Tag Archives: cancer

Review of Emerging 2018 Genomic Variants – a Genomenon Research Report

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2018 has been another banner year in the progression of Precision Medicine! Year over year, there has been a dramatic rise in the number of scientific studies and initiatives that resulted in meaningful published findings, and 2018 was another record-breaker. To demonstrate trends in genetics and genomics research seen through the lens of scientific publications, the Genomenon team mined the genomics data aggregated in Genomenon’s Mastermind Genomic Search Engine to reflect on these trends.

Genomenon’s Mastermind Genomic Search Engine has indexed the full text of millions of genomic articles and supplemental data to provide immediate insight into the published research for every disease, gene, and mutation found in the literature. Mastermind is used by hundreds of diagnostic labs around the world to accelerate genomic interpretation and by pharmaceutical companies in drug discovery for its comprehensive genomic landscape of every disease.

New Genomic Insights Indicate an Emergence of Drug Resistance in Cancer and Focus on Rare Disease Research

Aggregating the granular genomics data allowed us to see the bigger-picture patterns that emerged.

  • 2017 findings: Newly-emergent variants were predominantly associated with cancer and research was predominantly focused on resistance mechanisms or the development of new therapeutics.
  • 2018 findings: A continued trend of studies and new discoveries detailing drug resistance mechanisms, with several of the previously identified emerging variants re-appearing on the list of the top 300 newly discovered variants; an increasing number of emergent variants were found in non-cancer diseases. Notable results are summarized in Tables 1 and 2.

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Long Non-coding RNAs and Their Clinical Relevance in Cancer and Cancer Therapy

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Long non-coding RNAs (lncRNAs) are clinically relevant in at least two major ways: as biomarkers for cancer or carcinogenesis and as actual targets for cancer therapy.

LncRNAs as biomarkers for cancer and carcinogenesis

LncRNAs can be biomarkers for cancer or carcinogenesis, and can yield insight into possible sensitivity or resistance to potential anti-cancer therapies. A well-known example includes the FDA-approved PROGENSA PCA3 assay testing in urinary samples used as part of the screening paradigm for prostate cancer. This is one demonstration of a testable form of lncRNA that exists with sufficient stability in a non-invasive biological sample, highlighting the key attributes of stability and ability to be assayed of a viable biomarker.

LncRNAs as targets for cancer therapy

A number of lncRNA genes have been found to be expressed at elevated levels which correlate with various cancers. To investigate a possible causal connection, there are several options to reduce or knockout expression in vivo, where the technology has already been proven to be effective in in vitro or cell culture settings. These approaches include (Gutschner et al.,2018):

  • siRNAs that are complementary to lncRNA which takes advantage of the RISC/argonaute system to degrade the target molecule
  • anti-sense oligos (ASOs), refined with chemical modifications to enhance activity or stability, which have been demonstrated to function by targeting lncRNAs to the endogenous RNase H systems for destruction
  • the use of targeting ribozymes, deoxyribozymes, or CRISPR/Cas9-derived technologies which have been proposed for silencing lncRNA.

The evolving field of RNA biology and lncRNA

Image credit: Parasramka et al. (2016)

Once relegated to the ‘junk’ DNA category, large segments of the genome and their associated transcripts have long been ignored, or thought of as unimportant. Only a few Continue reading →

Genomenon’s Automated Genomic Search Engine Mastermind Illuminates Current Trends in Genomic Literature – A Look at the Top Cited Variants Across the Scientific Literature

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For this month’s “Company Spotlight” blog series we are taking a deeper look at Mastermind, an automated genomic search engine created by Genomenon, a University of Michigan spin-off. Mastermind, a comprehensive database of genomic disease-to-gene-to-variant associations, supports its users to search through millions of full text articles from the primary medical literature to identify variants of interest, prioritize them, and retrieve relevant articles for disease-gene-variant combinations. Rather than providing a regular Q&A with a company representative, we thought of illustrating the richness of Mastermind’s content and the associated functionalities via the retrieval of interesting citation data, as provided by Mark Kiel (CSO and co-Founder at Genomenon) and Lauren Chunn (Data Processing Intern at Genomenon). Specifically, the Genomenon team supplied a current trends analysis of widely cited variants within the genomic literature. Through this process they are able to paint a picture of the changing landscape of genomic research and medicine, from variants that have remained a common feature for decades to newly emerging variants over the last few years.

Genomenon is a 15 person company, headquartered in Ann Arbor, Michigan, and founded in 2014. To date, Genomenon has received $4.5M in funding (Angel, Venture investment and NIH SBIR Fast Track Grant), and has grown to become an independent company.

Mastermind is a genomic search engine comprising an index of titles, abstracts, and full text including figures and tables of 5.7 million prioritized primary articles. New Continue reading →

This year’s Bio-IT 2016 With Clinical Genetics as the Frontrunner

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BioITimage

This year’s Bio-IT conference – with theme Big Data – was clearly marked by the presence of clinical genetics: its data sharing, analysis, and interpretation challenges echoed throughout the many talks (and exhibit) whether it was Heidi Rhem’s opening plenary session or George Church’s genomics breakfast session, demonstrating that routine sequencing is within reach. Undoubtedly, there have been great developments in the software space in the past years, but scaling for massive genomics data still requires work! Interestingly, overlapping with Bio-IT 2016, the 13th International Congress of Human Genetics held in Kyoto further exemplified what was communicated Continue reading →

At AGBT 2016, the Winners Are Long Reads and Whole Solutions

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AGBT_logo_RGBThis year’s pilgrimage of geneticist, genomics scientists, and along with that commercial companies was to the JW Marriott in Orlando and not as usual to Marco Island – however, we were assured that the next two AGBT events are already confirmed to be held on Marco Island again. The Orlando Marriott setting seemed fine; nothing beats the Marco island environment with its beach setting which is well worth the extra hour bus ride from the airport to take you there. Having said this, the setting appeared to be more favorable for the vendors in particular, given the more open arrangement of large suites inviting easy access and interactions with conference attendees. Continue reading →