scholarly journals Gestational Psittacosis With Secondary Hemophagocytic Syndrome: A Case Report and Literature Review

2021 ◽  
Vol 8 ◽  
Author(s):  
Li Sun ◽  
Pulin Li ◽  
Bo Pang ◽  
Peipei Wu ◽  
Ran Wang
Keyword(s):  
Bone Marrow ◽  
Next Generation Sequencing ◽  
Hemophagocytic Syndrome ◽  
Nk Cell ◽  
Cell Activity ◽  
Lung Infection ◽  
Next Generation ◽  
Nk Cell Activity ◽  
Generation Sequencing

Gestational psittacosis and hemophagocytic syndrome (HPS) are rare clinical diseases. In this article, a case of gestational psittacosis concomitant with secondary HPS was reported. An analysis was performed on the clinical characteristics, signs, laboratory findings, progression, diagnosis, and treatment of a patient with gestational psittacosis concomitant with secondary HPS. Besides, the literature with respect to this disease was reviewed. This patient was definitively diagnosed through metagenomic next-generation sequencing techniques, bone marrow puncture and smear examination, and the determination of sCD25 level and natural killer (NK) cell activity. Anti-infectives such as doxycycline and etoposide combined with hormone chemotherapy achieved significant improvement in cough and expectoration, a return to normal temperature, and a significant improvement in oxygenation index. In addition, chest computed tomography revealed obvious absorption of lung lesions and a return of NK cell activity and sCD25 levels to normal ranges. Chlamydia psittaci pneumonia requires a clear determination of etiology, while HPS requires bone marrow puncture and smear examination, together with the determination of sCD25 level and NK cell activity in the blood. The findings of this study suggest that metagenomic next-generation sequencing is an effective instrument in clearly identifying pathogens that cause lung infection. Clinicians should consider atypical pathogens of lung infection in patients with poor response to empirical anti-infectives, and strive to design an effective treatment strategy as per an accurate diagnosis based on the etiology. As for patients suffering from long-term high fever and poor temperature control after broad-spectrum antibiotic treatment, non-infectious fever should be taken into account. A rapid and clear diagnosis would significantly improve patient prognosis.

A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data

2013 ◽  
Vol 2 (4) ◽  
pp. 86-98
Author(s):  
Chatzinikolaou Panagiotis ◽  
Makris Christos ◽  
Dimitrios Vlachakis ◽  
Sophia Kossida
Keyword(s):  
Next Generation Sequencing ◽  
Level Structure ◽  
Atomic Level ◽  
Protein Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Variant Analysis ◽  
Generation Sequencing

In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

scholarly journals A rare atypical chronic myeloid leukemia BCR-ABL1 negative with concomitant JAK2 V617F and SETBP1 mutations: a case report and literature review

2020 ◽  
Vol 11 ◽  
pp. 204062072092710
Author(s):  
Tianqi Gao ◽  
Changhui Yu ◽  
Si Xia ◽  
Ting Liang ◽  
Xuekui Gu ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Targeted Therapy ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Jak2 V617f ◽  
Next Generation ◽  
Bone Marrow Fibrosis ◽  
Atypical Chronic Myeloid Leukemia ◽  
Generation Sequencing ◽  
Marrow Fibrosis

Atypical chronic myeloid leukemia (aCML) BCR-ABL1 negative is a rare myelodysplastic syndromes/myeloproliferative neoplasm (MDS/MPN) for which no standard treatment currently exists. The advent of next-generation sequencing has allowed our understanding of the molecular pathogenesis of aCML to be expanded and has made it possible for clinicians to more accurately differentiate aCML from similar MDS/MPN overlap syndrome and MPN counterparts, as MPN-associated driver mutations in JAK2, CALR, or MPL are typically absent in aCML. A 55-year old male with main complaints of weight loss and fatigue for more than half a year and night sweats for more than 2 months was admitted to our hospital. Further examination revealed increased white blood cells, splenomegaly, and grade 1 bone marrow fibrosis with JAK2 V617F, which supported a preliminary diagnosis of pre-primary marrow fibrosis. However, in addition to JAK2 V617F (51.00%), next-generation sequencing also detected SETBP1 D868N (46.00%), ASXL1 G645fs (36.09%), and SRSF2 P95_R102del (33.56%) mutations. According to the 2016 World Health Organization diagnostic criteria, the patient was ultimately diagnosed with rare aCML with concomitant JAK2 V617F and SETBP1 mutations. The patient received targeted therapy of ruxolitinib for 5 months and subsequently an additional four courses of combined hypomethylating therapy. The patient exhibited an optimal response, with decreased spleen volume by approximately 35% after therapy and improved symptom scores after therapy. In diagnosing primary bone marrow fibrosis, attention should be paid to the identification of MDS/MPN. In addition to basic cell morphology, mutational analysis using next-generation sequencing plays an increasingly important role in the differential diagnosis. aCML with concomitant JAK2 V617F and SETBP1 mutations has been rarely reported, and targeted therapy for mutated JAK2 may benefit patients, especially those not suitable recipients of hematopoietic stem cell transplants.

The NK Cell MicroRNA Transcriptome Defined by Next-Generation Sequencing Identifies IL-15-Signaled Alterations In Mature MiR-223 Expression, and MiR-223 as a Potential Regulator of Murine Granzyme B

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 104-104
Author(s):  
Todd A Fehniger ◽  
Todd Wylie ◽  
Elizabeth Germino ◽  
Jeffrey W Leong ◽  
Vincent J Magrini ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Nk Cells ◽  
Real Time ◽  
Nk Cell ◽  
Granzyme B ◽  
Mrna Translation ◽  
Fold Increase ◽  
Next Generation ◽  
Altered Expression ◽  
Generation Sequencing

Abstract Abstract 104 Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g. granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the translation of their mRNA targets, and are therefore candidates mediating this control process. While the expression and importance of miRNAs in T and B lymphocytes has been established, little is known about miRNAs in NK cells. Here, we utilized two next-generation sequencing platforms, Illumina GA and SOLiD, to define the miRNA transcriptomes of resting and IL-15-activated primary murine NK cells. Using Illumina GA sequencing, we identified expression of 297 mature miRNA and 64 miRNA* sequences in NK cells at read counts of 1 to 507,369. The 5 miRNAs with the highest abundance (percent normalized read count) in resting NK cells were miR-21 (31.6%), miR-16 (8.3%), miR-142-5p (6.5%), miR-142-3p (3.8%), miR-24 (3.7%). Detection of known miRNA was similar using SOLiD sequencing in both resting (r2=0.79) and IL-15-activated (r2=0.75) NK cells, with most of the discordant detection arising in miRNAs with low expression (1-10 read counts). These results were further validated using real-time RT-qPCR and microarray profiling. A bioinformatics pipeline was developed that identified 37 novel miRNA genes that encoded 26 novel mature miRNA sequences, including miRNAs processed from snoRNAs. Of 84 miRNAs with significantly altered expression levels (Illumina, normalized read counts) following IL-15-activation, miR-223 demonstrated the greatest fold decrease (2.3, P=1.03E-10). The decrease in mature miR-223 following 24 hours of IL-15 activation was confirmed in SOLiD sequencing (7.7 fold-decrease, P=1.0E-10), qPCR (2.5 fold-decrease, P=0.01), and microarrays (4.6 fold-decrease, P=0.003). IL-15 induced reduction in mature miR-223 was time-dependent with fold decreases of 1.5 (NS) at 8 hours, 2.2 (P=0.003) at 24 hours, and 8.1 (P=0.012) at 48 hours, assessed by real-time qPCR. Decreases in mature miR-223 expression early following activation likely occur via regulation of the miRNA processing machinery, since primary and precursor miR-223 transcripts exhibited increased expression after 8 hours (2.1±0.3 fold increase, P=0.03) and 24 hours (2.5±0.3 fold increase, P=0.03) of IL-15-activation. MiR-223 is computationally predicted to bind to the murine GzmB 3'UTR sequence, and we therefore evaluated the ability of miR-223 to target the murine GzmB 3'UTR in vitro. Overexpression of miR-223 in 293T cells decreased luciferase protein signal controlled by the GzmB 3'UTR by 44±2% (P=0.002) without affecting negative controls (perforin 3'UTR or no 3'UTR). Moreover, mutating the miR-223 predicted binding site within the murine GzmB 3'UTR abrogated miR-223 mediated regulation. These data suggest that miR-223 directly targets the murine GzmB 3'UTR, and thereby contributes to tonic suppression of GzmB mRNA translation in resting NK cells. Thus, the sequenced and validated miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology. Disclosures: No relevant conflicts of interest to declare.

Mutation Analysis in 200 Cases of Newly Diagnosed Myelodysplastic Syndrome By Next Generation Sequencing: Association with Established Prognostic Variables and IPSS-R

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1703-1703
Author(s):  
Kankana Ghosh ◽  
Parsa Hodjat ◽  
Priyanka Priyanka ◽  
Beenu Thakral ◽  
Keyur P. Patel ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Next Generation Sequencing ◽  
Myelodysplastic Syndrome ◽  
Mutation Analysis ◽  
Conflicts Of Interest ◽  
International Prognostic Scoring System ◽  
P Value ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Generation Sequencing

Abstract INTRODUCTION Myelodysplastic syndrome (MDS) is known to have numerous genomic aberrations that predict response to treatment and overall survival. We aimed to assess various mutations in newly diagnosed MDS cases by next generation sequencing (NGS) and their association with various well-established clinicopathologic parameters and the Revised International Prognostic Scoring System (IPSS-R). MATERIALS AND METHODS We performed molecular studies on DNA extracted from bone marrow aspirate specimens in 200 newly diagnosed treatment naïve MDS patients presenting at a single institution from 08/2013 to 03/2015 as part of routine clinical work up in a CLIA certified molecular diagnostics laboratory. Cases met criteria for MDS per WHO 2008 criteria. The entire coding sequences of 28 genes (ABL1, ASXL1, BRAF, DNMT3A, EGFR, EZH2, FLT3, GATA1, GATA2, HRAS, IDH1, IDH2, IKZF2, JAK2, KIT, KRAS, MDM2, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PTPN11, RUNX1, TET2, TP53, WT1) were sequenced using a NGS-based custom-designed assay using TruSeq chemistry on Illumina MiSeq platform. FLT3 internal tandem duplications (ITD) and codon 835/836 point mutation were detected by PCR followed by capillary electrophoresis. CEBPA mutation analysis was performed by PCR followed by Sanger sequencing on 186 patients. RESULTS Median age was 67 years. Patients included 139 males (69.5%) and 61 females (30.5%). Hematologic parameters are as follows [median (range)]: Hb 9.6 g/dL (5-16.7), platelets 75 K/μ L (5-652), WBC: 2.8 K/μ L (0.4-20.8), ANC 1.3 K/μ L (0.0 -12.0), AMC 0.2 K/μ L (0.0-3). Bone marrow (BM) blasts [median (range)] were 4% (0-19). Of 192 patients with cytogenetic analysis performed, 65 (33.85%) had diploid karyotype, 53 (27.6%) had one, 21 (10.93%) had two, 13 (6.77%) had three, 40 (20.83%) had > three abnormalities. IPSS-R risk categorization of the 200 cases is as follows: very low (17 cases, 8.5%), low (46, 23%) intermediate (42, 21%), high (47, 23.5%), very high (48, 24%). Mutations identified by NGS are as detailed in Table 1. Of the 4 patients with FLT mutations detected, the breakdown is as follows: FLT3 ITD (3, 75%), FLT3 D835 (1, 25%), FLT3, ITD + D835 (0, 0%). CEBPA mutation was detected in 12 of 186 (6.45%) cases assessed. CEBPA was detected in 12 (6.45%). Sixty three (31.5%) cases had no mutations detected in the genes analyzed by NGS or PCR, 80 (40%) had mutations in one, 42 (21%) had mutations in two, 8 (4%) in three and 7 (3.5%) in > three genes. We found positive associations between mutated genes and various parameters as detailed in Table 2. No association was found between frequency of any particular mutation and the IPSS-R score. CONCLUSIONS: MDS is a heterogeneous group of myeloid neoplasms at the genetic level. Multiple genetic mutations in a large subset of cases likely indicate clonal evolution. A subset of mutations has significant association with well-established clinico-pathologic parameters like WBC and BM blast percentage. With longer follow-up, we could use this data to refine IPSS-R. Table 1. Number of cases % cases TP53 46 23 TET2 33 16.5 RUNX1 27 13.5 ASXL1 25 12.5 DNMT3A 17 8.5 EZH2 12 6 IDH2 8 4 IDH1 7 3.5 NRAS 7 3.5 JAK2 5 2.5 FLT3 4 2 PTPN11 3 1.5 EGFR 2 1 MPL 2 1 WT1 2 1 GATA2 1 0.5 KIT 1 0.5 KRAS 1 0.5 MYD88 1 0.5 NPM1 1 0.5 BRAF 1 0.5 Table 2. Mutated genes p value WBC ASXL1 <0.042 AEC TET2 <0.016 BM blast % RUNX1, CEBPA <0.008, p<0.02 BM myelocyte % TP53, TET2, RUNX1, DNMT3A <0.014, <0.014, <0.015, <0.038 AEC: absolute eosinophil count, BM: bone marrow Disclosures No relevant conflicts of interest to declare.

scholarly journals Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination

PLoS ONE ◽  
2013 ◽  
Vol 8 (9) ◽  
pp. e74249 ◽  
Author(s):  
Francesca Di Giallonardo ◽  
Osvaldo Zagordi ◽  
Yannick Duport ◽  
Christine Leemann ◽  
Beda Joos ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Error Rates ◽  
Next Generation ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Clinical Relevance of Diagnostic Criteria for Hemophagocytic Lymphohistiocytosis (HLH) and Survival Outcome of Adult HLH Patients: A Single-Center Prospective Cohort Study

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 3718-3718
Author(s):  
Joon Young Hur ◽  
Kang Kook Lee ◽  
Jun Ho Jang ◽  
Kihyun Kim ◽  
Chul Won Jung ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Diagnostic Criteria ◽  
Prospective Cohort ◽  
Nk Cell ◽  
Cell Activity ◽  
Diagnostic Value ◽  
Adult Patients ◽  
Nk Cell Activity ◽  
Soluble Cd25 ◽  
Underlying Causes

Abstract Introduction Hemophagocytic lymphohistiocytosis (HLH) is an immune-mediated life-threatening condition in which activated macrophages phagocytize hematopoietic cells in various clinical situations from physiologic reactions to pathologic conditions such as malignancy. The diagnosis of HLH is currently done according to the HLH-2004 criteria which were mainly based on pediatric experiences even though underlying causes and clinical features of adult patients with HLH are different from pediatric patients. However, there is little information about the value of each item and its clinical relevance in the diagnosis of adult patients. Thus, we analyzed the diagnostic value of HLH-2004 criteria in adult patients who had symptoms or signs suspicious of hemophagocytosis. Methods We have conducted a prospective cohort study for adult HLH since January of 2017 (Prospective cohort for adult hemophagocytosis: NCT03117010). Adult patients older than 18 years having at least one of the following problems could be enrolled onto this prospective cohort: 1) Pathologically confirmed hemophagocytosis in bone marrow or lymph nodes; 2) Presence of at least 3 conditions among 8 items of HLH-2004 diagnostic criteria. After obtaining written informed consent, we performed laboratory tests for the diagnosis of HLH including natural killer (NK)-cell activity and soluble CD25 in blood. The primary objective of this study was to explore the feasibility and clinical usefulness of HLH-2004 criteria in adult patients, and secondary objective was to analyze underlying causes and outcomes of adult HLH. Results At the time of analysis, 44 patients were enrolled in the cohort, and their median age was 51.5 years (range, 19-85 years). Male (n=27) was more common than female (n=17). All patients had fever (body temperature ≥ 38.5°C) and splenomegaly was found in 29 patients (66%, Figure 1). Although cytopenia such as neutropenia and thrombocytopenia was commonly found, only 20 patients had bi-lineage cytopenia (45%). Hypofibrinogenemia and/or hypertriglyceridemia were also less common findings (n=18, 41%). Hemophagocytosis in bone marrow or lymph nodes was pathologically confirmed in 27 patients (61%). Elevated serum level of ferritin (≥ 500 mg/L) and soluble CD25 (≥ 2400 U/mL) were 42 (95%) and 35 patients (80%), respectively. Among 33 patients whose NK-cell activity was evaluated, 22 patients had low or absent NK-cell activity (67%). According to diagnostic criteria, 28 patients having at least five conditions were diagnosed with HLH, and the remaining patients including 7 patients with bone marrow hemophagocytosis could not be diagnosed. Among 28 patients with HLH, T/NK-cell (n=8) and B-cell lymphomas (n=7) were the most common underlying disorders (n=15, 54%). Infection including EBV (n=6) and rheumatologic disorders (n=3) accounted for non-malignancy associated HLH whereas the remaining four patients' cause was not identified. At the time of analysis, 14 patients died due to uncontrolled HLH or underlying disorders or infectious complications during treatment. The median overall survival of all patients was 13.9 months (95% CI: 10.9 - 16.9), and patients with HLH was not significantly different from patients without HLH (p=0.655). The survival outcome of patients with lymphoma was significantly worse than patients without it regardless of HLH diagnosis (p<0.001). Conclusions Fever and elevated level of serum ferritin were the most frequent condition in patients having suspicious symptoms of HLH. Low or absent NK-cell activity and increased level of soluble CD25 could have additional diagnostic value for timely diagnosis of adult HLH. Considering lymphoma is frequently associated with adult HLH, immediate evaluation for lymphoma should be done in adult patients suspicious of HLH. Figure. Figure. Disclosures No relevant conflicts of interest to declare.

Sign in / Sign up

Export Citation Format

Share Document