Blueprint Genetics Aims to Automate and Improve Clinical Interpretation Processes with Software That Will Change the Industry

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This month’s “Company Spotlight” takes a closer look at Blueprint Genetics, a rare disease diagnostics company on a mission to deliver the highest quality standards for genetic diagnostics.

Tero-Pekka Alastalo, Chief Medical Officer of Blueprint Genetics discussed with us in detail Blueprint Genetics’ offerings, its approach to developing high quality diagnostics standards, and its vision to connect physicians across the globe to help them identify and address unique rare disease cases faster.

Blueprint Genetics is a company that started with an intellectual property, the OS-Seq™ Technology, developed at Stanford by a Finnish researcher. The company thus is bi-continental with headquarters both in the US (San Francisco) and in Finland (Helsinki). The 150-person company was founded in 2012 by Juha Koskenvuo, Samuel Myllykangas, Tero-Pekka Alastalo, and Tommi Lehtonen. Blueprint to date has secured $26.3M in funding which will be used to get closer to Blueprint Genetics’ vision to bring the use of genetic information to mainstream healthcare with uncompromised high quality, by elevating the sequencing technology and clinical data interpretation platform to the next level with increased efficiency and level of automation.

The following summarizes questions and answers from my dialogue with Tero-Pekka Alastalo.

EB: Tell us more about Blueprint Genetics. What is the history of Blueprint Genetics from when you started to today?

Tero-Pekka Alastalo: Originally Blueprint Genetics was a Stanford University spin-off. The company was founded around an innovative new Stanford DNA sequencing technology, the OS-Seq™ Technology (Nature Biotechnol., 2011), developed by a Finnish post-doc (Samuel Myllykangas). I myself am a medical doctor by training with expertise in pediatrics and pediatric cardiology. We got very excited about this innovative targeted sequencing technology and its opportunities in diagnostics. Since our initial career plans were to return back to Finland to continue our clinical and academic careers, we founded Blueprint Genetics in Finland in 2012. With Stanford being the place where the technology was developed and owned, we knew from day one that Stanford will always be a very close partner.

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JP Morgan 2019 – Drug pricing, drug development, immunotherapy, cancer moonshot, cell/gene-therapy, …

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As we all know the JP Morgan Healthcare conference is an invitation-only conference. For this reason, I have summarized various announcements for the purpose of this review. As we have witnessed in the past, exciting announcements happen here in San Francisco around or just before this annual conference, and some of the news spark what eventually will become the big trends throughout the year. One could say it is a window to what is just around the corner in 2019.

Several commercial tool providers and diagnostic companies used this venue to announce their strategies or to provide a status update:

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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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2018: Population Studies, Immunotherapy, CRISPR, Genomic Medicine,…2019

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2018 was full of significant developments in the life sciences, precision medicine, genetics, and genomics sector. Highlights and notable news included various technological advancements, new clinical applications of next-generation sequencing, success in population studies, genetics moving into the clinic, artificial intelligence and machine learning investments and potentials, immunotherapy further establishing itself as the leading weapon to attack cancer, the CRISPR technology being under fire, and more.

The significance of these developments is further manifested by clinical omics taking shape, hospitals adopting new applications, and testing and treatments coming into play that are based on next-generation sequencing or omics data. The results speak a clear language: improved diagnostic tests, and more precise therapeutics.

Here a few highlights – not an all-inclusive summary – of what made 2018 so exciting. Find a more complete list of 2018 news on the enlightenbio Industry News site.

Population studies taking shape

Various population studies/initiatives took shape this year, as demonstrated with projects such as…

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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.

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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 →

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.

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