Table 1.
Patient characteristics.
Fig 1.
(A) Mean and median coverage of each target region across all validation trials (n = 427). Target regions are sorted by chromosomal location. Targets on X chromosome are marked with a dotted line. (B) NA12878 coverage across all target regions from 17 independent setups. Target regions are sorted by % GC (orange dot). Standard deviation of coverage is shown (black bar). (C) Percentage of specimens that passed a base quality Q20 coverage of 100X, 250X, or 500X.
Fig 2.
(A) Inter-assay precision of 141 variants from 22 specimens repeated 3 times. The mean of the detected variant frequencies (orange dot) with standard deviation (closed vertical bar) and coefficients of variations (blue dot) are shown. (B) Intra-assay precision of 40 variants from 9 specimens replicated 3 times. The mean of the detected variant frequencies (orange dot) with standard deviation (closed vertical bar) and coefficients of variations (blue dot) are shown.
Fig 3.
(A) Number and type of variant used for accuracy study per gene. (B) Variant frequency distribution used for accuracy study. Variant frequency not provided by alternative method is categorized as undetermined. (C) Variant frequency concordance. Compared only if variant frequency is known by alternative method.
Table 2.
FLT3-ITD used for accuracy study.
Table 3.
Variant call concordance study using Genome in a Bottle reference specimens.
Table 4.
Summary of analytical sensitivity study result.
Fig 4.
Analytical sensitivity of the assay for various VAFs for each variant type.
Analytical sensitivity percentage represents the proportion of detected variants out of all variants tested at a given VAF.
Fig 5.
Variant call concordance study between the 48-gene panel for myeloid neoplasms and 35-gene panel for hematologic neoplasms.
(A) Number and type of variants compared per gene. (B) Scatter plot of VAFs (n = 1,094) across 141 trials detected by the 48-gene panel (x-axis) and 35-gene panel (y-axis).
Fig 6.
Detected variant frequency of a mutation-positive control (HD728) from 119 repeat tests over 10 months.
Expected variant frequency is indicated along with variant name.
Fig 7.
Pathogenic mutations (Tier I or Tier II) detected in 44 genes from the total cohort of 2,053 patients by the 48-gene NGS panel for myeloid neoplasms.
Fig 8.
Identified Tier I and Tier II mutations in 44 genes from the total cohort of 2,053 patients detected by the 48-gene NGS panel for myeloid neoplasms.
Each column in the x = axis represents a patient. Only patients with at least 1 mutation (n = 1,142) are shown. The percent of patients with Tier I and Tier II mutations in the indicated gene is presented.
Fig 9.
Frequency of patients harboring potentially actionable alterations.