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

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.

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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

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

Can 2017 top 2016?

In the life sciences, 2016 brought us many significant developments, and thank goodness, it’s mostly exciting and great to talk about those in length. I am talking here about technological advancements, the many new applications next-generation sequencing is seeing, genetics moving into the clinic, precision medicine finding its mark in oncology and beyond, immunotherapy establishing itself as the leading weapon to attack cancer, and more.

The significance of these developments is further manifested with clinical omics taking shape, hospitals adopting new applications, and testing and treatments that are based on next-generation sequencing, omics data, and more. 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 2016 so exciting.

2016

Next-generation sequencing matures

In 2016, we’ve reached a stage where the limitations of next-generation sequencing is not at the level of sequence data generation anymore, rather the limitations are associated Continue reading

The Need to Address the Ensuing Data Explosion is Imminent

Clearly, the DNA sequencing technology has matured and is continuously being optimized for performance while becoming increasingly affordable, thus opening an era of reliable and foreseeable quality data growth demanding high computational resources and data storage. With the rise of varied applications, be it in cancer research, infectious diseases, and other therapy areas, and with the launch of large initiatives (e.g. The Precision Medicine Initiative (PMI)), the need to address the ensuing data explosion is imminent.

Oncology is the dominant sector that currently benefits from next-generation sequencing followed by applications in inherited and rare disease understanding, infectious disease, the microbiome, and others. It is expected that soon, agriculture will also benefit from the technological developments that currently help propel both biomedical research and the clinical sector. Continue reading

Just Released – Our New NGS Data Analysis & Interpretation Ecosystem Analysis Report

Palo Alto, CA, August 22, 2016 – enlightenbio LLC, today announced the publication of its NGS Data Analysis & Interpretation Ecosystem Analysis Report. This new report details an extensive ecosystem analysis of 25 commercial companies in the NGS data analysis and interpretation space, market trends, unmet needs and challenges. 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 ecosystem analysis.

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This comparative ecosystem analysis of key commercial data analysis and interpretation tool providers reveals a range of capabilities that uniquely address both secondary and tertiary sequence data analysis needs. At first glance, the value propositions and communication of capabilities may seem overlapping or similar. However, a deeper analysis clearly uncovers substantial differences in the product characteristics related to analysis and interpretation, data management, data sharing and collaboration, reporting of findings, compliance and security mechanisms, and type of content made available for meaningful knowledge extraction.

While this report does not intend to provide direct recommendations to end-users for Continue reading

The Biologists and Clinicians Still Require Hand-Holding When it Comes to Sequence Data Analysis and Interpretation

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Bioinformaticians are a bottleneck and at high demand. They are hard to find, hire, and retain, while typically being an expensive investment. This realization is not new, but has escalated with the sequence data explosion and now puts a huge challenge on commercial tool providers to build optimal analysis and interpretation solutions that will be embraced by biologists and clinicians, i.e. the non-computational scientists. Almost all commercial tool providers state that they offer a solution that is easy to use and requires minimal upfront training. However, reality shows that this is not generally holding true, and biologists/clinicians are still overwhelmed with most offerings in the field. If a solution is too “simplified,” it can’t provide the capabilities required to do a high-quality analysis on complex data. On the flip side, if the solution is too complex, it cannot be deployed and effectively used without training, which is what the field is experiencing. Furthermore, Continue reading

Repositive Wants to Overcome Data Analysis and Sharing Challenges to Facilitate the Advancement of Science

Repositive-logoLast month I had a chance to meet Fiona Nielsen, CEO of Repositive, when she was visiting San Francisco for the BlackBox Connect program. I took this opportunity to learn more about Repositive, the platform the company has built, its intended application, and why data sharing is so important. This blog addresses genomic data questions related to data sharing, challenges encountered with analysis and sharing platforms, and what Repositive is focusing on to mitigate these issues.

The following summarizes questions and answers from my dialogue with Fiona Nielsen.

EB:  What are some of the biggest challenges when it comes to working with genomics data both in the research and the clinical setting, and what are suggested solutions to address these challenges? What are the promises and challenges of sharing clinical and research genomics data?

FN: All research in a data-intensive science is challenging and hard work. There are high demands put on research data management and efficient analysis tools. In addition, within genomics linked to studying human genetic diseases, you have to deal with the extra Continue reading