Additional file 4: Table S2. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Filtering Metrics. The criteria used to initially classify a variant in the training set for the quadratic discriminant model. (DOCX 14 kb

Additional file 5: Table S3. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

One thousand Genomes Population Codes. Abbreviations used to describe the populations from the 1000 Genomes Project. (DOCX 17 kb

Additional file 6: Figure S3. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Mapping coverage as a function of variant calls. (PNG 38 kb

Additional file 3: Figure S1. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Somatic Variant Calling Workflow. Illustrates a detailed workflow of the somatic variant calling process. The steps from “Transpose to pileup” and below are performed by the lumosVar software. (PNG 151 kb

Additional file 2: Table S1. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Definition of True Variants. Describes the criteria for counting a variant as a true variant. Germline variants were called by haplotype caller, samtools, and freebayes. Somatic variants were called by Mutect, Seurat, and Strelka. (DOCX 15 kb

Additional file 9: Figure S5. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Copy Number and Sample Fraction Across Dilutions. The copy number (left), minor allele copy number (center) and sample fraction of the copy number events (right) are plotted as heatmaps. (PNG 35 kb

Additional file 8: Figure S4. of A method to reduce ancestry related germline false positives in tumor only somatic variant calling

Variant Quality Filtering Across Dilutions. Shows the number of variants of each type, in each quality filtering category. Each graph represents a variant type, each bar represents a dilution, and the color of the bar represents the number of variants in each quality category. High quality positions have a PT > 0.99. Low quality positions have a PT < 0.99 but PV > 0.99. Artifacts have a PV < 0.99 and non variants are not considered by the tumor only caller (NaN). (PNG 43 kb

Additional file 1 of Molecular-guided therapy for the treatment of patients with relapsed and refractory childhood cancers: a Beat Childhood Cancer Research Consortium trial

Additional file 1: Table S1. Cell lines and mice models established. A total of 96 patients enrolled onto the NMTRC009 MGT trial had at least one tumor cell line generated in the laboratory setting. Since many subjects underwent multiple tumor biopsies and/or bone marrow biopsies, subjects may have >1 unique cell line, either from the same tumor obtained from different biopsy dates or from a different disease site (bone marrow). 47 subjects’ tumors underwent successful implantation into a NOD-SCID mouse to generate at least one PDX model. A total of 56 unique PDX models were generated