Probing cancer epigenetics with highly multiplexed PCR and targeted resequencing

2021 ◽  
Author(s):  
◽  
Andrew Johnston
Keyword(s):  
Cancer Epigenetics ◽  
Targeted Resequencing ◽  
Multiplexed Pcr

scholarly journals New Aspects of the Epigenetics of Pancreatic Carcinogenesis

Epigenomes ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 18
Author(s):  
Murat Toruner ◽  
Martin E. Fernandez-Zapico ◽  
Christopher L. Pin
Keyword(s):  
Pancreatic Cancer ◽  
Dna Methylation ◽  
Survival Rate ◽  
Epigenetic Mechanisms ◽  
Therapeutic Approaches ◽  
Cancer Epigenetics ◽  
Pancreatic Carcinogenesis ◽  
New Therapeutic Approaches ◽  
Environmental Events ◽  
Underlying Pathogenesis

Pancreatic cancer remains among the deadliest forms of cancer with a 5 year survival rate less than 10%. With increasing numbers being observed, there is an urgent need to elucidate the pathogenesis of pancreatic cancer. While both contribute to disease progression, neither genetic nor environmental factors completely explain susceptibility or pathogenesis. Defining the links between genetic and environmental events represents an opportunity to understand the pathogenesis of pancreatic cancer. Epigenetics, the study of mitotically heritable changes in genome function without a change in nucleotide sequence, is an emerging field of research in pancreatic cancer. The main epigenetic mechanisms include DNA methylation, histone modifications and RNA interference, all of which are altered by changes to the environment. Epigenetic mechanisms are being investigated to clarify the underlying pathogenesis of pancreatic cancer including an increasing number of studies examining the role as possible diagnostic and prognostic biomarkers. These mechanisms also provide targets for promising new therapeutic approaches for this devastating malignancy.

scholarly journals NGS-based identification and tracing of microsatellite instability from minute amounts DNA using inter-Alu-PCR

2020 ◽  
Author(s):  
Fangyan Yu ◽  
Ka Wai Leong ◽  
Alexander Makrigiorgos ◽  
Viktor A Adalsteinsson ◽  
Ioannis Ladas ◽  
...  
Keyword(s):  
Microsatellite Instability ◽  
Analysis Tool ◽  
Circulating Dna ◽  
Liquid Biopsies ◽  
Software Analysis ◽  
Multiplexed Pcr ◽  
Human Genomes ◽  
Custom Made ◽  
Alu Element ◽  
Next Generation Sequencing Ngs

Abstract Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new approach to detect MSI using inter-Alu-PCR followed by targeted NGS, that combines the practical advantages of multiplexed-PCR with the breadth of information provided by NGS. Inter-Alu-PCR employs poly-adenine repeats of variable length present in every Alu element and provides a massively-parallel, rapid approach to capture poly-A-rich genomic fractions within short 80–150bp amplicons generated from adjacent Alu-sequences. A custom-made software analysis tool, MSI-tracer, enables Alu-associated MSI detection from tissue biopsies or MSI-tracing at low-levels in circulating-DNA. MSI-associated indels at somatic-indel frequencies of 0.05–1.5% can be detected depending on the availability of matching normal tissue and the extent of instability. Due to the high Alu copy-number in human genomes, a single inter-Alu-PCR retrieves enough information for identification of MSI-associated-indels from ∼100 pg circulating-DNA, reducing current limits by ∼2-orders of magnitude and equivalent to circulating-DNA obtained from finger-sticks. The combined practical and informational advantages of inter-Alu-PCR make it a powerful tool for identifying tissue-MSI-status or tracing MSI-associated-indels in liquid biopsies.

scholarly journals Targeted Resequencing and Analysis of the Diamond-Blackfan Anemia Disease Locus RPS19

PLoS ONE ◽  
2009 ◽  
Vol 4 (7) ◽  
pp. e6172 ◽  
Author(s):  
Alvaro Martinez Barrio ◽  
Oskar Eriksson ◽  
Jitendra Badhai ◽  
Anne-Sophie Fröjmark ◽  
Erik Bongcam-Rudloff ◽  
...  
Keyword(s):  
Disease Locus ◽  
Targeted Resequencing ◽  
Diamond Blackfan Anemia

Lung cancer epigenetics: From knowledge to applications

2018 ◽  
Vol 51 ◽  
pp. 116-128 ◽  
Author(s):  
Michaël Duruisseaux ◽  
Manel Esteller
Keyword(s):  
Lung Cancer ◽  
Cancer Epigenetics

scholarly journals Overlapping pools for high-throughput targeted resequencing

2009 ◽  
Vol 19 (7) ◽  
pp. 1254-1261 ◽  
Author(s):  
S. Prabhu ◽  
I. Pe'er
Keyword(s):  
High Throughput ◽  
Targeted Resequencing

scholarly journals Cancer Epigenetics: New Therapies and New Challenges

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Eleftheria Hatzimichael ◽  
Tim Crook
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Hdac Inhibitors ◽  
Clinical Impact ◽  
Clinical Use ◽  
Cancer Epigenetics ◽  
Dnmt Inhibitors ◽  
Epigenetic Effects ◽  
New Challenges ◽  
Neoplastic Disorders

Cancer is nowadays considered to be both a genetic and an epigenetic disease. The most well studied epigenetic modification in humans is DNA methylation; however it becomes increasingly acknowledged that DNA methylation does not work alone, but rather is linked to other modifications, such as histone modifications. Epigenetic abnormalities are reversible and as a result novel therapies that work by reversing epigenetic effects are being increasingly explored. The biggest clinical impact of epigenetic modifying agents in neoplastic disorders thus far has been in haematological malignancies, and the efficacy of DNMT inhibitors and HDAC inhibitors in blood cancers clearly attests to the principle that therapeutic modification of the cancer cell epigenome can produce clinical benefit. This paper will discuss the most well studied epigenetic modifications and how these are linked to cancer, will give a brief overview of the clinical use of epigenetics as biomarkers, and will focus in more detail on epigenetic drugs and their use in solid and blood cancers.

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