Difference between revisions of "User:Shawndouglas/sandbox/sublevel4"

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[[File:Phlebotomy-drawing blood with a lancet.jpg|right|450px]]Often referred to as simply a medical or clinical laboratory, the clinical diagnostics lab performs tests on clinical specimens in order to get information about the health of a patient as it pertains to the diagnosis, treatment, and prevention of disease.<ref name="MedLabTech">{{cite book |title=Textbook of Medical Laboratory Technology |chapter=Chapter 1: Laboratory |author=Sood, R. |url=https://books.google.com/books?id=hpNhAQAACAAJ |pages=01–28 |year=2006 |publisher=Jaypee Brothers Publishers |isbn=818061591X}}</ref> There are, however, additional “flavors” of the clinical diagnostics lab — including the anatomical and clinical pathology labs, the physician office lab (POL), and the integrative medicine lab, among others — that provide more specific clinical diagnostic services, requiring unique functionality from its informatics solutions.
[[File:FISH (Fluorescent In Situ Hybridization).jpg|right|550px]]The molecular diagnostics lab will use one or more techniques (e.g., PCR, DNA sequencing, microarrays, gene expression profiling and cytogenetics) in their workflow, and the LIMS used in molecular diagnostics ideally will address those workflow needs. This is especially true for cytogenetics labs, which use specialty techniques like chromosome analysis or karyotyping, fluorescence ''in situ'' hybridization (FISH) and microarray-based assays such as comparative genomic hybridization.<ref name="AACCGenetic19">{{cite web |url=https://www.testing.com/genetic-testing-techniques/ |title=Genetic Testing Techniques |work=Testing.com |publisher=OneCare Media |date=09 November 2021 |accessdate=18 November 2021}}</ref><ref name="MayoClinicCyto">{{cite web |url=https://www.mayoclinic.org/departments-centers/laboratory-medicine-pathology/overview/specialty-groups/laboratory-genetics/cytogenetics-laboratory |title=Cytogenetics Laboratory |work=Departments and Centers: Laboratory Medicine and Pathology |publisher=Mayo Clinic |accessdate=18 November 2021}}</ref><ref name="YaleCyto">{{cite web |url=https://medicine.yale.edu/lab/cytogenetics/testing/ |title=Cytogenetics Lab Tests |work=Cytogenetics Lab |publisher=Yale School of Medicine |accessdate=18 November 2021}}</ref>


The ordinary clinical diagnostics lab will seek a LIMS that can provide, at a minimum, the essential functionality listed in section 2.3. Additionally, the LIMS may need to provide features and functions specific to one or more clinical diagnostic subtypes, described below.
In addition to the essential features of a standard LIMS, the molecular diagnostics and cytogenetics lab will also be looking for a system that can (or allows users to)<ref name="SunquestMitogen20">{{cite web |url=https://www.sunquestinfo.com/software-and-services/lims/ |title=Sunquest Mitogen LIMS |publisher=Sunquest Information Systems, Inc |date=2021 |accessdate=18 November 2021}}</ref><ref name="XifinMolec20">{{cite web |url=https://www.xifin.com/industry-solutions/laboratory/molecular-diagnostics |title=Molecular Diagnostics |publisher=XIFIN, Inc |date=2021 |accessdate=18 November 2021}}</ref><ref name="PsycheNucleoLIS20">{{cite web |url=https://psychesystems.com/enterprise-laboratory-information-software/nucleolis-molecular-lab-testing-software/ |title=NucleoLIS - Flexible & Modern LIS |publisher=Psyche Systems |date=2021 |accessdate=18 November 2021}}</ref><ref name="MyersLab18">{{cite journal |title=Laboratory Information Systems and Instrument Software Lack Basic Functionality for Molecular Laboratories |journal=Journal of Molecular Diagnostics |author=Myers, C.; Swadley, M.; Carter, A.B. |volume=20 |issue=5 |pages=591–99 |year=2018 |doi=10.1016/j.jmoldx.2018.05.011}}</ref>:


 
* Manage sample collection kits.
'''3.2.1.1 Anatomical and clinical pathology'''
* Manage informed consent documentation.
 
* Provide customized workflows for molecular and next-generation sequencing (NGS) testing.
In common medical practice, general pathology is mostly concerned with analyzing known clinical abnormalities that are markers or precursors for both infectious and non-infectious disease and is conducted by experts in one of two major specialties: anatomical pathology and clinical pathology. These two sciences have slightly differing workflows, and both bring with them the need for specific LIMS functionality to better address their unique workflows.
* Track specimen and aliquot lineage for cell lines, tissues, slides, etc.
 
* Track nucleic acid quantity and quality of specimens.
In addition to the essential features of a standard LIMS, the anatomical and clinical pathology lab will also be looking for a system that can (or allows users to)<ref name="LabWareAnatomic20">{{cite web |url=https://www.labware.com/industries/healthcare#anatomic |title=Anatomic Pathology |publisher=LabWare, Inc |date=2021 |accessdate=18 November 2021}}</ref><ref name="SunquestCoPath20">{{cite web |url=https://www.sunquestinfo.com/software-and-services/copathplus/ |title=Sunquest CoPathPlus |publisher=Sunquest Information Systems, Inc |date=2021 |accessdate=18 November 2021}}</ref><ref name="NovoPathHome20">{{cite web |url=https://www.novopath.com/ |title=NovoPath: Redefining Laboratory Information Systems |publisher=NovoPath, Inc |date=2021 |accessdate=18 November 2021}}</ref><ref name="TDMS_TDHistoCyto20">{{cite web |url=https://www.technidata-web.com/en-gb/solutions-services/solutions/histopathology |title=TD HistoCyto |publisher=Technidata SAS |date=2021 |accessdate=18 November 2021}}</ref>:
* Support a wide array of molecular testing and associated data fields, including biochemical and molecular genetics, carrier screening, immunology, molecular profiling, prenatal and newborn testing, and pharmacogenetics.
 
* Provide custom workflows for FISH, PCR, gel electrophoresis, cytogenetics, DNA sequencing and more.
* Configure the system using templates for histology and cytology case types.
* Support specialty testing reimbursement and other revenue management unique to this lab type.
* Add, view and link pre-generated organ maps and other diagrams.
* Support single sign-on with imaging platforms.
* Add, view and link custom annotated pathology imaging.
* Provide color coding for turn-around time and other testing statuses.
* Track abnormal results and provide trending reports for monitoring disease populations.
* Provide cleanly formatted rich-text reports customized for molecular diagnostics.
* Support blocks and slides as specimens, with predefined descriptions.
* Document grossing examinations.
* Print slides and cassettes.
* Provide case management, reporting and test requisition.
* Provide specialty workflow for autopsy.
* Provide specialty workflow for gynecological cytology, including HPV + Pap co-testing for cervical cancer.
* Provide stain panels and histology worksheets.
* Support shared management of tissue samples among departments.
* Support EHR integration.
* Support polymerase chain reaction (PCR) workflow and reporting.
* Support pathology-specific reflex testing.
* Provide the option to combine same-day anatomical and clinical pathology results and reporting.
* Flag unusual cases for conference or committee reporting.
 
 
'''3.2.1.2 Physician office'''
 
On average, the physician office laboratory (POL) may not produce the same level of daily specimen throughput as a larger clinical diagnostic laboratory, but that should not detract from the benefits a POL can gain from a laboratory informatics solution. The POL employing laboratory informatics will still need much of the same standard clinical functionality mentioned prior, and the system will still need to comply with data management and sharing regulations such as those found with HIPAA and CLIA.
 
If there is any additional consideration to be made for the POL seeking a LIMS or LIS, it will be with how well a given solution is able to interface with the electronic health record (EHR) solutions the POL and its stakeholders are using.  The POL should examine the potential integration capabilities of the LIMS solutions they are evaluating, as well as the currently used EHR and other clinical solutions. The lab should also be sure to consider any future potential of integrating their systems with other external data management systems, including those of other reference laboratories. A LIMS without the robust capability of integrating with other software systems only places additional burdens on the POL, now and into the future.
 
 
'''3.2.1.3 Integrative medicine'''
 
Integrative medicine is a type of personalized healthcare that takes a more holistic approach to the causes of illnesses. If an integrative medicine laboratory is using a laboratory informatics solution, their requirements will be nearly identical to a standard clinical diagnostic laboratory, meaning the standard clinical functionality mentioned in the second chapter will likely be suitable. If there is a major difference or required piece of additional functionality, it will have to do with a more extensive list of available tests and billing codes for them. This usually consists of expansions into nutritional, metabolic, and toxicity assays, as well as support for diagnostic imaging.<ref name="BralleyBasic">{{cite book |url=https://books.google.com/books?id=CpXVAwgOv7sC&pg=PT11 |chapter=Chapter 1: Basic Concepts |title=Laboratory Evaluations for Integrative and Functional Medicine |author=Bralley, J.A.; Lord, R.S. |publisher=MetaMetrix Institute |edition=2nd |pages=1–16 |year=2008 |isbn=0967394945}}</ref>


==References==
==References==
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{{Reflist|colwidth=30em}}

Revision as of 18:35, 9 March 2022

FISH (Fluorescent In Situ Hybridization).jpg

The molecular diagnostics lab will use one or more techniques (e.g., PCR, DNA sequencing, microarrays, gene expression profiling and cytogenetics) in their workflow, and the LIMS used in molecular diagnostics ideally will address those workflow needs. This is especially true for cytogenetics labs, which use specialty techniques like chromosome analysis or karyotyping, fluorescence in situ hybridization (FISH) and microarray-based assays such as comparative genomic hybridization.[1][2][3]

In addition to the essential features of a standard LIMS, the molecular diagnostics and cytogenetics lab will also be looking for a system that can (or allows users to)[4][5][6][7]:

  • Manage sample collection kits.
  • Manage informed consent documentation.
  • Provide customized workflows for molecular and next-generation sequencing (NGS) testing.
  • Track specimen and aliquot lineage for cell lines, tissues, slides, etc.
  • Track nucleic acid quantity and quality of specimens.
  • Support a wide array of molecular testing and associated data fields, including biochemical and molecular genetics, carrier screening, immunology, molecular profiling, prenatal and newborn testing, and pharmacogenetics.
  • Provide custom workflows for FISH, PCR, gel electrophoresis, cytogenetics, DNA sequencing and more.
  • Support specialty testing reimbursement and other revenue management unique to this lab type.
  • Support single sign-on with imaging platforms.
  • Provide color coding for turn-around time and other testing statuses.
  • Provide cleanly formatted rich-text reports customized for molecular diagnostics.

References

  1. ↑ "Genetic Testing Techniques". Testing.com. OneCare Media. 9 November 2021. https://www.testing.com/genetic-testing-techniques/. Retrieved 18 November 2021. 
  2. ↑ "Cytogenetics Laboratory". Departments and Centers: Laboratory Medicine and Pathology. Mayo Clinic. https://www.mayoclinic.org/departments-centers/laboratory-medicine-pathology/overview/specialty-groups/laboratory-genetics/cytogenetics-laboratory. Retrieved 18 November 2021. 
  3. ↑ "Cytogenetics Lab Tests". Cytogenetics Lab. Yale School of Medicine. https://medicine.yale.edu/lab/cytogenetics/testing/. Retrieved 18 November 2021. 
  4. ↑ "Sunquest Mitogen LIMS". Sunquest Information Systems, Inc. 2021. https://www.sunquestinfo.com/software-and-services/lims/. Retrieved 18 November 2021. 
  5. ↑ "Molecular Diagnostics". XIFIN, Inc. 2021. https://www.xifin.com/industry-solutions/laboratory/molecular-diagnostics. Retrieved 18 November 2021. 
  6. ↑ "NucleoLIS - Flexible & Modern LIS". Psyche Systems. 2021. https://psychesystems.com/enterprise-laboratory-information-software/nucleolis-molecular-lab-testing-software/. Retrieved 18 November 2021. 
  7. ↑ Myers, C.; Swadley, M.; Carter, A.B. (2018). "Laboratory Information Systems and Instrument Software Lack Basic Functionality for Molecular Laboratories". Journal of Molecular Diagnostics 20 (5): 591–99. doi:10.1016/j.jmoldx.2018.05.011. 
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