CRISPR Base Editors: An Upgrade for Treatment of Genetic Disease

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The CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9(CRISPR-associated system 9) technology, often touted as one of the greatest recent inventions to drive progress in biotechnology, is currently being challenged and viewed more critically as a recent flurry of articles is casting doubt on the overall safety of this rising technology which up to now has mostly seen positive press.

CRISPR gene editing recent news and controversies

CRISPR, also often referred to as CRISPR/Cas9, is a technically and scientifically fascinating biological system that promises to yield a revolution in treatment of genetic diseases. CRISPR also offers a basis for powerful and flexible tools for furthering our understanding of eukaryotic gene expression. The underlying biology – though rather obscure just a decade ago – is nowadays an enormously active area of research in both basic science and medical/technical applications.

CRISPR

CRISPR has such a promise that a cautionary article about issues with off-target genetic mutations in some CRISPR applications (Kosicki et al., 2018), also recently presented in the Wall Street Journal (WSJ) by Mohan and Marcus (2018) shook the research community. Both the study in question and the industry effects that the WSJ article touch upon are relevant when using the form of technology called CRISPR/Cas9 (Cas9 DNA nuclease paired with its targeting CRISPR RNA(s)). However, there are more advanced and specialized versions of CRISPR technology that may avoid those challenges, in this case referring to the ‘base editor’ versions of derived Cas9 (Komor et al., 2016, Nishida et al., 2016). More about the details of both will be discussed later in this post.

Image credit:  Cancer Research UK.

Recent “ruling by the European Court of Justice that gene editing equals genetic engineering”

The concerns over use of CRISPR-Cas9 in the context of therapeutic development have been further amplified with a recent ruling by the European Court of Justice that Continue reading →

Nebula Genomics’ Goal Is To Make The Value of Genome Sequencing a Reality

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This month’s “Company Spotlight” provides a closer look at Nebula Genomics, a human genome sequencing and health big data company on a mission to usher in the era of genomic sequencing by building a large and trusted genomic and health data marketplace for consumers, researchers and the medical community.

Kamal Obbad, CEO and cofounder of Nebula Genomics discussed Nebula Genomics’ marketplace, the need their platform is addressing, and where the future of genomics data sharing and access will lead to.

Nebula Genomics is using blockchain to ensure that consumers maintain control of their data and are compensated for its use, so that the Nebula marketplace will aggregate a critical mass of rich genetic information that researchers can analyze in order to accelerate drug development, streamline clinical trials, and usher in the era of truly personalized medicine. The eight-person company is headquartered in San Francisco, CA, and was founded in 2017 by Harvard Genomics pioneer George Church, along with Harvard researchers Dennis Grishin and Kamal Obbad. Nebula Genomics has recently secured $4.3M in funding from leading venture capital firms including Khosla Ventures, Mayfield and Arch Ventures. The funds will support the company’s mission to usher in the era of personal genome sequencing by creating a trusted, secure, and decentralized marketplace for genomic data. Nebula has also forged a partnership with Veritas Genetics, the leading whole genome sequencing and interpretation company, that will connect the Nebula marketplace to Veritas’ Arvados open-source software platform.

The following summarizes questions and answers from my dialogue with Kamal Obbad.

EB: Tell us more about Nebula Genomics – What scientific and business needs are you trying to address and what products/services do you offer? Blockchain is a critical component of Nebula Genomics – can you explain exactly how you apply this technology to your services?

Kamal Obbad: One of the main issues researchers and the pharma industry are facing today is access to large scale genomics data. The data as it exists today is very fragmented. It is generated in many different labs, by both nonprofit and for-profit Continue reading →

Now Available: Individual Clinical NGS Process Report Chapters

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We are currently offering the individual chapters and the full report at a 10% discount with promo code 10OFFCLINNGSNOW.

The recently released Clinical NGS Process Report – released January 12, 2018 – details the observations and learnings across the complex, multi-step informatics aspects following clinical NGS sample preparation and sequencing, and which includes data analysis, knowledge extraction, and clinical reporting of actionable findings.

You spoke – we listened: To make this report more accessible to individuals that only have an interest in a section we are now providing access to individual chapters. The following chapters are now available for separate purchase:

  1. Clinical End-User Feedback
    1. Conducted a series of end-user interviews to understand clinical needs, testing lab preferences, and challenges when receiving clinical variant data and communicating findings to the physician and the patient.
  2. Clinical NGS Market Trends
    1. NGS adoption challenges.
    2. Innovations and technology trends impacting clinical NGS applications.
    3. Mergers and acquisitions impacting clinical NGS.
  3. Ten Years of NGS Patents
    1. Studied the last ten years of NGS assignees across all NGS patent families, number of patents of leading commercial companies, and clinical-grade genetic/diagnostic testing providers.
    2. Top patent assignees across all NGS patent families.
    3. Contributed by our partner company Pramoedya Biointelligence.
  4. Clinical NGS Projects/Initiatives
    1. Detailed review of 38 global human genome-based initiatives.
  5. The Clinical NGS Data Analysis & Interpretation Ecosystem
    1. Evaluated 26 key commercial software and platform providers that offer a clinical NGS analysis or interpretation solution, to understand their product focus and offered capabilities, their strategy to address end-user needs, and more.
  6. Company/Product Profiles
    1. Reviewed 26 key companies with comprehensive solutions across the entire Clinical NGS Workflow, including genetic testing/diagnostics service providers their product focus, offered capabilities, and their strategy to address end-user needs, and more.

Continue reading →

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 →

Bio-IT World Conference 2018 – Data Science Has Replaced Bioinformatics

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This year’s conference kicked off with an interesting Data Science panel that included Tanya Cashorali (TCB Analytics), Jerald Schindler (Alkermes), John Reynders (Alexion Pharmaceuticals), and Lihua Yu (H3 Biomedicine). Without a doubt, data science is important and involves much more than big data, including the entire workflow of data creation, to insight generation, and decision-making. One key message that came across is that not all data is big data, and that we need improvements in data collection and infrastructure support for data analysis and management. Other key take-home messages: breaking down data silos, educating about responsibility, being responsible to not act independently on data, creating an environment that motivates everybody within a team to share, not rewarding bad data behavior, and being insensitive to data sharing to get more out in return. The big issue here is the culture. If the culture rewards Continue reading →

Happy National DNA Day

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The National DNA Day commemorates the 1953 Nature publication of the Structure of DNA by James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin, and colleagues. It has been….

Image credits: Zen Sutherland

  • 65 years since the publication of the Molecular Structure of Nucleic Acids
  • paper by Watson, Crick, and colleagues like Wilkins and Franklin,
  • 41 years since the release of the Sanger sequencing methodology,
  • 31 years since the launch of the first automated DNA sequencer by Applied Biosystems which eventually enabled the completion of the Human Genome Project in 2001,
  • 12 years since the launch of the Solexa Genome Analyzer, the first second-generation sequencing platform, which supported the sequencing of 1 GB of data in a single run,
  • 4 years since the $1,000 Genome has become a reality via Illumina’s introduction of the HiSeq X Ten platform and a 10,000-fold reduction in price relative to the cost of the human genome in 2004,
  • 3 years since the completion of the 1,000 Genomes Project and the start of the 100K Genomes Project and many other projects taking off.

Continue reading →

ACMG 2018 – “There is Still So Much We Have to Learn”

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This year’s ACMG conference in Charlotte, North Carolina, included a very well received first installment of TED-style talks which reflected on the evolution and impact of healthcare. All three talks delivered by Kaylene Ready (Director of Inherited Cancer and a Genetics Counselor, Counsyl), Christian Schaaf (Professor Clinical Genomics, University of Cologne), and Wendy Chung (Associate Professor of Pediatrics, Columbia University Irving Medical Center) were inspirational, and were considered a great addition to ACMG 2018. Takeaways and key messages included: “treat every patient like patient No. 1, always keeping them at the center of the work, and us working as mediators rather than as a barrier”. Image credit: @DeniseCalvert13

Some statistical numbers were eye-opening and challenging as it comes as no surprise that the community currently lacks genetic counselors (GCs), with fewer than 4,000 GCs and 2,000s medical geneticists in the US which translates to one geneticist per ~60,000 people. With new genetic tests generated every day, GCs need to take on the role of mediators. New operational solutions were discussed to address this shortcoming, and as such Kaylene Ready proposed the exploration of chatbots as alternatives to GC service delivery. While certainly an interesting suggestion, we will have to see whether the field with its customers (i.e. patients) is ready to discuss challenging genetics findings with a computer. As a result, it was suggested to decouple Continue reading →

Genohm Aims to Hit the Sweet Spot With a Customizable SLIMS + ELN Solution for Lab Information Management

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For this month’s “Company Spotlight” blog series we are reviewing Genohm with an interview with Nick Beckloff, Director of US Operations at Genohm. Genohm is a 50-person company headquartered in Lausanne, Switzerland. I took this opportunity to learn more about Genohm, and SLIMS (Sample Laboratory Information Management System), their sample and data management software offering intended to address today’s challenges of managing the sample and data throughput in clinical, NGS, and other types of labs.

The following summarizes questions and answers from my dialogue with Nick Beckloff.

EB: Tell us more about Genohm – what need are you trying to address and what products/services do you offer?

NB:  Genohm’s mission is to reduce the complexity of life in the lab by offering a software package that distills the important aspects of a LIMS while providing functionality across many relevant spectra. We offer a flexible and customizable solution Continue reading →

Just Released – Our New Clinical NGS Process Report

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Palo Alto, CA, January 12, 2018 – enlightenbio LLC, today announced the publication of its Clinical NGS Process Report. This new report details the observations and learnings across the complex, multi-step informatics aspects following clinical NGS sample preparation and sequencing, and which includes data analysis, knowledge extraction, and clinical reporting of actionable findings. Market trends, including listing of major initiatives, merger and acquisitions, and a summary of patents are detailed within this report, while also highlighted are clinical customer/end-users’ unmet interpretation and knowledge extraction needs and challenges, and genetic testing lab preferences. Finally, an extensive comparison of solution providers in the SaaS and PaaS sector for the analysis and interpretation of clinical NGS data is included. The report is unique, in that it is not a predictive market research report, but rather builds on data gathered from many end-user interviews combined with an extensive analysis of the clinical NGS sector.

While this report does not intend to provide direct recommendations on commercial offerings, the deep-dive analysis is an insightful review to help clinicians, researchers, commercial entities, and investors choose the best partner for success.

For a limited time only, apply Promo Code 10OFFCLINICALNGS and get 10% off when purchasing the report – valid until February 14, 2018.

Download Table of Contents to learn more about the report specifics 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 →