Massive, cheap computer power – often combined with AI – has facilitated much of the recent progress in understanding and working against cancer. Accordingly, it’s good to see that research against cancer will be one of the uses for the world’s most powerful supercomputer, which is headed for  the federal government’s Argonne Labs in Chicago’s western suburbs. To be operational in 2021, the supercomputer will operate at exaFLOP scale. What that heck does that mean? It means a quintillion calculations per second. What is a quintillion? It is a thousand raised to the power of six. It is a million raised to the power of five. In other words, it’s a really big number. It is a 1, followed by 18 zeros. See the chart for more. Amazing.

Hopefully this incredible machine will help researchers against cancer fulfill  Jeff Huber’s call to “find a better way” to take on cancer. Who is Jeff Huber? He is a University of Illinois computer science grad who., among other things, led the teams that developed Google Ads, Google Maps and Google Earth. He also is highly motivated against because his wife died in her 40s because of a colon cancer no one saw coming. He provided the commencement talk for the 2016 graduating class at the U of I, and drew a standing ovation after he aired the “find a better way” theme as a mantra for many problems facing societies, including cancer.

Mr. Huber presently serves as a member of the Board of Directors for Grail. Created in 2016, the company’s mission, as in seeking the holy grail, is to make it possible to find cancer early on by sifting through cells in blood to find and identify cancer cells long before a tumor manifests itself.  Grail  is one of a small handful of companies working to bring this type of “liquid biopsy” to mass markets.  Taking advantage of relatively cheap and massive computing power is part of the equation for getting things done against cancer. I’m looking forward to Chicago taking on a larger role in research against cancer, building on decades of marvelous computing work at the University of Illinois. See generally Transforming Science – “Petascale Day” – Celebrating “In Silico” Research and the Blue Waters Supercomputing Project at the National Center for Supercomputing Applications at the University of Illinois.

The March 18, 2019 press release from the Department of Energy is pasted below.

______________________________________________________________________________________________

CHICAGO, ILLINOIS – Intel Corporation and the U.S. Department of Energy (DOE) will build the first supercomputer with a performance of one exaFLOP in the United States. The system being developed at DOE’s Argonne National Laboratory in Chicago, named “Aurora”, will be used to dramatically advance scientific research and discovery. The contract is valued at over $500 million and will be delivered to Argonne National Laboratory by Intel and sub-contractor Cray Computing in 2021.

The Aurora systems’ exaFLOP of performance – equal to a “quintillion” floating point computations per second – combined with an ability to handle both traditional high performance computing (HPC) and artificial intelligence (AI) – will give researchers an unprecedented set of tools to address scientific problems at exascale. These breakthrough research projects range from developing extreme-scale cosmological simulations, discovering new approaches for drug response prediction, and discovering materials for the creation of more efficient organic solar cells. The Aurora system will foster new scientific innovation and usher in new technological capabilities, furthering the United States’ scientific leadership position globally.

“Achieving Exascale is imperative not only to better the scientific community, but also to better the lives of everyday Americans,” said U.S. Secretary of Energy Rick Perry. “Aurora and the next-generation of Exascale supercomputers will apply HPC and AI technologies to areas such as cancer research, climate modeling, and veterans’ health treatments. The innovative advancements that will be made with Exascale will have an incredibly significant impact on our society.”

Argonne's Aurora supercomputer will launch in 2021.
Aurora is expected to be completed by 2021. | Photo: Argonne National Laboratory

“Today is an important day not only for the team of technologists and scientists who have come together to build our first exascale computer – but also for all of us who are committed to American innovation and manufacturing,” said Bob Swan, Intel CEO.  “The convergence of AI and high-performance computing is an enormous opportunity to address some of the world’s biggest challenges and an important catalyst for economic opportunity.”

“There is tremendous scientific benefit to our nation that comes from collaborations like this one with the Department of Energy, Argonne National Laboratory, and industry partners Intel and Cray,” said Argonne National Laboratory Director, Paul Kearns.  “Argonne’s Aurora system is built for next-generation Artificial Intelligence and will accelerate scientific discovery by combining high-performance computing and artificial intelligence to address real world problems, such as improving extreme weather forecasting, accelerating medical treatments, mapping the human brain, developing new materials, and further understanding the universe – and that is just the beginning.”

The foundation of the Aurora supercomputer will be new Intel technologies designed specifically for the convergence of artificial intelligence and high performance computing at extreme computing scale. These include a future generation of Intel® Xeon® Scalable processor, a future generation of Intel® Optane™ DC Persistent Memory, Intel’s Xcompute architecture and Intel’s One API software.   Aurora will use Cray’s next-generation Shasta family which includes Cray’s high performance, scalable switch fabric codenamed “Slingshot”.

“Intel and Cray have a longstanding, successful partnership in building advanced supercomputers, and we are excited to partner with Intel to reach exascale with the Aurora system,” said Pete Ungaro, president and CEO, Cray. “Cray brings industry leading expertise in scalable designs with the new Shasta system and Slingshot interconnect. Combined with Intel’s technology innovations across compute, memory and storage, we are able to deliver to Argonne an unprecedented system for simulation, analytics, and AI.”

For more information about the work being done at DOE’s Argonne National Laboratory visit their website HERE.

The $15 billion or so Quebec class action verdict in Canada against tobacco companies was upheld late on Friday in a 440 page opinion, in French. It will interesting to watch the reactions of stock markets, and learn more as commentaries and English language translations are distributed. The Eye on the Trials blog is an excellent source of information about the case.

 

 

It’s world cancer day, a reminder of the biggest global terrorist and driver of much litigation.

The chart is from: Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer
statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36
cancers in 185 countries. CA Cancer J Clin. 2018 Nov;68(6):394-424. doi:
10.3322/caac.21492.

More and more molecular data will arrive over the next few years; some of it will be very valuable for more deeply understanding when and how diseases arise. Consider, for example, the fact that genes matter a great deal because they contain the instructions for producing proteins, but we need to know more about actual outputs of proteins coded for by the genes. The proteins, after all, are the actual doers of the work to promote health or fight off disease. Accordingly, it is useful to know which inherited or somatic mutations completely cut off production of a protein (null mutations), while other mutations may have a range of effects, from very little to material.

Today, researchers can answer many questions about the effect of mutations in some genes, and some combinations of genes. However, researchers seek to know more about the protein production results that arise from different combinations of inherited mutations.  With that in mind, consider the disease-related knowledge, questions and hypotheses that will arise from the following collaboration, which is described in a December 14, 2018 press release from SomaLogic and deCode.

___________________________________________

Largest-ever Protein Measurement Study Enhances deCODE’s Efforts in Basic Research, Drug Discovery and Novel Protein-based Diagnostics

deCODE genetics, an Amgen subsidiary, and SomaLogic, Inc. today announced a collaboration that brings together SomaLogic’s expertise in human proteins with deCODE’s expertise in human genetics. The collaboration combines deCODE’s rich data sets with SomaLogic’s leading protein measurement capabilities to enhance the understanding of how human disease and health are mediated through proteins to influence health outcomes.

“I am excited to see what deep proteomic analysis will add to what we already know about human health based on our study of genetics,” said Kári Stefánsson, M.D., Dr. Med., founder and chief executive officer of deCODE genetics. “SomaLogic’s ability to measure thousands of proteins brings a whole new dimension to our efforts, and we look forward to seeing the results.”

Under the collaboration agreement, SomaLogic will analyze up to 40,000 deCODE samples with the proprietary SOMAscan® assay, which can rapidly measure the levels of 5,000 proteins in each sample across a wide range of concentrations. deCODE will use the assay data for therapeutic drug discovery and development. SomaLogic will use the assay results and related clinical information to further develop clinical applications of the SOMAscan assay in an effort to improve health management.

“This collaboration with deCODE gives us an exciting opportunity to work with one of the most highly characterized and understood datasets in the world, as well as with world-class genomic and pharmaceutical scientists,” said Stephen Williams, M.D., chief medical officer at SomaLogic. “We are undertaking together the largest protein study ever performed — over 200 million individual protein measurements — to gain substantial new knowledge about normal and disease biology across many common and rare conditions.”

Specific details of the collaboration were not disclosed.

###

deCODE Contact
Jon Gustafsson
T: +354 664 1905
jon@decode.is

SomaLogic Contact 
Laura S. Mizoue, Ph.D.
Communications Specialist
T: 720 417 7509
lmizoue@somalogic.com

About deCODE genetics
Based in Reykjavik, Iceland, deCODE is a global leader in analyzing and understanding the human genome. Using its unique expertise and population resources, deCODE has discovered genetic risk factors for dozens of common diseases. The purpose of understanding the genetics of disease is to use that information to create new means of diagnosing, treating and preventing disease. deCODE is a wholly-owned subsidiary of Amgen.

About SomaLogic
SomaLogic seeks to empower a healthier world by delivering actionable health-management insights for every seeker and enabler of human health. These essential insights, which are provided through a global network of partners and users, are derived from SomaLogic’s unique ability to measure changes in thousands of individual human proteins over time with high precision, sensitivity and throughput. For more information, visit www.somalogic.com and follow @somalogic on Twitter.

Forward Looking Statement
This news release contains forward-looking statements that are based on the current expectations and beliefs of deCODE and its affiliates. All statements, other than statements of historical fact, are statements that could be deemed forward-looking statements, including statements regarding improvements in scientific understanding and drug discovery and development.  No forward-looking statement can be guaranteed and actual results may differ materially from those deCODE and its affiliates project. Results may be affected by clinical and regulatory developments and their research, testing and other operations are subject to extensive regulation by domestic and foreign government regulatory authorities. Discovery or identification of new product candidates or development of new indications for existing products cannot be guaranteed and movement from concept to product is uncertain; consequently, there can be no guarantee that any research and testing will lead to the identification of any particular product candidate or new potential indication for an existing product or aid in their development, or that the development of a particular product candidate or development of a new indication for an existing product will be successful and become a commercial product.

Today is the perfect day to buy a copy of “Cancer Rights Law: An Interdisciplinary Approach.” Why. Because today is the ABA’s annual cyber sale, with 40% off for law books and other written materials. This 2018 book was written  by the leaders of Triage Cancer, working with the ABA for publication.  Triage Cancer is a national not for profit that educates health professionals and patients regarding the entire range range of rights applicable during and after cancer. See https://triagecancer.org/.  It’s a wonderful group I am proud to serve as a member of the board and as a pro bono advocate for persons facing cancer-related issues. The authors are two smart, experienced pragmatic and compassionate lawyers, Monica Fawzy Bryant and Joanna Fawzy Morales. The book is online at the ABA – here. If you are thinking about taking on pro bono projects involving cancer, this book is one of a kind and comprehensive.

Age of exposure to toxins is receiving increasing attention from researchers. Below, the abstract from an interesting study of arsenic drinking water exposures in Chile.

https://academic.oup.com/aje/article-abstract/187/11/2297/5063615#.W98xc7qmSq8.email

“Abstract

Arsenic in drinking water is known to cause cancer and noncancer diseases, but little is known about its association with age at exposure. Here, we investigated age at arsenic exposure and mortality in Antofagasta, Chile, 30螔years after a distinct period of very high water arsenic concentrations (1958). We calculated standardized mortality ratios (SMRs) comparing Antofagasta with the rest of Chile for 2001by sex and age at potential first exposure. A remarkable relationship with age at first exposure was found for bronchiectasis, with increased risk in adults 30螔years after exposure being confined to those who were in utero (SMR = 11.7, 95% confidence interval (CI): 4.3, 25.4) or aged 1蝶years (SMR = 5.4, 95% CI: 1.1, 15.8) during the high-exposure period. Increased SMRs for lung, bladder, and laryngeal cancer were evident for exposures starting at all ages, but the highest SMRs were for exposures beginning at birth (for bladder cancer, SMR = 16.0 (95% CI: 10.3, 23.8); for laryngeal cancer, SMR = 6.8 (95% CI: 2.2, 15.8); for lung cancer, SMR = 3.8 (95% CI: 2.9, 4.9)). These findings suggest that interventions targeting early-life arsenic exposure could have major impacts in reducing long-term mortality due to arsenic 30螔years after exposure ends.” 

It’s good to see more lawyers focused on genomics as related to causation in mass tort cases. A group from Goldberg Segalla just wrote about the topic as part of a broader paper on alternative causation issues. The article was published in Mealey’s Asbestos; it is: Defense Strategies For Alternative Causation Arguments In Asbestos Case,  33-14 Mealey’s Litig. Rep. Asb. 31 (Aug. 29, 2018). The article also is online here at Asbestos Case Tracker.  

Some scientific findings provide both opportunities and risks for litigants in mass tort cases. The point is highlighted by a new paper by Panou and colleagues published in mid- August in the Journal of Clinical Oncology. The paper concludes that a significant proportion (12%) of patients with malignant mesotheliomas carry inherited (germline) mutations in cancer-associated genes, especially in peritoneal mesotheliomas. Overall, 24 germline mutations were identified in 13 cancer-associated genes from a cohort of 198 persons with mesothelioma. The subjects of the study were mainly persons treated at the University of Chicago during 2016-17.

The next few weeks include multiple events at which one can expect there will be discussion of the Panou paper and other topics related to genetics, asbestos and cancers of the lung: