Monthly Archives: February 2022

Companies Improve their Supply Chains with Artificial Intelligence – Logistics Viewpoints

Posted: February 28, 2022 at 7:57 pm

Machine Learning, a Form of Artifical Intelligence, Has Feedback Loops that Improve Forecasting

Many large enterprises use one form or another of a supply chain application to help manage their supply chains. Supply chain vendors have been touting their investments in artificial intelligence (AI) for the last several years. In the course of updating our annual research on the supply chain planning market, I talked to executives across the industry. Alex Pradhan, Product Strategy Leader John Galt Solutions, told me that all planning vendors have bold marketing around AI. But the trick is to find suppliers with field-proven AI/ML algorithms that have been delivered at scale.

Further, while artificial intelligence helps solve certain types of problems, Jay Muelhoefer the chief marketing officer at Kinaxis pointed out optimization and heuristics work better for other types of planning problems. This article, which is focused on the different types of artificial intelligence used and the types of problems they are solving, is aimed at helping practitioners cut through the hype.

Lets start with a definition: any device that can perceive its environment and takes actions that maximize its chance of success at some goal is engaged in some form of artificial intelligence (AI). AI can refer to several different types of math. But, in the supply chain realm, machine learning (ML) is where most of the activity surrounding artificial intelligence has been focused.

It is also worth pointing out, that based on this definition, not all forms of machine learning are particularly complicated. Planning applications dont work well if the master data they rely on is not accurate; this is known as the garbage in, garbage out problem. Artificial intelligence is beginning to be used to update the data. Lead times, for example, are a critical form of master data for planning purposes. Having an agent detect how long it takes to ship from a supplier site to a manufacturing facility, and then doing a running calculation on how the average lead time is changing, is trivial math. The agent technology is much more complicated than the math. Relying on humans to update this data has not worked at all well; people just dont want to do it.

But sometimes fixing the bad data problem is complicated. In process industries the supply chain models used for optimization are much more complex than those used in other industries. The processing units in an oil refinery, for example, operate at high temperature and high pressure. These constraints need to be understood. So, models for heavy process industries often include first principle parameters. First principles reflect physical laws such as mass balance, energy balance, heat transfer relations, and reaction kinetics. The first principles are important to understand yields, as well as the energy requirements for running the equipment.

AspenTech has developed in a process simulator which is tuned with real plant operating data. During development, the models automatically perform thousands of permutations and perturbations of the first principles model to create a large data set to which AI algorithms applied. The AspenTech models combine the classic first principles approach with the modern pure data-driven approach. Starting with a first principles model, according to AspenTech, improves accuracy significantly. They tell me, the model with either a first principles or pure data plus AI, the model accuracy would be in the 90-97% range. But hybrid models that combine first principles, data-driven models, and AI, they have 99+% accuracy.

A supply chain planning model learns when the planning application takes an output, like a forecast, observes the accuracy of the output, and then updates its own model so that better outputs will occur in the future.

When you look at machine learning this way, artificial intelligence for supply chain planning is nothing new. Machine learning has been used to improve demand forecasting since the early 2000s. But machine learning for demand forecasting is much better than it used to be. There are far more forecasts being made in far more planning horizons and at a greater degree of specificity today than 20 years ago. For example, forecasting how much of a particular product will be sold in a particular store is far more intensive than forecasting how many products in a product family will be sold in a region. This explosion in the number of forecasts would not be possible without the latest generation of machine learning. There were only a few SCP suppliers with mature capabilities in this area a few years ago. Since then, virtually every supplier I talked to in the process of updating this years Supply Chain Planning Market Analysis Study has said they are investing in this area.

One example of the value of machine learning in demand planning comes from Mahindra & Mahindra. Aniruddh Srivastava, Head of Demand and Supply Planning at Mahindra & Mahindra, said at Blue Yonders Icon user conference that artificial intelligence and machine learning algorithms are the cornerstone of their strategy. Through their partnership with Blue Yonder, Mahindra & Mahindra was able to increase forecast accuracy by 10%. A better forecast leads to carrying less inventory while maintaining or even improving service levels. The improvement in forecasting contributed to an increase in service levels by 10% while reducing inventory investment by 20%.

But that was pre-COVID. But after the pandemic hit their safety stock was increased by 30%. Post-COVID it was not about savings, Mr. Srivastava explained. The game changed to a global competition for the same set of raw materials. This division makes automotive spare parts, so the competition was to secure semiconductor chips.

During the pandemic, forecasting accuracy was terrible. Forecasting is based on the presumption that history repeats itself. As an E2open forecasting benchmarking report pointed out, for companies trying to predict demand in March of 2020 as the world was descending into lockdown and everything was being turned upside down, what happened in March of 2019 had little to no relevance.

But if there was any silver lining it was that companies that made use of planning systems that combined demand sensing the use of multiple, real-time signals (like sales in a particular store or shipments from a retailers warehouses to their stores) and machine learning, had significantly less error. And the companies that used these solutions, saw their forecasts improve much more quickly than traditional solutions.

In making demand forecasts, one can look at product history. An alternative is to look at customer behavior surrounding how clusters of customers buy these products. QAD Dynasys is one of several suppliers investing

One thing that is difficult to forecast are new product introductions. The way this forecasting is done is through the use of attributes. If you are looking at a purse, attributes would include the material it is made of, size, color, and other things as well. To the extent that one product is like another, it may be easier to forecast. But which attributes matter? Infor is using machine learning looking at attributes and past launches to make this determination. Solvoyo and Lily AI are using another form of AI, image recognition, to tackle this problem. Getting merchandisers to enter the attributes has not worked well. Merchandisers see this as an unimportant, dull task and they just dont take the time to do this properly.

One real trend ARC has seen this year, is the increasing investment supply chain planning suppliers are making to improve the ability of SCP to help companies reach their sustainability goals. Cyrus Hadavi, the CEO of Adexa, provides a good explanation for how SCP solutions can calculate the carbon footprint associated with a plan. The way this works is that every element in the supply chain is given a carbon index, absolute or relative. That is every machine, factory, DC, mode of transportation, supplier, product, material, etc. These indices then become attributes of these objects. Every time we plan and use any of these elements, the system can project the total carbon footprint of the projected plan. In addition to carbon emissions, these attributes can be used for other forms environmental and governance goals as well.

So, a plan can be produced that predicts the emissions. After a plan is executed, the actual emissions that occurred can be measured, and it is possible to see how close the plan came to what occurred. Just as a demand planning solution compares the forecast to what actually sold and uses machine learning to improve the machines forecasting capabilities, a similar feedback loop can exist with sustainability.

Artificial intelligence can also be used in supply and factory planning. But on the supply planning side it is not about using machine learning to select the right algorithms to improve the plans. When supply plans dont pan out it is less about the model than it is about a data quality issue or an unexpected occurrence. An example of an input issue would be, We thought it took 20 minutes to set up this machine to make product C, but it really takes 60 minutes when product A was made right before product C. An example of an unexpected occurrence would be a critical piece of machinery breaking down.

Machine learning is being used to predict machine breakdowns. But very few vendors are taking those alerts and automatically feeding them into their manufacturing planning solutions. AspenTech has probably done the most in this area. AspenTech, for example, is using predictive analytic inputs on when key machinery in a refinery will break down to allow alternative production schedules to be generated in a more autonomous manner. AspenTechs advantage is that they have both asset management (a solution that can use machine learning for the predictive maintenance alert) and the supply chain planning models those alerts can feed.

A less commonly used form of AI in supply chain applications is natural language processing (NLP). Googles Alexa uses NLP to understand a persons command and then play the music they want. There is a desire to use NLP to allow planners to tell a planning system what to do so they can focus more of their time on higher priority problems.

But Coupa and Oracle are also leveraging natural language processing for supplier risk assessment. Humans dont speak with a clarity that machines can understand. A company can go bankrupt, and a machine could be programmed to understand that. But on social media someone might say that a company is about to go belly up. Machines dont understand this type of unstructured data. NLP helps to make sense of these kinds of data. Oracles DataFox is accessing databases with important company information, but it also has web crawlers examining huge numbers of online news sites as well as social media to discover negative news about a company. That news could be an impending bankruptcy, unhappy customers, key executives leaving the company, or many other things. These events are turned into supplier scores, and if significant the score goes flagged in the Oracle procurement system. Now Oracle is working to connect these scores to the planning systems. At Coupa supplier risk is also flagged for single source or capacity constraints. This can then be leveraged by their supply chain design solution to improve risk mitigation.

Companies need to take machine learning driven demand-side predictions which are particularly good at granular short-term forecasts and adjust production accordingly. The closer in time a plans creation comes to the actual execution of an order, the more a planning system becomes an execution system. The idea is for supply planning application to digest a short horizon demand signals into meaningful plans by using machine learning to suggest courses of action for planners. These suggestions are based upon the way planners had previously solved the same kind of demand/supply disruption. However, this kind of AI does not work out of the box. The system observes planners actions over time and then learns to make the pertinent suggestions. QAD and Noodle.ai are among several suppliers working in this area.

In the last couple of years, RELEX Solutions has developed new capabilities for autonomous capacity balancing. In short, the AI algorithms can pull orders forward (for products with longer shelf-life) to level out the flow of goods into distribution centers and stores as well as to adhere to time-dependent capacity limits. Johanna Smros, Co-founder & Chief Marketing Officer at RELEX, points out the current difficulties in finding staff have really raised awareness of the value of being able to plan ahead to ensure availability and efficient use of human resources as well as to plan around this availability when it becomes a bottleneck in the supply chain.

Blue Yonder, in turn has developed a machine learning powered Dynamic Segmentation solution that automatically groups customers with similar fulfillment or procurement needs based on data changes, and then develops distinct supply chain operations to meet those specific requirements. This enables planners to provide differentiated service levels based on customer value and business parameters

While this article stemmed from research ARC is doing on the supply chain planning market, and most AI investments have been focused on planning applications, it is worth pointing out that AI investments are increasing in the supply chain execution realm as well. Companies like Oracle, Manhattan Associates, Koerber, and Blue Yonder, are all increasing the R&D in AI in their supply chain execution systems. A transportation system that applies machine learning to predict how long it will take a truck to make a delivery is one example of this. A warehouse management system that can digest a prediction of what ecommerce customers are apt to buy, and then drop the right work orders at the right time to the warehouse floor, is another example of this.

To sum it up, Madhav Durbha the vice president of supply chain strategy at Coupa Software said that artificial intelligence is becoming much more widely adopted due to progress occurring on several fronts at the same time. These include the development of new machine learning algorithms, computing power, big data analytics, and acceptance by industry leaders.

But remember, AI only fixes supply chains to a degree; this is not like waving a magic wand and seeing your supply chain problems suddenly vanish. Nevertheless, AI really is improving planning, and it is increasingly being used to improve order execution as well.

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Artificial Intelligence in Healthcare: Tomorrow and Today – ReadWrite

Posted: at 7:57 pm

It is a typically cold day in February and the peak of the flu season. Let alone the never-ending pandemic that seems to have been haunting this world forever. And it got me thinking can technology help battle all these nasty diseases and improve patient outcomes? And most importantly, will artificial intelligence have a hand in it? It seems so.

In 2021, weve reached another milestone in Artificial Intelligence adoption $6.9 billion of market size and counting. By 2027, the intelligent market in healthcare will grow to 67.4 billion. Hence, the future of AI in healthcare certainly looks bright, yet not serene.

Today, Ill walk you through the state of artificial intelligence in healthcare, its main application areas, and its current limitations. All these will help you build a holistic image of this technology in medical services.

Artificial Intelligence is now considered one of the most important IT research areas, promoting industrial growth. Just like the transformation of power technology led to the Industrial Revolution, AI is heralded today as the source of breakthrough.

Within the healthcare continuum, COVID-19 has accelerated investments in AI. Over half of healthcare leaders expect artificial intelligence (AI) to drive innovation in their organizations in the coming years. At the same time, around 90% of hospitals have AI strategies in place.

Now lets have a look at the top impacts of intelligent algorithms in medicine.

Today, only specific settings in clinical practice have welcomed the application of artificial intelligence.

Patients have been waiting for the deployment of augmented medicine since it allows for greater autonomy and more individualized care. However, clinicians are less encouraged because augmented medicine requires fundamental shifts in clinical practice.

Nevertheless, we already have enough AI use cases to assess its potential.

In most critical cases, the treatment prognosis depends on how early the disease is detected. AI-driven technology is currently used to amplify the accurate diagnosis of a disease like cancer in its earliest stages.

Machine learning algorithms can also process patient data from ECG, EEG, or X-ray images to prevent the aggravation of symptoms.

According to the American Cancer Society, 1 in every 2 women is misdiagnosed with cancer due to a high rate of erroneous mammography results. Hence, there is certainly an acute need for more accurate and effective disease identification. Mammograms are examined and interpreted 30 times faster with up to 99 percent accuracy with AI, reducing the need for biopsies.

This year, Alphabet has launched a company that uses AI for drug discovery. It will rely on the work of DeepMind, another Alphabet unit that has pioneered the use of artificial intelligence to predict the structure of proteins.

And its not the only instance of AI-enabled clinical research.

According to a Deloitte survey, 40% of drug discovery start-ups already used AI in 2019 to monitor chemical repositories for potential drug candidates. Over 20% leverage intelligent computing to identify new drug targets. Finally, 17% use it for computer-assisted molecular design.

The healthcare data explosion is something that has gained momentum in recent years. This sudden spike of data can be attributed to the massive digitalization of the healthcare industry and the proliferation of wearables.

With a single patient accounting for around 80 megabytes of data per year in imaging and EMH data, the compound annual growth rate of data is estimated to hit 36% by 2025.

Therefore, physicians need a fast and effective tool to make sense of this data flow to produce industry-changing insights. Predictive analytics is exactly one of those tools. In particular, AI-enabled data analytics helps uncover hidden trends in the spread of illness. This allows for proactive and preventive treatment, which further improves patient outcomes.

For example, the Centers for Disease Control and Prevention (CDC) implements analytics to predict the next flu outbreak. Using historical data, they assess the severity of future flu seasons which allows them to make strategic decisions beforehand.

The global pandemic wasnt an exception as well. Thus, The National Minority Quality Forum has launched its COVID-19 Index. The latter is a predictive tool that will help leaders prepare for future waves of coronavirus.

In the past year, labs performed over 2800 clinical trials to test life-saving medications and vaccines for the coronavirus. However, this large clinical trial field wasnt fruitful and has generated misleading expectations. But its old news.

The $52B clinical trials market has been long suffering from ineffective preclinical investigation and planning. One of the most difficult components of running clinical research is finding patients. However, many of these clinical trials particularly oncology trials have become more sophisticated, making it even more challenging to find the patients in a short window of time.

Artificial intelligence holds great potential for making the selection process faster. It can amplify the patient selection by:

As artificial intelligence enters the precision medicine landscape, it can help organizations benefit from precision medicine in multiple ways. First of all, personalized medicine may come in the form of digital solutions that allow one-to-one interaction with specialists without leaving the house.

According to statistics, there are currently over 53K healthcare apps on Google Play. Why are they so popular? Patients like the convenience that healthcare apps give. Patients can save money, get immediate access to tailored care, and have greater control over their health thanks to advancements in mobile healthcare technology.

Here are some encouraging statistics to demonstrate the importance of this tech boon:

Another face of personalization in healthcare is precision medicine. It is an innovative model of medical services that offers individualized healthcare customization through medical solutions, treatments, practices, or products tailored to a subset of patients. The tools underpinning precision medicine can include molecular diagnostics, imaging, and analytics.

However, precision medicine is impossible within the traditional medical approach. Instead, it requires access to massive amounts of data coupled with cutting-edge functionality. This data includes a wide span of patient data, including health records, personal devices, and family history. AI then computes this data and generates insights, enables the system to learn, and empowers clinician decision-making.

The clinical impact of machine intelligence holds great potential for disrupting healthcare, making it more accessible and affordable. However, the adoption of AI is currently at its early stages due to a great number of industry limitations. Some of them include:

Artificial intelligence in healthcare is a long-awaited disruption that has been ripening for quite a while. Its possibilities are virtually limitless and stretch from faster drug discovery to at-home diagnostics. In 2021, AI has seen significant growth due to the pandemic-induced crisis and acute need for automation. Although in its early stages, well see more of AI revolutionizing our healthcare sector.

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Artificial intelligence is only as ethical as the people who use it | TheHill – The Hill

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Artificial intelligence is revolutionary, but its not without its controversies. Many hail it as a chance for a fundamental upgrade to human civilization. Some believe it can take us down a dangerous path, potentially arming governments with dangerous Orwellian surveillance and mass control capabilities.

We have to remember that any technology is only as good or bad as the people who use it. Consider the EUs hailed blueprint for AI regulation and Chinas proposed crackdown on AI development; these instances seek to regulate AI as if it were already an autonomous, conscious technology. It isnt. The U.S. must think wisely before following in their footsteps and consider addressing the actions of the user behind the AI.

In theory, the EUs proposed regulation offers reasonable guidelines for the safe and equitable development of AI. In practice, these regulations may well starve the world of groundbreaking developments, such as in industry productivity or healthcare and climate change mitigation areas that desperately need to be addressed.

You can hardly go through a day without engaging with AI. If youve searched for information online, been given directions on your smartphone or even ordered food, then youve experienced the invisible hand of AI.

Yet this technology does not just exist to make our lives more convenient; it has been pivotal in our fight against the COVID pandemic. It proved instrumental in identifying the spike protein behind many of the vaccines being used today.

Similarly, AI enabled BlueDot to be one of the first to raise the alarm about the outbreak of the virus. AI has also been instrumental in supporting the telehealth communication services used to communicate information about the virus to populations, the start-up Clevy.io being one such example.

With so many beneficial use cases for AI, where does the fear stem from? One major criticism leveled at AI is that it is giving governments the ultimate surveillance tool. One report predicts there will be 1 billion surveillance cameras installed worldwide by the end of the year. There is simply not enough manpower to watch these cameras 24/7; the pattern-recognition power of AI means that every second or every frame can be analyzed. Whilst this has life-saving applications in social distancing and crowd control, it also can be used to conduct mass surveillance and suppression at an unprecedented scale.

Similarly, some have criticized AI for cementing race and gender inequalities with fears sparked from AI-based hiring programs displaying potential bias due to a reliance of historical data patterns.

So yes, this clearly shows that there is a need to bake the principles of trust, fairness, transparency and privacy into the development of these tools. However, the question is: Who is best suited to do this? Is it those closest to the development of these tools, government officials, or a collaboration of the two?

One thing is for certain: Understanding the technology and its nuances will be critical to advance AI in a fair and just way.

There is undoubtedly a global AI arms race going on. Over-regulation is giving us an unnecessary disadvantage.

We have a lot to lose. AI will be an incredibly helpful weapon when tackling the challenges we face, from water shortages to population growth and climate change. Yet these fruits will not be borne if we keep leveling suspicion at the technologies, rather than the humans behind them.

If a car crashes, we sanction the driver; we dont crush the car.

Similarly, when AI is used for human rights and privacy violations, we must look to the people behind the technology, not the technology itself.

Beyond these concerns, a growing crowd of pessimistic futurists predict that AI could, one day, surpass human general intelligence and take over the world. Herein lies another category mistake; no matter how intelligent a machine becomes, theres nothing to say that it would or could develop the uniquely human desire for power.

That said, AI is in fact helping drive the rise of a new machine economy, where smart, connected, autonomous, and economically independent machines or devices carry out the necessary activities of production, distribution, and operations with little or no human intervention. According to PwC, 70 percent of GDP growth in the global economy between now and 2030 will be driven by machines. This is a near $7 trillion dollar contribution to U.S. GDP based on the combined production from AI, robotics, and embedded devices.

With this in mind, the ethical concerns around AI are real and must be taken seriously. However, we must not allow these considerations to morph into restrictive, innovation-stopping interventionist policy.

We must always remember that it is the people behind the AI applications that are responsible for breaches of human rights and privacy, not the technology itself. We must use our democratic values to dictate what type of technologies we create. Patchy, ill-informed regulation in such a broad space will likely prevent us from realizing some of the most revolutionary applications of this technology.

Nations who over-regulate this space are tying their own shoelaces together before the starting pistol has even sounded.

Kevin Dallas, a former executive at Microsoft, is president & CEO of Wind River, a provider of secure intelligence software.

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Global Artificial Intelligence Education Technology Market Potential Growth, Share, Demand and Analysis of Key Players- Research Forecasts to 2027 to …

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The Global Artificial Intelligence Education Technology Market contains the latest market plans and new business developments. The actual expected results are assessed in the Artificial Intelligence Education Technology area, and the components that drive and drive the improvement of the business are included. Previous examples of progress, current progress, and new advanced continuous twists.

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Artificial Intelligence In Remote Patient Monitoring Market Look a Witness of Excellent Long-Term Growth | Cardiomo, Chronisense Medical, Medtronic …

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Region Included are: North America, Europe, Asia Pacific, Oceania, South America, Middle East & Africa

Country Level Break-Up: United States, Canada, Mexico, Brazil, Argentina, Colombia, Chile, South Africa, Nigeria, Tunisia, Morocco, Germany, United Kingdom (UK), the Netherlands, Spain, Italy, Belgium, Austria, Turkey, Russia, France, Poland, Israel, United Arab Emirates, Qatar, Saudi Arabia, China, Japan, Taiwan, South Korea, Singapore, India, Australia and New Zealand etc.

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Artificial Intelligence In Remote Patient Monitoring Market Look a Witness of Excellent Long-Term Growth | Cardiomo, Chronisense Medical, Medtronic ...

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CGView – Overview

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OverviewCGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, and as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file or a tab-delimited file. CGView converts the input into a graphical map (PNG, JPG, or SVG format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following:

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CGView - Overview

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Think of the Children? | Genomeweb – GenomeWeb

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In Nature News, Smriti Mallapaty describes the ethical debate surrounding care for the twin girls whose birth was reported by genome editing researcher He Jiankui.

He, who was jailed for his research, claims to have used CRISPR-Cas9-based gene editing to edit the CCR5 gene in twin embryos that were implanted in a woman who gave birth in 2018. A third genome-edited baby was born to other parents. CCR5 codes for a protein that HIV uses to make its way into human cells.

Two Chinese bioethicists would like to see a research center "dedicated to ensuring the well-being of the first children born with edited genomes," Mallapaty explains, though other experts "are concerned that the pair's approach would lead to unnecessary surveillance of the children."

While no other genome-edited babies have been reported, likely owing to He's punishment and backlash to the work in the scientific community, interest in the approach has persisted, she explains. In the meantime, experts are grappling with bioethical and practical issues surrounding the genome-edited children from their medical care and health testing to the potential social and psychological effects of their experience.

"Researchers say that the latest proposal, in a document by Qiu Renzong at the Chinese Academy of Social Science in Beijing and Lei Ruipeng at the Huanzhong University of Science and Technology in Wuhan, is the first to discuss how to manage the children's unique situation," Mallapaty writes. Among their recommendations, the pair calls for "regular sequencing of the children's genomes to check for 'abnormalities,' including conducting genetic tests of their embryos in the future."

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PacBio Supports SickKids to Investigate Use of HiFi Sequencing in Undiagnosed Genetic Conditions – Yahoo Finance

Posted: at 7:56 pm

Pacific Biosciences of California, Inc.

SickKids will use HiFi Sequencing to explore potential genetic causes of a range of medical and developmental conditions

MENLO PARK, Calif., Feb. 28, 2022 (GLOBE NEWSWIRE) -- PacBio, a leading provider of high-quality, highly accurate sequencing platforms, today announced it will be supporting The Hospital for Sick Children (SickKids) in Toronto, Canada in using HiFi whole genome sequencing (HiFi WGS) to potentially identify genetic variants that may be associated with medical and developmental conditions. Samples that will be examined using HiFi WGS were previously sequenced using short-read DNA sequencing technology, but still lack the identification of a disease-causing variant.

Even though more than 70 percent of rare disease, autism and intellectual disability have genetic causes, more than 50 percent lack an identified causative genetic alteration despite the use of microarrays, whole-exome or short-read whole-genome sequencing (srWGS).

SickKids will use HiFi WGS to analyze samples from research participants who are highly suspected to have a genetic condition but have not yet received a diagnosis despite previous genetic testing, including srWGS. The team will explore whether HiFi WGS can detect potential genetic causes for a range of conditions, such as autism spectrum disorder and congenital diseases.

HiFi sequencing allows us to investigate the entire genome in a way that is not accessible with other technologies, said Dr. Christian Marshall, Clinical Laboratory Director, Genome Diagnostics and Associate Director at The Centre for Applied Genomics (TCAG) at SickKids. We hope HiFi sequencing will enable us to take an exploratory look at classes of variation and large sections of the genome that were not detected previously, potentially showing unidentified causative genomic variants in these samples.

PacBios technology has been used to help genetic disease researchers explain mysteries where other technologies could not, said Edd Lee, Director of Human Genomics at PacBio. We are excited to support the SickKids team to hopefully uncover the answers they have been seeking.

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To learn more about the benefits of HiFi WGS in genetic disease, visit http://www.pacb.com/rare-disease.

About PacBioPacific Biosciences of California, Inc. (NASDAQ: PACB) is empowering life scientists with highly accurate sequencing platforms. The companys innovative instruments are based on Single Molecule, Real-Time (SMRT) Sequencing technology, which delivers a comprehensive view of genomes, transcriptomes, and epigenomes, enabling access to the full spectrum of genetic variation in any organism. Cited in thousands of peer-reviewed publications, PacBio sequencing systems are in use by scientists around the world to drive discovery in human biomedical research, plant and animal sciences, and microbiology. For more information, please visit http://www.pacb.com and follow @PacBio.

PacBio products are provided for Research Use Only. Not for use in diagnostic procedures.

Forward-Looking Statements This press release may contain forward-looking statements within the meaning of Section 21E of the Securities Exchange Act of 1934, as amended, and the U.S. Private Securities Litigation Reform Act of 1995, including statements relating to future availability, uses, accuracy, advantages, quality or performance of, or benefits or expected benefits of using, PacBio products or technologies; the suitability or utility of such products or technologies for particular applications or projects, including in connection with the SickKids collaboration; potential increases in variant detection and providing answers for rare disease samples, in the SickKids collaboration in particular and rare disease research in general; and other future events. Readers are cautioned not to place undue reliance on these forward-looking statements and any such forward-looking statements are qualified in their entirety by reference to the following cautionary statements. All forward-looking statements speak only as of the date of this press release and are based on current expectations and involve a number of assumptions, risks and uncertainties that could cause the actual results to differ materially from such forward-looking statements. Readers are strongly encouraged to read the full cautionary statements contained in the Companys filings with the Securities and Exchange Commission, including the risks set forth in the companys Forms 8-K, 10-K, and 10-Q. The Company disclaims any obligation to update or revise any forward-looking statements.

Contacts

Investors: Todd Friedmanir@pacb.com

Media:Lizelda Lopezpr@pacb.com

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PacBio Supports SickKids to Investigate Use of HiFi Sequencing in Undiagnosed Genetic Conditions - Yahoo Finance

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As New Zealand’s Omicron infections rise rapidly, genome surveillance is shifting gears – The Conversation AU

Posted: at 7:56 pm

Genomic sequencing has been a key tool throughout Aotearoas COVID-19 pandemic, with data generated here now part of the 8.5 million genomes shared globally.

It has helped us understand how cases arrived here and the extent of community outbreaks. It has also given us detailed insight into how the virus is transmitted from person to person, on a plane or quarantine facility.

As Omicron spreads rapidly across the country, it is important to consider how we best deploy genomics to achieve our public health goals. Which cases should we sequence and why? What is the role of wastewater when we know cases are already in our cities and regions?

Even as our testing and genomics capacity gets overwhelmed by the sheer number of cases, sequencing will continue to play an important role.

Firstly, we need to keep an eye open for new viral variants and keep track of those already circulating in the community. This is a core role of genomic surveillance and part of a global effort, with scientists around the world sequencing variants in their backyard.

Read more: How COVID-19 transformed genomics and changed the handling of disease outbreaks forever

One thing we are looking for is changes (mutations) in the virus that may affect its ability to transmit, evade our vaccines or immune defences, or cause even more serious disease. Particular scrutiny is given to mutations in the viral spike protein, on the outside of the virus, which allows it to latch onto cells and infect them.

The Pfizer vaccine we have used in Aotearoa essentially presents the body with a copy of the spike protein to train the immune system to create antibodies and other defences against it. Major changes in the spike might allow the virus to evade at least the first line of our immune defences as we have seen with the Omicron variant, which contains more than 30 different mutations in the spike protein.

With relatively few cases overall in New Zealand, and only the Delta variant that has persisted in the community for more than a few months, we have so far not seen any concerning new mutations or variants arise here. But small mutations or deletions in the viruss genetic code remain helpful for linking clusters and detecting new introductions into the community.

The majority of New Zealanders are now vaccinated, which means there is increasing pressure on the virus to escape our immunity. This is an arms race we have been playing with viruses for millennia. The game has changed somewhat as genomics allows us to watch viral evolution in real time.

By sequencing the virus from individual cases, we can tell exactly which variant the person has and, over time, we can detect patterns of variants rising in frequency or resulting in a more severe infection.

Currently, genomic surveillance tells us there is a mix of Omicron (including major variants BA.1, and BA.2) and a stubborn tail of Delta.

The BA.1 lineage was given an early boost at a wedding-related super-spreading event and now makes up 74% of Omicron cases. The remaining 26% of Omicron cases are BA.2 which was spread early on at the SoundSplash festival. In the last week, about 7% of cases sequenced were Delta. Without sequencing, we would be blind to this.

To maintain high-quality surveillance in the face of very high case numbers, we need to be selective in which samples we sequence and balance competing priorities.The top priority is the prevention of severe disease and there will be a focus on the genomes of cases in hospital. Overseas, many of the serious, hospitalised cases are Delta, not Omicron.

Some patients may have the misfortune of chronic COVID-19 infections. In such cases, multiple samples may be sequenced to see if the virus is changing within a single patient.

A leading hypothesis of how variants of concern such as Omicron and Delta have emerged is via chronically infected patients who act as an incubator for the virus. We need to continue monitoring patients with long-haul COVID.

We will also need to continue to monitor and sequence new cases that arrive at the border, either in MIQ or in recently returned travellers who test positive. Nearly all the genetic variation of SARS-CoV-2 we have seen in Aotearoa has been imported (as opposed to developed here), and this is a common pattern we see with other diseases such as influenza. By sequencing border cases, we get an early view of what we may need to prepare for.

Read more: Genomic sequencing: Here's how researchers identify omicron and other COVID-19 variants

Finally, to get a high-level view of cases and mutations, we sequence a random sample of cases across the country. Genomic sequences taken across time and space build a picture of which parts of the country are host to which variants and lineages. It is very much a case of know thy enemy.

Currently we are monitoring the areas where Delta is persisting. We can also monitor how the vaccine status of an individual affects the variant that is detected. Such data helps to build a picture of vaccine efficacy and population-level protection against a fast-changing virus.

The last piece of the genomic sequencing puzzle is wastewater testing for SARS-CoV-2. While sequencing from wastewater samples has been used for specific public health investigations in the past, low case numbers and quantities in most wastewater samples has made it difficult. Instead, wastewater testing has focused on using a sensitive method to allow for the early detection of the virus.

With the Omicron surge, we are now seeing an increase in both the number of positive wastewater samples and the amount of virus in those samples. This means we can use wastewater to indicate increasing or decreasing trends in cases at community level, and also to monitor known and new variants through sequencing and other tools.

In the weeks to come, there will be enough viral matter to make trends in wastewater data evident. In some cities, where regular sampling occurs, we will see viral wastewater loads trending up and down with case numbers. This information, along with regular case reporting, will inform the public about the relative risk of various regions. Such data may help people to understand the risks of travelling to a certain region or city.

Genomics remains a key tool in our pandemic management. There will be changes in how we use it, but it remains a core part of our surveillance toolkit. Prior to the genomics era, changes in the viral genetic blueprint were invisible to us. While many will dread another story about a new variant, we would be in a far worse position without this information.

If we step outside of our COVID-19 bubble for a second, the use of fast and affordable genomic technology in this pandemic also provides a glimpse of what genomic medicine may look like in the future but that is a discussion for another day.

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Massive Scale Genome Revolution: Changing the Rare Diseases Landscape – ETHealthworld.com

Posted: at 7:56 pm

by Dr Firoz AhmadThe landmark completion of the human genome project in 2003 and its subsequent refinement has undoubtedly marked the beginning of a new era for biomedical research. The human genome project helped us to understand the most accurate sequence of the 3 billion DNA base pairs that make up the human genome. With this development, we have witnessed a paradigm shift in which medicine became personalized, predictive and preventive especially in fatal disease like cancer and other chronic diseases. There has been growing interest in expanding these success stories to Rare diseases (RDs), which are often progressive, frequently devastating and life-threatening clinical conditions. Although RDs affect a limited fraction of individuals from the general population (1 in 5000 people or less in Indian context), in aggregate they represent a substantial challenge to global health systems.There are approximately 5,000 to 8,000 different rare diseases globally, and it comes in many forms and includes some cancers, auto-immune diseases, metabolic conditions, blood disorders, neurological disorders and inherited malformations. Available literature suggests that India is home to nearly 70 million affected people with rare diseases, and some of the common examples are primary immunodeficiencies, hemoglobinopathies, muscular dystrophies, Lysosomal storage disorders, Niemann-Pick Disease, Ethylmalonic Encephalopathy, familial hypercholesterolemia, Mucopolysaccharidoses type I and type II, Rhizomelic chondroplasia punctata type 1, pseudorheumatoid dysplasia, ichthyosis, dystrophic epidermolysis bullosa, sporadic acrokeratosis, Tay-Sachs disease, Von Willebrand disease, Werner syndrome, Spastic Paraplegia 79 and many more. Majority of these diagnosed RDs are so rare that it is extremely difficult to identify clinically, patient may need 7-8 medical consultations, and at times it takes several years to come to conclusive diagnosis (Fig-1). As far as the etiology of the RDs is concerned, the exact cause for many rare diseases remains unknown. Still, for a significant portion, the problem can be traced to mutations in a single gene (genetic origin).As these conditions are tough to recognize clinically, genetic and genomic testing have become the backbone of diagnostic modality in recent times. Identification of pathogenic DNA changes remained a big challenge in earlier days (late 70s), wherein basic information about the DNA sequence and genomic location of a abnormal gene had to be worked out through a tedious, time consuming and expensive laboratory process called cloning followed by first generation sanger sequencing of the cloned product. Technological progress in DNA sequencing spurred after 2003, with the introduction of first high-throughput sequencing (Next Generation Sequencing, NGS) technology by Roche in 2005, capable of detecting genetic variation with high precision and accuracy. In no time, NGS became the true game-changer and brought a complete Genome Revolution by offering the capability to read the entire genomes, rather than individual genes. This gave researchers the ability to identify potential disease-causing variants across the genome much more rapidly than had previously been possible. Last one and half decade has seen rapid progress in the NGS technologies in terms of sequencing chemistry, data output, longer read lengths and improved bioinformatics tools. This has significantly increased the outputs of sequencing data in the gigabase range per instrument run, resulted in much affordable cost compared to the traditional Sanger first-generation sequencing method, and at a much quicker pace. Today, broader multigene panels (checks few clinically relevant genes), whole exome sequencing (checks all the coding exons of the genome, WES), clinical exome sequencing (checks approx. 6000 genes known to cause human diseases, CES), and whole genome sequencing (checks all exons and non-coding regions of the genome, WGS), are the most preferred testing methodologies in RD diagnosis. Patients are now increasingly liberated from the long-standing diagnostic bottleneck. Many can receive a diagnosis in just 2-3 months using modern day genomics tools in comparison to 7-8 years of traditional way, with a precision that remains unparalleled in medicine.

Generally a referring doctor considers high end genomic testing, if a patient visits to his/her clinic with non-specific overlapping symptoms and unexplained illness, or known to have several affected family members, or couples who have undergone consanguineous marriage. Furthermore, many paediatricians prefer to do genomics testing if they see early disease onset in a child or repeated episodes of seizures in newborn babies. As depicted in (Fig-1), the strategy begins with collection of detailed clinical information of the patient and his/her family history. Based on the clinical suspicion and past knowledge on the molecular etiology of the suspected disorders, two different approaches are considered for the genetic screening. In case of clinically suspected but genetically characterized RDs, screening of known disease-associated candidate genes through a multigene targeted panel or Clinical exome based NGS approach is recommended.

Thanks to this recent technological advance in genomics, the number of Mendelian diseases that have a known genetic cause went from 1,257 in 2001 to 4,589 in 2022 . The Genome Revolution has opened the door for true personalization in disease management, and it is now truly improving peoples health. With several success stories emerging globally including India, genomics will become a mainstay for diagnosis of rare genetic diseases in the near future.

by Dr Firoz Ahmad, Section-Head, Molecular Pathology, SRL Diagnostics, Mumbai

(DISCLAIMER: The views expressed are solely of the author and ETHealthworld does not necessarily subscribe to it. ETHealthworld.com shall not be responsible for any damage caused to any person / organisation directly or indirectly.)

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Massive Scale Genome Revolution: Changing the Rare Diseases Landscape - ETHealthworld.com

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