scholarly journals Genomic and Functional Characteristics of Human Cytomegalovirus Revealed by Next-Generation Sequencing

Viruses ◽  
2014 ◽  
Vol 6 (3) ◽  
pp. 1049-1072 ◽  
Author(s):  
Steven Sijmons ◽  
Marc Van Ranst ◽  
Piet Maes
Keyword(s):  
Next Generation Sequencing ◽  
Human Cytomegalovirus ◽  
Next Generation ◽  
Functional Characteristics ◽  
Generation Sequencing

scholarly journals Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis

2019 ◽  
Author(s):  
Jiahui Wang ◽  
Yelei Han ◽  
Yang Zhou ◽  
Jing Feng
Keyword(s):  
Next Generation Sequencing ◽  
Human Cytomegalovirus ◽  
Predictive Value ◽  
Pulmonary Infection ◽  
Next Generation ◽  
Promising Technique ◽  
Infection Diagnosis ◽  
Conventional Tests ◽  
Conventional Test ◽  
Generation Sequencing

Abstract Background. Metagenomic next-generation sequencing (mNGS) is emerging as a promising technique for pathogens detection. However, reports on the application of mNGS in mixed pulmonary infection remain scarce. Methods. From July 2018 to March 2019, 55 cases were enrolled in this retrospective analysis. Cases were classified into mixed pulmonary infection (36 [65.5%]) and non-mixed pulmonary infection (19 [34.5%]) according to primary diagnoses. The performances of mNGS and conventional test on mixed pulmonary infection diagnosis and pathogen identification were compared. Results.The sensitivity of mNGS in mixed pulmonary infection diagnose was much higher than that of conventional test (97.2％ vs 13.9％;P<0.01) , but the specificity was the opposite (63.2％ vs 94.7％;P=0.07) . The positive predictive value of mNGS was 83.3% (95% CI: 68.0-92.5%) , and the negative predictive value was 92.3% (95% CI: 62.1-99.6%) . A total of 5 (9.1%) cases were identified as mixed pulmonary infection by both conventional tests and mNGS, however, the pathogens identification results were consistent between these two methods in only 1(1.8%) case. In summary, the pathogens detected by mNGS in 3 (5.5%) cases were consistent with those by conventional test, and only 1(1.8%) case was mixed pulmonary infection. According to our data, mNGS had a broader spectrum for pathogen detection than conventional tests. In particular, application of mNGS improved the diagnosis of pulmonary fungal infections. Within the 55 cases, mNGS detected and identified fungi in 31 (56.4%) cases, of which only 10 (18.2%) cases were positive for the same fungi by conventional test. The most common pathogen detected was Human cytomegalovirus in our study, which was identified in 19(34.5%) cases of mixed pulmonary infection. Human cytomegalovirus and Pneumocystis jirovecii, which were detected in 7(12.7%) cases, were the most common co-pathogens in the group of mixed pulmonary infection. Conclusions. mNGS is a promising technique to detect co-pathogens in mixed pulmonary infection, with potential benefits in speed and sensitivity.

scholarly journals Metagenomic next-generation sequencing for mixed pulmonary infection diagnosis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jiahui Wang ◽  
Yelei Han ◽  
Jing Feng
Keyword(s):  
Next Generation Sequencing ◽  
Human Cytomegalovirus ◽  
Predictive Value ◽  
Pulmonary Infection ◽  
Next Generation ◽  
Promising Technique ◽  
Infection Diagnosis ◽  
Conventional Tests ◽  
Conventional Test ◽  
Generation Sequencing

Abstract Background Metagenomic next-generation sequencing (mNGS) is emerging as a promising technique for pathogens detection. However, reports on the application of mNGS in mixed pulmonary infection remain scarce. Methods From July 2018 to March 2019, 55 cases were enrolled in this retrospective analysis. Cases were classified into mixed pulmonary infection (36 [65.5%]) and non-mixed pulmonary infection (19 [34.5%]) according to primary diagnoses. The performances of mNGS and conventional test on mixed pulmonary infection diagnosis and pathogen identification were compared. Results The sensitivity of mNGS in mixed pulmonary infection diagnosis was much higher than that of conventional test (97.2% vs 13.9%; P < 0.01), but the specificity was the opposite (63.2% vs 94.7%; P = 0.07). The positive predictive value of mNGS was 83.3% (95% CI, 68.0–92.5%), and the negative predictive value was 92.3% (95% CI, 62.1–99.6%). A total of 5 (9.1%) cases were identified as mixed pulmonary infection by both conventional tests and mNGS, however, the pathogens identification results were consistent between these two methods in only 1 (1.8%) case. In summary, the pathogens detected by mNGS in 3 (5.5%) cases were consistent with those by conventional test, and only 1 (1.8%) case was mixed pulmonary infection. According to our data, mNGS had a broader spectrum for pathogen detection than conventional tests. In particular, application of mNGS improved the diagnosis of pulmonary fungal infections. Within the 55 cases, mNGS detected and identified fungi in 31 (56.4%) cases, of which only 10 (18.2%) cases were positive for the same fungi by conventional test. The most common pathogen detected by mNGS was Human cytomegalovirus in our study, which was identified in 19 (34.5%) cases of mixed pulmonary infection. Human cytomegalovirus and Pneumocystis jirovecii, which were detected in 7 (12.7%) cases, were the most common co-pathogens in the group of mixed pulmonary infection. Conclusions mNGS is a promising technique to detect co-pathogens in mixed pulmonary infection, with potential benefits in speed and sensitivity. Trial registration (retrospectively registered): ChiCTR1900023727. Registrated 9 JUNE 2019.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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