Next-Generation Sequencing

Oncotarget

The cover for issue 29 of Oncotarget features Figure 2, "Categorisation of samples analysed," from Laes, et al.

- OncoDNA treatment recommendation followed in 60% of cases
- 93% of treatment decisions were made based on a holistic approach combining next generation sequencing (NGS) and multiple biomarker analysis provided by OncoDNA
- 27% of late-stage patients treated with OncoDNA-recommended therapies had overall survival less than 12 months, compared to a typical average of no more than six months
Gosselies, Belgium - April 17, 2018: OncoDNA ("OncoDNA or "the Company"), the healthcare technology company that collates and translates complex cancer biomarker data to make precision medicine a reality, is pleased to announce the publication of a study in the journal Oncotarget evaluating the utility of OncoDNA's comprehensive biomarker analysis and interpretation services in clinical settings.

The study, published online today and titled "The clinical impact of using complex molecular profiling strategies in routine oncology practice", found that combining advanced, comprehensive testing of cancer biomarkers with OncoDNA's proprietary cancer treatment knowledge database can enable oncologists to make better treatment decisions for their patients. This is because OncoDNA's testing combines immunohistochemistry, next generation sequencing (NGS), and other tests including inherited heart condition testing, DNA methylation, and microsatellite instability (MSI) testing, rather than the industry standard of NGS testing alone.

The study analysed samples from 1,057 late-stage and advanced grade cancer patients from over 30 different countries on four continents between January 2015 and January 2016 for whom at least one standard of care treatment had already failed. Samples were analysed either by the sequencing of a solid biopsy only - with either a hotspot panel or comprehensive panel including more than 400 genes - or the study of biomarkers determined by immunohistochemistry and other biomolecular tests, or a combination of both. In order to assess the utility of tumour profiling in clinical practice, the study also analysed the therapeutic decisions made by oncologists after receiving OncoDNA's tumour analysis and treatment recommendation.

Overall, OncoDNA's treatment recommendation was followed in 60.4% of cases and in 99% of the cases that did not follow the recommendation the cited reason was drug unavailability or cost, not clinical consideration. The vast majority of treatment decisions (93.4%) were made based on OncoDNA's combination of tests rather than NGS alone. This is a substantial increase on NGS testing alone, which will typically yield a treatment recommendation in only 30% of cases. For the cases in which OncoDNA's treatment recommendation was followed, 27% of patients had an overall survival of less than 12 months, a significant improvement for late-stage patients, who normally have a life expectancy of no more than six months.

Jean-Pol Detiffe, Chief Executive Officer of OncoDNA, said: "This dataset demonstrates the utility and power of OncoDNA's proprietary, living database and our holistic approach to genomic and molecular profiling. For oncologists, the study suggests our testing and analysis products could represent the best way to make informed therapeutic decisions in clinical practice. Not only were OncoDNA's recommendations followed in the majority of cases, but the study also suggests that our comprehensive testing and analyses could represent the best approach for obtaining useful molecular insight, while reducing physicians' exposure to irrelevant aberrations. As we continue to expand our business through Europe and beyond, these results will help raise awareness of the benefits of our product offering among oncologists and further the healthcare industry's ability to prescribe precision medicine."

Full text - https://www.oncotarget.com/article/24757/text/

Contact

OncoDNA+32 (0) 71 18 35 00

Jean-Pol Detiffe, CEO 
Jean-Francois Laes, CSO

Consilium Strategic Communications+44 (0)20 3709 5700

Amber Fennell, Sukaina Virji, Nicholas Brown, Hendrik Thys oncodna@consilium-comms.com

About Oncotarget

Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

To learn more about Oncotarget, please visit https://www.oncotarget.com or connect with:

SoundCloud - https://soundcloud.com/oncotarget
Facebook - https://www.facebook.com/Oncotarget/
Twitter - https://twitter.com/oncotarget
Instagram - https://www.instagram.com/oncotargetjrnl/
YouTube - https://www.youtube.com/c/OncotargetYouTube/
LinkedIn - https://www.linkedin.com/company/oncotarget
Pinterest - https://www.pinterest.com/oncotarget/
Reddit - https://www.reddit.com/user/Oncotarget/

Oncotarget is published by Impact Journals, LLC please visit https://www.ImpactJournals.com or connect with @ImpactJrnls

Media Contact
MEDIA@IMPACTJOURNALS.COM
18009220957

Author Insight: Unique Biomarker Analysis & Interpretation Platform in Clinical Decision-making

Oncotarget Volume 11, Issue 8 reported Independent validation cohorts of 599 cases of early-stage CRC and 91 cases of late-stage CRC were examined.

Multivariate and univariate survival analyses revealed that high expression of P4HA1 protein was an independent poor prognostic marker for patients with early-stage CRC, especially of the microsatellite stable subtype.

Dr. Michael H. Roehrl from the Department of Pathology, Memorial Sloan Kettering Cancer Center as well as the Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center said, "Colorectal cancer (CRC) is one of the most prevalent malignant tumors and the third leading cause of cancer deaths worldwide."

However, molecular biomarkers with more precise prognostic value, preferably with an underlying functional pathophysiologic rationale, are needed, as such markers would enable the scientists to better stratify risk of recurrence in resected early-stage CRC after resection and more accurately select patients for adjuvant therapy, while avoiding overtreatment in low-risk early-stage CRC.

Proteomics with latest-generation liquid chromatography-mass spectrometry can detect 5,000 - 10,000 proteins in one shotgun sequencing event, and such powerful and sensitive technology may enable the researchers to discover prognostic protein biomarkers for early-stage CRC that previous genomic and transcriptomic analyses would have missed.

Combining results from 712 patients, their study shows that collagen prolyl 4-hydroxylase alpha 1 protein expression robustly risk-stratifies early-stage CRC.

The discovery of P4HA1 outcome stratification in early-stage CRC and, in particular, its MSS subtype, may provide an avenue for early-stage CRC risk prognosis and thus improve cancer treatment outcomes by tailoring follow-up frequency and adjuvant therapy intensity.

The Roehrl Research Team concluded, in their Oncotarget Research Paper, that early-stage CRC presents frequent challenges in clinical patient management in that it is currently impossible to predict which patients will have aggressive disease and thus benefit the most from intensive adjuvant chemotherapy vs. those patients who will have less aggressive disease and benefit from surgery alone.

DOI - https://doi.org/10.18632/oncotarget.27491

Full text - https://www.oncotarget.com/article/27491/text/

Correspondence to - Michael H. Roehrl - roehrlm@mskcc.org

Keywords - P4HA1, colorectal cancer, biomarker, prognosis, pathology

About Oncotarget

Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

To learn more about Oncotarget, please visit https://www.oncotarget.com or connect with:

SoundCloud - https://soundcloud.com/oncotarget
Facebook - https://www.facebook.com/Oncotarget/
Twitter - https://twitter.com/oncotarget
Instagram - https://www.instagram.com/oncotargetj...
YouTube - https://www.youtube.com/c/OncotargetY...
LinkedIn - https://www.linkedin.com/company/onco...
Pinterest - https://www.pinterest.com/oncotarget/
Reddit - https://www.reddit.com/user/Oncotarget/

Oncotarget is published by Impact Journals, LLC please visit https://www.ImpactJournals.com or connect with @ImpactJrnls

Media Contact
MEDIA@IMPACTJOURNALS.COM
18009220957

Author Testimonial: Dr. Roehrl - Memorial Sloan Kettering Cancer Center

Author Insight: Prolyl 4-hydroxylase Alpha 1 Protein and Early Stage Colorectal Cancer

Oncotarget published "Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma" which reported that prior work has characterized changes in the mutation burden between primary and recurrent tumors; however, little work has characterized the changes in neoantigen evolution.

These authors characterized genomic and neoantigen changes between 23 paired primary and recurrent head and neck squamous cell carcinoma (HNSCC) tumors.

Within these tumors, they identified 6 genes which have predicted neoantigens in 4 or more patients.

Within HNSCC tumors examined in this Oncotarget research paper, there are neoantigens in shared genes by a subset of patients.

The presence of neoantigens in these shared genes may promote an anti-tumor immune response which controls tumor progression.

Dr. Brian A. Van Tine from The Washington University in St. Louis, The St. Louis Children's Hospital as well as The Siteman Cancer Center said, "Head and neck cancer are a group of heterogeneous tumors with an estimated 644,000 new cases per year worldwide."

The infiltration of immune cells, including T cells, into tumors is associated with improved outcomes and longer survival in HNSCC.

The infiltrating T cells release granules containing perforin and granzyme A and B which directly kill tumor cells or release other cytokines and chemokines that promote the anti-tumor immune response and alter the tumor microenvironment.

For example, infiltrating T cells release interferon gamma which increases expression of PD-L1 and CTLA-4, which may increase the efficacy of immune checkpoint therapy.

Multiple studies have characterized changes in mutation burden in HNSCC, when comparing primary and metastatic tumors, no studies have characterized the shifting neoantigen burden between primary and metastatic tumors within HNSCC.

In this Oncotarget study, the authors characterized the mutational and neoantigen burden between primary and first recurrence tumors in 23 patients with HNSCC.

The Van Tine Research Team concluded in their Oncotarget Research Output that there is a shifting neoantigen burden as there are unique neoantigens in primary tumors and different unique neoantigens in the recurrent/metastatic tumors.

The patients which have these neoantigens in shared genes are patients which have higher total numbers of neoantigens.

What is clear is that patients with neoantigens in these shared genes also tend to have increased duration of survival with disease.

The increase in neoantigens and duration of survival with disease tends to be associated with increased CD3 CD8 density in the tumor and CD8A expression.

This suggests that patients with these shared neoantigens are associated with increased CD8 T cell infiltration and increased cytotoxic activity, which extends the patient's life.

Sign up for free Altmetric alerts about this article -  - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.27907

DOI - https://doi.org/10.18632/oncotarget.27907

Full text - https://www.oncotarget.com/article/27907/text/

Correspondence to - Brian A. Van Tine - bvantine@wustl.edu

Keywords - head and neck squamous cell carcinoma, neoantigens, mutational evolution, tumor relapse, immune cell infiltration

About Oncotarget

Oncotarget is a bi-weekly, peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

To learn more about Oncotarget, please visit https://www.oncotarget.com or connect with:

SoundCloud - https://soundcloud.com/oncotarget
Facebook - https://www.facebook.com/Oncotarget/
Twitter - https://twitter.com/oncotarget
Instagram - https://www.instagram.com/oncotargetjrnl/
YouTube - https://www.youtube.com/c/OncotargetYouTube/
LinkedIn - https://www.linkedin.com/company/oncotarget
Pinterest - https://www.pinterest.com/oncotarget/
Reddit - https://www.reddit.com/user/Oncotarget/

Oncotarget is published by Impact Journals, LLC please visit https://www.ImpactJournals.com or connect with @ImpactJrnls

Media Contact
MEDIA@IMPACTJOURNALS.COM
18009220957

Author Insight: Genomic and Neoantigen Evolution in Head and Neck Squamous Cell Carcinoma

CD Genomics

RNA-Seq is the premier tool for mapping and quantifying transcriptomes by utilizing next-generation sequencing (NGS) technology. The transcriptome refers to the complete set of transcripts in a cell, which provides information on the transcript level for a specific developmental stage or physiological condition. Understanding the transcriptome is necessary for interpreting the functional elements of the genome and understanding development and disease. The key purpose of transcriptomics includes cataloging all species of transcripts; determining the transcriptional structure of genes; and quantifying the expression levels of each transcript under different conditions.

The Development and Workflow of RNA-seq, Learn more at https://www.cd-genomics.com/resourse-Bioinformatics-Workflow-of-RNA-Seq.html

Principle and Workflow of RNA Sequencing

As a leading provider of NGS services, CD Genomics is providing an integrated portfolio of methylation sequencing services. Whole genome bisulfite sequencing (WGBS) is an effective and reliable strategy to identify individually methylated cytosines on a genome-wide scale. With over 10 years of experience and the state-of-the-art next-generation sequencing platforms, we can totally meet your project requirements and budgets in the exploration of methylome.


https://www.cd-genomics.com/Whole-Genome-Bisulfite-Sequencing.html

Principle and Workflow of Whole Genome Bisulfite Sequencing

CD Genomics has extensive experience in providing support for the selection and design of microsatellite markers for a wide range of plant and animal species. Besides microsatellite genotyping, we also provide genotyping by sequencing (GBS) method, which saves time and resources.  https://www.cd-genomics.com/Microsatellite-Genotyping-Service.html

Learn Microsatellite Genotyping Service  at CD Genomics

Highly integrated single-base resolution DNA methylation patterning; Providing insights into gene cell-fate commitment and reprogramming, as well as gene regulation; Identifying novel epigenetic markers and targets for disease· Unable to distinguish between 5mC and 5hmC.
More information at https://www.cd-genomics.com/5mc-5hmc-sequencing-1.html

5mC and 5hmC Sequencing Methods

To support the increasing research interest in small RNA, CD Genomics is offering the qualified small RNA sequencing service that covers novel small RNA discovery, mutation characterization, and expression profiling of small RNAs by leveraging of advanced NGS technologies and data analysis pipeline.	https://www.cd-genomics.com/Small-RNA.html

Next-Generation Sequencing

Refine By

Keep up to date with all your favourite videos and channels.

Get personalised notifications on new releases and channel content by subscribing to the LabTube eNewsletter.