scholarly journals SeqAnt 2012: Recent Developments in Next-Generation Sequencing Annotation

10.5772/53339 ◽  
2012 ◽  
Author(s):  
Matthew Ezewudo ◽  
Promita Bose ◽  
Kajari Mondal ◽  
Viren Patel ◽  
Dhanya Ramachandran ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Recent Developments ◽  
Generation Sequencing

scholarly journals The long tail and rare disease research: the impact of next-generation sequencing for rare Mendelian disorders

2015 ◽  
Vol 97 ◽  
Author(s):  
TONY SHEN ◽  
ARIEL LEE ◽  
CAROL SHEN ◽  
C.JIMMY LIN
Keyword(s):  
Next Generation Sequencing ◽  
Rare Diseases ◽  
The United States ◽  
Next Generation ◽  
Recent Developments ◽  
Low Incidence ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

SummaryThere are an estimated 6000–8000 rare Mendelian diseases that collectively affect 30 million individuals in the United States. The low incidence and prevalence of these diseases present significant challenges to improving diagnostics and treatments. Next-generation sequencing (NGS) technologies have revolutionized research of rare diseases. This article will first comment on the effectiveness of NGS through the lens of long-tailed economics. We then provide an overview of recent developments and challenges of NGS-based research on rare diseases. As the quality of NGS studies improve and the cost of sequencing decreases, NGS will continue to make a significant impact on the study of rare diseases moving forward.

scholarly journals Integrating next-generation sequencing to endoscopic retrograde cholangiopancreatography (ERCP)-obtained biliary specimens improves the detection and management of patients with malignant bile duct strictures

Gut ◽  
2019 ◽  
Vol 69 (1) ◽  
pp. 52-61 ◽  
Author(s):  
Aatur D Singhi ◽  
Marina N Nikiforova ◽  
Jennifer Chennat ◽  
Georgios I Papachristou ◽  
Asif Khalid ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bile Duct ◽  
Endoscopic Retrograde Cholangiopancreatography ◽  
Elevated Serum ◽  
Next Generation ◽  
Endoscopic Retrograde ◽  
Pathological Evaluation ◽  
Recent Developments ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ObjectiveDespite improvements in imaging, serum CA19-9 and pathological evaluation, differentiating between benign and malignant bile duct strictures remains a diagnostic conundrum. Recent developments in next-generation sequencing (NGS) have opened new opportunities for early detection and management of cancers but, to date, have not been rigorously applied to biliary specimens.DesignWe prospectively evaluated a 28-gene NGS panel (BiliSeq) using endoscopic retrograde cholangiopancreatography-obtained biliary specimens from patients with bile duct strictures. The diagnostic performance of serum CA19-9, pathological evaluation and BiliSeq was assessed on 252 patients (57 trainings and 195 validations) with 346 biliary specimens.ResultsThe sensitivity and specificity of BiliSeq for malignant strictures was 73% and 100%, respectively. In comparison, an elevated serum CA19-9 and pathological evaluation had sensitivities of 76% and 48%, and specificities of 69% and 99%, respectively. The combination of BiliSeq and pathological evaluation increased the sensitivity to 83% and maintained a specificity of 99%. BiliSeq improved the sensitivity of pathological evaluation for malignancy from 35% to 77% for biliary brushings and from 52% to 83% for biliary biopsies. Among patients with primary sclerosing cholangitis (PSC), BiliSeq had an 83% sensitivity as compared with pathological evaluation with an 8% sensitivity. Therapeutically relevant genomic alterations were identified in 20 (8%) patients. Two patients withERBB2-amplified cholangiocarcinoma received a trastuzumab-based regimen and had measurable clinicoradiographic response.ConclusionsThe combination of BiliSeq and pathological evaluation of biliary specimens increased the detection of malignant strictures, particularly in patients with PSC. Additionally, BiliSeq identified alterations that may stratify patients for specific anticancer therapies.

scholarly journals Translational Bioinformatics for Diagnostic and Prognostic Prediction of Prostate Cancer in the Next-Generation Sequencing Era

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Jiajia Chen ◽  
Daqing Zhang ◽  
Wenying Yan ◽  
Dongrong Yang ◽  
Bairong Shen
Keyword(s):  
Prostate Cancer ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Cancer Biomarkers ◽  
Translational Bioinformatics ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Recent Developments ◽  
Generation Sequencing

The discovery of prostate cancer biomarkers has been boosted by the advent of next-generation sequencing (NGS) technologies. Nevertheless, many challenges still exist in exploiting the flood of sequence data and translating them into routine diagnostics and prognosis of prostate cancer. Here we review the recent developments in prostate cancer biomarkers by high throughput sequencing technologies. We highlight some fundamental issues of translational bioinformatics and the potential use of cloud computing in NGS data processing for the improvement of prostate cancer treatment.

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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