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DNA Extraction 4 Point Guide: Extracting Excellence

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DNA extraction and purification is a vital step involved in several molecular biology and genomics-based research methods. This is because it determines the quality of your samples for downstream experiments. Without high quality, pure DNA samples to work from, researchers run the risk of getting erroneous results in their subsequent investigations. In this article we break down what is involved in this process and four of the biggest challenges that face researchers when attempting to extract DNA from their samples.

DNA extraction involves isolating sufficient amounts of genomic/plasmid DNA from samples (which are often precious and/or irreplaceable). After you have extracted DNA from your samples it is not yet ready for experimentation, a purification step is also necessary. Purifying your samples is crucial since it reduces the contaminants (lipids and proteins) present in your DNA samples that can compromise your research and reduce their “shelf-life” for future experimentation.

A simplified workflow for DNA extraction:

Lyse your cell/tissue samples using the most appropriate method for your samples. This could include mechanical disruption, chemically treating cells or enzymatic digestions.

Once samples are lysed, nucleic acids are isolated from contaminants using a suitable buffer solution and are either filtered, centrifuged or magnetically cleared.

The soluble fraction of the lysate is then treated to obtain purified DNA. One common method involves the addition of magnetic beads that have a matrix coating that binds to DNA present the lysate fraction.

The magnetic beads, now bound to DNA, are then removed and washed with a solution that removes lipids and unwanted proteins to purify the samples.

A charge is applied to the magnetic beads that changes their polarity and separates the DNA collected from the beads, the magnetic beads are removed leaving purified samples.

DNA Extraction performed on Perkin Elmer Chemagic 360

What are the challenges facing DNA extraction?

Most commercial labs require DNA for their downstream applications such as PCR and molecular cloning. However, they may also have limited supplies of cell/tissue samples which means that optimizing the extraction from their limited resources becomes key to successful downstream applications. The four biggest challenges to overcome in this process can be largely summarized as:

  1. The need for automation
  2. Employing high-throughput solutions
  3. Saving time
  4. Lack of expertise

Automation

Labs that are scaling up, or looking to scale up, can turn to automation to streamline their experiments and increase data output. The same principle can be applied to this process since the advantages of automation are hard to argue with. By selecting a platform such as Perkin Elmer’s Chemagic 360 instrument, researchers can step away from manually extracting DNA from samples and save time whilst minimizing the number of human errors seen in these workflows. Automation is costly however, since not only are you having to pay high prices to outright purchase the automated platform, but there are also lab space concerns and the extra overhead involved such as maintenance and annual service fees.

High-throughput solutions

Similarly, labs that are scaling up or ones that deal with large numbers of samples inevitably require platforms with High-throughput solutions to keep up with their increasing sample count. A platform that can deal with large volumes of samples will also almost always be an automated one and so the two features are complimentary. Taking a look at Perkin Elmer’s Chemagic 360 platform as an example, the platform is capable of being able to process 12x 10ml samples, 24x 2ml samples or 96 well plates with 400ul volumes with ease. The platform’s ability to handle a wide range of volumes means that it can be used as a “one-stop shop” for DNA extraction since it means one instrument can handle a wide variety of sample types. This saves time for researchers since they only need to become familiar with one platform, however this optimization requires intensive training and experience to be invested by individuals and teams.

Saving time

This process can take hours of active and passive work by researchers. In many cases researchers actively spend hours extracting and purifying samples between overnight incubation periods. Saving time is another important feature of automated, high-throughput platforms. Typically, a researcher spends 3 hours of overall “hands-on time” to extract DNA from large sample volumes such as 12x 10ml samples of blood. For the same number and volume of samples, automated platforms can perform the process in under 2 hours. Moreover, for samples with volumes of 400ul or below, it can take up to 6 hours to extract by hand, whereas an automated platform can successfully achieve this goal in just over an hour. Saving time in this manner allows researchers to focus on other aspects of their research as well as allowing them to start experiments which require purified DNA, much faster.

Lack of expertise

Not all samples can be treated the same way. Even though most cell/tissue samples can have DNA extracted from them easily and using automated platforms, there are always exceptions. Samples derived from mouse tails for example sometimes require phase separation steps to be completed which means employing methods that require “salting out” DNA. Even if you have samples that can be worked with easily, a batch of cells/tissue that has not been optimally stored or have even undergone some degradation will likewise require to be salted out in order to obtain pure DNA. The question must be addressed: Is it better to optimize methods to salt out DNA yourself or is it smarter to outsource the whole process to a company who can deliver processed samples on-time and efficiently.

DNA extraction at Sampled

With decades of experience and a success rate of over 99.9% for DNA extraction, the Sampled team are ready to accept your samples no matter how large or small your sample volumes and quantities are. We have multiple automated, high-throughput platforms such as Perkin Elmer’s Chemagic 360 and Qiagen’s Qia Symphony instruments that can take multiple different sample types and volumes depending on your needs. By outsourcing your needs to us, you can spend more time on the research that matters to you and not have to sacrifice bench space and costs towards scaling up lab processes.

Our experts are ready to take any questions you may have or discuss bespoke DNA extraction workflows with you, for more information click here

Managing success: How sample management can make or break a business

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It goes without saying that executing accurate and reproducible scientific research is at the heart of any successful research group or biotech. However, as research progresses so inevitably does the number of cell/tissue samples increase from a manageable level to thousands, or even hundreds of thousands of samples. At a certain point a limit is reached whereby the number of samples that must be stored or managed simultaneously becomes too much to handle internally. Having an endless sea of cells in a spreadsheet, or worse, multiple spreadsheets that are each updated without proper cross-communication, could easily lead to samples being misplaced. How academic groups and businesses manage their ever-increasing numbers of samples from various studies invariably becomes a hurdle to overcome for their continued success.

Why rigorous sample management matters

When academic groups and scaling biotech companies grow, the obvious hurdle that they must overcome is how to scale their sample management appropriately. This means at a certain point in time, it is no longer feasible for them to rely on one or more scientists to spend ever increasing amounts of time barcoding, labeling and digitally storing the information on a spreadsheet. What if the spreadsheet isn’t updated correctly? What if the file becomes corrupted and information is lost? These are frighteningly common situations that could spell disaster as precious samples that cannot be replaced become unidentifiable forever.

Not only is there an increasing amount of time dedicated to correctly labelling, sorting and storing samples, the time and resources dedicated to sample processing also increases greatly too. For example, blood samples would need to be fractionated into constituent components, including peripheral blood mononuclear cells, plasma or serum and red blood cells. Each fraction would then have to be cryopreserved under controlled conditions and stored. Likewise, for DNA and RNA samples extracted from tissues (e.g., blood) concentration, purity and identity must be determined prior to storage. These bioprocessing steps require more time and resources as the number of samples increases.

These are just a few reasons many companies and research groups turn to Sampled to manage and store samples on their behalf. Sampled utilizes LIMS software to ensure that each time a sample is handled, analyzed or stored, the sample is scanned via its barcode and the activity is logged. Tracking the chain of custody from the moment a sample is picked up from a client’s lab to the moment it is stored in a freezer ensures full transparency and great precision in real time.

Navigating the maze of shipping samples

It is well known that sample handling errors almost always occur in the field, this can be because a phlebotomist has mislabeled a blood sample, for example. It is therefore necessary to have the staff and resources to be able to understand how these errors occur as well as what the regulatory and customs agencies of various countries require for efficient shipping. Most scaling businesses simply cannot dedicate the required staff or time to deal with these inevitable hiccups which is where Sampled can help. Since we have trained staff on hand, we take care of all shipping and handling to remove the headache of paperwork from businesses so they can focus on what they do best. Our staff prepare customized kits for clients so that they simply fill the pre-barcoded sample vessels and ship them in the appropriate cryovessel we provide. Using our LIMS system, we can ensure that the correct samples arrive at the right place at the right time. At each stage the samples are scanned to ensure a clear chain of custody which is crucial for certain clients such as those looking to capture this data for clinical trials.

In short, Sampled can make a real impact by correctly managing and even storing client’s samples using properly trained staff and LIMS software. In doing so, researchers focus on the important research that matters, instead of tracking down lost samples or wasting time on the phone talking to customs agents.

If you would like to contact one of our experts about how Sampled provide sample management solutions that are tailor-made to your research, click here

Published Research Shows Initial Results from SARS-CoV-2 Surveillance Studies Support U.S. Public Health Initiatives

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INNOVATIVE RESPONSE SUPPORTS FUTURE RESPONSES AGAINST SIMILAR PANDEMIC THREATS

  • First results from the CDC SARS-CoV-2 U.S. variant surveillance program to be published
  • Positive COVID samples sequenced for variant surveillance in general public
  • Samples processed using industry first EUA saliva collection & assay methodology for SARS-CoV-2

PISCATAWAY, N.J. – April 26th, 2022: Infinity BiologiX LLC d/b/a Sampled, a next generation SMART Lab, and co-authors report results from the CDC SARS-CoV-2 variant surveillance program.

In May 2020, Sampled received the first Saliva based EUA for industry leading COVID-19 testing and has tested over 12 million samples to date. In March of 2021, the Centers for Disease Control and Prevention contracted with Sampled and other large commercial diagnostics labs to sequence the viral genome of SARS-CoV-2 positive patient samples across the U.S.  Sampled has sequenced over 100,000 SARS-CoV-2 genomes as part of this program. In the recent peer reviewed study published and co-authored by Goswami and Sheldon et al in BMC Infectious Disease, entitled ‘Identification of SARS‑CoV‑2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program’ the authors highlight the importance of sequencing platform, sample collection methods and RT-PCR results in guiding variant surveillance efforts.

“These surveillance studies evaluating genetic changes of SARS‑CoV‑2 have been identified as critical by the CDC and impacts many aspects of public health including transmission, disease severity, diagnostics, therapeutics and vaccines. Working with industry leading sequencing technologies and protocols such as the Illumina COVIDSeq™ were critical to support these initiatives.” Said Shareef Nahas, Chief Scientific Officer at Sampled and the corresponding author.

“This research shows the value of the scientific community coming together to find innovative solutions in response to events that impact public health. As an organization we are focused on the storage, management, analysis, research and transport of biological samples through our Sampled SMART Labs concept to make it faster and easier for health innovators to improve human health.” Said Robin Grimwood, Chief Executive Officer, Sampled.

The study is now available publicly and can be downloaded directly from the BMC Infectious Diseases website https://rdcu.be/cL6fu. This research marks an important contribution to future responses to similar pandemic level threats to global public health.  It is the first publication from the CDC SARS-CoV-2 U.S. variant surveillance program.

About Sampled:

Sampled is a next-generation laboratory that unlocks the valuable data in any biological sample. Through our integrated Sampled SMART Lab, we can Store, Manage, Analyze, Research and Transport biological materials, offering partners a seamless solution for all research samples. Our vision is a world where we make it faster and easier for health innovators to improve human health, Sampled SMART Labs mission is to be the lab behind every transformative health innovation. Sampled is headquartered in Piscataway, N.J. with labs across the US and Europe and partner labs in the Netherlands, China and Australia.

Infinity BiologiX LLC, Roylance Stability Storage Limited and Roylance Scientific Limited are doing business as Sampled.

For more information, please visit www.sampled.com  Media Contact: Mike Thurogood Mike.Thurogood@sampled.com

Autism Acceptance Month

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April is Autism Acceptance Month, starting with Autism Awareness Day on April 2nd. On March 4, 2021, The Autism Society of America made an important verbiage change – what was once Autism Awareness Month is now officially known as Autism Acceptance Month.

Autism is one of the leading developmental disabilities in the world, affecting 1 in 44 people, and if diagnosed by age 4, children are 50 times more likely to receive services and care that they need. As it is a spectrum disorder with many varying behaviors and symptoms, the care needed is unique to the individual’s needs. This is why Autism awareness, and most importantly acceptance, is so important – those with autism are able to lead full and rich lives with their diagnoses. The Autism Society strives “to create connections, empowering everyone in the Autism community with the resources needed to live fully,” and has been for 57 years. This is their 4th year in a row promoting the #CelebrateDifferences campaign, aiming to inform, educate, and connect those in need with the appropriate resources to live a full life. The Autism Society of America website is a wealth of resources, so if you’re looking to get involved, donate, or promote Autism Acceptance within your own community, they are a great place to start: autismsociety.org/autism-acceptance-month.

Key Autism Stats

  • Defined as “Spectrum Condition” as it has a certain set of behaviors that affect different individuals to varying degrees
  • Affects 1 in 44 children in the US according to CDC studies
  • Can be diagnosed as early as age 2, most are diagnosed after age 4
  • ⅓ of autistic children also have an intellectual disability
  • 31% of children with autism have an intellectual disability, 25% are in the borderline range, 44% have IQ scores in the average to above average range 
  • Affects all people, across ethnic and socioeconomic groups, though minorities tend to be diagnosed later and less often
  • 40% of people with autism are nonverbal
  • Nearly half “wander” or “bolt from safety”
  • Nearly 28% have self-injurious behaviors – headbanging, arm biting, skin scratching
  • Boys are 4 times as likely to develop autism as girls their age. Recent research suggests girls show signs of autism differently than boys, possibly leading to a lower rate of diagnosis.
  • Children who are diagnosed with autism by age 4 are 50x more likely to receive services
  • No known cure, but treatments are available to reduce symptoms
  • “Autism” derives from the Greek word “autos” meaning self – “Autism” is defined as “alone”
  • Research indicates genetics are involved in the majority of autism cases
Forwards, Faster.

Sampled working with key Autism organizations

Here at Sampled, we are immensely proud to be able to support two of the leading research centres that investigate the genetic causes of autism. Sampled initially began working with Autism Speaks in 1998 and then began working with The Simons Foundation in 2007 and have since maintained close ties with both groups.

The Simons Foundation established the Simons Foundation Autism Research Initiative (SFARI) with a mission to improve the understanding, diagnosis and treatment of autism spectrum disorders by funding innovative research of the highest quality and relevance. With Sampled’s labs, the Simons Simplex Collection (SSC) was developed as the gold standard of collecting and safely storing thousands of DNA samples associated with detailed phenotypic data from parents and children. In an effort that continues to this day, this collection of samples has enabled researchers to identify a number of genes that have the potential to yield valuable insights into the causes of and potential therapies for autism.

By working closely with Autism Speaks, Sampled was able to participate in the launch of the Autism Genetic Research Exchange (AGRE). AGRE is an collection of DNA samples processed by Sampled that have been sequenced and analyzed by researchers around the world. It is the largest private, open-access repository of clinical and genetic information dedicated to help autism research. Research on the samples in these two collections resulted in the publication of hundreds of papers advancing our understanding of the genetic components in autism and related behavioural disorders.

If you are interested in the work we do in Autism or other developmental disabilities, reach out to a member of our team today here.

Autism Society:

-National Today:

-Autism Speaks:

-AGRE:

-Simons Foundation:

Infinity BiologiX becomes Sampled

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Sampled

PISCATAWAY, N.J. – Date April 5th, 2022: Today Infinity Biologix (IBX) and Roylance Pharma announced the rebrand of both organisations as “Sampled”.

Sampled is a next-generation laboratory that unlocks valuable data from any biological sample. By focusing on the genetic causes of common, complex diseases, Sampled aims to discover diagnoses, treatments and, eventually, cures. Through its integrated “SMART Labs” services, the company can Store, Manage, Analyze, Research and Transport biological materials, offering partners a seamless solution for all research samples.

Robin Grimwood, Sampled Chief Executive Officer, said: “At Sampled, we play a vital role in improving human health by offering the quality, speed and scale our partners need to develop and bring products to market faster. With our proven technology and deep expertise, Sampled aims to be the SMART lab behind every new transformative health innovation.”

Since commercializing outside of Rutgers in 2020, the company has rapidly expanded its capabilities and partnerships, while launching several ground-breaking new products. In May of 2020, the company developed the first COVID-19 test utilizing saliva, for which it received FDA emergency use authorization and became the first company to offer at-home collection with this methodology. In 2021, the company acquired Roylance Pharma, a leader in biomaterial expertise, expanding its footprint with a UK hub to better service Europe.

Amit Bhalla, Sampled Chief Financial Officer, said: “In the last two years, we drove incredible growth across our core services while also demonstrating our ability to quickly scale up during the COVID-19 crisis. The rebrand to Sampled has helped us further integrate our services and laying a strong foundation to continue investing in expanding our capabilities and international presence.”

The Sampled SMART Labs approach puts partner’s samples at the center, supported by five fully-integrated categories of service: Storage, Management, Analysis, Research and Transport. Throughout the lifecycle, samples are handled with utmost integrity and trust and partners have access to a global network of experts and specialists.

Aaron Venables, Sampled Chief Commercial Officer, said: “I’m enormously proud to bring the Sampled SMART Labs proposition to our existing and new clients, offering an unparalleled level of integrated, global service in support of health innovation. As a partner that genuinely understands their challenges, we are here to do the heavy lifting so clients can do what they do best – bring their products to market, faster.”

Sampled’s deep industry expertise – the executive team alone holds 180 years of cumulative life sciences experience – has enabled the company to stay at the cutting edge of test design and innovation.

Isabella Britton, Head of People, said: “Our people set Sampled apart. We pride ourselves on a deep bench of scientists and subject matter experts who share an unparalleled dedication towards improving human health. This rebrand further focuses our work on our ultimate mission, while helping ensure we continue to develop and attract the finest talent in our industry.”

About Sampled:

Sampled is a next-generation laboratory that unlocks the valuable data in any biological sample. Through our integrated “SMART Lab” services, we can Store, Manage, Analyze, Research and Transport biological materials, offering partners a seamless solution for all research samples. Our vision is a world where we make it faster and easier for health innovators to improve human health, with a mission to be the SMART Lab behind every transformative health innovation. Sampled is headquartered in Piscataway, N.J. with labs across the US and Europe and partner labs in the Netherlands, China and Australia.

Infinity BiologiX LLC, Roylance Stability Storage Limited and Roylance Scientific Limited are doing business as Sampled.

For more information, please visit www.sampled.com 

Media Contact: Mike Thurogood Mike.Thurogood@sampled.com  

Don’t delay your research: How outsourcing sample analysis could lead to your next breakthrough

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With laboratory automation becoming easier to access and more commonplace in pharmaceutical companies as well as academic groups, the need for quick and robust sample analysis has never been higher. Concurrently, as scientific fields become more and more interdisciplinary, the breadth of equipment and expertise must also increase to meet the demand. This means investigators and group leaders face difficult decisions: Should they invest in expensive equipment, that requires resources and expertise which they may not possess, or should they outsource this part of their research?

Benefits to outsourcing sample analysis

We understand that for both academic groups and growing businesses, the cost of buying NGS systems can run into millions of dollars. Worse still, the service contracts for such systems can cost anywhere from $100,000-200,000 per year. This can put smaller groups/businesses in a difficult position since a branch of their research could be underpinned by NGS studies they cannot afford for example. For this reason, more and more researchers turn to Sampled to carry out bespoke, customer-orientated analytical assays using the same instruments and systems the researchers cannot afford to purchase themselves. By working with Sampled, researchers save themselves from enormous costs and time since they can focus on the research they do best and still get the answers they seek. We work with clients to understand exactly what type of sample analysis they wish to conduct and generate customised reports that feedback the data in a manner that best suits the researcher.

However, this isn’t the only advantage to outsourcing sample analysis to Sampled. Some researchers simply lack the manpower to analyse the growing number of samples that are piling up in their labs. An example of this is how a number of groups representing the States of New Jersey and Minnesota, among others, approached Sampled during the pandemic in order to identify positive COVID biosamples through PCR and store these samples for future studies. The Center for Disease Control (CDC) awarded Sampled one of six contracts in the US to analyze COVID-positive samples by NGS to identify specific variant strains. The raw data from these studies was then uploaded to CDC’s database for further study. By outsourcing this sample analysis to Sampled the CDC saved precious time and resources in combating the virus and were able to learn about the emergence and spread of variant strains faster than if they had conducted the research internally.

A better way to validate research?

Outsourcing sample analysis also acts a third-party validation service which helps to confirm reproducibility of new methodologies or experimental results. As previously mentioned, Sampled utilizes cutting edge technologies from numerous companies including Illumina, PacBio, 10X genomics etc. This allows us to tailor-make any assays using specific pieces of equipment the researcher selects, giving them all the benefits of conducting cutting-edge research, without the overhead costs or in-house expertise.

Whether it be due to costs, lack of expertise, lack of manpower or simply to validate results acquired by another party, Sampled has the infrastructure, the equipment you desire and the customisation capability to take your research to the next level. If you wish to discuss your research needs with us, feel free to contact us here.