Difference between revisions of "User:Shawndouglas/sandbox/sublevel1"

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A June 2020 report by Weemaes ''et al.'' in the ''Journal of the American Medical Informatics Association'' describes the bottlenecks they encountered in their test workflows at the Belgian National Reference Center, and how they updated their LIS with functionality to resolve those bottlenecks.<ref name="WeemaesLab20">{{cite journal |title=Laboratory information system requirements to manage the COVID-19 pandemic: A report from the Belgian national reference testing center |journal=JAMIA |author=Weemaes, M.; Martens, S.; Cuypers, L. et al. |at=ocaa081 |year=2020 |doi=10.1093/jamia/ocaa081 |pmid=32348469 |pmc=PMC7197526}}</ref> In addition to adding a COVID-19–specific order set into the [[computerized physician order entry]] (CPOE) module integrated with both their LIS and [[electronic health record]] (EHR), they included an up-to-date triage criteria component, a tool for optimizing sampling and packaging, a COVID-19 status button, and improved reporting modules for automating reference testing and epidemiological reporting. They also added extra database and data mining functionality to facilitate research and insights into epidemiologies and treatments. Their conclusion: "Rapidly developed, agile extendable LIS functionality and its meaningful use alleviates the administrative burden on laboratory personnel and improves turnaround time of SARS-CoV-2 testing."<ref name="WeemaesLab20" /> The Association of Public Health Laboratories comes to a similar conclusion in regard to laboratory informatics solutions and public health laboratories' COVID-19 testing.<ref name="APHLLIMS20">{{cite web |url=https://www.aphl.org/aboutAPHL/publications/Documents/INFO-2020-LIMS.pdf |format=PDF |title=LIMS (Laboratory Information Management System) |author=Association of Public Health Laboratories |publisher= Association of Public Health Laboratories |date=2020 |accessdate=18 August 2020}}</ref>
Table 3 lists the major vendors developing and selling PCR, isothermal amplification, and NGS supplies, instruments, and software for both clinical diagnostics and life science research. "Research use only" equipment like Siemens Healthcare's Fast Track Cycler was ignored for completing the table. The vendor list was largely compiled from vendors identified in a handful of online market reports on PCR, with an added sprinkling of a few additional reagent vendors (e.g., Jena Bioscience, LGC, and New England BioLabs) who address isothermal amplification supplies in addition to PCR. Note that this is not an endorsement for any particular vendor.
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  ! style="background-color:white; text-align:left; font-weight: normal; padding-left:10px; padding-right:10px;" colspan="13"|'''Table 3.''' Major players operating in the global diagnostic PCR, isothermal amplification, and NGS market
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  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Vendor
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Shop all products
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR machines
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Nucleic acid extraction<br />and purification machines
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Immunoassay analyzers<br />and assays
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR and qPCR assays
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|PCR and qPCR enzymes<br />and master mixes
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|DNA/RNA purification,<br />quantitation, and<br />amplification supplies
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|LAMP assays
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Isothermal amplification<br />enzymes and <br />master mixes
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|NGS supplies
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Supporting labware<br />and supplies
  ! style="background-color:#e2e2e2; padding-left:10px; padding-right:10px;"|Software
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Abbott
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.molecular.abbott/us/en/offerings/products Abbott products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Agilent Technologies
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.agilent.com/en-us/products Agilent products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Becton, Dickinson and Company
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bd.com/en-us/offerings/capabilities BD products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Bio-Rad Laboratories, Inc.
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.bio-rad.com/en-us/life-science-research?ID=1100 Bio-Rad products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|bioMérieux SA
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.biomerieux-usa.com/az bioMérieux products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Danaher Corporation and its companies
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.cepheid.com/ Cepheid products],<br />[https://www.beckmancoulter.com/en/products Beckman Coulter products], and<br />[https://www.beckman.com/ Beckman Life Sciences products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|F. Hoffmann-La Roche AG
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.roche.com/products/diagnostics-portfolio.htm Roche Diagnostics products]
  | style="background-color:white; padding-left:10px; padding-right:10px;"|✓
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Jena Bioscience GmbH
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.jenabioscience.com/ Jena Bioscience products]
  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|LGC Limited and its companies
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.lucigen.com/products.html Lucigen products]
  | style="background-color:white; padding-left:10px; padding-right:10px;"| -
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Merck KGaA
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.sigmaaldrich.com/US/en/life-science/covid Sigma-Aldrich products] and<br />[https://www.emdmillipore.com/US/en/products/vMqb.qB.GdEAAAE_Mhd3.Lxj,nav Millipore Sigma products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|New England BioLabs, Inc.
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.neb.com/products NEB products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Promega
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.promega.com/products/ Promega products] and [https://www.promega.com/products/catalog/ catalog]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|QIAGEN N.V.
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.qiagen.com/us/products/ QIAGEN products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Siemens Healthcare GmbH
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.siemens-healthineers.com/products-services Siemens Healthcare products]
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  | style="background-color:white; padding-left:10px; padding-right:10px;"|Thermo Fisher Scientific, Inc.
  | style="background-color:white; padding-left:10px; padding-right:10px;"|[https://www.thermofisher.com/us/en/home/order.html Thermo Fisher products] and<br />[https://www.fishersci.com/us/en/browse/90217008/pcr-equipment-and-supplies Fisher Scientific products]
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As such, adding COVID-19 and other respiratory illness testing to your workflow may necessitate an information management system, or an upgrade of your existing software systems. You may experience many of the same bottlenecks the Belgian National Reference Center experienced, especially if you're still working primarily with paper-based test ordering. Those researchers found that paper-based COVID-19 test requests often<ref name="WeemaesLab20" />:
The "Software" column of Table 3 represents whether or not the vendor offers laboratory informatics software such as a LIMS or LIS. Those vendors' solutions may or may not be tailored to handle the specific requirements of a clinical diagnostic or virology lab handling COVID-19 and other viruses. (See the next chapter for more in-depth information about working an informatics solution into COVID-19 and other viral testing workflow.) A non-endorsed, representative example of vendors who do include:


* omitted critical clinical status and contact information;
* [[Abbott Informatics Corporation]] - [https://www.starlims.com/us/en/covid19-testing-and-reporting/starlims-covid19 STARLIMS LIMS]
* slowed down epidemiological and research studies;
* [[AgileBio]] - [https://labcollector.com/solutions/applications/lp-covid19-pack/ COVID-19 LC]
* hindered proper pre-analytical biosafety procedures; and
* [[Autoscribe Informatics, Inc.]] -  [https://www.autoscribeinformatics.com/lims/matrix-covid-lims Matrix Covid LIMS]
* impeded rapid response to evolving test criteria and clinical insights through test ordering protocols.
* [[BioSoft Integrators, LLC]] - [https://biosoftintegrators.com/covid-19/ LabOptimize LIMS for COVID-19]
* [[CloudLIMS.com, LLC]] - [https://cloudlims.com/industries/covid-19-lims-software.html CloudLIMS for COVID-19]
* [[Common Cents Systems, Inc.]] - [https://resources.apollolims.com/blog/covid-19-testing-and-the-important-role-of-a-lims Apollo LIMS for COVID-19]
* [[Comp Pro Med, Inc.]] - [https://www.comppromed.com/covid-19-rapid-deployment-lis/ COVID-19 Rapid Deployment LIS]
* [[Illumina, Inc.]] - [https://blog.software.illumina.com/2020/04/14/efficient-accurate-lab-management-for-covid-19-research/ BaseSpace Clarity LIMS for COVID-19]
* [[Junction Concepts, Inc.]] - [https://qbench.net/qbench-covid-19-lims-laboratory-information-management-system/ QBench]
* [[LabLynx, Inc.]] - [https://www.covidlims.com/ COVIDLiMS]
* [[LabVantage Solutions, Inc.]] - [https://www.labvantage.com/your-lab-type/labvantage-covid-19-lims/ LabVantage COVID-19 LIMS]
* [[Physion, LLC]] - [https://www.ovation.io/covid-19/ Ovation LIMS for COVID-19]
* [[Sunquest Information Systems, Inc.]] - [https://www.sunquestinfo.com/docs/sunquest-covid19-mitogen-lims-product-focus.pdf Mitogen LIMS for COVID-19] (PDF)
* [[Third Wave Analytics, Inc.]] - [https://thirdwaveanalytics.com/covid19/ Lockbox LIMS for SARS-CoV-2 Clinical Testing]


How interoperable your laboratory software solution is with other systems such as EHRs is also worth consideration. The next chapter addresses system interoperability in greater detail, but it's worth mentioning it here in the context of adding software to improve testing workflows for SARS-CoV-2 and other respiratory viruses. Broadly speaking, improving interoperability among [[clinical informatics]] systems—whether at the point of care or within a specific laboratory—is recognized as an important step towards improving health outcomes.<ref name="KunImprov08">{{cite journal |title=Improving outcomes with interoperable EHRs and secure global health information infrastructure |journal=Studies in Health Technology and Informatics |author=Kun, L.; Coatrieux, G.; Quantin, C. et al. |volume=137 |pages=68–79 |year=2008 |pmid=18560070}}</ref><ref name="GCHIImproving">{{cite web |url=http://s3.amazonaws.com/rdcms-himss/files/production/public/Improving-Patient-Carethrough-Interoperability.pdf |format=PDF |title=Improving Patient Care through Interoperability |author=Global Center for Health Innovation |publisher=Global Center for Health Innovation |date=n.d. |accessdate=16 August 2020}}</ref> However, while developers of EHRs and other clinical informatics systems have intended to improve their software's interoperability, the COVID-19 pandemic has, at times, unfortunately shown the inadequacies still inherent in that software's overall design.<ref name="GlaserItsTime20">{{cite web |url=https://hbr.org/2020/06/its-time-for-a-new-kind-of-electronic-health-record |title=It’s Time for a New Kind of Electronic Health Record |author=Glaser, J. |work=Harvard Business Review |date=12 June 2020 |accessdate=18 August 2020}}</ref><ref name="LimoliPhys20">{{cite web |url=https://medcitynews.com/2020/07/physicians-deserve-better-software-covid-19-has-shown-why-medical-records-need-to-adapt/ |title=Physicians deserve better software: Covid-19 has shown why medical records need to adapt |author=Limoli, C.; Papathomas, G. |work=MedCity News |date=07 July 2020 |accessdate=18 August 2020}}</ref><ref name="JasonEHR20">{{cite web |url=https://ehrintelligence.com/news/ehr-optimization-health-it-projects-needed-after-covid-19-surge |title=EHR Optimization, Health IT Projects Needed After COVID-19 Surge |author=Jason, C. |work=EHR Intelligence |date=23 July 2020 |accessdate=18 August 2020}}</ref><ref name="ReevesTheClin21">{{cite journal |title=The Clinical Information Systems Response to the COVID-19 Pandemic |journal=Yearbook of Medical Informatics |author=Reeves, J.J.; Pageler, N.M.; Wick, E.C. et al. |volume=30 |issue=1 |pages=105–25 |year=2021 |doi=10.1055/s-0041-1726513 |pmid=34479384 |pmc=PMC8416224}}</ref> As such, any research into acquiring a [[laboratory information management system]] (LIMS), LIS, or other clinical information management solution should take into account how well that solution is able to integrate with your other clinical systems, as well as any other third-party systems like physician or hospital EHRs. And it's not just the software solutions you'll want to consider. Will the new instruments you add for getting your lab rolling with clinical respiratory illness testing integrate with your software?
Additionally, when in-house knowledge is lacking, a consultant may be required. These consultants are meant to be representative examples of those laboratory consulting firms indicating they have the knowledge to help a laboratory with COVID-19-related testing and other issues. This list is not an endorsement for any particular consultant:


Finally, although rare, you may find you don't have the in-house expertise to fully implement a COVID-19 testing line to your laboratory. In such a case, you may need to turn to a laboratory services consultancy with experience in SARS-CoV-2 test method validation, instrument procurement and implementation, and legal matters. (See the next section for a representative example of consultants advertising COVID-19 testing knowledge and services for labs.)
* [https://www.aruplab.com/consulting ARUP Laboratories] (Utah)
 
* [https://www.colaborate.com/covid-19-lab-consulting/ Colaborate] (Florida)
==References==
* [https://elitediagnostics.com/verticals/infectious-disease/ Elite Diagnostics] (North Carolina)
{{Reflist|colwidth=30em}}
* [https://www.freedassociates.com/news/freed-associates-launches-a-covid-19-consulting-service-for-health-care-organizations/ Freed Associates] (California)
* [https://www.lighthouselabservices.com/consulting/infectious-disease/ Lighthouse Lab Services] (North Carolina)
* [https://optimumhit.com/ehr-services/covid-19-support/ Optimum Healthcare IT] (Florida)
* [https://thecovidconsultants.com/ The COVID Consultants] (Colorado)
* [https://www.triumvirate.com/coronavirus Triumverate Environmental] (Massachusetts)

Revision as of 19:48, 3 February 2022

Table 3 lists the major vendors developing and selling PCR, isothermal amplification, and NGS supplies, instruments, and software for both clinical diagnostics and life science research. "Research use only" equipment like Siemens Healthcare's Fast Track Cycler was ignored for completing the table. The vendor list was largely compiled from vendors identified in a handful of online market reports on PCR, with an added sprinkling of a few additional reagent vendors (e.g., Jena Bioscience, LGC, and New England BioLabs) who address isothermal amplification supplies in addition to PCR. Note that this is not an endorsement for any particular vendor.

Table 3. Major players operating in the global diagnostic PCR, isothermal amplification, and NGS market
Vendor Shop all products PCR machines Nucleic acid extraction
and purification machines
Immunoassay analyzers
and assays
PCR and qPCR assays PCR and qPCR enzymes
and master mixes
DNA/RNA purification,
quantitation, and
amplification supplies
LAMP assays Isothermal amplification
enzymes and
master mixes
NGS supplies Supporting labware
and supplies
Software
Abbott Abbott products - - - - - -
Agilent Technologies Agilent products - - - -
Becton, Dickinson and Company BD products - - - - - - - -
Bio-Rad Laboratories, Inc. Bio-Rad products - - - -
bioMérieux SA bioMérieux products - - - - - -
Danaher Corporation and its companies Cepheid products,
Beckman Coulter products, and
Beckman Life Sciences products
- - - - - -
F. Hoffmann-La Roche AG Roche Diagnostics products - - - -
Jena Bioscience GmbH Jena Bioscience products - - - - -
LGC Limited and its companies Lucigen products - - - - - -
Merck KGaA Sigma-Aldrich products and
Millipore Sigma products
- - - - - -
New England BioLabs, Inc. NEB products - - - - -
Promega Promega products and catalog - - - - - -
QIAGEN N.V. QIAGEN products - - - -
Siemens Healthcare GmbH Siemens Healthcare products - - - - - - -
Thermo Fisher Scientific, Inc. Thermo Fisher products and
Fisher Scientific products
- -

The "Software" column of Table 3 represents whether or not the vendor offers laboratory informatics software such as a LIMS or LIS. Those vendors' solutions may or may not be tailored to handle the specific requirements of a clinical diagnostic or virology lab handling COVID-19 and other viruses. (See the next chapter for more in-depth information about working an informatics solution into COVID-19 and other viral testing workflow.) A non-endorsed, representative example of vendors who do include:

Additionally, when in-house knowledge is lacking, a consultant may be required. These consultants are meant to be representative examples of those laboratory consulting firms indicating they have the knowledge to help a laboratory with COVID-19-related testing and other issues. This list is not an endorsement for any particular consultant: