University of Southern California, Children's Oncology Group, St. Jude Children's Research Hospital, University of Minnesota, Hospital for Sick Children, Children's Hospital of Philadelphia, Children's Mercy Hospital, Harvard University, Dana-Farber Cancer Institute

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Variable analysis

independent variables

Diagnostic and remission BM or PB samples
Relapse specimens

dependent variables

Presence of mutations in exon 8 and 17 of the KIT gene

control variables

Integrity of samples confirmed by agarose gel visualization
Entire coding region of KIT gene analyzed using targeted exome capture sequencing

controls

Positive control: Not specified
Negative control: Not specified

Annotations

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