Table 1. Quality parameters for a 10-plex Human Papillomavirus (HPV) Sequencing Bead Array (SBA) assay.
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a.
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b.
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c.
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| AVG | STDEV | AVG | STDEV | AVG | STDEV | |||
| I. Reporter population | 6.87x105 | ±7.18% | 1.46x104 | ±29.67% | 2.04x105 | ±30.44% | ||
| II. Polyclonality | 35.20% | ±3.95% | 19.65% | ±7.16% | 39.59% | ±2.22% | ||
| III. Low quality | 9.68% | ±1.85% | 58.47% | ±14.61% | 31.74% | ±5.57% | ||
| IV. Uncalled reporters | 3.07% | ±0.22% | 1.50% | ±0.44% | 1.57% | ± 0.33% | ||
| V. Called reporters | 52.04% | ±2.68% | 20.38% | ±7.40% | 27.10% | ±3.89% | ||
| VI. Bead density | 5.93x105 | ±15.11% | N/A | N/A | N/A | N/A | ||
Average (AVG) calls and standard deviation percentages (STDEV) for assay parameters. (a) Library variability of six identical individually constructed reporter libraries (metadata Table S2). (b) Background noise of six parallel negative (water) selections (metadata Table S3). (c) Six parallel quintuple HPV selections (metadata Table S4). The Ion Personal Genome Machine (PGM) Torrent Suite software automatically filters parameters I-III during a sequencing run, while IV and V are generated during Sphix analysis, and VI was quantitatively estimated via fluorescent readout data. I) Reporter population denotes the number of reporters that yield a strong enough sequencing read signal. II) Polyclonality denotes filtering of reporters with mixed sequence reads due to beads containing two or more different sequences, or loading of multiple beads in the same well (rare). III) Low quality denotes filtering of sequence reads with low signal quality and other abnormalities. To this category we have also included the smaller contributing primer-dimer filer (removes inserts < 8-bp), which has been merged for simplified interpretation. IV) Uncalled reporters denote obtained sequence reads that do not match any of the ID traces (caused by sequencing errors and alike). V) Called reporters denote obtained sequence reads that match ID traces. VI) Bead density denotes a quantitative estimate of the amount of beads/μl for a constructed reporter library. Bead density measurements were not performed in (b and c).