Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms

Rosenthal, S. H.; Gerasimova, A.; Ma, C.; Li, H.-R.; Grupe, A.; Chong, H.; Acab, A.; Smolgovsky, A.; Owen, R.; Elzinga, C.; Chen, R.; Sugganth, D.; Freitas, T.; Graham, J.; Champion, K.; Bhattacharya, A.; Racke, F.; Lacbawan, F.

doi:10.1101/2020.11.30.403634

bioRxiv · 10.1101/2020.11.30.403634

Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms

Rosenthal, S. H.·Gerasimova, A.·Ma, C.·Li, H.-R.·Grupe, A.·Chong, H.·Acab, A.·Smolgovsky, A.·Owen, R.·Elzinga, C.·Chen, R.·Sugganth, D.·Freitas, T.·Graham, J.·Champion, K.·Bhattacharya, A.·Racke, F.·Lacbawan, F.

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Abstract

Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. However, due to lack of standard NGS protocols, the application of NGS for hematologic malignancies into clinical settings remains limited. We report development and validation of a 48-gene NGS panel for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies [≥]5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n=2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n=2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms.

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Rosenthal, S. H., Gerasimova, A., Ma, C., Li, H.-R., Grupe, A., Chong, H., Acab, A., Smolgovsky, A., Owen, R., Elzinga, C., Chen, R., Sugganth, D., Freitas, T., Graham, J., Champion, K., Bhattacharya, A., Racke, F., Lacbawan, F.. 2020-11-30. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. https://doi.org/10.1101/2020.11.30.403634

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