Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Selection
2.2. Nucleic Acid Isolation
2.3. Library Preparation and Next-Generation Sequencing
2.4. Bioinformatics Pipeline and Statistical Analyses
3. Results
3.1. Sequencing Performance
3.2. Accuracy
3.2.1. SNVs and Indels
3.2.2. Gene Fusions
3.2.3. CNVs
3.2.4. MSI
3.2.5. TMB and HRD
3.3. Limit of Detection
3.3.1. SNVs and Indels
3.3.2. Gene Fusions
3.4. Precision
3.4.1. SNVs and Indels
3.4.2. Gene Fusions
3.4.3. CNVs and Genomic Signatures
3.5. Performance on Clinical Specimens
3.5.1. SNVs and Indels
3.5.2. CNVs
3.5.3. Gene Fusions
3.5.4. TMB and MSI
3.5.5. HRD
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene (Variant) | Expected VAF (%) | OCA+ VAF (%) |
---|---|---|
EGFR (p.E746_A750delELREA) | 25.0 ± 1.6 | 23.8 ± 4.7 |
KRAS (p.A146T) | 4.3 ± 0.6 | 3.4 ± 0.7 |
KRAS (p.G12C) | 6.2 ± 0.8 | 6.7 ± 1.4 |
PIK3CA (p.E542K) | 4.1 ± 0.7 | 3.8 ± 0.5 |
Gene Fusion | OCA+ (Read Counts) |
---|---|
KIF5B::RET | 64,018 |
ETV6::NTRK3 | 49,745 |
TPM3::NTRK1 | 49,052 |
EML4::ALK | 46,932 |
TMPRSS2::ERG | 42,573 |
LMNA::NTRK1 | 35,393 |
PAX8::PPARG | 34,650 |
TFG::NTRK1 | 38,610 |
SLC34A2::ROS1 | 28,861 |
CD74::ROS1 | 25,762 |
MET Exon 14 Skipping | 29,684 |
FGFR3::TACC3 | 29,571 |
NCOA4::RET | 17,646 |
EGFR::SEPT14 | 14,389 |
SLC45A3::BRAF | 15,719 |
FGFR3::BAIAP2L1 | 15,502 |
CCDC6::RET | 7894 |
EGFRvIII | 5336 |
Sample ID | FISH Results | OCA+ Result | |
---|---|---|---|
Average HER2 CN 1 per Cell | HER2/chr 17 Ratio | ERBB2 CNV (×) | |
BHL_F13 | 5.38 | 1.31 | 6.1 |
BHL_F15 | 23.70 | 6.58 | 22.9 |
BHL_F16 | 15.70 | 10.83 | 10.8 |
Seraseq® RM | Expected Score | OCA+ Score |
---|---|---|
gDNA TMB Mix Score 7 | 7.2 ± 0.2 | 7.7 ± 0.0 |
gDNA TMB Mix Score 26 | 25.8 ± 0.5 | 20.3 ± 0.4 |
FFPE HRD Negative | 31 ± 2 | 35 ± 6 |
FFPE HRD Low-Positive | 54 ± 2 | 54 ± 2 |
FFPE HRD High-Positive | 72 ± 3 | 68 ± 4 |
Gene | Variant Type | Mutation | Target VAF (%) | OCA+ VAF (%) |
---|---|---|---|---|
MPL | SNV | p.W515L | 10.0 | 6.8 |
AKT1 | SNV | p.E17K | 10.0 | 9.8 |
APC | SNV | p.R1450* | 10.0 | 10.3 |
GNA11 | SNV | p.Q209L | 10.0 | 10.4 |
GNAQ | SNV in HP 3N | p.Q209P | 10.0 | 11.4 |
KIT | SNV | p.D816V | 10.0 | 11.4 |
PIK3CA | SNV | p.E545K | 10.0 | 12.1 |
PDGFRA | SNV | p.D842V | 10.0 | 13.6 |
EGFR | DEL | p.E746_A750delELREA | 10.0 | 4.5 |
EGFR | INS | p.D770_N771insG | 10.0 | 4.5 |
SMAD4 | INS | p.A466fs*28 | 10.0 | 11.7 |
APC | INS in HP 7N | p.T1556fs*3 | 10.0 | 6.3 |
ERBB2 | INS | p.A775_G776insYVMA | 10.0 | 9.9 |
JAK2 | SNV in HP 3N | p.V617F | 7.0 | 4.1 |
TP53 | SNV | p.R248Q | 7.0 | 7.0 |
EGFR | SNV | p.L858R | 7.0 | 7.1 |
TP53 | SNV | p.R175H | 7.0 | 7.3 |
TP53 | SNV | p.R273H | 7.0 | 7.6 |
KRAS | SNV | p.G12D | 7.0 | 7.7 |
CTNNB1 | SNV | p.T41A | 7.0 | 7.8 |
NRAS | SNV | p.Q61R | 7.0 | 7.9 |
GNAS | SNV | p.R201C | 7.0 | 8.9 |
PTEN | DEL 6N > 5N | p.K267fs*9 | 7.0 | Not Called |
TP53 | DEL | p.C242fs*5 | 7.0 | 8.0 |
PTEN | INS | p.P248fs*5 | 7.0 | 7.6 |
RET | SNV | p.M918T | 4.0 | 3.9 |
EGFR | SNV | p.T790M | 4.0 | 4.2 |
IDH1 | SNV | p.R132C | 4.0 | 4.2 |
FOXL2 | SNV | p.C134W | 4.0 | 4.5 |
BRAF | SNV | p.V600E | 4.0 | 4.8 |
FLT3 | SNV | p.D835Y | 4.0 | 5.5 |
PIK3CA | SNV | p.H1047R | 4.0 | 5.9 |
FGFR3 | SNV | p.S249C | 4.0 | 6.7 |
ATM | DEL | p.C353fs*5 | 4.0 | 9.6 |
TP53 | DEL 5N > 4N | p.S90fs*33 | 4.0 | Not Called |
PDGFRA | INS | p.S566fs*6 | 4.0 | 6.1 |
Gene (Variant) | Library Prep. | Day 1 | Day 2 | Day 3 | Intra-Run | Inter-Run | ||
---|---|---|---|---|---|---|---|---|
Expected VAF (%) | Chip 1.1 | Chip 1.2 | Chip 1.3 | Chip 2 | Chip 3 | CV (%) 1 | CV (%) | |
EGFR (p.E746_ A750delELREA) | 25.0 | 19.7 | 20.9 | 23.0 | 23.9 | 31.6 | 7.9 | 19.5 |
KRAS (p.A146T) | 4.3 | 4.2 | 3.5 | 3.9 | 2.6 | 2.6 | 9.1 | 21.9 |
KRAS (p.G12C) | 6.2 | 5.4 | 7.7 | 7.5 | 7.8 | 5.0 | 18.6 | 20.4 |
MET (p.T1010I) | 6.2 | 7.1 | 7.0 | 7.2 | 7.0 | 8.2 | 1.4 | 7.0 |
PIK3CA (p.E542K) | 4.1 | 4.0 | 4.2 | 4.0 | 3.0 | 4.0 | 2.8 | 12.4 |
Sample ID | Library Prep. | Day 1 (Tech. 1) | Day 2 | Day 3 | Intra-Run | Inter-Run | ||
---|---|---|---|---|---|---|---|---|
Gene/Signature (Unit) | Replicate 1 | Replicate 2 | Replicate 3 | Tech. 2 | Tech. 3 | CV (%) 1 | CV (%) | |
BHL_C03 | IL7R Gain (×) | 10.8 | 10.0 | 9.6 | 11.4 | 7.3 | 6.0 | 16.0 |
BHL_C61 | MDM2 Gain (×) | 18.3 | 13.4 | 12.70 | 16.0 | 17.9 | 20.6 | 16.3 |
BHL_F03 | ERBB2 Gain (×) | 64.9 | 58.7 | 61.1 | 62.9 | 33.4 | 5.1 | 23.0 |
BHL_C11 | MSS (MSI Score) | 8.2 | 8.1 | 8.5 | 5.2 | 4.3 | 2.3 | 28.2 |
BHL_C40 | MSI-H (MSI Score) | 25.3 | 18.7 | 18.25 | 16.7 | 31.4 | 19.3 | 28.1 |
BHL_C66 | MSI-H (MSI Score) | 78.7 | 73.3 | 81.1 | 48.6 | 84.8 | 5.1 | 19.6 |
BHL_C03 | TMB-L (mut/Mb) 2 | 4.8 | 4.8 | 4.8 | 6.7 | 4.8 | 0.5 | 16.3 |
BHL_C40 | TMB-H (mut/Mb) | 17.1 | 19.0 | 17.1 | 20.1 | 19.2 | 6.2 | 7.1 |
BHL_C66 | TMB-H (mut/Mb) | 40.5 | 37.7 | 40.3 | 39.9 | 41.6 | 4.0 | 3.6 |
BHL_C05 | gLOH (%) | 4.9 | 1.8 | 5.5 | 4.2 | 4.1 | 48.8 | 34.2 |
BHL_C10 | gLOH (%) | 13.9 | 14.5 | 16.9 | 9.6 | 14.2 | 10.5 | 19.1 |
BHL_C55 | gLOH (%) | 25.5 | 26.0 | 25.7 | 26.5 | 26.5 | 1.0 | 1.8 |
Sample ID | Tumor Type | Tumor Content (%) | Expected Fusion (Exon Junctions) | OCA+ Result (Exon Junctions) |
---|---|---|---|---|
BHL_C09 | Prostate Cancer | 25 | TMPRSS2::ERG 1 | TMPRSS2::ERG (T1E2) |
BHL_C13 | MASC | 85 | ETV6-Fusion 1 | ETV6::NTRK3 (E5N15) |
BHL_C14 | NSCLC | 30 | FGFR3::TACC3 (F17T8) | FGFR3::TACC3 (F17T8) |
BHL_C15 | Prostate Cancer | 30 | TMPRSS2::ERG (T1E4) | TMPRSS2::ERG (T1E4) |
BHL_C16 | NSCLC | 50 | FGFR3::TACC3 (F17T8) | FGFR3::TACC3 (F17T8) |
BHL_C17 | NSCLC | 70 | METex14 (M13M15) 2 | METex14 (M13M15) |
BHL_C18 | NSCLC | 70 | KIF5B::RET (K15R12) | KIF5B::RET (K15R12) |
BHL_C19 | NSCLC | 70 | ETV6::NTRK3 (E5N15) | ETV6::NTRK3 (E5N15) |
BHL_C20 | NSCLC | 5 | EML4::ALK (E6A19) | EML4::ALK (E6A19) |
BHL_C21 | NSCLC | 50 | CCDC6::RET (C1R12) | CCDC6::RET (C1R12) |
BHL_C22 | NSCLC | 20 | EML4::ALK (E13A20) | EML4::ALK (E13A20) |
BHL_C23 | NSCLC | 50 | EML4::ALK (E20A20) | EML4::ALK (E20A20) |
BHL_C24 | NSCLC | 5 | CD74::ROS1 (C6R34) | CD74::ROS1 (C6R34) |
BHL_C25 | Prostate Cancer | 50 | TMPRSS2::ERG (T2E4) | TMPRSS2::ERG (T2E4) |
BHL_C26 | NSCLC | 30 | EML4::ALK (E2A20) | EML4::ALK (E2A20) |
BHL_C27 | NSCLC | 10 | METex14 (M13M15) | METex14 (M13M15) |
BHL_C28 | NSCLC | 40 | KIF5B::RET (K15R12) | KIF5B::RET (K15R12) |
BHL_C29 | NSCLC | 10 | METex14 (M13M15) | METex14 (M13M15) |
BHL_C30 | NSCLC | 10 | METex14 (M13M15) | METex14 (M13M15) |
BHL_C31 | NSCLC | 50 | EML4::ALK (E6ALK20) | EML4::ALK (E6ALK20) |
Sample ID | HRD Class | HRR Mutated Gene | Reference Score Type | Reference Score | OCA+ Score Type | OCA+ Score |
---|---|---|---|---|---|---|
BHL_C04 | HRD-NEG | ATM | %LOH | 1 | nLOH | 6 |
BHL_C12 | HRD-NEG | FANCG | %LOH | 0 | nLOH | 1 |
BHL_C67 | HRD-NEG | None | %LOH | 9 | nLOH | 5 |
BHL_C73 | HRD-NEG | None | %LOH | 0 | nLOH | 2 |
BHL_C68 | HRD-NEG | None | GIS | 1 | HRD | 2 |
BHL_C69 | HRD-NEG | None | GIS | 12 | HRD | 24 |
BHL_C70 | HRD-NEG | None | GIS | 3 | HRD | 7 |
BHL_C71 | HRD-NEG | None | GIS | 19 | HRD | 29 |
BHL_C72 | HRD-POS | BRCA2 | GIS | 64 | HRD | 53 |
BHL_C74 | HRD-POS | BRCA1 | GIS | 75 | HRD | 58 |
BHL_C06 | HRD-POS | BRCA2 | GIS | + 1 | HRD | 71 |
Sample ID | HRD Class | HRD Score (v5.18) | OCA+ GIM (v5.20) |
---|---|---|---|
BHL_C08 | HRD-NEG | 1 | 0 |
BHL_C73 | HRD-NEG | 2 | 0 |
BHL_C68 | HRD-NEG | 2 | 0 |
BHL_C09 | HRD-NEG | 6 | 0 |
BHL_C70 | HRD-NEG | 7 | 0 |
BHL_C12 | HRD-NEG | 12 | 0 |
BHL_C11 | HRD-NEG | 13 | 0 |
BHL_C05 | HRD-NEG | 17 | 3 |
BHL_C04 | HRD-NEG | 20 | 1 |
BHL_C67 | HRD-NEG | 23 | 4 |
BHL_C69 | HRD-NEG | 24 | 7 |
BHL_C03 | HRD-NEG | 26 | 5 |
BHL_C71 | HRD-NEG | 29 | 4 |
BHL_C07 | HRD-NEG | 32 | 15 |
BHL_C01 | HRD-NEG | 38 | 10 |
BHL_C02 | HRD-NEG | 40 | 13 |
BHL_C72 | HRD-POS | 53 | 16 |
BHL_C10 | HRD-POS | 56 | 16 |
BHL_C74 | HRD-POS | 58 | 19 |
BHL_C06 | HRD-POS | 71 | 24 |
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Dumur, C.I.; Krishnan, R.; Almenara, J.A.; Brown, K.E.; Dugan, K.R.; Farni, C.; Ibrahim, F.Z.; Sanchez, N.A.; Rathore, S.; Pradhan, D.; et al. Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors. J. Mol. Pathol. 2023, 4, 109-127. https://doi.org/10.3390/jmp4020012
Dumur CI, Krishnan R, Almenara JA, Brown KE, Dugan KR, Farni C, Ibrahim FZ, Sanchez NA, Rathore S, Pradhan D, et al. Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors. Journal of Molecular Pathology. 2023; 4(2):109-127. https://doi.org/10.3390/jmp4020012
Chicago/Turabian StyleDumur, Catherine I., Ramakrishnan Krishnan, Jorge A. Almenara, Kathleen E. Brown, Kailyn R. Dugan, Christiana Farni, Fatima Z. Ibrahim, Naomi A. Sanchez, Sumra Rathore, Dinesh Pradhan, and et al. 2023. "Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors" Journal of Molecular Pathology 4, no. 2: 109-127. https://doi.org/10.3390/jmp4020012