Whole-Genome Sequencing of AML Tumors

We performed whole-genome sequencing of the primary tumor and matched normal skin samples from 50 patients (with data from 24 of these patients reported previously^{17 (link)}) and exome capture and sequencing for another 150 paired samples of AML tumor and skin (see Table S3 in the Supplementary Appendix for coverage data for the 200 samples).
All 200 patients who were selected for this study were enrolled in a single-institution tissue-banking protocol approved by the human studies committee at Washington University. Written informed consent for whole-genome sequencing was obtained from all study participants.
The samples, which were banked between November 2001 and March 2010, were selected from a set of more than 400 samples to reflect a real-world distribution of subtypes. Sample inventory and quality issues also had to be considered in the selection process, since the samples were analyzed on several different platforms. We identified candidate somatic variants using several algorithms (see the Methods section in the Supplementary Appendix), and all the variants for the 200 samples were verified with the use of hybridization capture–based methods and deep digital sequencing.^{18 (link)} We performed RNA-expression profiling on the Affymetrix U133 Plus 2 platform for 197 samples, RNA sequencing for 179 samples, microRNA (miRNA) sequencing for 194 samples, Illumina Infinium Human Methylation 450 BeadChip profiling for 192 samples, and Affymetrix SNP Array 6.0 for both tumor and normal skin samples from all 200 patients. Data sets were not completed for all samples on all platforms because of assay failures and availability and quality issues for some samples. The complete list of data sets is provided in Table S4 in the Supplementary Appendix. All data sets are available through the Cancer Genome Atlas (TCGA) data portal (https://tcga-data.nci.nih.gov/tcga).

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Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. (2013). The New England journal of medicine, 368(22), 2059-2074.

Publication 2013

Assay Cancer Deep Exome Genome Human Hybridization Methylation Microrna 194 Patients Rna expression Skin Somatic Tumor

Corresponding Organization :

Other organizations : Washington University in St. Louis, Brown University, Providence College, University of British Columbia, University of North Carolina at Chapel Hill, University of Southern California, Massachusetts Institute of Technology, Seattle Cancer Care Alliance, Seattle University, Johns Hopkins University, The University of Texas MD Anderson Cancer Center, Nationwide Children's Hospital, National Institutes of Health, Temple University, University of Chicago, Philadelphia University, University of Pennsylvania

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Protocol cited in 267 other protocols

Variable analysis

independent variables

Whole-genome sequencing of the primary tumor and matched normal skin samples from 50 patients
Exome capture and sequencing for another 150 paired samples of AML tumor and skin

dependent variables

Identified candidate somatic variants
RNA-expression profiling on the Affymetrix U133 Plus 2 platform for 197 samples
RNA sequencing for 179 samples
MicroRNA (miRNA) sequencing for 194 samples
Illumina Infinium Human Methylation 450 BeadChip profiling for 192 samples
Affymetrix SNP Array 6.0 for both tumor and normal skin samples from all 200 patients

control variables

Matched normal skin samples from 50 patients
Normal skin samples from 150 paired samples of AML tumor and skin

Annotations

Based on most similar protocols

Utilize two rounds of hybridization to increase specificity of exome capture (Protocol 2, Protocol 3)

Perform real-time PCR quantification of capture pools to ensure proper library quantification prior to sequencing (Protocol 2, Protocol 3)

Run 5-6 lanes of sequencing per AML tumor sample and 3 lanes per matched skin biopsy sample to achieve sufficient sequencing depth (Protocol 2, Protocol 3)

Develop a custom 11.9 Mb capture library to validate all previously reported AML variants and new variants detected in the study (Protocol 2, Protocol 3)

Apply the custom 11.9 Mb capture library to sequence 96 specimens that had been previously subjected to whole exome sequencing to validate variant calls (Protocol 2, Protocol 3)

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