Extended Data Fig. 10: In vitro pooled and sequenced biopsy material recapitulates the average genotypes of constituent input samples and in silico merged samples.
a. Concordance between somatic mutation variant allele frequency (VAF, left column), gene copy number log ratios (center column), and tumor fraction (right column) between in vitro combined versus mean input sample (black), in vitro versus in silico combined samples (blue), and in silico combined versus mean input sample (green). Note that in vitro log ratio values were normalized using white blood cell DNA (rather than source-matched pooled benign tissue as per the other comparator samples). Seven patients are included and the number of mutations assessed is indicated on each plot. b. Genomic status of TP53, PTEN, and RB1 in primary, in silico combined, and in vitro combined samples. Copy number is corrected for tumor fraction. Heterozygous single-nucleotide polymorphism (SNP) variant allele fraction greater than 60% was considered a heterozygous loss. LOH: loss of heterozygosity.
