Tag Archives: NGS

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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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 →

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 →

Diploid Tackles the Challenges of Rare Disease Diagnostics

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enlightenbio is excited to introduce our new “Company Spotlight” blog series where we will review some of the exciting work that is currently ongoing in up- and-coming companies. Moving forward we plan on reviewing and profiling some of these companies and their products on a regular basis.

At ASHG, I had a chance to meet with Peter Schols, CEO of Diploid, a small seven person company located in Leuven, Belgium. I took this opportunity to learn more about Diploid, and Moon, the software the company has built, and its intended application to help diagnose rare disease.

The following summarizes questions and answers from my dialogue with Peter Schols.

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

PS: Diploid is a privately funded, rare disease diagnostics company founded in 2014. Diploid started with offering an interpretation service, helping our customers analyze rare disease sequence data. Customers send us NGS data of a patient together with a description of the phenotype, and we deliver a report listing the most likely candidate variants. We focus exclusively on rare disease testing and currently support the Continue reading →

AHSG 2017 Roundup – A Shout Out to the Women in Science

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This year’s ASHG conference in Orlando was kicked off with an inspiring plenary talk by the ASHG President Dr. Nancy Cox, celebrating diversity, inviting refugees to join the human genetics research mission, and longing for the day when contributions by female scientists will be as valued and as acknowledged as those of men. She concluded with highlighting contributions of women to genetics and science thus far, and by sharing her desire that the future will have a more positive outlook in this regard.

This powerful opening talk was followed by a presentation by Bill Gates and a conversation between Bill Gates and Dr. Francis Collins on global health and genomics. Gates highlighted different projects the Bill & Melinda Gates Foundation had been Continue reading →

Bio-IT 2017 – Data Security, Data Sharing, Data Access, Data Integration, Data …

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The 15th annual Bio-IT conference – with the theme “Building a global network for precision medicine by uniting the Bio-IT community” – clearly had as its underlying theme the many different aspects of data that need to be addressed to make precision medicine a true reality, as echoed throughout the many talks and discussions. This was reflected in both the keynotes, as well as the panel discussions that focused on data regulations, security, and getting patients to feel good about sharing their data. The first hackathon launched by Bio-IT World had the focus on FAIR [findable, accessible, interoperable, and reproducible] data. Many commercial announcements or recent advancements in artificial intelligence revolved around new and improved data analysis solutions. This year’s Best in Show award selections featured Starfish Storage’s Starfish V4, SciBite LaunchPad, SolveBio’s Operating System for Molecular Information, Dana Farber Cancer Institute / The Hyve’s MatchMiner v1.0, and Seven Bridges’ CAVATICA.

Coinciding with Bio-IT were a number of major announcements as listed below: Continue reading →

AGBT 2017, a Mix of Single Cell Genomics, Long Read Technology, and More

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This year’s meeting followed the true and tested script of past AGBT installments. Similarly to last year’s conference, the technological advancements seemed to have slowed and somewhat resulting in no breakthrough announcements, while a larger emphasis was put on the scientific talks. Software analysis announcements related to secondary and tertiary sequence data analysis solutions were almost not present.

images_agbt2017

Interestingly, the much liked software demo session was mostly reduced to three open source demonstrations and a demonstration of Optalysys, a light-based sequence alignment technology. Too bad, as the software demo part provided a great opportunity to get up to speed with the latest developments across the many commercial solutions Continue reading →

PMWC 2017 Silicon Valley: Data sharing, privacy, and security

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pmwc2017sv-logoThis year’s Precision Medicine World Conference (PMWC 2017 Silicon Valley) was comprised of many exciting sessions and presentations (almost 300 speakers across four tracks) in the area of next-generation sequencing, different diagnostics applications, precision medicine, big data analysis, the microbiome, large cohort studies, biobanking, and data interpretation/knowledge extraction. In addition to providing a great set of overview talks on latest developments and achievements across the health care sector, in pharma, and related to regulatory aspects, this latest rendition of PMWC also featured a government presence (the former FDA Commissioner Dr. Robert Califf and the former Cancer Moonshot Task Force Director Greg Simon) and Elizabeth Baca (Health Advisor to Governor Brown’s Office of Planning and Research) among others that shared with the audience their respective Continue reading →