Setting Up a CLIA Lab

2. to CLIA or not to CLIA
(is there a question)
Prof. Wim Van Criekinge, CSO
9th of march 2013

3. Agenda
 MDxHealth
– Epigenetics
– Business Model
 CLIA
– Regulatory Agencies
– Categorization
– CLIA 88: QMS/QC/QA
 Howto
– MDxHealth, a CLIA lab setup

4. Defining Epigenetics
Genome
DNA  Reversible changes in gene
expression/function
 Without changes in DNA
Chromatin sequence
Epigenome
 Can be inherited from precursor
cells
Gene Expression  Allows to integrate intrinsic with
environmental signals (including
Phenotype
diet)

5. Actionable Epigenome

6. (Epi)Genetic Editing ‘Root’ of Cancer Growth
Tumor
Tumor
Development
and
Growth
Epigenetically
altered, self-
renewing cancer
stem cells

7. Outside Oncology ?

8. Genetics
Whole-genome Probes
MSP
Bisulphite seq (450-27K)
Full genome bp
109 108 107 106 105 104 103 102 101 1

9. Genetics
Whole-genome Enrichment seq Enrichment
G PCR
sequencing (Exome) Targeted Panels
E
N
E Full genome bp
T
I 109 108 107 106 105 104 103 102 101 1
C

10. Genetics
Instrument and Assay providers
Whole-genome Enrichment seq Enrichment
G PCR
sequencing (Exome) Targeted Panels
E
N
E Full genome bp
T
I 109 108 107 106 105 104 103 102 101 1
C

11. Genetics
Instrument and Assay providers
Whole-genome Enrichment seq Enrichment
G PCR
sequencing (Exome) Targeted Panels
E
N
E Full genome bp
T
I 109 108 107 106 105 104 103 102 101 1
C
CLIA Lab service providers

12. Monetize Epigenetic
Capabilities in Two Markets
ClinicalMDx <-R&D-> PharmacoMDx
Prostate, Lung Next Gen Sequencing Companion Diagnostics
CLIA Lab Epigenetic PCR R&D Lab
Direct sales force Business development
Physicians IP Pharma companies
Reimbursement Contracts + royalties
Market size > $2 Billion Proprietary Tests Market size >$3.4 billion

13. Agenda
 MDxHealth
– Epigenetics
– Business Model
 CLIA
– Regulatory Agencies
– Categorization
– CLIA 88: QMS/QC/QA
 Howto
– MDxHealth, a CLIA lab setup

14. CLIA ?
Congress established the Clinical
Laboratory Improvement
Amendments (CLIA) in 1988 to
ensure that patients' laboratory
tests were being handled by labs
qualified to handle them. Every lab
in the United States that handles
human test samples is required to
obtain CLIA certification.
Program administered by
CDC,FDA, CMS

15. Federal Regulatory Agencies
 U.S. Department of Health and Human Services
(hhs.gov)

18. Federal Regulatory Agencies
 U.S. Department of Health and Human Services
(hhs.gov)
– Food and Drug Administration (fda.gov)

21. Federal Regulatory
Agencies
 U.S. Department of Health and Human Services
(hhs.gov)
– Food and Drug Administration (fda.gov)
• Centers for Devices and Radiological Health (CDRH)
• Eg CDx typically requires a Premarket Approval (PMA)
submitted to FDA as 4 module

23. The FDA is responsible for test categorization
Categorization applies to all laboratory
test systems on materials derived from
the human body conducted for the
purpose of diagnosis, prevention or
treatment, or assessment of the health

24. What is Categorization?
 Process of assigning new commercially marketed
tests to one of 3 CLIA categories:
waived, moderate, high
 The key to understanding categorization; the
analyst/operator and the complexity of testing
 Regulations that govern categorization
– 42 CFR 493.17, categorization of specific laboratory
tests by level of complexity
• 7 Criteria: Knowledge, Training and
experience, Characteristics of operational
Steps, Calibration, QC, PT
materials, Troubleshooting, Maintenance, Interpretation
and judgment

25. Moderate, High
42 CFR 493.17
• 7 criteria scored as 1, 2, or 3
• Score of 1 = minimum
• Score of 3 = specialized
• Total scores of 12 or less = moderate
• 13 or higher = high
• e.g. PCR = high complexity

26. Most Common Waived Tests
Urine pregnancy – 34%
All other tests – 20%
Blood glucose (OTC) – 18%
Urine dipstick/tablet chemistries-19%
Ovulation tests – 5%
Fecal occult blood – 4%

27. FDA Databases

28. FDA Databases

29. Federal Regulatory Agencies
 U.S. Department of Health and Human Services
(hhs.gov)
– Food and Drug Administration (FDA)
– Centers for Medicare and Medicaid Services (CMS)
• Oversee regulations of all clinical laboratories (225,000) that
perform testing on human samples for diagnosis, prevention
or treatment, or for the assessment of an individual’s
health..
• “CLIA” or “CLIA 88”

30. Other Regulatory Agencies
 The College of American Pathologists (CAP) is an
independent accreditation agency that has been
awarded “deemed status” by CMS and performs
accreditations inspections for CLIA
 State and Regulatory Agencies
– Washington and New York State are exempt from
CLIA

31. CMS database
Total Number of Laboratories: 214,875
–Compliance 19,178
–Accredited 16,095
–Waived 134,778
–Provider Performed Microscopy 38,509
–Exempt 6,315
• NY 3,103
• WA 3,212
31

32. CMS database

33. Agenda
 MDxHealth
– Epigenetics
– Business Model
 CLIA
– Regulatory Agencies
– Categorization
– CLIA 88: QMS/QC/QA
 Howto
– MDxHealth, a CLIA lab setup

34. Why CLIA?
 Enacted as result of reports of inaccurate test
results from Pap smears (In U.S., estimated
44,000 to 98,000 deaths / year due to “medical
errors”)
 Questions were raised about how labs functioned
and what quality control procedures existed

35. Error Source
Ross and Boone1 Plebani et al.2
Pre-analytical 46% 68%
Analytical 7% 13%
Post-analytical 47% 19%
1Ross and Boone, Inst. of Critical Issues in Health Lab Pract,
DuPont Press, 1991
2Plebani and Carraro, Clin Chem 43:1348, 1997

36. Why CLIA?
Enacted as result of reports of inaccurate
test results from Pap smears (In U.S.,
estimated 44,000 to 98,000 deaths / year due to
“medical errors”)
Questions were raised about how labs
functioned and what quality control
procedures existed
Quality results for Quality healthcare
Adopt insights from Quality Management

37. QC
Quality Control (QC)
A set of procedures designed to monitor the test method and test results to
ensure appropriate test system performance

38. QC|A
Quality Control (QC)
A set of procedures designed to monitor the test method and test results to
ensure appropriate test system performance
Quality Assurance (QA)
The practice that encompasses all procedures and activities directed toward
ensuring that a specified quality of product is achieves and maintained

39. QC|A|MS
Quality Control (QC)
A set of procedures designed to monitor the test method and test results to
ensure appropriate test system performance
Quality Assurance (QA)
The practice that encompasses all procedures and activities directed toward
ensuring that a specified quality of product is achieves and maintained
Quality management (QMS) is what the organization does to
enhance customer satisfaction, and achieve continual improvement of its
performance

41. QMS evolving standards (CLIA-CLSI-ISO)
1988
CLIA’88
2003
CLIA
Final QC Rule

42. Quality Management System
Essentials
These CLSI and ISO standards apply a core set of 12 quality
system essentials basic to any organization across all
operations in the health-care path of workflow that defines
how a particular product or service is provided.

43. Quality Management System
Essentials
These CLSI and ISO standards apply a core set of 12 quality
system essentials basic to any organization across all
operations in the health-care path of workflow that defines
how a particular product or service is provided.
• The laboratory must be part of an organization that has
sufficient facilities to operate in a safe manner.

44. Quality Management System
Essentials
These CLSI and ISO standards apply a core set of 12 quality
system essentials basic to any organization across all
operations in the health-care path of workflow that defines
how a particular product or service is provided.
• The laboratory must be part of an organization that has
sufficient facilities to operate in a safe manner.
• Adequate personnel should be trained and competent to
perform the procedure, and the equipment must be
validated prior to patient testing and have regular ongoing
maintenance.

45. Quality Management System
Essentials
These CLSI and ISO standards apply a core set of 12 quality
system essentials basic to any organization across all
operations in the health-care path of workflow that defines
how a particular product or service is provided.
• The laboratory must be part of an organization that has
sufficient facilities to operate in a safe manner.
• Adequate personnel should be trained and competent to
perform the procedure, and the equipment must be
validated prior to patient testing and have regular ongoing
maintenance.
• All supplies must be traceable by lot and shipment and
performance verified prior to use on samples.

46. Quality Management System
Essentials
 The process of analysis must be controlled and documented.

47. Quality Management System
Essentials
 The process of analysis must be controlled and documented.
 Records of patient testing must be maintained and all
procedures and policies must be under document control to
prevent unexpected changes without supervisory approval.

48. Quality Management System
Essentials
 The process of analysis must be controlled and documented.
 Records of patient testing must be maintained and all
procedures and policies must be under document control to
prevent unexpected changes without supervisory approval.
 Management of information is thus important, both in
protecting confidentiality and for providing traceability of the
testing process from sample to reagent to result.

49. Quality Management System
Essentials
 The process of analysis must be controlled and documented.
 Records of patient testing must be maintained and all
procedures and policies must be under document control to
prevent unexpected changes without supervisory approval.
 Management of information is thus important, both in
protecting confidentiality and for providing traceability of the
testing process from sample to reagent to result.
 Finally, the laboratory must assess the quality of its
results, and respond to complaints and occurrences.
 Customer satisfaction should be monitored and performance
improved when issues are noted.

50. Quality Control
Quality control is a set of procedures designed to monitor the
test method and test results to ensure appropriate test
system performance.
CLIA' 67 was the first quality law for clinical laboratories in the
United States that mandated the performance of two levels of
quality control, at a normal and abnormal concentration of
analyte, each day of patient testing. CLIA 88 reinforced this
need for two levels of controls at least every 24h of testing
Two levels of controls each day of testing have thus
become the de facto historical standard for good
laboratory practice.

51. The Role of the Laboratory Director
The laboratory director plays a central leadership role in
laboratory management. The laboratory director holds a
CLIA' 88 certificate that allows the laboratory to perform
testing under the director's supervision. The laboratory
director must ensure compliance with all legal and
regulatory aspects of CLIA88.
The laboratory director has ultimate responsibility for the
quality of laboratory results reported under his or her
direction. Although the laboratory director can delegate some
functions within the laboratory, he or she is ultimately
responsible for ensuring compliance.

52. The Role of the Laboratory Director
The federal government takes laboratory directorship seriously
and wants directors to play an active role in laboratory
management rather than just apply their name to licensing
paperwork.
Laboratory inspectors look for documentation of active
participation by the laboratory director, through meeting minutes,
signatures on policies and procedures, review of control and
proficiency test results, and participation in performance
improvement or other laboratory committees and activities.
For this reason, a laboratory director can only hold a maximum
of five CLIA 88 certificates.

53. Quality assurance (QA)
Quality assurance (QA) is an objective assessment of a laboratory's
capability and commitment to produce repeatable, defendable, and
accurate data. QA includes regulation of the quality of raw materials,
assemblies, products, and components; services related to production; and
management, production, and inspection processes. Two key principles
characterize QA: "fit for purpose" and "right at the first time." It is
important to realize also that quality is determined by the intended users.
Appropriate measures for QA should be
• Using validated methods of analysis
• Using internal quality control (QC) procedures
Participating in proficiency testing schemes
• Becoming accredited to an International Standard

54. Biomarker Fit-for-Purpose Validation
Definition Verification Development Validation Accuracy (final Regulatory /
Phase Phase Phase Phase clinical studies) Product
Sequence area
Choose regions
Initial Designs
Design Verification
Final design
Transfer to CLIA as service

55. Biomarker Fit-for-Purpose Validation
Definition Verification Development Validation Accuracy (final Regulatory /
Phase Phase Phase Phase clinical studies) Product
Phase II/III / Pre-IDE
Preparation for phase II/III study:
• Move product to development phase
• Start FFP validation for clinical studies
• Obtain IDE
• Accuracy based on therapeutic responses

56. Biomarker Fit-for-Purpose Validation
Definition Verification Development Validation Accuracy (final Regulatory /
Phase Phase Phase Phase clinical studies) Product
Preparation for Regulatory submission:
• Finalize manufacturing
• Supply agreements, reagents, instruments, software etc
• Produce multiple lots
• Validate as final assay “fit” for the recruitment of patients
• Submit with drug as CDx

57. “right at the first time” –> Method Validation
Validation of methods is an integral part of QA to demonstrate
the applicability for the intended use. According to IUPAC
technical report, typical performance characteristics of
analytical methods are applicability, selectivity, calibration,
trueness, precision, recovery, operating range, limit of
quantification, limit of detection, sensitivity, and
ruggedness. Additional parameters may be relevant for
particular analytical purpose.
For quantitative bioanalytical procedures, at least the
following validation parameters should be evaluated :
selectivity, calibration model, precision, bias, limit of
detection, the lower limit of quantification (LLOQ),
statistical process control, and measurement uncertainty.

58. Precision
Precision can be the "within-laboratory reproducibility,
where operator and/ or equipment and/or time and/or
calibration can be varied, but in the same laboratory." It is
usually specified as standard deviation (SD).
Method: Analysis of five to six replicates per level under
repeatability conditions. Control samples at low and high
concentrations relative to calibration range.
Acceptance criteria: Relative standard deviation (RSD)
within ±15% (±20% near LLOQ).

59. Limit of Detection
The limit of detection (LOD) is the smallest amount or
concentration of an analyte that can be reliably distinguished
from zero. Depending on the intended use, it must not be part
of the validation procedure. For practical use, the LOD can be
determined with a simple procedure. The values for this
"practical" LOD were greater than the possible "instrumental"
LOD.
Method: Analysis of the LOD using spiked samples with
decreasing concentrations of the analyte.
Acceptance criteria: Checking for compliance with
identification criteria or a signal-to-noise ratio (SNR) >= 3.

60. The Lower Limit of Quantification
The LLOQ defines the concentration below which the
analytical method cannot operate with an acceptable
precision.
Method: Control samples with an analyte
concentration near the LOQ. Alternatively, analysis of
spiked samples with decreasing concentrations of the
analyte.
Acceptance criteria: Compliance with accuracy and
precision data of control samples near LLOQ or a
SNR >= 10.

61. CDx: Fit-for-Purpose / Minimizing Error
Definition Verification Development Validation Accuracy (final Regulatory /
Phase Phase Phase Phase clinical studies) Product
Manufactured Components
No
LOD
LOD, LOQ, LLOQ, LLOD
LOQ
Precision
Selectivity
Reproducibility
Precision
Robustness
Linearity
Linearity
Accuracy
Cutoff determination
Accuracy

66. CLIA vs ISO/CLSI
CLIA –more specific in some areas, eg
– Personnel
– Quality control
– PT
– Record retention
ISO/CLSI –more general, e.g.
– Applies to all laboratories, regardless of test
complexity
– Management system
– Internal and external assessment

67. Agenda
 MDxHealth
– Epigenetics
– Business Model
 CLIA
– Regulatory Agencies
– Categorization
– CLIA 88: QMS/QC/QA
 Howto
– MDxHealth, a CLIA lab setup

69. to CLIA or to CLIA
(there no question)
Prof. Wim Van Criekinge, CSO
9th of march 2013