scholarly journals A Novel NGS-Based Simultaneous Detection of DNA and RNA Biomarkers Using Total Nucleic Acid (TNA) for Acute Lymphocytic Leukemia (ALL)

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1875-1875
Author(s):  
Archana Ramesh ◽  
Samuel Koo ◽  
Soo Jin Kang ◽  
Abhisek Ghosal ◽  
Francys Alarcon ◽  
...  

Abstract Background: Acute Lymphocytic Leukemia (ALL) is the most common childhood cancer and accounts for about a quarter of adult acute leukemias. Current NCCN recommendations for clinical testing for risk stratification and treatment guidance include karyotyping, FISH testing for translocations, and RT-PCR for gene fusions and sequencing for DNA mutations detection. Most NGS based approaches test DNA mutations and RNA fusions separately, thereby requiring higher input material and multiple workflows adding to the cost and turn-around-time. An NGS based assay for the detection of DNA variants (NeoGenomics Heme NGS assay) in heme malignancies using Total Nucleic Acid (TNA) is already available in our clinical laboratory and complements FISH based fusion detection and karyotyping but an integral assay to detect both DNA and RNA alterations with a simple workflow for ALL is needed. Methods: We used TNA or RNA spiked-in with DNA to simulate TNA samples, extracted from 93 bone marrow and peripheral blood samples from patients and healthy donors, along with commercial fusion reference myeloid samples Seraseq Myeloid Fusion RNA Mix (SeraCare Inc.) controls. DNA/RNA libraries were prepared using a custom amplicon based Multimodal NGS panel (Qiagen Inc.) targeting 297 genes and 213 genes (select exons) for DNA and RNA fusion detection, respectively. The enriched dual indexed amplicon libraries were sequenced on an Illumina NovaSeq 6000. The sequence data was processed with a customized bioinformatic pipeline for DNA variant as well as a novel machine learning algorithm for RNA fusion detection. We analyzed sensitivity, specificity, accuracy, reproducibility, and repeatability for clinical use. The DNA variants were orthogonally confirmed using other NGS assays, and the RNA fusions were confirmed on an RNA-seq Archer assay or RT-Sanger confirmation assays. Results: Here, we developed and validated a single tube comprehensive NGS panel using a custom multimodal chemistry that uses TNA as input for simultaneous dual detection of DNA and RNA abnormalities in ALL patients' samples. We performed the analytical validation of our Heme NGS assay for the RNA panel to detect fusions in ALL, using TNA input for comprehensive DNA and RNA mutation detection. The fusion concordance was 95% for the RNA fusion panel. The assay detected BCR-ABL1 (7/7), ETV6-RUNX1 (1/1), KMT2A fusions (4/5), TCF3-PBX1 (1/1), and PCM1-JAK2(1/1). The specificity was determined at 100% using a set of 42 fusion negative samples. The limit of detection (LOD) was analyzed using serial dilutions to up to 3 log reduction (LR) using a the Seraseq Myeloid Fusion sample. The fusions were detected down to 1 LR. The reproducibility was tested using a positive fusion and Seraseq samples across three runs and was reported at 100%. Next, a small cohort of ALL samples (n=8) was included as part of this study to simultaneously evaluate DNA and RNA mutations. We detected pathogenic DNA variants in genes previously reported in ALL that included NOTCH1, PTEN, FLT3, IKZF1, JAK1, JAK2, KRAS, NF1, PAX5, U2AF1, TP53, and also RNA fusion BCR-ABL1, and the results were confirmed by an orthogonal NGS assay (NexCourse and RNA-Seqv1 for fusions). One sample carrying a BCR-ABL1 fusion (detected by RNA panel) also harbored mutations in IKZF1 in DNA (detected by DNA panel) that is reported as unfavorable prognostic biomarker for Ph-Like ALL demonstrating comprehensive panel could identify multiple variants within the same sample, demonstrating the advantage DNA+RNA testing has over the classical single gene FISH/RT-PCR testing for the efficient risk stratification and treatment in ALL patients. Conclusions: In this study, we demonstrated that the single tube TNA based NeoGenomics NGS assay can simultaneously detect the DNA and RNA biomarkers associated with ALL for improved diagnostic and prognostic recommendations. The single-tube assay for detection of both RNA fusions and DNA variants using the same sample could offer comprehensive and cost-effective solution for clinical laboratory test for ALL patient care. This is a promising approach that might be used as a dual DNA/RNA alterations detection on other hematological neoplasia. Disclosures Ramesh: Neo Genomics Laboratories: Current Employment. Koo: Neo Genomics Laboratories: Current Employment. Kang: Neo Genomics Laboratories: Current Employment. Ghosal: NeoGenomics Laboratories: Current Employment. Alarcon: NeoGenomics Laboratories: Current Employment. Gyuris: Neo Genomics Laboratories: Current Employment. Jung: NeoGenomics Laboratories, Inc.: Current Employment. Magnan: NeoGenomics Laboratories, Inc.: Current Employment. Nam: NeoGenomics Laboratories, Inc.: Current Employment. Thomas: NeoGenomics Laboratories, Inc.: Current Employment. Fabunan: NeoGenomics Laboratories, Inc.: Current Employment. Petersen: Neo Genomics Laboratories: Current Employment. Lopez-Diaz: NeoGenomics Laboratories, Inc.: Current Employment. Bender: NeoGenomics Laboratories, Inc.: Current Employment. Agersborg: NeoGenomics Laboratories, Inc.: Current Employment. Ye: Neo Genomics Laboratories: Current Employment. Funari: NeoGenomics Laboratories, Inc.: Current Employment.

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 38-39
Author(s):  
Ha Jin Lim ◽  
Jun Hyung Lee ◽  
Ju-Hyeon Shin ◽  
Seung Yeob Lee ◽  
Hyun-Woo Choi ◽  
...  

Introduction Targeted RNA sequencing (RNA-seq) is a highly accurate method for sequencing transcripts of interest and can overcome limitations regarding resolution, throughput, and multistep workflow. However, RNA-seq has not been widely performed in clinical molecular laboratories due to the complexity of data processing and interpretation. We developed a customized targeted RNA-seq panel with a data processing protocol and validated its analytical performance for gene fusion detection using a subset of samples with different hematologic malignancies. Additionally, we investigated its applicability for identifying transcript variants and expression analysis using the targeted panel. Methods The target panel and customized oligonucleotide probes were designed to capture 84 genes associated with hematologic malignancies. Libraries were prepared from 800 to 1,500 ng of total RNA using GeneMediKit NGS-Leukemia-RNA kit (GeneMedica, Gwangju, Korea) and sequenced using Miseq reagent kit v3 (300 cycles) and MiseqDx (Illumina, San Diego, CA, USA). The diagnostic samples included one reference DNA (NA12878), one reference RNA (Cat no. 740000, Agilent Technologies), 14 normal peripheral blood (PB) samples, four validation bone marrow (BM) samples with known gene fusions, and 30 clinical BM or PB samples from seven categories of hematologic malignancies. The clinical samples included 27 BM aspirates and three PB samples composed of six acute myeloid leukemia, nine B-lymphoblastic leukemia/lymphoma, four T-lymphoblastic leukemia/lymphoma, three mature B-cell neoplasms, six MPN, one myelodysplastic/myeloproliferative neoplasm, and one myeloid/lymphoid neoplasm with eosinophilia and gene rearrangement. For the analytical validation of fusion detection, target gene coverage, between-run and within-run repeatability, and dilution tests (1:2 to 1:8 dilution) were performed. For the comparative analysis of fusion detection, the RNA-seq data were analyzed by STAR-Fusion and FusionCatcher and processed with stepwise filtering and prioritization strategy (Figure 1), and the result was compared to those of multiplex RT-PCR (HemaVision kit; DNA Technology, Aarhus, Denmark) or FISH (MetaSystems Gmbh, Althusseim, Germany) using 30 clinical samples. The RNA-seq data from clinical samples were additionally analyzed by FreeBayes for variant detection and by StringTie for expression profiling (Figure 1). Results First, the analytical validation showed reliable results in target gene coverage, between-run and within-run repeatability, and linearity tests. The uniformity of coverage (% of base pairs higher than 0.2 × total average depth) was calculated to be 99.8%, which revealed even coverage for the target genes in the panel using the reference DNA. Both in the within-run and between-run tests, the read counts and FFPM (fusion fragments per million) of all replicates showed reliable repeatability (r2 = 0.9655 and 0.9874, respectively). The FFPM of the diluted analytical samples including BCR-ABL1 and PML-RARA showed linear log2-fold-changes (r2 = 0.9852 and 0.9447, respectively). Second, compared to multiplex RT-PCR and FISH using 30 clinical samples, targeted RNA-seq combined with filtering and prioritization strategies detected all 13 known fusions and newly detected 17 fusions. Finally, 16 disease- and drug resistance-associated variants on the expressed transcripts of ABL1, GATA2, IKZF1, JAK2, RUNX1, and WT1 were simultaneously designated and expression analysis showed distinct four clusters of clinical samples according to the cancer subtypes and lineages. Conclusions Our customized targeted RNA-seq system provided a stable analytical performance and a more sensitive identification of gene fusions than conventional molecular methods in various clinical samples. In addition, clinically significant variants in the transcripts and expression profiling could be simultaneously identified directly from the RNA-seq data without the need for additional parallel testing. Our study identified the advantages of the clinical laboratory-oriented targeted RNA-seq system to enhance the diagnostic yield for gene fusion detection and to simplify the diagnostic steps as providing a comprehensive tool for analyzing hematologic malignancies in the clinical laboratory. Figure 1 Disclosures Lee: National Research Foundation of Korea: Research Funding.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 29-30
Author(s):  
Yongxin Yu ◽  
Francys Alarcon ◽  
Yanglong Mou ◽  
Segun C Jung ◽  
Hyunjun Nam ◽  
...  

Background: A cost effective and comprehensive genomic profiling (CGP) approach for diagnosis, risk stratification and therapy would be useful for the evaluation of oncologic specimens. Available approaches involving additive testing for DNA and RNA abnormalities through traditional methods (e.g. Sanger, FISH, cytogenetics, qRT-PCR) are not comprehensive, require multiple different workflows and are sample consuming, often resulting in incomplete testing. While there are next generation sequencing (NGS) assays designed for detecting DNA and RNA abnormalities, they have separate workflows that require twice the amount of sample and effort. To address this, we developed a novel total nucleic acid (TNA) extraction method and single tube workflow utilizing TNA and a custom multimodal chemistry designed for hematologic malignancies. This consolidated workflow enables an efficient discovery based approach for both DNA/RNA abnormalities including single nucleotide variants (SNVs), InDels, copy number variants (CNVs), large structural changes from DNA and gene fusions and gene expression levels from RNA. This method maximizes data derived from valuable samples while delivering a comprehensive profile of the patient's tumor which can help guide therapeutic and clinical decisions. Methods: Total nucleic acid (TNA) was extracted from bone marrow and peripheral blood of 95 patients (CML, CMML, CLL, AML and myeloid disorders). 297 genes that have DNA mutations specific to hematological cancers were targeted, along with 213 genes that were targeted for clinically significant RNA abnormalities. Enriched genomic and transcriptomic regions of interest from 85 patients were successfully sequenced with unique dual indices on an Illumina NovaSeq 6000. DNA variant detection as well as fusion detection from RNA were compared to traditional orthogonal NGS assays that use DNA input or compared to qRT-PCR and Sanger sequencing assays that use RNA as input. Results: In this study, we developed an efficient and high-quality TNA extraction method that can purify enough total nucleic acid from bone marrow, peripheral blood, cytogenetic pellets, flow suspension, and FFPE samples for the downstream NGS assay. The average OD 260/280 value was 1.9 and the OD 260/230 was 2.18. After sequencing, 256/262 (97.7% accuracy) SNV and Indel variants that were candidate pathogenic mutations were concordant from 38 patients. Meanwhile, 100% (7/7) of all BCR/ABL1 gene fusions which had an international scale (IS) value above 6.4% were concordant. In addition, 69 fusion positive samples containing 20 unique gene fusions which had been previously reported by an independent ArcherDX assay designed specifically for gene fusions were also evaluated with this chemistry. Analysis revealed a 92.5% (64/69) concordance. More importantly, the QIAseq multimodal TNA NGS assay detected both DNA and RNA abnormalities in a single tube. For example, in one myeloid leukemia patient, we not only identified pathogenic variants of ASXL1 and JAK2 which had been previously detected by a DNA NGS assay, but also detected a concurrent BCR-FGFR1 fusion which had been previously reported by a FISH assay. Moreover, we were able to provide more comprehensive genomic profiling by investigating many DNA and RNA abnormalities simultaneously. In our study, for 5 patients that previously been tested for BCR-ABL1 fusion only, we are able to assess BCR-ABL1 fusion status from RNA as well as identify pathogenic DNA variants at the same time, including JAK2 p.V617F, U2AF1 p.S34F, ASXL1 p.E635Rfs*15, BRCA p.S1982Rfs*22, and DNMT3A p.S708Vfs*71, which provides valuable information to assist diagnosis and treatment in a cost effective and efficient way. Conclusions: We developed a single tube TNA based workflow with a custom multimodal chemistry that simultaneously detects many DNA and RNA abnormalities in a cost effective and efficient way while reducing sample requirements. This unique TNA NGS assay provides comprehensive genomic profiling for hematologic malignancies and improves the diagnostic testing options for precise patient care. Disclosures Yu: NeoGenomics: Current Employment. Alarcon:NeoGenomics: Current Employment. Mou:NeoGenomics: Current Employment. Jung:NeoGenomics: Current Employment. Nam:NeoGenomics: Current Employment. Thomas:NeoGenomics: Current Employment. Keeler:NeoGenomics: Current Employment. Shinbrot:NeoGenomics: Current Employment. Magnan:NeoGenomics: Current Employment. Bender:NeoGenomics: Current Employment. Jiang:NeoGenomics: Current Employment. Agersborg:NeoGenomics: Current Employment. Weiss:Bayer: Other: speaker; Genentech: Other: Speaker; Merck: Other: Speaker; NeoGenomics: Current Employment. Ye:NeoGenomics: Current Employment. Funari:NeoGenomics: Current Employment.


2009 ◽  
Vol 161 (1) ◽  
pp. 70-74 ◽  
Author(s):  
Imadeldin E. Aradaib ◽  
Mohamed E.H. Mohamed ◽  
Mohamed A. Abdalla
Keyword(s):  
Rt Pcr ◽  

2022 ◽  
Vol 99 (12) ◽  
pp. 7-12
Author(s):  
T. I. Kalenchits ◽  
S. L. Kabak ◽  
S. V. Primak ◽  
N. M. Shirinaliev

The article describes a case of polysegmental destructive viral-bacterial pneumonia complicated with acute pulmonary abscess, pleural empyema, and pneumopleurofibrosis in a 50-year-old female patient infected with the SARS-CoV-2 virus. The first clinical, laboratory and radiological signs of purulent-necrotic inflammation appeared only 20 days after receiving a positive RT-PCR test result with a nasopharyngeal swab. A month later, an emerging abscess in the lower lobe of the right lung was diagnosed. Subsequently, it spontaneously drained into the pleural cavity.Coagulopathy with the formation of microthrombi in small pulmonary vessels is one of the causative factors of lung abscess in patients infected with the SARS-CoV-2 virus.


2022 ◽  
Vol 12 ◽  
Author(s):  
Xiaorui Liu ◽  
Lingling Xie ◽  
Zhixu Fang ◽  
Li Jiang

We investigated the existence and potential pathogenicity of a SLC9A6 splicing variant in a Chinese boy with Christianson Syndrome (CS), which was reported for the first time in China. Trio whole-exome sequencing (WES) was performed in the proband and his parents. Multiple computer prediction tools were used to evaluate the pathogenicity of the variant, and reverse transcription-polymerase chain reaction (RT-PCR) analysis and cDNA sequencing were performed to verify the RNA splicing results. The patient presented with characteristic features of CS: global developmental delay, seizures, absent speech, truncal ataxia, microcephaly, ophthalmoplegia, smiling face and hyperkinesis with electrical status epilepticus during sleep (ESES) detected in an electroencephalogram (EEG). A SLC9A6 splicing variant was identified by WES and complete skipping of exon 10 was confirmed by RT-PCR. This resulted in altered gene function and was predicted to be pathogenic. ESES observed early in the disease course is considered to be a significant feature of CS with the SLC9A6 variant. Combined genetic analysis at both the DNA and RNA levels is necessary to confirm the pathogenicity of this variant and its role in the clinical diagnosis of CS.


F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 1362
Author(s):  
Colin L. Hisey ◽  
Petr Tomek ◽  
Yohanes N.S. Nursalim ◽  
Lawrence W. Chamley ◽  
Euphemia Leung

Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and YBX1, as well as long-noncoding RNAs HOTAIR, ZFAS1, and AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that BIRC5 and HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.


F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 1362
Author(s):  
Colin L. Hisey ◽  
Petr Tomek ◽  
Yohanes N.S. Nursalim ◽  
Lawrence W. Chamley ◽  
Euphemia Leung

Extracellular vesicles (EVs) are emerging as key players in breast cancer progression and hold immense promise as cancer biomarkers. However, difficulties in obtaining sufficient quantities of EVs for the identification of potential biomarkers hampers progress in this area. To circumvent this obstacle, we cultured BT-474 breast cancer cells in a two-chambered bioreactor with CDM-HD serum replacement to significantly improve the yield of cancer cell-associated EVs and eliminate bovine EV contamination. Cancer-relevant mRNAs BIRC5 (Survivin) and YBX1, as well as long-noncoding RNAs HOTAIR, ZFAS1, and AGAP2-AS1 were detected in BT-474 EVs by quantitative RT-PCR. Bioinformatics meta-analyses showed that BIRC5 and HOTAIR RNAs were substantially upregulated in breast tumours compared to non-tumour breast tissue, warranting further studies to explore their usefulness as biomarkers in patient EV samples. We envision this effective procedure for obtaining large amounts of cancer-specific EVs will accelerate discovery of EV-associated RNA biomarkers for cancers including HER2+ breast cancer.


2010 ◽  
Vol 4 (3) ◽  
pp. 146-151 ◽  
Author(s):  
Reham W. Salim ◽  
Khairalla M.S. Khairalla ◽  
Awadalkareem A. Eljamal ◽  
Abdelrahim E. Karrar ◽  
Imadeldin E. Aradaib

Background: Novel coronavirus outbreak that originated in Wuhan, province of China has now been declared as one of the deadliest pandemics inflicting humankind in last hundred years. Method: In the present study, we have inferred the clinical, laboratory, radiological, and microbiological findings of five patients in a family cluster who presented with unexplained pneumonia after coming back from overseas and touchdown right here in India on 1st March 2020 earlier than lockdown and another member of the family who didn’tvisit thiscountry. Results: From March 10, 2020, we enrolled a family of six patients who travelled to SingaporeonJanuary 10th 2020and returned on March 1st 2020. Of six family members who travelled to Singapore, five were recognised as affected with the radical coronavirus (COVID 19). Additionally, one family member, who did not travel to overseas also became infected with the virus post14 days of staying with four of the family members. Five family members (aged 30–55 years) presented with symptoms like fever, upper or lower respiratory tract symptoms, or diarrhoea, or a combination of these 3–6 days after exposure. Phylogenetic evaluation of these five subjects’ RT-PCR amplicons and two full genomes by nextgeneration sequencing presented that this is a novel coronavirus, which is closest to the severe acute respiratory syndrome (SARS)-related coronaviruses. Conclusion: Our findings are steady with person-to-person transmission of this novel coronavirus in hospital (nosocomial) and family settings, and the reports of infected travellers in other geographical regions.


Leukemia ◽  
1998 ◽  
Vol 12 (8) ◽  
pp. 1326-1327 ◽  
Author(s):  
J Moravcová ◽  
S Muchová ◽  
R Kalbáčová ◽  
C Haškovec
Keyword(s):  
Rt Pcr ◽  

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