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SPRI Bead-Based Purification: Optimizing PCR Cleanup for Superior NGS Results
In molecular biology, precision and purity are everything. Whether you’re prepping for next-generation sequencing (NGS), cloning, or qPCR, the quality of your DNA directly influences your results. PCR cleanup is one of those essential steps that can make or break your downstream applications. And when it comes to PCR cleanup, Solid Phase Reversible Immobilization (SPRI) bead-based purification is the method of choice for researchers worldwide.
SPRI bead-based methods combine efficiency, scalability, and versatility in one simple workflow. They’ve become indispensable for high-throughput labs, small academic teams, and commercial genomic facilities alike. In this article, we’ll explore how SPRI beads work, best practices for optimizing PCR cleanup, and how cost-effective solutions like MagBio Genomics’ HighPrep™ PCR Clean-Up Kit are transforming the purification landscape.
What is SPRI Technology?
SPRI stands for Solid Phase Reversible Immobilization. This method uses paramagnetic beads that bind nucleic acids in the presence of polyethylene glycol (PEG) and salt. The DNA binds to the beads, while unwanted components like salts, primers, enzymes, and nucleotides remain in the solution.
Key benefits include:
Size-selective binding
High recovery rates for DNA fragments ranging from 100 bp to >10 kb
Simple workflows that replace spin-column protocols
Automation-friendly—ideal for 96- and 384-well plates
The Role of PCR Cleanup in NGS Workflows
NGS library preparation involves several steps that require precise DNA handling. After amplification, it’s critical to remove unwanted materials such as leftover primers, free nucleotides, and enzymes. These contaminants can:
Inhibit adapter ligation
Interfere with quantification and normalization
Reduce overall sequencing quality
SPRI beads simplify this process. Add the beads, bind the DNA, wash away the contaminants, and elute clean DNA that’s ready for the next step.
Key Advantages of SPRI-Based PCR Cleanup
1. Efficiency
SPRI workflows reduce the number of steps and eliminate centrifugation. This makes them ideal for high-throughput pipelines and minimizes user error.
2. Scalability
From a handful of samples to thousands, SPRI bead protocols are easily scaled and automation-compatible.
3. Customizability
You can fine-tune your purification with bead-to-sample ratios:
1.8x for total DNA recovery
0.6x to exclude smaller fragments (<300 bp)
0.8x to retain larger DNA for long-read workflows
How to Optimize SPRI Bead-Based PCR Cleanup
Choose the Right Bead-to-Sample Ratio
This is perhaps the most important variable. Use:
1.8x for complete fragment retention
0.8x to remove primer dimers and small artifacts
Avoid Overdrying the Beads
After ethanol washing, beads should be air-dried until no visible liquid remains. Overdrying can make it difficult to elute DNA and decrease recovery.
Use Fresh Ethanol
Old or cold ethanol can decrease the wash efficiency and lead to poor DNA purity.
Elute in the Right Volume
Using 20–50 μL of elution buffer ensures efficient recovery while keeping the DNA concentration high enough for downstream use.
Common Applications in Molecular Biology
SPRI beads aren’t just for NGS. Their versatility spans across:
PCR cleanup: Removing enzymes, primers, dNTPs
Cloning: Preparing inserts for ligation
Sanger sequencing: Enhancing read clarity by removing noise
qPCR: Ensuring template purity for quantification
cDNA synthesis and RNA-seq: Purifying double-stranded cDNA
HighPrep™ PCR Clean-Up Kit: A Reliable SPRI-Based Solution
MagBio Genomics’ HighPrep™ PCR Clean-Up Kit is designed to deliver all the benefits of SPRI bead-based purification at a more accessible cost.
Key Features:
Compatible with all major NGS platforms
Comparable or better recovery than AMPure XP
Validated for manual and automated protocols
Stable shelf life and consistent batch quality
HighPrep™ beads use the same SPRI chemistry as traditional solutions but come at a fraction of the cost, making them perfect for cost-sensitive labs without sacrificing performance.
Automation and High-Throughput Compatibility
As research scales up, automation becomes essential. HighPrep™ PCR Clean-Up is compatible with liquid-handling platforms like:
Thermo Fisher KingFisher Flex
Hamilton Microlab STAR
Tecan Fluent and Evo
These integrations allow genomic core facilities to streamline operations and reduce sample-to-sample variation.
Testimonials and Case Studies
“Switching to HighPrep™ not only cut our cleanup costs in half, but also gave us flexibility with automation. We saw no drop in yield or data quality.” — Senior Scientist, Biotech Startup
“We routinely process 10,000 samples a month, and HighPrep™ has been instrumental in keeping our workflow smooth and cost-effective.” — Genomics Core Facility, UK
Sustainability and Supply Chain Reliability
Unlike spin columns, SPRI beads reduce plastic usage. HighPrep™ PCR Clean-Up is also offered in bulk formats to minimize packaging waste. And unlike some competitors, MagBio ensures consistent availability with a stable supply chain.
Cost Comparison

When to Use SPRI-Based Purification
SPRI bead cleanup is ideal when you need:
Fast and reproducible DNA purification
High throughput compatibility
Flexible size selection for fragment trimming or retention
Reliable performance for sensitive applications like NGS
Final Thoughts
SPRI bead-based purification has changed the game for PCR cleanup and beyond. The simplicity, accuracy, and scalability of this approach make it indispensable in modern molecular biology. With cost-effective and high-performing kits like HighPrep™ PCR Clean-Up from MagBio Genomics, it’s easier than ever to streamline your workflow, reduce costs, and get consistent, high-quality results.
Upgrade Your PCR Cleanup Workflow
Explore the power of SPRI-based purification with the HighPrep™ PCR Clean-Up Kit. It’s the perfect solution for efficient, cost-effective DNA purification in any lab setting.
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Introducing our game-changing Automated RNA Clean-up Kit! Our cutting-edge technology harnesses the power of nano-magnetic beads, ensuring high-quality and cost-effective RNA extraction and purification. Perfect for researchers, our kit simplifies the process, saving you time and effort.
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DNA and RNA Sample Preparation Market – Insights
DNA and RNA sample preparation provides accessibility to nucleic acids in a natural form and removes unwanted contaminants. DNA and RNA sample preparation process has become highly refined and multi-national companies are focusing on faster and accurate products. Market players are focused on launching automated workstations to enable faster, refined, and consistent DNA and RNA extraction. These workstations are compatible with various kits, reagents and lab ware.
The global DNA and RNA sample preparation market is estimated to account for US$ 1,541.3 Mn in terms of value in 2018 and is expected to reach US$ 2,327.7 Mn by the end of 2027.
Global DNA and RNA Sample Preparation Market: Drivers
Increasing funding in life science research is expected to boost growth of the global DNA and RNA sample preparation market over the forecast period. For instance, in February 2020, Purdue-affiliated Amplified Sciences LLC and Brightlamp Inc. received approvals for up to US$ 250,000 each from the Purdue Foundry Investment Fund for R&D in life science technologies.
Moreover, collaborative efforts and initiatives to identify therapies for difficult-to-treat illnesses is also expected to aid in growth of the market. For instance, in February 2020, Cellectricon (Molndal), a Sweden–based pharmaceutical company collaborated with StressMarq Biosciences, a Canada-based life sciences reagents supplier, for R&D in neurodegenerative diseases.
North America region held dominant position in the global DNA and RNA sample preparation market in 2018, accounting for 40.6% share in terms of value, followed by Europe.
Global DNA and RNA Sample Preparation Market: Restraints
High cost of products and low investments are expected to hinder growth of the global DNA and RNA sample preparation market. Researches in the life science sector are complex and have uncertainties in terms results. This in turn increases R&D and product cost and deters users from investing in such expensive products.
Moreover, challenges in handling RNA are also expected to limit growth of the market. The presence of RNases is a major challenge in isolating, manipulating, or analyzing RNA. RNases are extremely stable and very active nucleases capable of degrading the RNA.
Global DNA and RNA Sample Preparation Market: Opportunities
Using quality control tools to obtain information on nucleic acid quantification, integrity, and sizing of fragments in next-generation sequencing is expected to offer lucrative growth opportunities for players in the market. Quality control tools can aid in maintaining clean samples that are free from contaminants.
Moreover, market players can also focus on digitalization in the life science sector through adoption of technologies such as wearable devices and artificial intelligence. Digital technology can be used for routine tasks such regulatory filings.
DNA sample preparation segment in the global DNA and RNA sample preparation market was valued at US$ 570.9 Mn in 2018 and is expected to reach US$ 932.0 Mn by 2027 at a CAGR of 5.5% during the forecast period.
Market Trends/Key Takeaways
The market is witnessing emergence of new field of scientific investigation in the form of RNA interference (RNAi). It is a biological process targeted mRNA molecule are neutralized to inhibit gene expression or translation in RNA molecules.
Major companies are focused on R&D in COVID-19 virus. For instance, in February 2020, Covaris, Inc. launched two new kits for viral RNA extraction from nasal or throat swab sample collection devices that include truXTRAC Viral RNA Extraction kit using Puritan Swabs and truXTRAC-PCR Direct Viral RNA Extraction kit.
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Global DNA and RNA Sample Preparation Market: Competitive Landscape
Major players operating in the global DNA and RNA sample preparation market include, Agilent Technologies, Inc., Becton, Dickinson and Company, Bio-Rad Laboratories Inc., DiaSorin S.p.A, F. Hoffmann-La Roche, Miroculus, Inc., Illumina, Inc., PerkinElmer, Inc., QIAGEN, Sigma Aldrich Corp., Tecan Group AG, and Thermo Fisher Scientific, Inc.
Global DNA and RNA Sample Preparation Market: Key Developments
Major players in the market are focused on launching new products to expand their product portfolio. For instance, in February 2020, Miroculus, Inc. launched Miro Canvas, a system that can simplify, automate, and miniaturize complex protocols such as next generation sequencing library preparation, at the Advances in Genome Biology and Technology conference held in the U.S.
Major players in the market are also focused on adopting collaboration strategies to expand their product portfolio. For instance, in March 2020, Fluidigm Corporation, a provider of microfluidics technology, partnered with Next Gen Diagnostics, a provider of automation in pathogen bioinformatics, under which the later will use the Fluidigm Juno system for pathogen whole genome sequencing sample preparation in exchange of milestone payments starting in 2020 and additional revenue to Fluidigm Corp.
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DNA and RNA sample preparation provides accessibility to nucleic acids in a natural form and removes unwanted contaminants. DNA and RNA sample preparation process has become highly refined and multi-national companies are focusing on faster and accurate products. Market players are focused on launching automated workstations to enable faster, refined, and consistent DNA and RNA extraction. These workstations are compatible with various kits, reagents and lab ware.
The global DNA and RNA sample preparation market is estimated to account for US$ 1,541.3 Mn in terms of value in 2018 and is expected to reach US$ 2,327.7 Mn by the end of 2027.Increasing funding in life science research is expected to boost growth of the global DNA and RNA sample preparation market over the forecast period. For instance, in February 2020, Purdue-affiliated Amplified Sciences LLC and Brightlamp Inc. received approvals for up to US$ 250,000 each from the Purdue Foundry Investment Fund for R&D in life science technologies.
We do offer sample of this report. Kindly go through the follow information in order to access sample copy:- https://www.coherentmarketinsights.com/insight/request-sample/3620
Moreover, collaborative efforts and initiatives to identify therapies for difficult-to-treat illnesses is also expected to aid in growth of the market. For instance, in February 2020, Cellectricon (Molndal), a Sweden–based pharmaceutical company collaborated with StressMarq Biosciences, a Canada-based life sciences reagents supplier, for R&D in neurodegenerative diseases.North America region held dominant position in the global DNA and RNA sample preparation market in 2018, accounting for 40.6% share in terms of value, followed by Europe.High cost of products and low investments are expected to hinder growth of the global DNA and RNA sample preparation market. Researches in the life science sector are complex and have uncertainties in terms results. This in turn increases R&D and product cost and deters users from investing in such expensive products.
Moreover, challenges in handling RNA are also expected to limit growth of the market. The presence of RNases is a major challenge in isolating, manipulating, or analyzing RNA. RNases are extremely stable and very active nucleases capable of degrading the RNA.
Using quality control tools to obtain information on nucleic acid quantification, integrity, and sizing of fragments in next-generation sequencing is expected to offer lucrative growth opportunities for players in the market. Quality control tools can aid in maintaining clean samples that are free from contaminants.
Moreover, market players can also focus on digitalization in the life science sector through adoption of technologies such as wearable devices and artificial intelligence. Digital technology can be used for routine tasks such regulatory filings. DNA sample preparation segment in the global DNA and RNA sample preparation market was valued at US$ 570.9 Mn in 2018 and is expected to reach US$ 932.0 Mn by 2027 at a CAGR of 5.5% during the forecast period.The market is witnessing emergence of new field of scientific investigation in the form of RNA interference (RNAi). It is a biological process targeted mRNA molecules are neutralized to inhibit gene expression or translation in RNA molecules.
Major companies are focused on R&D in COVID-19 virus. For instance, in February 2020, Covaris, Inc. launched two new kits for viral RNA extraction from nasal or throat swab sample collection devices that include truXTRAC Viral RNA Extraction kit using Puritan Swabs and truXTRAC-PCR Direct Viral RNA Extraction kit.
Major players operating in the global DNA and RNA sample preparation market include, Agilent Technologies, Inc., Becton, Dickinson and Company, Bio-Rad Laboratories Inc., DiaSorin S.p.A, F. Hoffmann-La Roche, Miroculus, Inc., Illumina, Inc., PerkinElmer, Inc., QIAGEN, Sigma Aldrich Corp., Tecan Group AG, and Thermo Fisher Scientific, Inc.
Major players in the market are focused on launching new products to expand their product portfolio. For instance, in February 2020, Miroculus, Inc. launched Miro Canvas, a system that can simplify, automate, and miniaturize complex protocols such as next generation sequencing library preparation, at the Advances in Genome Biology and Technology conference held in the U.S.
Major players in the market are also focused on adopting collaboration strategies to expand their product portfolio. For instance, in March 2020, Fluidigm Corporation, a provider of microfluidics technology, partnered with Next Gen Diagnostics, a provider of automation in pathogen bioinformatics, under which the later will use the Fluidigm Juno system for pathogen whole genome sequencing sample preparation in exchange of milestone payments starting in 2020 and additional revenue to Fluidigm Corp.
Get the main link:- https://www.coherentmarketinsights.com/market-insight/dna-and-rna-sample-preparation-market-3620
ContactUs: Mr.Shah Coherent Market ,Insights 10014thAve, #3200 Seattle,WA98154 Tel:+1-206-701-6702 Email: [email protected]
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What Takes So Long? A Behind-The-Scenes Look At The Steps Involved In COVID-19 Testing
After a slow start, testing for COVID-19 has ramped up in recent weeks, with giant commercial labs jumping into the effort, drive-up testing sites established in some places and new types of tests approved under emergency rules set by the Food and Drug Administration.
But even for people who are able to get tested (and there’s still a big lag in testing ability in hot spots across the U.S.), there can be a frustratingly long wait for results — not just hours, but often days. Sen. Rand Paul (R-Ky.) didn’t get his positive test results for six days and is now being criticized for not self-quarantining during that time.
We asked experts to help explain why the turn-around time for results can vary widely — from hours to days or even a week — and how that might be changing.
It’s A Multistep Process
First, a sample is taken from a patient’s nose or throat, using a special swab. That swab goes into a tube and is sent to a lab. Some large hospitals have on-site molecular test labs, but most samples are sent to outside labs for processing. More on that later.
That transit time usually runs about 24 hours, but it could be longer, depending on how far the hospital is from the processing lab.
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Once at the lab, the specimen is processed, which means lab workers extract the virus’s RNA, the molecule that helps regulate genes.
“That step of cleaning, the RNA extraction step, is one limiting factor,” said Cathie Klapperich, vice chair of the department of biomedical engineering at Boston University. “Only the very biggest labs have automated ways of extracting RNA from a sample and doing it quickly.”
After the RNA is extracted, technicians also must carefully mix special chemicals with each sample and run those combinations in a machine for analysis, a process called polymerase chain reaction (PCR), which can detect whether the sample is positive or negative for COVID.
“Typically, a PCR test takes six hours from start to finish to complete,” said Kelly Wroblewski, director of infectious disease programs at the Association of Public Health Laboratories.
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Some labs have larger staffs and more machines, so they can process more tests at a time than others. But even for those labs, as demand grows, so does the backlog.
Capacity Is Expanding, But Not Enough
Initially, only a few public health labs and the federal Centers for Disease Control and Prevention processed COVID-19 tests. Problems with the first CDC test kits also led to delays.
Now the CDC has a better kit, and 94 public health labs across the country do COVID-19 testing, said Wroblewski.
But those labs can’t possibly do all that’s needed. In normal times, their main function is regular public health surveillance — detecting more common threats such as outbreaks of measles or monitoring seasonal influenza — “but not to do diagnostic testing of the magnitude that is required in this response,” she said.
Large commercial labs like those run by companies such as Quest Diagnostics and LabCorp were given the go-ahead late last month by the FDA to start testing, too.
The FDA has said it won’t stop certain private labs — those that are already certified to perform complex testing — and diagnostic companies from developing their own test kits. Labs at some big-name hospital systems, such as Advent Health, the Cleveland Clinic and the University of Washington, are among those doing this.
In addition, the FDA has approved more than a dozen testing kits by various manufacturers or labs under special emergency rules designed to speed the process. Those include tests by Quest Diagnostics, LabCorp, Roche, Quidel Corp. and others. The kits are used in PCR machines, either in hospital labs or large commercial labs.
“A chief medical officer on the East Coast said that, up until two days ago, on average it was taking 72 hours to get results,” said Susan Van Meter, executive director of AdvaMedDx, a division of the Advanced Medical Technology Association, a device and diagnostics industry trade group. “That will get better as our member companies come on the market.”
Even so, supply is not keeping up with demand, Roche CEO Severin Schwan told CNBC on March 23. Roche won the first approval from the FDA for a test kit under emergency rules, and it has delivered more than 400,000 kits so far.
“Demand continues to be much higher than supply,” Schwan told CNBC. “So we are glad that overall capacity is increasing, but the reality is that broad-based testing is not yet possible.”
How Many Tests Can Be Done At A Time?
That varies. Large commercial labs can do a lot. LabCorp, for example, said it is processing 20,000 tests a day — and hopes to do more soon. Other test kit makers and labs are also ramping up capacity.
Smaller labs — such as molecular labs at some hospitals — can do far fewer per day but get results to patients faster because they save on transit time.
Still, it’s usually only large academic medical centers and some health systems that have their own molecular testing labs, which require complex equipment.
One of those is Medstar Georgetown University Hospital in Washington, D.C.
“From beginning to results can take five to six hours,” said Joeffrey Chahine, technical director for the molecular pathology division there.
Even at such hospitals, the tests are often prioritized for patients who have been admitted and staff who might have been exposed to COVID-19, said Chahine. His lab can process 93 samples at a time and run a few cycles a day, up to about 280, he said. Last week, it did 186 a day, three days in a row.
But hospitals with this ability are generally “not testing from their outpatient centers or the ER,” he said. In other words, the in-house labs aren’t running tests from walk-in patients.
Those tests are sent to large outside labs “so as not to overwhelm the hospital lab.” While those outside labs have large staffs, “the demand is so high that these outpatient clinics and ERs say the turnaround time can be four to seven business days,” he said.
Supply Shortages Are Slowing Test Production
As the worldwide demand for testing has grown, so, too, have shortages of the chemical agents used in the test kits, the swabs used to get the samples, and the protective masks and gear used by health workers taking the samples.
“There is an inadequate supply of so many things associated with testing,” said Wroblewski, which is why her group, along with officials in states including New York and cities including Los Angeles, recommend prioritizing who should be tested for COVID-19.
At the front of the line, she said, should be health care workers and first responders; older adults who have symptoms, especially those living in nursing homes or assisted living residences; and people who may have other illnesses that would be treated differently if they were infected. Bottom line: prioritizing who is tested will help speed the turnaround time for getting results to people in these circumstances and reduce their risk of spreading the illness.
Still, urgent shortages of some of the chemicals needed to process the tests are hampering efforts to test health care workers, including at hospitals such as SUNY Downstate medical center in hard-hit New York.
Looking forward, companies are working on quicker tests. Indeed, the FDA in recent days has approved tests from two companies that promise results in 45 minutes or less. Those will be available only in hospitals that have special equipment to run them. One of those companies, Cepheid of Sunnyvale, California, says about 5,000 U.S. hospitals already have the equipment needed to process these tests. Both firms say they will ship to the hospitals soon but have given few specifics on quantity or timing.
But many public health officials say doctors and clinics need a truly rapid test they can use in their offices, one like the tests already in use for influenza or strep throat.
A number of companies are moving in that direction. Late Friday, for instance, Abbott Laboratories announced that the FDA has given emergency-use authorization for the company’s rapid, point-of-care test, which can deliver positive results in as little as five minutes and negative results in 13.
The tests are processed on a small device already installed in thousands of medical offices, ERs, urgent care clinics and other settings. Abbott said it will begin this week to make 50,000 tests available per day.
“That’s going to make a meaningful difference,” said Van Meter at AdvaMedDx, who believes the rapid tests are a critical piece in the continuum of available testing.
Even though lab-based PCR tests, which are done at large labs and academic medical centers, can take several hours to produce a result, the machines used can test high numbers of cases all at once. The rapid test by Abbott — and other, similar tests now under development — do far fewer at a time but deliver results much faster.
“This can be provided in a doctor’s office or an ER, helping to triage patients who are waiting to get in,” said Van Meter. “It’s a very fine complement to the testing that exists.”
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What Takes So Long? A Behind-The-Scenes Look At The Steps Involved In COVID-19 Testing
After a slow start, testing for COVID-19 has ramped up in recent weeks, with giant commercial labs jumping into the effort, drive-up testing sites established in some places and new types of tests approved under emergency rules set by the Food and Drug Administration.
But even for people who are able to get tested (and there’s still a big lag in testing ability in hot spots across the U.S.), there can be a frustratingly long wait for results — not just hours, but often days. Sen. Rand Paul (R-Ky.) didn’t get his positive test results for six days and is now being criticized for not self-quarantining during that time.
We asked experts to help explain why the turn-around time for results can vary widely — from hours to days or even a week — and how that might be changing.
It’s A Multistep Process
First, a sample is taken from a patient’s nose or throat, using a special swab. That swab goes into a tube and is sent to a lab. Some large hospitals have on-site molecular test labs, but most samples are sent to outside labs for processing. More on that later.
That transit time usually runs about 24 hours, but it could be longer, depending on how far the hospital is from the processing lab.
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Once at the lab, the specimen is processed, which means lab workers extract the virus’s RNA, the molecule that helps regulate genes.
“That step of cleaning, the RNA extraction step, is one limiting factor,” said Cathie Klapperich, vice chair of the department of biomedical engineering at Boston University. “Only the very biggest labs have automated ways of extracting RNA from a sample and doing it quickly.”
After the RNA is extracted, technicians also must carefully mix special chemicals with each sample and run those combinations in a machine for analysis, a process called polymerase chain reaction (PCR), which can detect whether the sample is positive or negative for COVID.
“Typically, a PCR test takes six hours from start to finish to complete,” said Kelly Wroblewski, director of infectious disease programs at the Association of Public Health Laboratories.
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‘Red Dawn Breaking Bad’: Officials Warned About Safety Gear Shortfall Early On, Emails Show Mar 28
CDC Coronavirus Testing Decision Likely To Haunt Nation For Months To Come Mar 23
Telemedicine Surges, Fueled By Coronavirus Fears And Shift In Payment Rules Mar 27
Some States Are Reporting Incomplete COVID-19 Results, Blurring The Full Picture Mar 25
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Some labs have larger staffs and more machines, so they can process more tests at a time than others. But even for those labs, as demand grows, so does the backlog.
Capacity Is Expanding, But Not Enough
Initially, only a few public health labs and the federal Centers for Disease Control and Prevention processed COVID-19 tests. Problems with the first CDC test kits also led to delays.
Now the CDC has a better kit, and 94 public health labs across the country do COVID-19 testing, said Wroblewski.
But those labs can’t possibly do all that’s needed. In normal times, their main function is regular public health surveillance — detecting more common threats such as outbreaks of measles or monitoring seasonal influenza — “but not to do diagnostic testing of the magnitude that is required in this response,” she said.
Large commercial labs like those run by companies such as Quest Diagnostics and LabCorp were given the go-ahead late last month by the FDA to start testing, too.
The FDA has said it won’t stop certain private labs — those that are already certified to perform complex testing — and diagnostic companies from developing their own test kits. Labs at some big-name hospital systems, such as Advent Health, the Cleveland Clinic and the University of Washington, are among those doing this.
In addition, the FDA has approved more than a dozen testing kits by various manufacturers or labs under special emergency rules designed to speed the process. Those include tests by Quest Diagnostics, LabCorp, Roche, Quidel Corp. and others. The kits are used in PCR machines, either in hospital labs or large commercial labs.
“A chief medical officer on the East Coast said that, up until two days ago, on average it was taking 72 hours to get results,” said Susan Van Meter, executive director of AdvaMedDx, a division of the Advanced Medical Technology Association, a device and diagnostics industry trade group. “That will get better as our member companies come on the market.”
Even so, supply is not keeping up with demand, Roche CEO Severin Schwan told CNBC on March 23. Roche won the first approval from the FDA for a test kit under emergency rules, and it has delivered more than 400,000 kits so far.
“Demand continues to be much higher than supply,” Schwan told CNBC. “So we are glad that overall capacity is increasing, but the reality is that broad-based testing is not yet possible.”
How Many Tests Can Be Done At A Time?
That varies. Large commercial labs can do a lot. LabCorp, for example, said it is processing 20,000 tests a day — and hopes to do more soon. Other test kit makers and labs are also ramping up capacity.
Smaller labs — such as molecular labs at some hospitals — can do far fewer per day but get results to patients faster because they save on transit time.
Still, it’s usually only large academic medical centers and some health systems that have their own molecular testing labs, which require complex equipment.
One of those is Medstar Georgetown University Hospital in Washington, D.C.
“From beginning to results can take five to six hours,” said Joeffrey Chahine, technical director for the molecular pathology division there.
Even at such hospitals, the tests are often prioritized for patients who have been admitted and staff who might have been exposed to COVID-19, said Chahine. His lab can process 93 samples at a time and run a few cycles a day, up to about 280, he said. Last week, it did 186 a day, three days in a row.
But hospitals with this ability are generally “not testing from their outpatient centers or the ER,” he said. In other words, the in-house labs aren’t running tests from walk-in patients.
Those tests are sent to large outside labs “so as not to overwhelm the hospital lab.” While those outside labs have large staffs, “the demand is so high that these outpatient clinics and ERs say the turnaround time can be four to seven business days,” he said.
Supply Shortages Are Slowing Test Production
As the worldwide demand for testing has grown, so, too, have shortages of the chemical agents used in the test kits, the swabs used to get the samples, and the protective masks and gear used by health workers taking the samples.
“There is an inadequate supply of so many things associated with testing,” said Wroblewski, which is why her group, along with officials in states including New York and cities including Los Angeles, recommend prioritizing who should be tested for COVID-19.
At the front of the line, she said, should be health care workers and first responders; older adults who have symptoms, especially those living in nursing homes or assisted living residences; and people who may have other illnesses that would be treated differently if they were infected. Bottom line: prioritizing who is tested will help speed the turnaround time for getting results to people in these circumstances and reduce their risk of spreading the illness.
Still, urgent shortages of some of the chemicals needed to process the tests are hampering efforts to test health care workers, including at hospitals such as SUNY Downstate medical center in hard-hit New York.
Looking forward, companies are working on quicker tests. Indeed, the FDA in recent days has approved tests from two companies that promise results in 45 minutes or less. Those will be available only in hospitals that have special equipment to run them. One of those companies, Cepheid of Sunnyvale, California, says about 5,000 U.S. hospitals already have the equipment needed to process these tests. Both firms say they will ship to the hospitals soon but have given few specifics on quantity or timing.
But many public health officials say doctors and clinics need a truly rapid test they can use in their offices, one like the tests already in use for influenza or strep throat.
A number of companies are moving in that direction. Late Friday, for instance, Abbott Laboratories announced that the FDA has given emergency-use authorization for the company’s rapid, point-of-care test, which can deliver positive results in as little as five minutes and negative results in 13.
The tests are processed on a small device already installed in thousands of medical offices, ERs, urgent care clinics and other settings. Abbott said it will begin this week to make 50,000 tests available per day.
“That’s going to make a meaningful difference,” said Van Meter at AdvaMedDx, who believes the rapid tests are a critical piece in the continuum of available testing.
Even though lab-based PCR tests, which are done at large labs and academic medical centers, can take several hours to produce a result, the machines used can test high numbers of cases all at once. The rapid test by Abbott — and other, similar tests now under development — do far fewer at a time but deliver results much faster.
“This can be provided in a doctor’s office or an ER, helping to triage patients who are waiting to get in,” said Van Meter. “It’s a very fine complement to the testing that exists.”
What Takes So Long? A Behind-The-Scenes Look At The Steps Involved In COVID-19 Testing published first on https://smartdrinkingweb.weebly.com/
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What Takes So Long? A Behind-The-Scenes Look At The Steps Involved In COVID-19 Testing
After a slow start, testing for COVID-19 has ramped up in recent weeks, with giant commercial labs jumping into the effort, drive-up testing sites established in some places and new types of tests approved under emergency rules set by the Food and Drug Administration.
But even for people who are able to get tested (and there’s still a big lag in testing ability in hot spots across the U.S.), there can be a frustratingly long wait for results — not just hours, but often days. Sen. Rand Paul (R-Ky.) didn’t get his positive test results for six days and is now being criticized for not self-quarantining during that time.
We asked experts to help explain why the turn-around time for results can vary widely — from hours to days or even a week — and how that might be changing.
It’s A Multistep Process
First, a sample is taken from a patient’s nose or throat, using a special swab. That swab goes into a tube and is sent to a lab. Some large hospitals have on-site molecular test labs, but most samples are sent to outside labs for processing. More on that later.
That transit time usually runs about 24 hours, but it could be longer, depending on how far the hospital is from the processing lab.
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Once at the lab, the specimen is processed, which means lab workers extract the virus’s RNA, the molecule that helps regulate genes.
“That step of cleaning, the RNA extraction step, is one limiting factor,” said Cathie Klapperich, vice chair of the department of biomedical engineering at Boston University. “Only the very biggest labs have automated ways of extracting RNA from a sample and doing it quickly.”
After the RNA is extracted, technicians also must carefully mix special chemicals with each sample and run those combinations in a machine for analysis, a process called polymerase chain reaction (PCR), which can detect whether the sample is positive or negative for COVID.
“Typically, a PCR test takes six hours from start to finish to complete,” said Kelly Wroblewski, director of infectious disease programs at the Association of Public Health Laboratories.
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Some labs have larger staffs and more machines, so they can process more tests at a time than others. But even for those labs, as demand grows, so does the backlog.
Capacity Is Expanding, But Not Enough
Initially, only a few public health labs and the federal Centers for Disease Control and Prevention processed COVID-19 tests. Problems with the first CDC test kits also led to delays.
Now the CDC has a better kit, and 94 public health labs across the country do COVID-19 testing, said Wroblewski.
But those labs can’t possibly do all that’s needed. In normal times, their main function is regular public health surveillance — detecting more common threats such as outbreaks of measles or monitoring seasonal influenza — “but not to do diagnostic testing of the magnitude that is required in this response,” she said.
Large commercial labs like those run by companies such as Quest Diagnostics and LabCorp were given the go-ahead late last month by the FDA to start testing, too.
The FDA has said it won’t stop certain private labs — those that are already certified to perform complex testing — and diagnostic companies from developing their own test kits. Labs at some big-name hospital systems, such as Advent Health, the Cleveland Clinic and the University of Washington, are among those doing this.
In addition, the FDA has approved more than a dozen testing kits by various manufacturers or labs under special emergency rules designed to speed the process. Those include tests by Quest Diagnostics, LabCorp, Roche, Quidel Corp. and others. The kits are used in PCR machines, either in hospital labs or large commercial labs.
“A chief medical officer on the East Coast said that, up until two days ago, on average it was taking 72 hours to get results,” said Susan Van Meter, executive director of AdvaMedDx, a division of the Advanced Medical Technology Association, a device and diagnostics industry trade group. “That will get better as our member companies come on the market.”
Even so, supply is not keeping up with demand, Roche CEO Severin Schwan told CNBC on March 23. Roche won the first approval from the FDA for a test kit under emergency rules, and it has delivered more than 400,000 kits so far.
“Demand continues to be much higher than supply,” Schwan told CNBC. “So we are glad that overall capacity is increasing, but the reality is that broad-based testing is not yet possible.”
How Many Tests Can Be Done At A Time?
That varies. Large commercial labs can do a lot. LabCorp, for example, said it is processing 20,000 tests a day — and hopes to do more soon. Other test kit makers and labs are also ramping up capacity.
Smaller labs — such as molecular labs at some hospitals — can do far fewer per day but get results to patients faster because they save on transit time.
Still, it’s usually only large academic medical centers and some health systems that have their own molecular testing labs, which require complex equipment.
One of those is Medstar Georgetown University Hospital in Washington, D.C.
“From beginning to results can take five to six hours,” said Joeffrey Chahine, technical director for the molecular pathology division there.
Even at such hospitals, the tests are often prioritized for patients who have been admitted and staff who might have been exposed to COVID-19, said Chahine. His lab can process 93 samples at a time and run a few cycles a day, up to about 280, he said. Last week, it did 186 a day, three days in a row.
But hospitals with this ability are generally “not testing from their outpatient centers or the ER,” he said. In other words, the in-house labs aren’t running tests from walk-in patients.
Those tests are sent to large outside labs “so as not to overwhelm the hospital lab.” While those outside labs have large staffs, “the demand is so high that these outpatient clinics and ERs say the turnaround time can be four to seven business days,” he said.
Supply Shortages Are Slowing Test Production
As the worldwide demand for testing has grown, so, too, have shortages of the chemical agents used in the test kits, the swabs used to get the samples, and the protective masks and gear used by health workers taking the samples.
“There is an inadequate supply of so many things associated with testing,” said Wroblewski, which is why her group, along with officials in states including New York and cities including Los Angeles, recommend prioritizing who should be tested for COVID-19.
At the front of the line, she said, should be health care workers and first responders; older adults who have symptoms, especially those living in nursing homes or assisted living residences; and people who may have other illnesses that would be treated differently if they were infected. Bottom line: prioritizing who is tested will help speed the turnaround time for getting results to people in these circumstances and reduce their risk of spreading the illness.
Still, urgent shortages of some of the chemicals needed to process the tests are hampering efforts to test health care workers, including at hospitals such as SUNY Downstate medical center in hard-hit New York.
Looking forward, companies are working on quicker tests. Indeed, the FDA in recent days has approved tests from two companies that promise results in 45 minutes or less. Those will be available only in hospitals that have special equipment to run them. One of those companies, Cepheid of Sunnyvale, California, says about 5,000 U.S. hospitals already have the equipment needed to process these tests. Both firms say they will ship to the hospitals soon but have given few specifics on quantity or timing.
But many public health officials say doctors and clinics need a truly rapid test they can use in their offices, one like the tests already in use for influenza or strep throat.
A number of companies are moving in that direction. Late Friday, for instance, Abbott Laboratories announced that the FDA has given emergency-use authorization for the company’s rapid, point-of-care test, which can deliver positive results in as little as five minutes and negative results in 13.
The tests are processed on a small device already installed in thousands of medical offices, ERs, urgent care clinics and other settings. Abbott said it will begin this week to make 50,000 tests available per day.
“That’s going to make a meaningful difference,” said Van Meter at AdvaMedDx, who believes the rapid tests are a critical piece in the continuum of available testing.
Even though lab-based PCR tests, which are done at large labs and academic medical centers, can take several hours to produce a result, the machines used can test high numbers of cases all at once. The rapid test by Abbott — and other, similar tests now under development — do far fewer at a time but deliver results much faster.
“This can be provided in a doctor’s office or an ER, helping to triage patients who are waiting to get in,” said Van Meter. “It’s a very fine complement to the testing that exists.”
from Updates By Dina https://khn.org/news/what-takes-so-long-a-behind-the-scenes-look-at-the-steps-involved-in-covid-19-testing/
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Looking to improve NGS Sample Prep?
NGS (Next-Generation Sequencing) has aided rapid strides in genomics data generation but getting to the results may prove labor and time-consuming. Sample prep can be complicated if samples are damaged or degraded. However, experts recommend the following tips to accelerate and simplify the sample prep.
Accept that you will hit bottlenecks
A sequence may have a natural variation or the variation may result from the NGS workflow. There are different steps in sample prep and any of them could be responsible for variation, for example, inaccurate pipetting can impact data. After a long NGS process, if you find that you have bad data, you would have to start again. This means more sample requirements as well as added reagent and labor costs. This is why NGS sample prep needs to be consistent and repeatable.
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The automated RNA Clean-up Kit enables fast and simple purification and concentration. The highly concentrated and purified RNAs are suitable for all subsequent analyses and molecular manipulations.
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GC Biotech products
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