Supplementary data: Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with UMI error correction

Supplementary
Figure 1. Ratio of forward-to-reverse reads is no useful quality criterion
for UMI-libraries after error-correction bioinformatics. The
density plots show the position balance of forward reads to reverse reads at
each genomic position, from targeted sequencing of the PIK3CA coding regions. The position balance was computed with
GenSearchNGS, with 1 being optimal and 0 being worst. (A) Position balance in
the four non-UMI-libraries (TruSeq 776-1, 776-2, 779-1, 779-2). The majority
of genomic positions have a near-optimal read balance. (B) Position balance
in the two UMI-libraries (Oncology 776, 779). Nearly all positions are
covered by error-corrected reads oriented in just one genomic direction. The
conventional quality check of forward/reverse balance is therefore no longer
useful after UMI-based error-correction has been performed.

Supplementary Table 3: Deduplication (removal of
redundant sequences) increases the allele frequency of signal noise (PCR or
sequencing errors) and reduces the effective sequencing depth

Supplementary Table 2: Allelic frequency of PIK3CA
p.E545K mutation for non-UMI libraries vs UMI libraries and bioinformatic
non-filtering vs filtering, in wild-type standard HD776 (0.00%) and mutated
standard HD779 (0.13%)

Supplementary Table 1: Bioinformatic tools, versions,
and settings that were used