Feasibility and clinical impact of routine molecular testing of gastrointestinal cancers at a tertiary centre with a multi-gene, tumor-agnostic, next generation sequencing panel

Sequencing of the human genome has led to the definition of the genes for most of the relevant blood group systems, and the polymorphisms responsible for most of the clinically relevant blood group antigens are characterized. Molecular blood group typing is used in situations where erythrocytes are not available or where serological testing was inconclusive or not possible due to the lack of antisera. Also, molecular testing may be more cost-effective in certain situations. Molecular typing approaches are mostly based on either PCR with specific primers, DNA hybridization, or DNA sequencing. Particularly the transition of sequencing techniques from Sanger-based sequencing to next-generation sequencing (NGS) technologies has led to exciting new possibilities in blood group genotyping. We describe briefly the currently available NGS platforms and their specifications, depict the genetic background of blood group polymorphisms, and discuss applications for NGS approaches in immunohematology. As an example, we delineate a protocol for large-scale donor blood group screening established and in use at our institution. Furthermore, we discuss technical challenges and limitations as well as the prospect for future developments, including long-read sequencing technologies.

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P2.14-29 Clinical Impact of Next-Generation Sequencing (NGS) in Blood Liquid Biopsies for Treatment Decisions in Advanced NSCLC

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2019.08.1814 ◽

2019 ◽

Vol 14 (10) ◽

pp. S840-S841

Author(s):

M. Garcia Pardo ◽

I. Martinez Delfrade ◽

I. Aparicio Salcedo ◽

M. Arregui Valles ◽

M. Alva Bianchi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Advanced Nsclc ◽

Treatment Decisions ◽

Clinical Impact ◽

Next Generation ◽

Liquid Biopsies ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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Routine molecular testing of resected early-stage lung adenocarcinoma with targeted next-generation sequencing demonstrates a high rate of actionable mutations

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2015.12.075 ◽

2016 ◽

Vol 11 (2) ◽

pp. S44-S45 ◽

Cited By ~ 1

Author(s):

Brendon M. Stiles ◽

Abu Nasar ◽

Mohamed Kamel Hussein ◽

Galal Rafik Ghaly ◽

Mohamed Rahouma Ahmed ◽

...

Keyword(s):

Next Generation Sequencing ◽

Lung Adenocarcinoma ◽

Early Stage ◽

High Rate ◽

Molecular Testing ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Clinical Impact of Plasma Metagenomic Next-generation Sequencing in a Large Pediatric Cohort

The Pediatric Infectious Disease Journal ◽

10.1097/inf.0000000000003395 ◽

2021 ◽

Vol Publish Ahead of Print ◽

Author(s):

Denver T. Niles ◽

Paula A. Revell ◽

Daniel Ruderfer ◽

Lucila Marquez ◽

J. Chase McNeil ◽

...

Keyword(s):

Next Generation Sequencing ◽

Clinical Impact ◽

Next Generation ◽

Generation Sequencing

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

PLoS ONE ◽

10.1371/journal.pone.0243683 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0243683

Author(s):

Sun Hee Rosenthal ◽

Anna Gerasimova ◽

Charles Ma ◽

Hai-Rong Li ◽

Andrew Grupe ◽

...

Keyword(s):

Next Generation Sequencing ◽

Myeloproliferative Neoplasms ◽

Simultaneous Detection ◽

Molecular Testing ◽

Next Generation ◽

Analytical Validation ◽

Bioinformatics Pipeline ◽

Myeloid Neoplasms ◽

Clinically Significant ◽

Generation Sequencing

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. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging 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 even in technically challenging genes.

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Next-Generation Sequencing Analysis of Endometrial Screening Liquid-Based Cytology Specimens: A Comparative Study to Tissue Specimens

10.21203/rs.3.rs-19269/v3 ◽

2020 ◽

Author(s):

Toshiaki Akahane ◽

Ikumi Kitazono ◽

Shintaro Yanazume ◽

Masaki Kamio ◽

Shinichi Togami ◽

...

Keyword(s):

Endometrial Cancer ◽

Next Generation Sequencing ◽

Gene Panel ◽

Molecular Testing ◽

Sequencing Analysis ◽

Cancer Gene ◽

Next Generation ◽

Ffpe Tissues ◽

Liquid Based Cytology ◽

Generation Sequencing

Abstract Background: Liquid-based cytology (LBC) is now a widely used method for cytologic screening and cancer diagnosis. Since the cells are fixed with alcohol-based fixatives, and the specimens are stored in a liquid condition, LBC specimens are suitable for genetic analyses. Methods: Here, we established a small cancer gene panel, including 60 genes and 17 microsatellite markers for next-generation sequencing, and applied to residual LBC specimens obtained by endometrial cancer screening to compare with corresponding formalin-fixed paraffin-embedded (FFPE) tissues. Results: A total of 49 FFPE and LBC specimens (n=24) were analyzed, revealing characteristic mutations for endometrial cancer, including PTEN, CTNNB1, PIK3CA, and PIK3R1 mutations. Eight cases had higher scores for both tumor mutation burden (TMB) and microsatellite instability (MSI), which agree with defective mismatch repair (MMR) protein expression. Paired endometrial LBC, and biopsied and/or resected FFPE tissues from 7 cases, presented almost identical mutations, TMB, and MSI profiles in all cases. Conclusion: These findings demonstrate that our ad hoc cancer gene panel enabled the detection of therapeutically actionable gene mutations in endometrial LBC and FFPE specimens. Endometrial cancer LBC specimens offer an alternative and affordable source of molecular testing materials.

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Synchronous Pulmonary Adenocarcinomas

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqaa023 ◽

2020 ◽

Vol 154 (1) ◽

pp. 57-69

Author(s):

Carlos A Pagan ◽

Catherine A Shu ◽

John P Crapanzano ◽

Galina G Lagos ◽

Mark B Stoopler ◽

...

Keyword(s):

Next Generation Sequencing ◽

Gene Panel ◽

Driver Mutations ◽

Molecular Testing ◽

Next Generation ◽

Synchronous Tumors ◽

Targeted Next Generation Sequencing ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Objectives To determine concordance/discordance between morphology and molecular testing (MT) among synchronous pulmonary carcinomas using targeted next generation sequencing (NGS), with and without comprehensive molecular review (CMR), vs analyses of multiple singe genes (non-NGS). Methods Results of morphologic and MT assessment were classified as concordant, discordant, or indeterminate. For discordant cases, comprehensive histologic assessment (CHA) was performed. Results Forty-seven cases with 108 synchronous tumors were identified and underwent MT (NGS, n = 23 and non-NGS, n = 24). Histology and MT were concordant, discordant, and indeterminate in 53% (25/47), 21% (10/47), and 26% (12/47) of cases, respectively. CHA of the 10 discordant cases revised results of three cases. Conclusions There is discordance between histology and MT in a subset of cases and MT provides an objective surrogate for staging synchronous tumors. A limited gene panel is sufficient for objectively assessing a relationship if the driver mutations are distinct. Relatedness of mutations require CMR with a larger NGS panel (eg, 50 genes).

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