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Journal articles on the topic 'NGS'

Author: Grafiati

Published: 4 June 2021

Last updated: 29 March 2025

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1

Tatebale, Rivaldo, Orbanus Naharia, and Helen J. Lawalata. "Isolation and Identification of Lactic Acid Bacteria from Red Dragon Fruit (Hylocereus polyrhicus) as Exopolysaccharide Producers." Indonesian Biodiversity Journal 5, no. 1 (April 28, 2024): 8–19. https://doi.org/10.53682/ibj.v5i1.7730.

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Cherry tomatoes are a type of Red Dragon Fruit that has various benefits, including lowering cholesterol levels, preventing colon cancer, and strengthening the working power of muscles. Isolation of LAB isolated from Dragon Fruit as a production material for EPS. This study aims to isolate and identify LAB as a producer of EPS from red dragon fruit (Hylocereus polyrhiruz), which can produce exopolysaccharides. This research uses a descriptive research method. Data from experimental research in the laboratory obtained 10 LAB isolates, namely isolates NG1, NG2, NG3, NG4, NG5, NG6, NG7, NG8, NG9 and NG10. Based on the identification results, isolate NG1 has similarities with the genus Lactococcus (spherical, gram-positive, nonmotile, non-spore). While isolates NG2, NG3, NG4, NG5, NG6, NG7, NG8, NG9 and NG10 have similarities with the genus Lactobacillus (rod form, nonmotile, gram-positive). Based on the morphological characteristics, which are gram-positive, catalase-negative and non-spore. The ten isolates of lactic acid bacteria are capable of producing EPS. these are the results of EPS acquisition, namely: NG1(152.1 mg/L), NG2(127.9 mg/L), NG3(134.6 mg/L), NG4(130.9 mg/L), NG5(137 mg/L), NG6(139.2 mg/L), NG7(204.9 mg/L), NG8(156.2 mg/L), NG9(136.4 mg/L), and NG10 (157, 3 mg/L). The highest amount of EPS was isolated NG7 at 204.9 mg/L. Meanwhile, the lowest EPS was isolated NG4 at 130.9 mg/L.

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2

Tunis, Sean. "Reimbursing NGS Testing." Clinical OMICs 2, no. 1 (January 2015): 21–23. http://dx.doi.org/10.1089/clinomi.02.01.08.

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3

Zemlo, Tamara. "Democratizing NGS Platforms." Genetic Engineering & Biotechnology News 32, no. 5 (March 2012): 16–18. http://dx.doi.org/10.1089/gen.32.5.05.

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4

Tunis, Sean. "Reimbursing NGS Testing." Genetic Engineering & Biotechnology News 35, no. 3 (February 2015): 5–6. http://dx.doi.org/10.1089/gen.35.03.03.

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5

Kim, Annette S., Angela N. Bartley, Julia A. Bridge, Kelly Devereaux, A. John Iafrate, Lawrence Jennings, Suzanne Kamel-Reid, et al. "31. The PT alphabet soup: LDT, FDA, NGS, non-NGS, @#$!%." Cancer Genetics 233-234 (April 2019): S13. http://dx.doi.org/10.1016/j.cancergen.2019.04.037.

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6

Szabo, Kathrin, Burkhard Malorny, and Manfred Stoyke. "Etablierung der § 64 LFGB Arbeitsgruppen „NGS – Bakteriencharakterisierung“ und „NGS – Speziesidentifizierung“." Journal of Consumer Protection and Food Safety 15, no. 1 (October 22, 2019): 85–89. http://dx.doi.org/10.1007/s00003-019-01255-z.

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Zusammenfassung Das Next-Generation Sequencing (NGS) besitzt großes Potential im Bereich der Lebensmittelsicherheit und der Authentizitätsprüfung von Lebensmitteln. Die Gesamtgenomsequenzierung mikrobieller Genome kombiniert mit bioinformatischen Auswerteprogrammen ersetzt zunehmend die klassischen Typisierungsmethoden und gilt aufgrund ihres außerordentlichen Auflösungsvermögen mittlerweile als Methode der Wahl im Rahmen von Ausbruchsuntersuchungen. Zur Authentizitätskontrolle z. B. von Fleisch- und Fischproben finden NGS-Methoden als Metabarcoding immer häufiger Anwendung, um Täuschung und Irreführung bis hin zu Lebensmittelbetrug aufzudecken. Einige Untersuchungsbehörden verfügen bereits über die NGS-Technologie und setzen diese auch erfolgreich ein, weitere Einrichtungen werden folgen. Um den mit der Lebensmittelüberwachung betrauten Behörden validierte, leistungsfähige und standardisierte NGS-Methoden zur Verfügung zu stellen, ist eine Aufnahme dieser Methoden in die „Amtliche Sammlung von Verfahren zur Probenahme und Untersuchung von Lebensmitteln“ (ASU) durch die Gründung zweier neuer § 64 LFGB Arbeitsgruppen mit unterschiedlichen thematischen Schwerpunkten vorgesehen. Die Arbeitsgruppe „NGS – Bakteriencharakterisierung“ bearbeitet NGS-Verfahren für die Sequenzierung bakterieller Erreger im Rahmen von Ausbruchsuntersuchungen. Die Arbeitsgruppe „NGS – Speziesidentifizierung“ beschäftigt sich mit NGS-Methoden zur Tierartendifferenzierung in Lebensmitteln. Am 6. März 2019 fand das erste Treffen der Arbeitsgruppe „NGS – Speziesidentifizierung“ und am folgenden Tag, dem 7. März 2019 das der Arbeitsgruppe „NGS – Bakteriencharakterisierung“ auf Einladung des Bundesamts für Verbraucherschutz und Lebensmittelsicherheit (BVL) in Berlin statt. Auf den Sitzungen wurden durch die Mitglieder der Gruppen NGS-Methoden zur Bakteriencharakterisierung bzw. zur Tierartendifferenzierung in Lebensmitteln vorgestellt. Anschließend diskutierten die Mitglieder die ersten thematischen Schwerpunkte der Methodenentwicklung, Validierungskonzepte, Qualitätskontrollmaßnahmen und den Einsatz dieser Methoden in der Lebensmittelüberwachung. Es wurde beschlossen, durch laborübergreifende Vorringversuche die Vergleichbarkeit der verschiedenen NGS-Technologien zu ermitteln sowie die entsprechenden Auswerteparameter, Qualitätskriterien und Validierungsparameter für eine laborübergreifende Validierungsstudie zu erarbeiten.

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7

Veldman, Abigail, Mensiena B. G. Kiewiet, Margaretha Rebecca Heiner-Fokkema, Marcel R. Nelen, Richard J. Sinke, Birgit Sikkema-Raddatz, Els Voorhoeve, et al. "Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead." International Journal of Neonatal Screening 8, no. 1 (February 24, 2022): 17. http://dx.doi.org/10.3390/ijns8010017.

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Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe the aim and set-up of the NGS-first for the NBS (NGSf4NBS) project, which will proceed in three steps. In Step 1, we will identify IMDs eligible for NGS-first testing, based on treatability. In Step 2, we will investigate the feasibility, limitations and comparability of different technical NGS approaches and analysis workflows for NBS, eventually aiming to develop a rapid NGS-based workflow. Finally, in Step 3, we will prepare for the incorporation of this workflow into the existing Dutch NBS program and propose a protocol for referral of a child after a positive NGS test result. The results of this study will be the basis for an additional analytical route within NBS that will be further studied for its applicability within the NBS program, e.g., regarding the ethical, legal, financial and social implications.

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8

Ardeshirdavani, Amin, Erika Souche, Luc Dehaspe, Jeroen Van Houdt, Joris Vermeesch, and Yves Moreau. "NGS-Logistics : Federated analysis of NGS sequence variants across multiple locations." Genome Medicine 6, no. 9 (2014): 71. http://dx.doi.org/10.1186/preaccept-3696327041308731.

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9

May, Ali, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, and Bernd W. Brandt. "NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL." Nucleic Acids Research 43, W1 (April 15, 2015): W301—W305. http://dx.doi.org/10.1093/nar/gkv346.

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10

Ravasio, Viola, Marco Ritelli, Andrea Legati, and Edoardo Giacopuzzi. "GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS." Bioinformatics 34, no. 17 (April 14, 2018): 3038–40. http://dx.doi.org/10.1093/bioinformatics/bty303.

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11

Shotelersuk, V. "NGS for rare diseases." Clinica Chimica Acta 530 (May 2022): S459. http://dx.doi.org/10.1016/j.cca.2022.04.780.

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12

Heiden, Lisa. "NGS Propels Personalized Oncology." Clinical OMICs 2, no. 4 (April 2015): 16–21. http://dx.doi.org/10.1089/clinomi.02.04.07.

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13

Schrezenmeier, Hubert. "NGS und neue Erkrankungen." Transfusionsmedizin - Immunhämatologie, Hämotherapie, Immungenetik, Zelltherapie 7, no. 01 (March 13, 2017): 7–8. http://dx.doi.org/10.1055/s-0043-100088.

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14

Weißmann, R., and C. Gilissen. "NGS Datenanalyse und Qualitätskontrolle." medizinische genetik 26, no. 2 (June 2014): 239–45. http://dx.doi.org/10.1007/s11825-014-0448-6.

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15

Gomes, Ellia, Efi Melista, Krisztina Rigó, Panna Vass, and Peter Meintjes. "P254 NGS Superpowers II." Human Immunology 78 (September 2017): 240. http://dx.doi.org/10.1016/j.humimm.2017.06.314.

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Heiden, Lisa. "NGS Propels Personalized Oncology." Genetic Engineering & Biotechnology News 35, no. 6 (March 2015): 1,30–32. http://dx.doi.org/10.1089/gen.35.06.02.

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17

Szabo, Kathrin, Burkhard Malorny, and Manfred Stoyke. "Correction to: Etablierung der § 64 LFGB Arbeitsgruppen „NGS – Bakteriencharakterisierung“ und „NGS – Speziesidentifizierung“." Journal of Consumer Protection and Food Safety 15, no. 1 (December 17, 2019): 91. http://dx.doi.org/10.1007/s00003-019-01262-0.

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18

Kim, Sung-Min, Jung-Ah Kim, Dajeong Jeong, Jiwon Yun, Kyu Min Lim, Sang Mee Hwang, Sung-Soo Yoon, and Dong Soon Lee. "Next Generation Flow for Multiple Myeloma Minimal Residual Disease: Igh Rearrangement NGS Is Complement to the NGF." Blood 132, Supplement 1 (November 29, 2018): 5609. http://dx.doi.org/10.1182/blood-2018-99-120333.

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Abstract Background: Detection of leukemia-associated aberrant immuno-phenotype is used to assess minimal residual disease (MRD) by multi-parameter flow cytometry (MFC). However, detection of MRD by MFC remains to be a challenging due to the possible change in aberrant immunophenotype during disease progress. In our present study, we compared International Myeloma Working group (IMW) treatment response and NGF MRD, including BM PC% and cytogenetics. Thereon, we conducted IgH rearrangement study by NGS in cases showing discrepant results. Methods: A total of 35 BM (35 myeloma patients at follow-up) was enrolled. We performed NGF using 8-color antibody panel using Navios flow cytometer and Infinicyt. Linearity of NGF was validated with myeloma cell line (U266) and BM specimen at initial diagnosis in myeloma patient. IgH rearrangement NGS was performed using Immunoseq assay (Adaptive Biotechnologies, Seattle, WA, USA). Paired specimen at initial diagnosis BM and follow-up BM were subjected to NGS study. Results: Detection sensitivity of NGF was <0.001%. Patients who achieved CR or sCR showed MRD negativity in 63.6% (7/11). Twenty-three patients showed neoplastic PCs above LLOQ and their response criteria were 1 sCR, 3 CR, 2 VGPR, 3 PR, 1 MR, 5 SD, 3 progressive disease, 3 relapse, and 2 with unavailable response. Four patients who did not achieve CR (1 VGPR, 1 PR, 1 MR, and 1 SD) showed MRD negativity by NGF. In 4 patients with discrepancy between IMW treatment response and NGF, we compared the results of IgH NGS at initial BM with those after treatment. NGS revealed a persistence of residual clone in 1 patient and an acquisition of new clone after treatment. One patient had same dominant clone both initial diagnosis BM (95.2%; proportion of clone) and follow-up BM (45.8%). The other patient had newly appeared clones in follow-up BM (6.12%, 5.63%, 3.42%, 3.11%, 3.09%) which clones were absent in initial diagnosis BM. The other 2 patients showed heterogeneous clones without dominant clone at follow-up BM by NGS. Results of FISH and immunofixation are summarized in Table 1. This results show IgH rearrangement NGS can detect malignant clone that could not be identified by using NGF. Conclusions: Thirty-six percent of patients who did not achieve CR showed NGF MRD negativity and NGS revealed residual clones in half of them. Switching of immunophenotypes of neoplastic PC can escape monitoring of NGF, and complementary NGS test is needed to catch such drifting clones for monitoring of MRD in MM. Disclosures No relevant conflicts of interest to declare.

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Wong, William Bruce, Daniel Sheinson, Sarika Ogale, Carlos Flores, and Cary Philip Gross. "The association between Medicare’s next generation sequencing (NGS), national coverage decision (NCD), and NGS utilization." Journal of Clinical Oncology 38, no. 29_suppl (October 10, 2020): 98. http://dx.doi.org/10.1200/jco.2020.38.29_suppl.98.

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98 Background: In 2018, Medicare released a NGS NCD memo which would facilitate reimbursement for NGS tests for patients (pts) with advanced or metastatic cancer who had not been previously tested using NGS for the same cancer and genetic content. We examined the association between the NCD and: a) NGS utilization trends in commercially-insured and Medicare pts and b) repeat NGS testing. Methods: We conducted a retrospective study of pts with advanced non-small cell lung cancer (aNSCLC), metastatic colorectal cancer (mCRC), metastatic breast cancer (mBC) or advanced melanoma (aM), diagnosed 2011 (2013 for mCRC) through Dec. 2019 using the Flatiron Health EHR-derived de-identified database, comprising data from over 280 (largely community based) cancer clinics (~800 sites of care). Pts were classified as Medicare or Commercially insured based on age and insurance type, and grouped into quarters based on their advanced or metastatic diagnosis date. NGS testing rates per quarter were based on evidence of first NGS test within 60 days from diagnosis. We used an interrupted time series analysis to assess NGS utilization trends pre- and post-NCD policy effective date (March 2018). The frequency of repeat NGS testing was assessed among those pts with only 1 primary cancer. Results: The utilization analysis included 70,290 pts while the repeat NGS testing analysis included 51,385 pts. Across the 4 tumors combined, the use of NGS was < 1% in 2011 (both insurance types) and increased to 41% in commercially-insured pts and 37% in Medicare in 2019. In each tumor, NGS utilization was < 6% in Q1 2014; however, the rate of increase varied by tumor, with aNSCLC increasing to 58% in commercial and 48% in Medicare, while mBC and aM remained < 20% in Q4 2019. Among pts with aNSCLC, mCRC, or mBC, the quarterly rate of increase in NGS testing was higher post-NCD compared to pre-NCD (p < 0.05 for pre-post difference in rate of NGS increase within each cancer type). The difference in trends pre- and post-NCD was not significantly different between commercial and Medicare in any of the tumors (p > 0.05 within each cancer type). Repeat NGS testing increased over time from 17.8% (in Q3 2014 to Q2 2016) to 29.6% (in Q2 2018 to Q4 2019). Conclusions: NGS utilization trends significantly changed post-NCD, however the rate of change was not significantly different by insurance, indicating private insurers may also be following the guidance of the NCD. We observed an increase in repeat NGS testing, despite the NCD not covering repeat testing with the same NGS test.

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Urushihara, Ryota, Naoki Takezako, Takeshi Yoroidaka, Takeshi Yamashita, Shinji Nakao, and Hiroyuki Takamatsu. "Comparison of MRD Detection in Autografts in Multiple Myeloma between Novel High-Sensitivity Euroflow-NGF and NGS." Blood 138, Supplement 1 (November 5, 2021): 3950. http://dx.doi.org/10.1182/blood-2021-149041.

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Abstract Background: Autologous stem cell transplantation (ASCT) remains the gold-standard treatment for multiple myeloma (MM). To date, we have reported the prognostic value of minimal residual disease (MRD) detection in autografts in an ASCT setting using EuroFlow next-generation flow (NGF) and next-generation sequencing (NGS) (Takamatsu et al., ASH 2018, 2020). The main problem with NGF is its lower sensitivity (2 × 10 -6) compared with that of NGS (<1 × 10 -6). Methods: We reanalyzed 11 autografts in which the MRD were negative on NGF but positive (n = 7) or negative (n = 4) on NGS (Takamatsu et al., ASH 2018, abstract #258) using 5-20 mL of autografts with NGF to increase the sensitivity of MRD detection. Additionally, we enrolled 9 patients with newly diagnosed MM, from whom 5-20 mL of apheresed autografts were cryopreserved. We included 20 patients with newly diagnosed MM. The median age at ASCT was 60 (range, 45-67) years, and the patients included 12 men and 8 women at International Staging System I (n = 3), II (n = 13), and III (n = 4), 6 of whom harbored high-risk chromosomal abnormalities, including t(4;14) (n = 3), t(14;16) (n = 1), del17p (n = 1), and t(4;14) and del 17p (n = 1). All patients received bortezomib-based chemotherapy for induction followed by melphalan at a dose of 200 mg/m 2 for conditioning before ASCT. Three patients received consolidation therapy with carfilzomib-lenalidomide-dexamethasone (n = 2) or bortezomib-lenalidomide-dexamethasone (n = 1), and 18 patients received lenalidomide (n = 16), thalidomide (n = 1), or thalidomide and lenalidomide (n = 1) maintenance. Frozen autografts (n = 20) were thawed for MRD assessment using NGF and NGS. The NGF method was based on a previous report (Flores-Montero et al., Leukemia 2017). NGS-based MRD assessment was performed using Adaptive's standardized NGS-MRD assay (Seattle, WA) (Ching et al., BMC Cancer 2020). The NGF method was modified to increase the sensitivity of MRD detection by capturing up to 6 × 10 7 cells. Results: Frozen autografts were used in this study; therefore, we performed a sensitivity test using a dilution of frozen/thawed primary MM cells in an autograft with NGF. The sensitivity test revealed a strong correlation between 5 × 10 -7 and 1 × 10 -4 MRD levels (Figure 1A; r = 0.999, P <0.0001). Next, MRD in autografts (n = 20) was evaluated using NGF and NGS. The sensitivity of NGS was 1.7 × 10 -7-8.7 × 10 -5 (median, 7 × 10 -7) using 2-4 mL of autografts; the sensitivity of NGF was 1.6 × 10 -7-3.7 × 10 -6 (median, 3 × 10 -7) using up to 20 mL of autografts based on the detection of ≥10 abnormal cells. MRD levels in autografts using NGF and NGS were correlated (Figure 1B; r = 0.979, P <0.0001). There was no discrepancy in the MRD negativity between both methods except for two cases (MRD-negative on NGF/positive on NGS [n = 2]). All high-risk chromosomal abnormality cases (n = 6) revealed MRD levels <10 -5 butonly three patients achieved MRD levels <10 -6. The best responses included 16 cases of a stringent complete response and 4 of a very good partial response. Three patients with positive MRD in the autograft exhibited progression. With a median follow-up period of 41 months after ASCT, the 3-year progression-free survival (PFS) was 90%, and the 3-year overall survival was 95%. There was no significant difference in the PFS based on the MRD levels between NGF and NGS. MRD negative cases tended to show better PFS than MRD positive ones (Figure 1C; P = 0.077 by NGF; P = 0.111 by NGS). Conclusion: The modified EuroFlow-NGF method may be used to assess MRD in frozen/thawed autografts, and its sensitivity may increase up to 5 × 10 -7, which is comparable to that of NGS. Figure 1 Figure 1. Disclosures Yamashita: Janssen: Honoraria; Bristol-Myers Squibb: Honoraria; celgene: Honoraria; Takeda: Honoraria. Nakao: Novartis Pharma: Honoraria; Symbio: Consultancy; Kyowa Kirin: Honoraria; Alexion Pharma: Research Funding. Takamatsu: Adaptive Biotechnologies, Eisai: Honoraria; SRL: Consultancy; Bristol-Myers Squibb: Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding.

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Ruark, Elise, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, and Nazneen Rahman. "The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis." F1000Research 5 (March 22, 2016): 386. http://dx.doi.org/10.12688/f1000research.8219.1.

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To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 730 sites; 409 sites with variants and 321 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 286 indel variants and 275 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.

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Ruark, Elise, Anthony Renwick, Matthew Clarke, Katie Snape, Emma Ramsay, Anna Elliott, Sandra Hanks, Ann Strydom, Sheila Seal, and Nazneen Rahman. "The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis." F1000Research 5 (September 5, 2018): 386. http://dx.doi.org/10.12688/f1000research.8219.2.

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To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 704 sites; 416 sites with variants and 288 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 293 indel variants and 247 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.

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An, Omer, Kar-Tong Tan, Ying Li, Jia Li, Chan-Shuo Wu, Bin Zhang, Leilei Chen, and Henry Yang. "CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing." International Journal of Molecular Sciences 21, no. 11 (May 28, 2020): 3828. http://dx.doi.org/10.3390/ijms21113828.

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Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus.edu.sg/csingsportal.

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Singer, Jochen, Hans-Joachim Ruscheweyh, Ariane L. Hofmann, Thomas Thurnherr, Franziska Singer, Nora C. Toussaint, Charlotte K. Y. Ng, et al. "NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis." Bioinformatics 34, no. 1 (August 28, 2017): 107–8. http://dx.doi.org/10.1093/bioinformatics/btx540.

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Yoroidaka, Takeshi, Hiroyuki Takamatsu, Mitsuhiro Itagaki, Satoshi Yoshihara, Kota Sato, Naoki Takezako, Shuji Ozaki, et al. "Prospective Comparison Study of Prognostic Value of MRD Detected By 8-Color MFC (EuroFlow-NGF) and NGS in Patients with Multiple Myeloma in ASCT Setting." Blood 138, Supplement 1 (November 5, 2021): 3946. http://dx.doi.org/10.1182/blood-2021-146441.

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Abstract Background: Novel agents capable of inducing deeper responses dramatically improve the prognosis of patients with multiple myeloma (MM). Innovative technologies such as multiparameter flow cytometry (MFC) and next-generation sequencing (NGS) are utilized to assess minimal residual disease (MRD) for further stratification of patients who achieve a complete response (CR). EuroFlow-next-generation flow (EuroFlow-NGF) is one of the gold standard MFC methods. Recently, both NGF and NGS have been used in many clinical trials to assess MRD levels associated with progression-free survival (PFS) and overall survival (OS). The present study prospectively assessed MRD levels by both NGF and NGS to elucidate the prognostic impact of both methods and clarify their characteristics in MM patients in an autologous stem cell transplantation (ASCT) setting. Methods: We prospectively assessed the response in Japanese patients with newly diagnosed MM who underwent ASCT and lenalidomide-based maintenance therapy at multiple Japanese medical centers between September 2016 and July 2021. The diagnosis of MM and patients' responses to therapy were assessed using the IMWG criteria. Only patients with CR or stringent CR on days 100-365 post-ASCT were included, and bone marrow (BM) samples were obtained to assess MRD. Four milliliters of BM was divided equally. Cells derived from 2 mL BM were analyzed by the NGF method (Flores-Montero et al., Leukemia 2017) at Kanazawa University, and DNA extracted from the remaining 2 mL BM cells was processed by Adaptive Biotechnologies' standardized NGS-MRD assay (Seattle, WA) (Ching et al., BMC Cancer 2020) to assess MRD levels. MRD levels in BM were also monitored at 1-year (± 20 days) and 2-year (± 20 days) post-ASCT. The prognostic value of MRD levels in BM was assessed, and their correlation between NGF and NGS was compared at a cut-off value of 1×10 -5. Sustained MRD negativity was defined as the maintenance of MRD negativity in the BM for more than 6 months. BM cells were analyzed for high-risk cytogenetics (del(17p), t(4;14), and t(14;16)) by FISH. Results: A total of 60 patients (male = 29, female = 31) underwent bortezomib-based induction therapy, ASCT conditioned with high-dose melphalan, and lenalidomide-based maintenance. The median age was 62 years at the ASCT (range 36-71; ISS 1 [n = 13], 2 [n = 24], and 3 [n = 23]). Thirty-three percent of patients showed high-risk chromosomal abnormalities (del17p (n=11), t(4;14) (n=10), t(14;16) (n=2)), 3 patients had double hit diseases, and five patients had extramedullary diseases. With a median follow-up of 3 years, the 3-year progression-free survival (PFS) and 3-year overall survival (OS) rates were 69.2% and 94.2%, respectively. In total, 148 samples were analyzed using NGF and 138 were analyzed using NGS. The rates of MRD negativity at least once using NGF and NGS were 80% and 61%, respectively. The patients who achieved at least one MRD negativity exhibited significantly better 3-year PFS (82.9% by NGF; 84.8% by NGS) than those who did not (P < 0.0001, 0% by NGF; P = 0.005, 49.1% by NGS). Patients who sustained MRD negativity for more than 6 months also showed significantly better 3-year PFS (96.7% by NGF; 92.3% by NGS) compared with those without sustained MRD negativity (Figure; P < 0.0001, 37.1% by NGF; P < 0.01, 50.9% by NGS). The MRD levels between the NGF and NGS methods were significantly correlated with each other (r = 0.9295, P < 0.0001). Among the 17 patients who developed PD after ASCT, seven cases showed discrepancies in the MRD results and two cases in which one case was MRD-positive and the other was MRD-negative by both methods progressed with extramedullary diseases. Five of the seven cases were MRD-positive by NGS and MRD-negative by NGF. Conclusions: In this prospective comparison study of MRD assessment in BM cells using EuroFlow-NGF and NGS approaches, MRD levels highly correlated with each other, and MRD negativity and sustained MRD negativity were significantly associated with prolonged PFS. Multiple MRD assessments by NGF or NGS are essential for predicting durable remission and prolonged clinical outcomes. Figure 1 Figure 1. Disclosures Takamatsu: Bristol-Myers Squibb: Honoraria, Research Funding; Adaptive Biotechnologies, Eisai: Honoraria; SRL: Consultancy; Janssen: Consultancy, Honoraria, Research Funding. Yoshihara: Bristol-Myers Squibb: Honoraria; Janssen: Honoraria; Novartis: Honoraria. Matsumoto: Sanofi: Honoraria; Janssen: Honoraria; Ono: Honoraria; Bristol-Myers Squibb: Honoraria. Yamashita: Janssen: Honoraria; Bristol-Myers Squibb: Honoraria; celgene: Honoraria; Takeda: Honoraria. Fuchida: Takeda Pharmaceutical Co., Ltd.: Honoraria; Ono Pharmaceutical Co., Ltd.: Honoraria; Janssen Pharmaceutical K.K.: Honoraria; Sanofi: Honoraria; Bristol-Myers Squibb Co., Ltd.: Honoraria; Celgene Co., Ltd.: Honoraria. Hiragori: BML: Current Employment. Suzuki: Amgen: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; ONO: Honoraria; Novartis: Honoraria; Sanofi: Honoraria; Abie: Honoraria; Janssen: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Bristol-Myers Squibb: Honoraria, Research Funding. Nakao: Symbio: Consultancy; Kyowa Kirin: Honoraria; Novartis Pharma: Honoraria; Alexion Pharma: Research Funding. Durie: Amgen: Other: fees from non-CME/CE services ; Amgen, Celgene/Bristol-Myers Squibb, Janssen, and Takeda: Consultancy.

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Tang, Chengfang, Lixin Li, Ting Chen, Yulin Li, Bo Zhu, Yinhong Zhang, Yifan Yin, et al. "Newborn Screening for Inborn Errors of Metabolism by Next-Generation Sequencing Combined with Tandem Mass Spectrometry." International Journal of Neonatal Screening 10, no. 2 (March 29, 2024): 28. http://dx.doi.org/10.3390/ijns10020028.

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The aim of this study was to observe the outcomes of newborn screening (NBS) in a certain population by using next-generation sequencing (NGS) as a first-tier screening test combined with tandem mass spectrometry (MS/MS). We performed a multicenter study of 29,601 newborns from eight screening centers with NBS via NGS combined with MS/MS. A custom-designed panel targeting the coding region of the 142 genes of 128 inborn errors of metabolism (IEMs) was applied as a first-tier screening test, and expanded NBS using MS/MS was executed simultaneously. In total, 52 genes associated with the 38 IEMs screened by MS/MS were analyzed. The NBS performance of these two methods was analyzed and compared respectively. A total of 23 IEMs were diagnosed via NGS combined with MS/MS. The incidence of IEMs was approximately 1 in 1287. Within separate statistical analyses, the positive predictive value (PPV) for MS/MS was 5.29%, and the sensitivity was 91.3%. However, for genetic screening alone, the PPV for NGS was 70.83%, with 73.91% sensitivity. The three most common IEMs were methylmalonic academia (MMA), primary carnitine deficiency (PCD) and phenylketonuria (PKU). The five genes with the most common carrier frequencies were PAH (1:42), PRODH (1:51), MMACHC (1:52), SLC25A13 (1:55) and SLC22A5 (1:63). Our study showed that NBS combined with NGS and MS/MS improves the performance of screening methods, optimizes the process, and provides accurate diagnoses.

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Owen, Dwight, Rotem Ben-Shachar, Josephine Feliciano, Lisa Gai, Kyle A. Beauchamp, Zachary Rivers, Adam J. Hockenberry, et al. "Actionable Structural Variant Detection via RNA-NGS and DNA-NGS in Patients With Advanced Non–Small Cell Lung Cancer." JAMA Network Open 7, no. 11 (November 4, 2024): e2442970. http://dx.doi.org/10.1001/jamanetworkopen.2024.42970.

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ImportanceThe National Comprehensive Cancer Network (NCCN) guidelines for non–small cell lung cancer suggest that RNA next-generation sequencing (NGS) may improve the detection of fusions and splicing variants compared with DNA-NGS alone. However, there is limited adoption of RNA-NGS in routine oncology clinical care today.ObjectiveTo analyze clinical evidence from a diverse cohort of patients with advanced lung adenocarcinoma and compare the detection of NCCN-recommended actionable structural variants (aSVs; fusions and splicing variants) via concurrent DNA and RNA-NGS vs DNA-NGS alone.Design, Setting, and ParticipantsThis multisite, retrospective cohort study examined patients sequenced between February 2021 and October 2023 within the deidentified, Tempus multimodal database, consisting of linked molecular and clinical data. Participants included patients with advanced lung adenocarcinoma and sufficient tissue sample quantities for both RNA-NGS and DNA-NGS testing.ExposuresReceived results from RNA-NGS and DNA-NGS solid-tissue profiling assays.Main Outcomes and MeasuresDetection rates of NCCN guideline–based structural variants (ALK, ROS1, RET and NTRK1/2/3 fusions, as well as MET exon 14 skipping splicing alterations) found uniquely by RNA-NGS.ResultsIn the evaluable cohort of 5570 patients, median (IQR) age was 67.8 (61.3-75.4) years, and 2989 patients (53.7%) were female. The prevalence of actionable structural variants detected by either RNA-NGS or DNA-NGS was 8.8% (n = 491), with 86.7% (n = 426) of these detected by DNA-NGS. Concurrent RNA-NGS and DNA-NGS identified 15.3% more patients harboring aSVs compared with DNA-NGS alone (491 vs 426 patients, respectively), including 14.3% more patients harboring actionable fusions (376 vs 329 patients) and 18.6% more patients harboring MET exon 14 skipping alterations (115 vs 97 patients). There was no significant association between the assay used for aSV detection and aSV-targeted therapeutic adoption or clinical outcome. Emerging structural variants (eSVs) were found to have a combined prevalence to be 0.7%, with only 47.5% of eSVs detected by DNA-NGS.Conclusions and RelevanceIn this cohort study, the detection of structural variants via concurrent RNA-NGS and DNA-NGS was higher across multiple NCCN-guideline recommended biomarkers compared with DNA-NGS alone, suggesting that RNA-NGS should be routinely implemented in the care of patients with advanced NSCLC.

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Christy, Alap Lukiyas, Eatu Das, Jasmin Surana, Pradnya Padhye, Kedar Shirodkar, Rakhi Bajpai Dixit, and Kirti Chadha. "Expanding the screening of newborns for detecting inborn errors in metabolism using next generation sequencing following mass spectrometry/immunoassay." International Journal of Clinical Biochemistry and Research 10, no. 4 (February 15, 2024): 332–38. http://dx.doi.org/10.18231/j.ijcbr.2023.059.

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Inborn errors of metabolism are rare inherited disorders which leads to significant morbidity and mortality in patients. Very few studies have been conducted in India to assess prevalence of Inborn Errors of Metabolism (IEM) in newborns. We proposed testing by TMS/TR-FIA followed by NGS. This pilot study would be one of the ﬁrst expanded NBS studies in India.The aim of this study was to determine the prevalence of IEM in newborns based on the samples received at Metropolis Global Reference Lab, India. Next-generation sequencing (NGS) was done as a conﬁrmational analysis for patients tested presumptive positive on Newborn screening using Tandem Mass spectrometry (TMS) and Time-resolved fluoroimmunoassay (TR-FIA). Two years retrospective study was conducted based on incidences of IEM using TMS and TR-FIA. NGS testing was performed on presumptive positive newborns for cystic fibrosis (CF), galactosemia and urea cycle disorder/ organic academia (UCD /OA) who had undergone NBS by TMS and TR-FIA. Highestprevalence of 1.98% & 1.58% was detected for G6PD and TSH respectively by TR-FIA. Prevalence of AA disorders (3.20%), OA (1.60%) and UCD (1.43%) was observed to be the highest amongst the diseases detected by TMS. Presumptive positive case of Argininemia and Cystic Fibrosis were found to be concordant with NGS. Out of three presumptive positive cases, one presumptive positive case of CF and two of galactose were found discordant. Our prevalence study showed similarities to the prevalence reports published by other Asian countries. Expanded NBS program can be improved by including NGS as a first follow-up test after detection of abnormal metabolites in DBS. This approach will help in reducing the encumbrance of false-positive as well as false-negative cases. Our study will be influential in conducting more prospective studies and routine implementation of NGS-based analysis in NBS in India.

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Luo, Xiaomei, Ruifang Wang, Yanjie Fan, Xuefan Gu, and Yongguo Yu. "Next-generation sequencing as a second-tier diagnostic test for newborn screening." Journal of Pediatric Endocrinology and Metabolism 31, no. 8 (August 28, 2018): 927–31. http://dx.doi.org/10.1515/jpem-2018-0088.

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Abstract Background Tandem mass spectrometry (MS/MS) has been used for newborn screening (NBS) of inherited metabolic diseases (IMDs) for decades. However, the traditional approach can yield false-positive or false-negative results and is affected by biochemical substrate-level fluctuations. To overcome the current limitations, we explored the possibility of using next-generation sequencing (NGS) as a second-tier diagnostic test to detect gene mutations in samples with abnormal MS/MS results. Methods Genomic DNA was extracted from dried blood spots and we designed a multigene panel, comprising 77 genes related to over 40 IMDs, for NBS. The prepared libraries were sequenced on the Ion Personal Genome Machine (PGM) platform. Thirty-eight samples identified as abnormal by MS/MS were tested for the diagnostic accuracy of NGS compared with Sanger sequencing. Results The concentration of DNA extracted from the 38 dried blood spots was sufficient for library preparation. The coverage and depth of the sequencing data were sufficient for the analysis. For all samples, the NGS results were consistent with the Sanger sequencing results. Conclusions The genomic DNA extracted from dried blood spots could be used for NGS, generating reliable sequencing results, and NGS may function as a second-tier diagnostic test for NBS. Ion PGM could facilitate the molecular diagnosis of IMDs with appropriate primers designed for candidate genes.

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Voigt, Benjamin, Oliver Fischer, Christian Krumnow, Christian Herta, and Piotr Wojciech Dabrowski. "NGS read classification using AI." PLOS ONE 16, no. 12 (December 22, 2021): e0261548. http://dx.doi.org/10.1371/journal.pone.0261548.

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Clinical metagenomics is a powerful diagnostic tool, as it offers an open view into all DNA in a patient’s sample. This allows the detection of pathogens that would slip through the cracks of classical specific assays. However, due to this unspecific nature of metagenomic sequencing, a huge amount of unspecific data is generated during the sequencing itself and the diagnosis only takes place at the data analysis stage where relevant sequences are filtered out. Typically, this is done by comparison to reference databases. While this approach has been optimized over the past years and works well to detect pathogens that are represented in the used databases, a common challenge in analysing a metagenomic patient sample arises when no pathogen sequences are found: How to determine whether truly no evidence of a pathogen is present in the data or whether the pathogen’s genome is simply absent from the database and the sequences in the dataset could thus not be classified? Here, we present a novel approach to this problem of detecting novel pathogens in metagenomic datasets by classifying the (segments of) proteins encoded by the sequences in the datasets. We train a neural network on the sequences of coding sequences, labeled by taxonomic domain, and use this neural network to predict the taxonomic classification of sequences that can not be classified by comparison to a reference database, thus facilitating the detection of potential novel pathogens.

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Doan, Tri. "Investigator-Completed NGS Data Analysis." Clinical OMICs 1, no. 10 (September 24, 2014): 22–23. http://dx.doi.org/10.1089/clinomi.01.10.08.

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Durfee, Tim, Dan Nash, Ken Dullea, Jacqueline Carville, Marjorie Beggs, Jon Wilson, Chris Larsen, and Frederick R. Blattner. "Validating NGS-Based Genetic Tests." Clinical OMICs 2, no. 3 (March 2015): 22–24. http://dx.doi.org/10.1089/clinomi.02.03.09.

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Romero, Diana. "NGS reveals relevant resistance mutations." Nature Reviews Clinical Oncology 17, no. 4 (January 21, 2020): 197. http://dx.doi.org/10.1038/s41571-020-0330-1.

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Souilmi, Yassine, Jae-Yoon Jung, Alex Lancaster, Erik Gafni, Saaid Amzazi, Hassan Ghazal, Dennis Wall, and Peter Tonellato. "COSMOS: cloud enabled NGS analysis." BMC Bioinformatics 16, Suppl 2 (2015): A2. http://dx.doi.org/10.1186/1471-2105-16-s2-a2.

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D., Y. M. "bioMérieux : accord dans le NGS." Option/Bio 26, no. 521 (February 2015): 7. http://dx.doi.org/10.1016/s0992-5945(15)30012-x.

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Crowther, Greg. "NGS Advances Spawn Novel Challenges." Genetic Engineering & Biotechnology News 32, no. 5 (March 2012): 32–35. http://dx.doi.org/10.1089/gen.32.5.13.

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Liao, Sha, Bobby Chavli, and Annette Summers. "Sample-Prep Automation in NGS." Genetic Engineering & Biotechnology News 33, no. 18 (October 15, 2013): 30–31. http://dx.doi.org/10.1089/gen.33.18.12.

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Brookman-Amissah, Nicola, and Ibrahim Jivanjee. "Increasing On-Target NGS Reads." Genetic Engineering & Biotechnology News 34, no. 6 (March 15, 2014): 24. http://dx.doi.org/10.1089/gen.34.06.12.

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Bolz, Hanno J., and Alexander Hoischen. "NGS: Gestern, heute und morgen." medizinische genetik 31, no. 2 (June 1, 2019): 185–90. http://dx.doi.org/10.1007/s11825-019-0240-8.

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Lee, Suman, and Joomyeong Kim. "NGS-based deep bisulfite sequencing." MethodsX 3 (2016): 1–7. http://dx.doi.org/10.1016/j.mex.2015.11.008.

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Dutton, Gail. "Enzymatics Enriches NGS with AMP." Genetic Engineering & Biotechnology News 34, no. 14 (August 2014): 10–11. http://dx.doi.org/10.1089/gen.34.14.05.

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Durfee, Tim, Dan Nash, Ken Dullea, Jacqueline Carville, Marjorie Beggs, Jon Wilson, Chris Larsen, and Frederick R. Blattner. "Validating NGS-Based Genetic Tests." Genetic Engineering & Biotechnology News 35, no. 4 (February 15, 2015): 20–21. http://dx.doi.org/10.1089/gen.35.04.11.

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Huggett, Jim F., Justin O’Grady, and Stephen Bustin. "qPCR, dPCR, NGS – A journey." Biomolecular Detection and Quantification 3 (March 2015): A1—A5. http://dx.doi.org/10.1016/j.bdq.2015.01.001.

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Mandlik, Jyoti S., Amol S. Patil, and Sarita Singh. "Next-Generation Sequencing (NGS): Platforms and Applications." Journal of Pharmacy and Bioallied Sciences 16, Suppl 1 (February 2024): S41—S45. http://dx.doi.org/10.4103/jpbs.jpbs_838_23.

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ABSTRACT The demand for accurate, faster, and inexpensive sequencing of deoxyribonucleic acid (DNA) is increasing and is driving the emergence of next-generation sequencing (NGS) technologies. NGS can provide useful insights to help researchers and clinicians to develop the right treatment options. NGS has wide applications in novel fields in biology and medicine. These technologies are of great aid to decode mysteries of life, to improve the quality of crops to detect the pathogens, and also useful in improving life qualities. Thousands to millions of molecules can be sequenced simultaneously in parallel using various NGS methods. NGS can identify and characterize the microbial species more comprehensively than culture-based methods. Recently, the NGS approach has been used for oral microbial analysis.

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Piñero, Paula, Rocio Gonzalez, Elena Marin, Marina Gonzalez, Vanesa Diaz, Javier Lopez, Pablo Manresa, and Fabian Tarin. "Integrating Next Generation Flow Cytometry and Next-Generation Sequencing for an Enhanced Detection of Measurable Residual Disease in Acute Myeloid Leukemia with Myelodysplasia-Related Gene Mutations." Blood 144, Supplement 1 (November 5, 2024): 6165. https://doi.org/10.1182/blood-2024-198602.

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Background: The diagnosis of acute myeloid leukemia (AML) has evolved significantly with the last classifications of hematopoietic neoplasms (WHO and ICC 5th edition).1,2 A key update is the addition of a new AML group with myelodysplasia (MDS)- related molecular alterations, that allows categorization of many patients previously classified as AML-NOS3. The monitoring of minimal residual disease (MRD) in this AML group using molecular approaches is challenging, due to the unfeasibility of creating a specific PCR assay for each single alteration in the clinical practice, which leaves flow cytometry as the only option for the monitoring of MRD. In order to improve MRD evaluations we proposed an automated Next Generation Flow Cytometry approach (NGF-MRD) that provides a highly sensitive, specific, and reproducible MRD strategy. However, the molecular alterations in those patients might also be monitored thanks to the advances in Next Generation Sequencing (NGS-MRD), that can detect any mutations and gene rearrangements at very low frequencies. However, the complex subclonal architecture of leukemic hematopoiesis and the prevalence of pre-existing and non-specific mutations complicate the interpretation of NGS-MRD studies. Aims To study the correlation between NGF-MRD and NGS-MRD in AML patients with MDS-related mutations. To investigate the phenotypic and molecular characteristics of subpopulations potentially monitorable Patients and methods We studied bone marrow samples from 51 patients that reached complete remission after induction (26 after 3+7 protocol, and 25 after 21 days of Aza-Venetoclax). We used a highly sensitive flow cytometry protocol, based on an automatized data-base guided strategy, as previously described4. The acquisition was performed on a FACSCANTO II flow cytometer (BD Biosciences). FCS files were analyzed using the Infinicyt Software V 2.0 (Cytognos). We performed an NGS study following the international recommendations for myeloid pathology at diagnosis 5. NGS libraries were synthesized using the QIAseq Targeted Human Myeloid Neoplasms DNA Panel DHS-003Z (Qiagen). The same panel was used for the evaluation of NGS-MRD. This was possible thanks to the use of unique molecular index (UMIs), which allows the reliable detection of variants at very low frequencies. Data analysis was performed using the CLC Genomics Workbench software and the QCInterpret platform. The study received ethical approval from the Hospital ethics committee, and all participants provided informed consent in accordance with the Declaration of Helsinki. Results All patients presented at least one mutation, not monitorable by PCR, at the time of diagnosis (Me= 3, range 1-7). In patients considered NGF-MRD positive, the mutations detected at diagnosis were also found in the NGS-MRD study (VAF= 1.3%-46%). The correlation analysis revealed a strong association between NGF-MRD and NGS-MRD results (χ2: 18.844, p<0.05). NGF-MRD negative cases often exhibited a disappearance of the initial pathogenic mutations (excluding DNMT3A, TET2, and ASXL1). On the contrary, NGF-MRD+ cases retained any of the initial pathogenic alterations and, additionally, we detected an emerging subclonal TP53 mutation. Interestingly, most of those patients (84.9%) exhibited a high proportion (≥5%) of leukemic cells (LSCs) characterized by a stem cell phenotype CD34+ CD38- CD133++ at diagnosis. Discordances between NGF-MRD and NGS-MRD were observed only in 9% of NGF-MRD negative cases that showed the persistence of mutations from diagnosis. Interestingly, the detection of emerging mutations (whose meaning is still unknown) was significantly more frequent in the NGF-MRD negative group. In spite of the small patient cohort and the relatively short follow-up period, double-negative cases for both NGF-MRD and NGS-MRD correlate with a particularly favorable outcome (13-month SLE: 95.2% vs. 66.6%, Median SLE non reached). Conclusions The combination of NGF-MRD and NGS-MRD demonstrated high level of concordance and sensitivity in AML patients with MDS-related mutations. The dual evaluation of MRD revealed synergistic assessment capabilities, helping to reach safer conclusions. The combined use of both techniques refines risk group definitions and helps to select optimal post-remission therapies. Further research will be essential to elucidate the clinical implications of emerging alterations.

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Surrey, Lea F., Fredrick D. Oakley, Jason D. Merker, Thomas A. Long, Patricia Vasalos, Joel T. Moncur, and Annette S. Kim. "Next-Generation Sequencing (NGS) Methods Show Superior or Equivalent Performance to Non-NGS Methods on BRAF, EGFR, and KRAS Proficiency Testing Samples." Archives of Pathology & Laboratory Medicine 143, no. 8 (March 13, 2019): 980–84. http://dx.doi.org/10.5858/arpa.2018-0394-cp.

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Context.— There has been a rapid expansion of next-generation sequencing (NGS)–based assays for the detection of somatic variants in solid tumors. However, limited data are available regarding the comparative performance of NGS and non-NGS assays using standardized samples across a large number of laboratories. Objective.— To compare the performance of NGS and non-NGS assays using well-characterized proficiency testing samples provided by the College of American Pathologists (CAP) Molecular Oncology Committee. A secondary goal was to compare the use of preanalytic and postanalytic practices. Design.— A total of 17 343 responses were obtained from participants in the BRAF, EGFR, KRAS, and the Multigene Tumor Panel surveys across 84 different proficiency testing samples interrogating 16 variants and 3 wild-type sequences. Performance and preanalytic/postanalytic practices were analyzed by method. Results.— While both NGS and non-NGS achieved an acceptable response rate of greater than 95%, the overall performance of NGS methods was significantly better than that of non-NGS methods for the identification of variants in BRAF (overall 97.8% versus 95.6% acceptable responses, P = .001) and EGFR (overall 98.5% versus 97.3%, P = .01) and was similar for KRAS (overall 98.8% and 97.6%, P = .10). There were specific variant differences, but in all discrepant cases, NGS methods outperformed non-NGS methods. NGS laboratories also more consistently used preanalytic and postanalytic practices suggested by the CAP checklist requirements than non-NGS laboratories. Conclusions.— The overall analytic performance of both methods was excellent. For specific BRAF and EGFR variants, NGS outperformed non-NGS methods and NGS laboratories report superior adherence to suggested laboratory practices.

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Nittur, Vinay, Karam Ashouri, Blake Adnani, Jennifer Hwang, Denaly Chen, Kimberly Schiff, Lakshmi Savitala-Damerla, et al. "Comparison of next-generation sequencing and flow cytometry in detecting minimal residual disease in adult acute lymphoid leukemia: Evaluating clinical outcomes in a single-center study." Journal of Clinical Oncology 41, no. 16_suppl (June 1, 2023): 7033. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.7033.

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7033 Background: Detection of measurable residual disease (MRD) is an important biomarker to direct treatment for adult patients with acute lymphoblastic leukemia (ALL). Currently, multiparameter flow cytometry (MFC) is standard of care and can detect residual leukemia cells in 1 out of 100,000 cells (1 × 10−5). Routine use of next-generation sequencing (NGS) assays with higher levels of sensitivity may improve disease-free survival and overall survival in adult ALL patients. The clonoSEQ MRD assay (Adaptive Biotechnologies Corporation, USA) can detect MRD at a sensitivity of 1 × 10−6 . In this study, we compare the detection of MRD by clonoSEQ assay and MFC in adult ALL patients at a single institution. Methods: We performed a retrospective study evaluating 92 adult patients with B- or T-ALL admitted to Norris Comprehensive Cancer Center between 2014 and 2022. Patients were excluded if they did not achieve complete remission (N=9) or if they presented with prior relapse (N=27). Median time to first complete remission (CR1) was 2.38 months. Among our cohort (N=56 patients), all patients underwent pre-treatment bone marrow sampling which was used for Clonoseq assay. 52 patients had contemporaneous MFC which was used for comparative analysis. MRD on MFC was defined as residual leukemia cells at a sensitivity of 1 × 10−5. MRD on Clonoseq assay was evaluated at 1 × 10−6; residual cells under this limit were considered MRD−. Results: Demographics are summarized in the table. Median time to follow-up from MRD assessment was 18.0 months. 10 patients relapsed (17.9%), 3 patients died (5.4%), and 20 patients (35.7%) underwent allogeneic transplant during first remission. Among 52 patients analyzed by both MFC and NGS at CR, 26 (50%) were concordantly MRD− by NGS and NGF, 13 (25%) were discordantly MRD− by NGF but MRD+ by NGS, and 13 (25%) concordantly MRD+ by NGS and NGF. Residual cell levels between NGS and NGF were strongly correlated (R-Squared = 0.6744, p<0.001), however, MRD status was significantly different between NGS and NGF (p<0.001 using Fisher’s Exact Test). This difference was likely driven by disparities in the limits of detection between both methods. Conclusions: Assessment of MRD using the clonoSEQ assay over a standard MFC-based approach adds crucial prognostic information among adult ALL patients who achieved CR. [Table: see text]

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Mujamammi, Ahmed H. "Insights into National Laboratory Newborn Screening and Future Prospects." Medicina 58, no. 2 (February 11, 2022): 272. http://dx.doi.org/10.3390/medicina58020272.

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Newborn screening (NBS) is a group of tests that check all newborns for certain rare conditions, covering several genetic or metabolic disorders. The laboratory NBS is performed through blood testing. However, the conditions that newborn babies are screened for vary from one country to another. Since NBS began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders, and there is a national trend to further expand the NBS program. The use of mass spectrometry (MS) for the diagnosis of inborn errors of metabolism (IEM) obviously helps in the expansion of the screening panels. This technology allows the detection of different metabolic disorders at one run, replacing the use of traditional techniques. Analysis of the targeted pathogenic gene variant is a routine application in the molecular techniques for the NBS program as a confirmatory testing to the positive laboratory screening results. Recently, a lot of molecular investigations, such as next generation sequencing (NGS), have been introduced in the routine NBS program. Nowadays, NGS techniques are widely used in the diagnosis of IMD where its results are rapid, confirmed and reliable, but, due to its uncertainties and the nature of IEM, it necessitates a holistic approach for diagnosis. However, various characteristics found in NGS make it a potentially powerful tool for NBS. A range of disorders can be analyzed with a single assay directly, and samples can reduce costs and can largely be automated. For the implementation of a robust technology such as NGS in a mass NBS program, the main focus should not be just technologically biased; it should also be tested for its long- and short-term impact on the family and the child. The crucial question here is whether large-scale genomic sequencing can provide useful medical information beyond what current NBS is already providing and at what economical and emotional cost? Currently, the topic of newborn genome sequencing as a public health initiative remains argumentative. Thus, this article seeks the answer to the question: NGS for newborn screening- are we there yet?

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Raskin, William, Parneet Cheema, Kirstin Perdrizet, Marco Iafolla, Shaan Dudani, and Brandon Sheffield. "Rapid point of care NGS in colorectal cancer." Journal of Clinical Oncology 40, no. 4_suppl (February 1, 2022): 172. http://dx.doi.org/10.1200/jco.2022.40.4_suppl.172.

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172 Background: Next generation sequencing (NGS) is the laboratory cornerstone of precision oncology treatment. In advanced colorectal cancer (CRC), current guidelines recommend testing RAS, BRAF and MMR biomarkers as standard of care. The added value of comprehensive genomic profiling is so far unclear. Traditional NGS operations are complicated, requiring specialized equipment and personnel. In many jurisdictions, cancer patients are treated in publicly-funded community hospitals, where NGS is not typically utilized and access to testing via send-out services is associated with lengthy turnaround times. Here, we have validated and implemented one of the world's first "point of care" NGS services. Our early experience on NGS implementation and impact in CRC patients is described. Methods: All NGS studies were performed using the Oncomine Precision Assay (OPA) on the genexus integrated sequencer. NGS was performed at the request of the treating physician. All NGS was performed in a local community pathology lab by histotechnologists, simultaneously responsible for IHC testing (such as MMR) and interpreted by anatomic pathologists in conjunction with routine diagnostic pathology services. Retrospective chart review was performed for all patients undergoing sequencing studies and key data, including turnaround time and NGS findings were extracted from the electronic medical record for analysis. Results: A total of 51 cases with CRC were tested using point of care NGS from November 2020-August 2021, initiated by treating physicians. The median turnaround time for results was 3 days. Oncogenic driver events were identified in 46 (90%) cases, including canonical mutations in KRAS, NRAS and BRAF (Table). Actionable mutations were identified in 13 (25%) samples that would not have been identified with single-gene testing. Conclusions: Here, we show that comprehensive NGS can reveal occult resistance mechanisms to standard therapy and identify actionable biomarkers in a substantial proportion of patients with CRC. NGS added valuable information compared to guideline-recommended testing standards. Our study demonstrates that local testing can have rapid turnaround times. To our knowledge, this is the first report of “point of care” NGS in CRC. Further follow up is needed to explore the utility of these expanded roles for NGS testing. [Table: see text]

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Takamatsu, Hiroyuki, Naoki Takezako, Takeshi Yoroidaka, Takeshi Yamashita, Ryoichi Murata, Atsuko Yamazaki, Masahiro Takeuchi, et al. "Minimal Residual Disease in Autografts and Bone Marrow of Patients with Multiple Myeloma: 8-Color Multiparameter Flow Cytometry (EuroFlow-NGF) Vs. Next-Generation Sequencing." Blood 136, Supplement 1 (November 5, 2020): 22–23. http://dx.doi.org/10.1182/blood-2020-137014.

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Background: Autologous stem cell transplantation (ASCT) in conjunction with novel therapeutic drugs can dramatically improve response rates and the prognoses of patients with multiple myeloma (MM). However, most patients with MM ultimately relapse due to minimal residual disease (MRD). Next-generation multiparameter flow cytometry (MFC) (EuroFlow-NGF) and next-generation sequencing (NGS) are currently the standard methods to assess MRD. Aims: To compare the prognostic value of MRD detection in autografts and bone marrow (BM) cells using 8-color MFC (EuroFlow-NGF) and NGS (Adaptive Biotechnologies), and also MRD levels between fresh and cryopreserved autografts using NGF. Methods: The study enrolled 52 newly-diagnosed MM patients who underwent ASCT. The median age ASCT was 61 (range 41-69) years and included 29 males and 23 females at ISS I (n = 17), II (n = 23), and III (n = 12). Of these, 18 patients harbored high-risk chromosomal abnormalities including t(4;14) (n = 15), del17p and t(4;14) (n = 2), and complex (n = 1). Bortezomib-based chemotherapy was used for induction together with melphalan at 140 mg/m2 (n = 1) and 200 mg/m2 (n = 51) for conditioning before ASCT. 39 of 52 (75%) patients received maintenance therapy until progressive disease. The best responses achieved post-ASCT included 30 sCR, 4 CR, 15 VGPR, and 3 PR. Forty autografts, one from each MM patient, were analyzed using NGF and NGS protocols, and BM cells at pre/post-ASCT and autografts derived from 16 patients were analyzed using NGS. The EuroFlow-NGF method uses standard sample preparation; large numbers of cells are evaluated using an optimized 8-color antibody panel that facilitates accurate identification of discrimination between phenotypically aberrant plasma cells (aPCs) and their normal counterparts (Flores-Montero et al., Leukemia 2017). NGS-based MRD assessment was performed using Adaptive's standardized NGS-MRD Assay (Seattle, WA) (Martinez-Lopez et al., Blood 2014). Eight additional autografts were used to assess MRD in both fresh and cryopreserved samples by NGF. Results: MRD was evaluated in 48 of 52 autografts (92%) using NGF and in 44 of 52 autografts (85%) using NGS. We identified aPCs in autografts based on multivariate analysis of individual cell populations (e.g., CD56+, CD19−, CyIgκ+, and CD117+). As the results of NGF revealed a strong correlation with respect to MRD in fresh vs. thawed autografts (r = 0.999, P < 0.0001), MRD was subsequently evaluated in thawed autografts. The sensitivity of NGF was 1 × 10−5-2 × 10−6; the sensitivity of NGS was 1 × 10−6. 28 of 48 (58%) of the autografts were MRD-positive by NGF; 30 of 44 (68%) of the autografts were MRD-positive by NGS. MRD levels in autografts using NGF and NGS correlated with one another (r = 0.69, P < 0.0001; Fig. 1A). MRD negative in autografts by NGF cases (MRDNGF (-)) and MRDNGS (-) tended to show better progression-free survival (PFS) than MRDNGF (+) (P = 0.195) and MRDNGS (+) (P = 0.156), respectively. Furthermore, MRDNGS (-) showed significantly better overall survival (OS) than MRDNGS (+) (P = 0.03) (Fig. 1C) while MRDNGF (-) showed better OS than MRDNGF (+) (P = 0.09) (Fig. 1B). Our data revealed only a minimal correlation between MRD in the autografts (median 1.1 × 10−5,range 0-7.29 × 10−4) and in the BM cells at pre-ASCT (median 5.05 × 10−3,range 6 × 10−6-2.64 × 10−1; r = 0.09, P = 0.7) or at post-ASCT (median 2.11 × 10−4,range 0-9.09 × 10−3; r = 0.14, P = 0.6); MRD detected in the autografts was > 27 times lower than that detected in pre-ASCT BM cells, and MRD detected in the post-ASCT BM cells was > 3 times lower than that detected in pre-ASCT BM cells except for one case in which the ratio was increased by two times. Interestingly, while MRD was detected in all BM cells at pre-ASCT (n = 16), 4 of 16 (25%) of these autografts were MRDNGS-negative. The median of MRD levels of the 4 cases in pre-ASCT and post-ASCT BM cells were 4.14 × 10−4 (range 6-583 × 10−6)and 1.8 × 10−5 (range 0-27 × 10−6), respectively. Conclusion: Although EuroFlow-NGF is a rapid and accurate method for detecting MRD, NGS was more sensitive and provided greater prognostic value than EuroFlow-NGF. Disclosures Takamatsu: Adaptive Biotechnologies: Honoraria; Bristol-Myers Squibb: Honoraria, Research Funding; Janssen Pharmaceutical: Consultancy, Honoraria, Research Funding; Ono pharmaceutical: Honoraria, Research Funding; SRL: Consultancy, Research Funding. Takezako:Bristol-Myers Squibb: Honoraria, Research Funding; Takeda: Honoraria, Research Funding; Janssen: Research Funding; Abbvie: Research Funding. Nakao:Symbio: Consultancy; Kyowa Kirin: Honoraria; Alexion: Research Funding; Novartis: Honoraria.

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