Biochemical Genetic Test Establishment and

2015 Webinar Series
Biochemical Genetic Test Establishment and Verification
4/8/2015
Speakers
Tina M. Cowan, PhD, Associate Professor of Pathology and Director, Clinical Biochemical Genetics Laboratory,
Stanford University, Palo Alto, CA
Tina Cowan is an Associate Professor of Pathology at Stanford University Director of the Stanford Clinical
Biochemical Genetics Laboratory. She received her PhD in Genetics from UCLA and postdoctoral fellowship training
in Medical Genetics at the Universtiy of Maryland Baltimore. She is certified by the American Board of Medical
Genetics and Genomics in Clinical Biochemical Genetics, has served on a number of national committees and
boards for medical genetics, education, and laboratory quality.
Chunli Yu, M.D., FACMG, Associate Professor, Director of Biochemical Genetics Division, Mount Sinai Genetic
Testing Laboratory, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New
York, NY
Dr. Yu is currently an Associate Professor of Genetics and Genomic Sciences Department at Icahn School of
Medicine at Mount Sinai and Director of Biochemical Genetics Division at Mount Sinai Genetic Testing Laboratory.
Dr. Yu was board certified in clinical biochemical genetics in 1999 and has extensive experiences in directing large
academic biochemical genetics laboratories. Dr. Yu’s professional career has been focused on the laboratory
diagnosis and monitoring of patients with inborn errors of metabolism of carbohydrates, fatty acids, amino acids, and
organic acids, as well as porphyrias and lysosomal storage diseases. She is particularly interested in applications of
LC-MS/MS technology in biochemical genetic testing and new assay development.
Objectives
At the conclusion of this program, participants will be able to:

Describe the basic elements of analytical test validation and their application to biochemical genetics testing.

Recognize the importance of addressing clinical validity in addition to analytical validity in the development of new biochemical
genetics tests.
Continuing Education Credit
4/8/15 – 10/8/15
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laboratory sciences by the ASCLS P.A.C.E.® Program. Participants who successfully complete each program will be awarded 1.0
®
contact hours. P.A.C.E. is accepted by all licensure states except Florida. APHL is a Florida and CPH-recertification approved CE
provider; each course has been approved for 1.0 contact hours.
10/9/15 – 4/8/16
No CEU credit, but after completing the evaluation you will receive a certificate of attendance.
Evaluation/Printing Certificate
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d. 4/8/15 – 10/8/15
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e.
10/9/15-4/8/16
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Faculty Disclosure
Analysis. Answers. Action.
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Biochemical Genetic Test
Establishment and Verification
The Association of Public Health Laboratories adheres to established standards
regarding industry support of continuing education for healthcare professionals.
The following disclosures of personal financial relationships with commercial
interests within the last 12 months as relative to this presentation have been
made by the speaker(s):
“Nothing to disclose”
Chunli Yu, MD
Tina Cowan, PhD
Analysis. Answers. Action.
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Objectives
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Regulations and Guidelines
for Test Establishment
• Describe the basic elements of analytical test validation
and their application to biochemical genetics testing.
• Recognize the importance of addressing clinical validity
in addition to analytical validity in the development of
new biochemical genetics tests.
CLSI
CLIA
ACMG
CAP
MMWR
Analysis. Answers. Action.
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LDTS: Validation vs. Verification
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ANALYTIC VALIDATION:
1. Establishment of performance specifications:
A type of in vitro diagnostic test that is designed,
manufactured and used within a single laboratory
• Validation
Process to confirm with objective evidence that a
laboratory-developed or modified FDA-cleared/approved
test performs as intended
• Verification
a.
b.
c.
d.
e.
f.
g.
Accuracy
Precision
Analytical sensitivity
Analytical specificity to include interfering substances
Reportable range of test results for the test system
Reference intervals (normal values)
Any other performance characteristic required for test performance
2. Determination of calibration and control procedures
3. Documentation
Process to confirm with objective evidence that
performance claims of a test have been met
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Test Establishment: 42 CFR §493.1253
• Laboratory Developed Test (LDT)
Analysis. Answers. Action.
Analysis. Answers. Action.
[68 FR 3703, Jan. 24, 2003; 68 FR 50724, Aug. 22, 2003]
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Analysis. Answers. Action.
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Test Validation Elements
Clinical validity
Analytic validity
Analysis. Answers. Action.
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Clinical Validity – MMWR Guidelines
Laboratories should ensure that tests are clinically relevant
and can be interpreted for specific clinical situations
Sensitivity
Specificity
Positive predictive value
Negative predictive value
• Documentation of clinical validity from available information
sources
• Establishment of clinical validity based on internal studies
using previously characterized positive and normal samples
Accuracy/Precision
Analytic sensitivity
Analytic interference
Reportable range
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• Determination of test results that suggest imminent or
potentially life-threatening conditions, or of critical values or
alert values that warrant immediate medical attention
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Clinical Validity Elements
Analysis. Answers. Action.
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Definition of Terms
accuracy with which a test identifies a particular condition
Sensitivity
• proportion of people with condition
who test positive
Specificity
• proportion of people without
condition who test negative
Test Result
Positive
Positive
of people with positive
predictive value • proportion
result who have the condition
(PPV)
Test Result
Negative
Negative
of people with negative
predictive value • proportion
result who do not have the condition
(NPV)
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Burke W. Clinical validity and clinical utility of
genetic tests. Curr Protoc Hum Genet. 2009
Jan;Chapter 9:Unit 9.15.
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Condition
Positive
Condition
Negative
True
Positive
False
Positive
PPV
False
Negative
True
Negative
NPV
Sensitivity
Specificity
Analysis. Answers. Action.
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Factors Influencing Clinical Performance
Genetic Influences on Test Performance
• Analytic test performance (more later)
• Intermittent or subtle nature of some abnormalities
Certain fatty acid oxidation disorders (MCAD, VLCAD)
Intermittent maple syrup urine disease
Glutaric acidemia type I (low-excretor variant)
• Other clinical considerations
Diet (e.g., TPN, protein restriction, MCT)
Medication (e.g., antibiotics, antiepileptics)
Other therapies (e.g., dopamine, arginine, IVIG)
Clinical status (e.g., hypoxia, renal or hepatic failure,
pregnancy, catabolic state)
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• Enzyme pseudodeficiencies
e.gαglucosidase, β-hexosaminidase
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Analysis. Answers. Action.
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The Interpretation – General Guidelines
F1.2 In most cases, the analytical methods used by
biochemical genetics laboratories are similar to
those of standard clinical chemistry laboratories.
Accordingly, procedures for test validation, quality
control, quality assurance, and monitoring of safety
and equipment performance are generally the
same in both settings.
https://www.acmg.net/
Importantly, the biochemical genetics laboratory
differs from the clinical chemistry laboratory in the
extent of interpretation required in order to provide
a valid and meaningful result. Interpretation of
biochemical genetics tests should be provided by
an American Board of Medical Genetics (ABMG)certified clinical biochemical geneticist, ideally
taking into consideration the clinical history, results
of other tests, and other relevant parameters.
Ensuring a Meaningful Interpretation
Information provided to the laboratory
• Indication for testing
– Clinical presentation, abnormal NBS, positive family history, follow-up
of known condition
• Clinical history
– Diet, medications, nutritional status, other relevant factors
• Labs should seek information when needed
Knowledge of normal and disease states
• Elevated BCAA in catabolism vs. MSUD
• Enzyme pseudodeficiency
• Experience with as many conditions as possible
– Testing a broad range of known positives (challenging)
– Staying current with literature
– Collaboration is essential!
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Recognition of a Medical Emergency
MMWR: Determination of test results that suggest
imminent or potentially life-threatening conditions, or of
critical values or alert values that warrant immediate
medical attention
• Setting guidelines (vs. critical values)
– Determined by Medical Director
– Examples:
• New diagnosis in a previously unknown patient
• Elevated galactose-1-phosphate in a newborn
• Very high leucine or citrulline
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Pre-Validation Considerations (LC-MS/MS)
•
Thorough optimization of LC and mass spec parameters
•
Qualifier/quantifier SRM transition ratios
•
Selection of appropriate internal standards and concentrations
– Stable isotope labeled
– Structural analog
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Evaluation of carryover
•
Evaluation of background noise level
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Analysis.
Answers.
Action.
CLSI C62-A
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Analysis. Answers. Action.
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Analytic Validity
performance characteristics with which a test measures a particular analyte or analytes
Accuracy
Precision
• Closeness of agreement between an
individual value and a true value
• Closeness of agreement between multiple
independent test results
Analytic
sensitivity
• Lower limit of detection (LLOD)
• Lower limit of quantification (LLOQ)
Analytic
interference
• The laboratory must be aware of common
interferences by performing studies or
having available studies performed
elsewhere
Reportable
range
• Analytic measurement range (AMR), the
range of analyte values that a method can
directly measure on the specimen without
any dilution or concentration
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CLSI Statispro software
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Quantitative Evaluation of Matrix Effects
(LC-MS/MS)
• Matrix effects (ME)
ME (%)= B/A x 100
• Recovery (RE)
RE (%) = C/B x 100
• Process efficiency (PE)
PE (%) = C/A x 100
• A: Neat standards
• B: Standards spiked to
the extracted matrix
• C: Standards spiked to
matrix and then
processed
Matuszewski BK, et al, Strategies for the assessment of matrix effect in quantitative bioanalytical methods
based on HPLC-MS/MS. Anal Chem. 2003; 75 (13): 3019-3030.
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Analyte and Matrix Stability
Analytic Accuracy
• No absolute guidance on experiment design
• Stability of analyte and sample matrix from collection to
result
• Testing homogenous aliquots under different conditions
over time
e.g. extreme temp, room temp, 4C, -20C
• Amino acids
• Acylcarnitines
Analysis.
• Enzymes
Answers.
Action.
– Biotinidase, GALT
closeness of agreement between an individual value
and a true value
• Approaches to evaluating accuracy:
– Measure recovery of spiked samples
– Split samples with an established laboratory
(CLSI EP09-A3: n = 40)
– Test known PT samples, compare to participant consensus
ERNDIM (http://www.erndimqa.nl/)
CAP BGL (carnitine)
CDC NSQAP
• Evaluate throughout entire analytic measurement range
Low (near LLOQ), mid, and high (near ULOQ)
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Analytic Precision
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Analytic Sensitivity
closeness of agreement between independent test
results
• Lower limit of detection (LLOD)
Signal/noise ratio >3.0
• Repeat testing over time
Patient samples, standards, QC material
• Lower limit of quantification (LLOQ)
• Within-run precision (repeatability)
 20% precision;  20% bias
e.g., 20 replicates of same prep
(CLSI EP17-A2)
• Between-run precision (reproducibility)
e.g., repeat entire testing process daily for 20 days
• Calculation of coefficient of variation (CV%)
• Clinical implications of LLOQ
Careful validation of metabolites with clinical significance
at very low concentrations (e.g., citrulline in proximal urea
cycle defects)
= SD/mean x 100
• Comparison to acceptance criteria
e.g.,   10-15%,   20% at LLOQ or ULOQ
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Reportable Range
Analytic Measurement Range (AMR)
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Analytic Interference
• Identification and characterization of interferents
• Analyze replicates throughout concentration range
• Calculate precision and bias at each concentration level
Acceptance criteria, e.g., CV  20%, Bias  20%
• Evaluate linearity, compare to criteria
e.g., R2>0.995
Literature search
Testing samples with known or potential sources of
interference
Hemolysis, icterus, lipemia, various collection tube additives
• Specific examples for biochemical genetics:
Amino acid analysis
Hemolysis (glu, asp, tau); ampicillin (phe)
• Other considerations
Matrix effects
Clinical reportable range
Dilution protocol
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Analysis.
Answers.
Action.
Acylcarnitine profile
Pivalic acid containing antibiotics (C5); cefotaxime and IV dextrose
(C16-OH)
Biotinidase
Sulfa drugs
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Analysis. Answers. Action.
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Considerations of Enzyme Testing
Reference Interval
• Analytic specificity
• Pediatric samples might be challenging to obtain
• Certain specimen types are difficult to obtain
– CSF, muscle, fibrablasts
• Normal ranges vs disease ranges
– Affected range (enzyme)
– Carrier range (Hex A%)
• Comparing to published literature ranges
• Periodic verification after test implementation
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– Use of specific inhibitors
• Pompe disease - acarbose
• Fabry disease – α-N-acetylgalactosamine
• Interference from clinical status
– Pregnancy, diabetes, prematurity
• Reference interval
– Normal range and affected range
– Non-carrier range and carrier range
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Test Implementation – The Basics
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Clinical validity (literature references or internal studies)
Analytic validity
Quality plan
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Standard operating procedure
Proficiency testing procedures
Personnel training and competency
Documentation and review of validation study
Analysis. Answers. Action.
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Test Implementation – Other Details
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– QC material, frequency, thresholds, QA review and documentation
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Practitioner and patient education materials
Sample collection and handling instructions
Test requisition form
Billing codes
Lab website, test directory, CAP activity menu
Results reporting
– Format
– Disclaimer (COM.40630)
Reports for laboratory-developed tests (LDTs) contain a statement that the assay was developed
by the laboratory.
Example: "This test was developed and its performance characteristics determined by <Laboratory X>. It
has not been cleared or approved by the FDA. The laboratory is regulated under CLIA as qualified to
perform high-complexity testing. This test is used for clinical purposes. It should not be regarded as
investigational or for research.”
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Last But Not Least….
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• New tests must be completely validated, even if they
have already been validated by another laboratory
There is a summary statement, signed by the laboratory director (or designee who
meets CAP director qualifications) prior to use in patient testing, that includes the
evaluation of validation/verification studies and approval of each test for clinical
use.
The summary statement must include a written assessment of the validation/verification study, including the
acceptability of the data. The summary must also include a statement approving the test for clinical use with the
approval signature such as, "This validation study has been reviewed, and the performance of the method is considered
acceptable for patient testing."
For … LDTs, the summary must address analytical sensitivity, analytical specificity and any other parameter that is
considered important to assure that the analytical performance of a test (e.g. specimen stability, reagent stability,
linearity, carryover, and cross-contamination, etc.), as appropriate and applicable.
If the laboratory makes clinical claims about its tests, the summary must address the validation of these claims.
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In Summary
COM.40000
Method Validation/Verification Approval
Analysis. Answers. Action.
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• The laboratory is responsible for assuring and
documenting clinical claims and analytic performance
• Clinical validation should be performed and
documented wherever possible, but can be
challenging for some areas of biochemical genetics
• Analytic validation requirements do not differ from
other laboratory sections, but approaches for
implementation may be unique
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Analysis. Answers. Action.
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Thank you!!
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