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

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, …

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

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

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

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

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

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

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

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

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

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

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

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