Fig. 1

IDMseq for detection of subclonal variants. a Schematic representation of IDMseq. Individual DNA molecules are labeled with unique UMIs and amplified for sequencing on appropriate platforms (e.g., Illumina, PacBio, and Nanopore). During data analysis, reads are binned by UMIs to correct errors introduced during amplification and sequencing. Both SNV and SV calling are included in the analysis pipeline. b Examples of Integrative Genomics Viewer (IGV) tracks of UMI groups in which the spike-in SNV in the 1:10,000 population was identified by IDMseq and VAULT. The knock-in SNV is indicated by the red triangle in the diagram of the EPOR gene on top, and also shown as red “T” base in the alignment map. The gray bars show read coverage. The ten colored bars on the left side of the coverage plot represent the UMI sequence for the UMI group. Individual Nanopore (top) and Illumina (bottom) reads within the group are shown under the coverage plot. c Large SVs detected by IDMseq in the 1:1000 population on the PacBio platform. Three UMI groups are shown with the same 2375-bp deletion. Group 1 represents one haplotype, and groups 2 and 3 represent a different haplotype. Colored lines represent the SNPs detected in each group. Thick blue boxes: exons; thin blue boxes: UTRs. Thin vertical red lines in the gene diagram represent PCR primer location. d Distribution of SNVs detected by PacBio sequencing in conjunction with IDMseq and VAULT. One of the SNVs was also found in the Nanopore dataset. The spike-in SNV (1:1000) is indicated by the red triangle. The table on the right summarizes the frequency of SNV-associated records in different annotation categories. The numbers in the table represent annotation records from all transcript isoforms, so the same SNV may be recorded more than once. e Frequency distribution of the variant allele fraction of SNVs detected by IDMseq in PacBio sequencing of the EPOR locus. f The spectrum of base changes among somatic SNVs. The majority of base changes are G to A and C to T. g Comparison between observed VAF and expected VAF in different experiments and sequencing platforms