scholarly journals Gestational Psittacosis Resulting in Neonatal Death Identified by Next-Generation RNA Sequencing of Postmortem, Formalin-Fixed Lung Tissue

2018 ◽  
Vol 5 (8) ◽  
Author(s):  
Litty Paul ◽  
Jessica Comstock ◽  
Kornelia Edes ◽  
Robert Schlaberg
Keyword(s):  
Rna Sequencing ◽  
Infant Death ◽  
Neonatal Death ◽  
Pathogen Detection ◽  
Severe Disease ◽  
Adverse Outcomes ◽  
Premature Delivery ◽  
Next Generation ◽  
Death Studies ◽  
Formalin Fixed

Abstract Psittacosis is a rare zoonosis that can cause severe disease and adverse outcomes during pregnancy. We identified a previously elusive case of psittacosis causing premature delivery and infant death by next-generation RNA sequencing of postmortem tissues. Hypothesis-free pathogen detection in postmortem specimens can increase the yield of epidemiologic and cause-of-death studies.

Next-generation RNA Sequencing of Archival Formalin-fixed Paraffin-embedded Urothelial Bladder Cancer

2014 ◽  
Vol 66 (6) ◽  
pp. 982-986 ◽  
Author(s):  
Yu Liu ◽  
Aidan P. Noon ◽  
Eduardo Aguiar Cabeza ◽  
Jess Shen ◽  
Cynthia Kuk ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Rna Sequencing ◽  
Next Generation ◽  
Urothelial Bladder Cancer ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Urothelial Bladder ◽  
Formalin Fixed

scholarly journals Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David S. Fischer ◽  
Meshal Ansari ◽  
Karolin I. Wagner ◽  
Sebastian Jarosch ◽  
Yiqi Huang ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Ex Vivo ◽  
Severe Disease ◽  
Human Leukocyte ◽  
Cell Receptor ◽  
Single Cell Rna Sequencing

AbstractThe in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.

scholarly journals Suitability of Bronchoscopic Biopsy Tissue Samples for Next-Generation Sequencing

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 391
Author(s):  
Shuji Murakami ◽  
Tomoyuki Yokose ◽  
Daiji Nemoto ◽  
Masaki Suzuki ◽  
Ryou Usui ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Success Rate ◽  
Rna Sequencing ◽  
Surface Area ◽  
Endobronchial Ultrasound ◽  
Next Generation ◽  
Endobronchial Ultrasonography ◽  
Tissue Surface ◽  
The Impact ◽  
Generation Sequencing

A sufficiently large tissue sample is required to perform next-generation sequencing (NGS) with a high success rate, but the majority of patients with advanced non-small-cell lung cancer (NSCLC) are diagnosed with small biopsy specimens. Biopsy samples were collected from 184 patients with bronchoscopically diagnosed NSCLC. The tissue surface area, tumor cell count, and tumor content rate of each biopsy sample were evaluated. The impact of the cut-off criteria for the tissue surface area (≥1 mm2) and tumor content rate (≥30%) on the success rate of the Oncomine Dx Target Test (ODxTT) was evaluated. The mean tissue surface area of the transbronchial biopsies was 1.23 ± 0.85 mm2 when small endobronchial ultrasonography with a guide sheath (EBUS-GS) was used, 2.16 ± 1.49 mm2 with large EBUS-GS, and 1.81 ± 0.75 mm2 with endobronchial biopsy (EBB). The proportion of samples with a tissue surface area of ≥1 mm2 was 48.8% for small EBUS-GS, 79.2% for large EBUS-GS, and 78.6% for EBB. Sixty-nine patients underwent ODxTT. The success rate of DNA sequencing was 84.1% and that of RNA sequencing was 92.7% over all patients. The success rate of DNA (RNA) sequencing was 57.1% (71.4%) for small EBUS-GS (n = 14), 93.4% (96.9%) for large EBUS-GS (n = 32), 62.5% (100%) for EBB (n = 8), and 100% (100%) for endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) (n = 15). Regardless of the device used, a tissue surface area of ≥ 1 mm2 is adequate for samples to be tested with NGS.

scholarly journals Serum albumin concentrations are associated with disease severity and outcomes in coronavirus 19 disease (COVID-19): a systematic review and meta-analysis

2021 ◽  
Author(s):  
Panagiotis Paliogiannis ◽  
Arduino Aleksander Mangoni ◽  
Michela Cangemi ◽  
Alessandro Giuseppe Fois ◽  
Ciriaco Carru ◽  
...  
Keyword(s):  
Systematic Review ◽  
Serum Albumin ◽  
Disease Severity ◽  
Meta Analysis ◽  
Severe Disease ◽  
Geographic Area ◽  
Adverse Outcomes ◽  
Poor Outcome ◽  
Standard Mean Difference ◽  
Meta Regression Analysis

AbstractCoronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the most threatening pandemic in modern history. The aim of this systematic review and meta-analysis was to investigate the associations between serum albumin concentrations and COVID-19 disease severity and adverse outcomes. A systematic literature search was conducted in PubMed, from inception to October 30, 2020. Sixty-seven studies in 19,760 COVID-19 patients (6141 with severe disease or poor outcome) were selected for analysis. Pooled results showed that serum albumin concentrations were significantly lower in patients with severe disease or poor outcome (standard mean difference, SMD: − 0.99 g/L; 95% CI, − 1.11 to − 0.88, p < 0.001). In multivariate meta-regression analysis, age (t =  − 2.13, p = 0.043), publication geographic area (t = 2.16, p = 0.040), white blood cell count (t =  − 2.77, p = 0.008) and C-reactive protein (t =  − 2.43, p = 0.019) were significant contributors of between-study variance. Therefore, lower serum albumin concentrations are significantly associated with disease severity and adverse outcomes in COVID-19 patients. The assessment of serum albumin concentrations might assist with early risk stratification and selection of appropriate care pathways in this group.

scholarly journals Liver dysfunction in COVID-19: a useful prognostic marker of severe disease?

2020 ◽  
pp. flgastro-2020-101689
Author(s):  
James Lok ◽  
Markus Gess
Keyword(s):  
Liver Function ◽  
Acute Phase ◽  
Liver Dysfunction ◽  
Acute Phase Proteins ◽  
Severe Disease ◽  
Ventilatory Support ◽  
Length Of Hospital Stay ◽  
Abnormal Liver Function ◽  
Adverse Outcomes ◽  
High Dependency

BackgroundCOVID-19 is a global pandemic caused by the novel coronavirus SARS-CoV-2. Risk factors and prognostic markers of severe disease remain to be fully determined, although some studies have suggested a correlation between abnormal liver function and adverse outcomes. Further studies are needed to investigate this further.MethodsThis retrospective study enrolled patients with a confirmed diagnosis of COVID-19 who were admitted to Kingston Hospital in the UK. Data collected included age, sex, ethnicity, comorbidity profile, biochemical markers of liver function and the acute phase response, and overall outcome.ResultsBetween 16 March 2020 and 30 April 2020, a total of 343 patients were admitted to the acute medical team at Kingston Hospital. Excluding those with a history of liver disease, 299 patients had liver function tests performed with abnormalities demonstrated in 44.8% of individuals. Derangement of liver function was associated with greater need for ventilatory support (p<0.001), admission to high dependency unit or intensive care (p<0.001) and increased length of hospital stay (p<0.001). Of note, liver dysfunction was more common in those of non-white ethnicity (p=0.007) and correlated with higher levels of C reactive protein (p=0.01) and ferritin (p<0.001).ConclusionAbnormal liver function is associated with a negative outcome among those hospitalised with COVID-19. The cause for this association is unclear, but correlation between abnormal liver function and higher serum levels of acute phase proteins suggest that dysregulation of the immune system in response to SARS-CoV-2 may be contributory.

scholarly journals The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michal Marczyk ◽  
Chunxiao Fu ◽  
Rosanna Lau ◽  
Lili Du ◽  
Alexander J. Trevarton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Rna Extraction ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
The Impact ◽  
Formalin Fixed

Abstract Background Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA. Methods Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche). All RNA samples underwent whole transcriptome RNA sequencing (wtRNAseq) and targeted RNA sequencing for 31 transcripts included in a signature of sensitivity to endocrine therapy. We assessed the effect of RNA extraction kit on the reliability of gene expression levels using linear mixed-effects model analysis, concordance correlation coefficient (CCC) and differential analysis. All protein-coding genes in the wtRNAseq and three gene expression signatures for breast cancer were assessed for concordance. Results Despite variable quality of the RNA extracted from FFPE samples by different kits, all had similar concordance of overall gene expression from wtRNAseq between matched FF and FFPE samples (median CCC 0.63–0.66) and between technical replicates (median expression difference 0.13–0.22). More than half of genes were differentially expressed between FF and FFPE, but with low fold change (median |LFC| 0.31–0.34). Two out of three breast cancer signatures studied were highly robust in all samples using any kit, whereas the third signature was similarly discordant irrespective of the kit used. The targeted RNAseq assay was concordant between FFPE and FF samples using any of the kits (CCC 0.91–0.96). Conclusions The selection of kit to purify RNA from FFPE did not influence the overall quality of results from wtRNAseq, thus variable reproducibility of gene signatures probably relates to the reliability of individual gene selected and possibly to the algorithm. Targeted RNAseq showed promising performance for clinical deployment of quantitative assays in breast cancer from FFPE samples, although numerical scores were not identical to those from wtRNAseq and would require calibration.

scholarly journals Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0127353 ◽  
Author(s):  
Danielle Mercatante Carrick ◽  
Michele G. Mehaffey ◽  
Michael C. Sachs ◽  
Sean Altekruse ◽  
Corinne Camalier ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Generation Sequencing ◽  
Formalin Fixed

scholarly journals Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses

Apmis ◽  
2016 ◽  
Vol 124 (1-2) ◽  
pp. 127-139 ◽  
Author(s):  
Martin Sokol ◽  
Karen Margrethe Jessen ◽  
Finn Skou Pedersen
Keyword(s):  
Rna Sequencing ◽  
Endogenous Retroviruses ◽  
Next Generation ◽  
Human Endogenous Retroviruses

Church Attendance, Religious Affiliation and Parental Responses to Sudden Infant Death, Neonatal Death and Stillbirth

1995 ◽  
Vol 31 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M. J. Thearle ◽  
J. C. Vance ◽  
J. M. Najman ◽  
G. Embelton ◽  
W. J. Foster
Keyword(s):  
Infant Death ◽  
Neonatal Death ◽  
Church Attendance ◽  
Religious Affiliation ◽  
Well Being ◽  
Sudden Infant Death ◽  
Sudden Infant ◽  
Religion And Health ◽  
Life Styles ◽  
A Prospective Study

There is an association between religion and health: those who are religious have healthier life-styles resulting in less physical illness and improved longevity. Some evidence shows that there may be a beneficial association between religion and psychological well-being. With bereavement, some may “turn to God” while others “turn away from God”; this occurrence may be reflected in their church attendance. In a prospective study, families who had experienced death from Sudden Infant Death Syndrome, Neonatal Death, or Stillbirth were compared for anxiety, depression, and church attendance with control families who had not experienced such bereavement A traditionally held belief that religion offers consolation for the grief of bereavement and that the bereaved “turn to God” as reflected in church attendance was not confirmed. There is the suggestion that the bereaved who attend church regularly have less anxiety and depression compared with the irregular or non-church attenders.

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