Molecular and Genetic
Clinical Diagnostics
An Introduction to Use,
Application, Technology and
Coding
February 16, 2011
1
Results For Life: The Value of Laboratory Medicine
• Message
– Laboratory medicine central to
medical decisions
– Laboratory medicine changes
course of diagnosis, treatment,
management
• Audience
– Congress, media, thought leaders
• Tools
– Briefings, OpEds, advertising
2
ACLA Members and Associate Members
Associate Members
ACLA Member Sponsors
Aculabs
Agendia
Arista Laboratories
ARUP Laboratories
Aureon Laboratories
Aurora Diagnostics
Axial Biotech
Berkeley Heartlab
Biodesix
BioReference Laboratories
bioTheranostics
CBLPath
Clarient
Cleveland Clinic Foundation
CorePlus
DaVita
DCI Laboratory
Genomic Health
Genoptix
GI Pathology, PLLC
Joint Venture Hospital Labs
Laboratory Corp of America
Laboratory Partners
Machaon Diagnostics
Mayo Clinic
MEDTOX Laboratories
Meridian Laboratories
Myriad Genetics
NeoGenomics Laboratories
NMS Labs
PathNet Esoteric Lab Inst
Pathology Associates
Medical Laboratories
Pathology
PerkinElmer Genetics
Precision Therapeutics
Quest Diagnostics Incorporated
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RedPath Integrated Pathology
Satellite Laboratory Services
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American Medical Technologists
Aperio
Cgate Health
HillCo Health
LipoScience
McKesson Health Solutions-Adv Diagn. Mgt
Roche
Siemens
Sysmex
XIFIN
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A revolution in science requires a revolution in thinking
• What disease is
• How to identify and treat disease
• When it is best to take action
• Which individuals are at risk
• The size of the population we treat
• The economics of utilization and health spending
• The ability to reduce adverse events, side effects, inappropriate
use
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Because we know vastly more about disease…
Diagnose more precisely
More effective treatment
Select specific treatment
that best fits disease
Avoid adverse drug reaction
Improve utilization
Predict risk before
symptoms occur
Earlier treatment
Preventive action
Manage more effectively
Better timing
Adjustments as disease changes
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Today
• The basics of genetic testing
Presentation
• The use and value of genetic testing
– Personalized medicine
– Pharmacogenomics
– Emerging Technologies
• Laboratory procedures and coding
Speakers

Vicky Pratt, Ph.D., FACMG, Quest Diagnostics

Sherri Bale, Ph.D., FACMG, GeneDX

Kaye Jones, MLS (ASCP), CPC, LabCorp
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THE BASICS OF GENETIC TESTING
Presented by
Victoria Pratt, Ph.D., FACMG
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One of the most fundamental “basics”
• Diagnostic laboratory testing drives health
decisions
– 70% of healthcare decisions based on diagnostic data
• Diagnostic data yields essential information
– Helps identify trends for public health
– Enables physicians to care for individual patients
– Facilitates new test development
• Continuum of diagnostic lab testing
– From diagnosis to predictive and personalized medicine
• Diagnostic data increasingly…
– … is providing actionable insights physicians can use to
improve patient healthcare outcomes
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DNA » RNA » Protein
DNA
Cell
membrane
Nucleus
DNA
bases
mRNA
Chain of
amino
acids
Gene
Protein
Ribosome
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Gene Tests: Three Common Methods
Mutation Absent
Mutation Present
Chromosome
Cytogenetics
DNA
Molecular Genetics
Protein
Biochemical Genetics
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Types of Mutations
• Single nucleotide - traditional
–
–
–
–
Missense
Nonsense (creation of stop codon)
Splicing
Regulatory sequences (promoter, 3’ end)
• Deletions/Insertions – copy number variants (CNVs)
– In frame
– frameshift
• Expansions (triplet repeat disorders)
• Epigenetic (methylation)
• Translocations and inversions
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Alleles
Quiet! I’ll speak
for both of us!
Dominant
Allele
I’ll have to be
in charge now!
Normal
Allele
Recessive
Allele
Damaged
Allele
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Human Chromosomes
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
X Y
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Gene Mutations
Mismatch
Insertion
Deletion
Deletion
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General Principles
• Hereditary disorders can affect multiple organs
• Penetrance can be influenced by modifiers:
genes + environment
• Complexity of mutational spectrum varies
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Different Genes, Different Functions
Bone Cell
Pancreas Cell
Brain Cell
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Gene inheritance is complex
Gene Changes in Cystic Fibrosis
Mucus Production Gene
Normal
Mutation 1
Mutation 2
Mutation 3
No
Symptoms
Severe
Symptoms
Mild
Symptoms
No
Symptoms
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Continuum of Diagnostic Lab Testing
Diagnostic
Predictive
Personalized
Confirm diagnosis
Identify higher
chance for disease
before symptoms
Tailor drug
treatment to
genotype
Example
Example
Example
Cystic Fibrosis
Huntington
Disease
HIV Therapy
Physician
Patient
Pharma
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Common genetic disorders
• Inherited (predictive or diagnostic)
–
–
–
–
Cystic fibrosis
Thrombophilia
Hereditary hemochromatosis
Fragile X syndrome
• Acquired (predictive or diagnostic)
– Chronic myelogenous leukemia (CML)
• Pharmacogenetics (personalized)
– Cytochrome P450s
– HLA
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New Assay/Biomarker Progression
Retrospective
clinical trials
CLINICAL
RESEARCH
Biomarker
associated
with
disease
Prospective
clinical trials
TEST
TRANSLATION
Lab test
developed Analytical
validation
CLINICAL
VALIDITY
Test can
predict
clinical
outcomes
CLINICAL
UTILITY
Benefits
patients
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THE USE AND VALUE OF GENETIC TESTS
FOR PATIENTS
Presented by
Sherri J Bale, Ph.D., FACMG
Victoria Pratt, Ph.D., FACMG
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Genetic Tests for Constitutional Mutations
• Cytogenetic Tests
• Molecular Tests
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Cytogenetic Test
• Standard karyotype, used to look for gross
chromosomal anomalies in children with
development delays, congenital anomalies,
mental retardation
• FISH, used to look at 1 or 2 specific chromosomal
regions suspected by the physician
• BAC arrays, used to look at many (100s)
chromosomal regions at once, using FISH
technology
• CGH array, used to look at MANY (50K-200K)
regions at once, and identify specifically which
genes are involved in the chromosomal anomaly
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Child with Multiple Congenital Anomalies and/or Autism
Standard karyotype
CGH array - “molecular karyotype”
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Patient with Tetralogy of Fallot, Suspected 22q11 Deletion
• FISH test, 2 probes:
–
–
–
–
used in baby
found deletion
confirmed dx
Provided prognostic
info to family.
• Parents tested by FISH:
– Negative
– Provided information
re: risk in future
children
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Child with Multiple Anomalies and Autism;
No Specific Syndrome Suspected
• Karyotype normal
• CGH array followed Karyotype.
– Identified deletion involving end of one arm of
chromosome 3
• Parents tested by FISH and dad found to be
balanced carrier of the deletion
• Prenatal diagnosis by quantitative PCR is now
possible for the family.
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Molecular Test – PCR, followed by sequencing, for
identification of mutation
• Used to identify mutation in a patient with
inherited disease
• Number of times PCR is done and how much
sequencing is required depends on SIZE of
gene, MANY UNITS.
• Once mutation is identified, testing of parents,
sibs, other relatives for ONLY that mutation, is
needed. ONE or ONLY a FEW UNITS.
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Molecular diagnosis of Gorlin Syndrome
• 13 yo child presented to dentist with a jaw cyst – surgery
performed but tooth was lost. Referred to geneticist.
• Geneticist suspected Gorlin Syndrome
• Molecular diagnosis involved PCR and sequencing, 26 “units”
(large gene). Mutation identified.
• Prognosis now known: This individual would develop many
skin cancers, more jaw cysts.
• Regular surveillance by dermatologist and dentist allowed
early identification, less expensive treatment, and good
clinical outcome:
– Teeth were saved; Minimal damage to nose, ears, eyes
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Use and Value of Genetic Tests
• Diagnosis
– Enables physicians to properly care for patient
• Prognosis
– Appropriate surveillance leading to early care and
intervention
• Risk Information
– Is it inherited? What is the recurrence risk in future
pregnancies?
• Prenatal/Pre-symptomatic diagnosis
– Allows informed decision making, preventive care
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Personalized Medicine, Pharmacogenetics
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Chronic Myelogenous Leukemia
Science
Patient Care
Fusion of BCR/ABL genes
Better response rates, less toxicity
FISH, Quantitative PCR to identify
Complete remission in many patients
Treatable with Gleevac
5-year survival rate: 69% in 2001, 89%
now
Some patients become resistant to
Gleevac
Mutations in tyrosine kinase
domains (DNA sequencing)
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Clopidogrel (Plavix®)
Science
Patient Care
To inhibit blood clots in coronary
artery disease, peripheral artery
disease, and cerebrovascular disease.
Prevention of vascular ischemic events
in patients with symptomatic
artherosclerosis
Metabolized by cytochrome P450
2C19 to active form
Also used, along with aspirin, for
preventing thrombosis after placement
of intracoronary stent
FDA: clopidogrel cannot be taken
with Prilosec (omeprazole) and
Nexium (esomeprazole)
Inhibitors of 2C19
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EMERGING TECHNOLOGIES AND TESTING
Presented by
Victoria Pratt, Ph.D., FACMG
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The genome is complex
• High throughput DNA sequencing
• microRNAs
• Copy Number Variants (CNVs)
• Epigenetics
– methylation
• Proteomics
– Up and down regulation
– Disease-specific patterns
34
New high throughput DNA (NextGen) sequencing
methods
• Reduced the cost
• Increased sequencing capacity
• 454 (Roche)
• Solexa (Illumina)
• SOLiD (ABI)
35
MicroRNAs (miRNA)
• Single-stranded RNA molecules
– 21-23 nt
– Transcribed from non-coding DNA
• Regulate gene expression
• Cancer
– May enable classification of cancers (CUP = cancer of
unknown primary)
– Determine therapy
36
Copy Number Variants (CNVs) (Variome)
• Large deletions or duplications of DNA
– Usually cannot be detected by DNA sequencing
– Newer technologies
• aCGH
• Impacts
–
–
–
–
–
Autism
Alzheimer disease
Parkinson disease
susceptibility to HIV-1
some forms of color blindness
37
Epigenetics
• Changes in chromatin structure (how DNA is
packaged) or alters gene activity without
changing the DNA
– DNA methylation
– Modification of histones
– Position effects
• Cancer and imprinting disorders
38
Genetic tests find mutations, not disease
Chances of Developing Breast Cancer by Age 65
8
100
7
80
6
60
5
40
4
20
3
0
With BRCA 1
Gene
Without BRCA 1
Gene
2
1
Normal BRCA1
0
Altered BRCA1
39
LABORATORY PROCEDURES AND CODING
Presented by
Kaye Jones, MLS(ASCP), CPC
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Objective
• To improve your understanding of current molecular
diagnostic CPT coding
41
Molecular Codes
• CPT codes 83890-83914 represent steps
performed during molecular diagnostic
procedures
• CPT codes are assigned based on the different
steps and the number of times each type of step
is performed.
• Example: 83898 Amplification x3
83896 Nucleic acid probe,
each x25
42
Molecular Codes
• Different molecular methods may be used for
the same analyte
• Those methods may vary among different
laboratories.
• Therefore, different labs may code their tests
differently
43
Molecular Codes
• No clear written guidelines for how to assign
units of service
• Example: When a Cystic Fibrosis procedure
for 23 mutations is performed by two
different labs
– One lab bills for 23 probes (1 per mutation).
– The other lab bills for 46 probes (2 per mutation
because you need a normal and a mutant probe
for each in order to interpret the assay).
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Molecular Codes
• All industry stakeholders recognize the
issues surrounding the assignment and
billing of molecular diagnostic procedures
• A number of organizations and entities are
engaged in a collaborative process to
review and address coding issues in an
effort to increase transparency
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Cytogenetics
• This is another area where CPT codes are
assigned based on the procedural steps
performed.
• Routine chromosome analysis typically requires
three steps to complete the procedure.
– 88230 Tissue culture
– 88262 Karyotyping
– 88291 Interpretation and report with a picture of the
actual chromosomes
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Cytogenetics
• Cytogenetic FISH is often necessary to
diagnose constitutional defects
• Cytogenetic FISH may also be a stand
alone order necessary to evaluate
leukemias such as CML and MM
• Units of service are determined by the
number of FISH probes and specific
procedures needed to evaluate the
cells
47
Molecular Diagnostics and Cytogenetics
• Think of newer CGH procedure as a
combination of molecular diagnostic
procedural steps needed to prepare the
patient’s sample, and the cytogenetic CGH chip
analysis
• There is much confusion within the industry
regarding how to assign CPT codes to CGH
procedures
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Molecular Diagnostics and Cytogenetics
• Array CPTs 88384-88386 are in the Surgical
Pathology section of CPT.
• These codes are
– global codes with Technical and Professional
components,
– only represent the work needed for the array chip and
I&R
– sample preparation is coded with molecular
diagnostic codes
– only appropriate for when a physician/pathologist
performs the I&R
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Molecular and Cytogenetic Codes
• In summary:
– Molecular procedures are coded based on the
procedural steps
– Units of service are determined by the number of
times each step is performed
– Different procedures may exist for the same analyte,
which makes the CPT coding different
– Lack of standardized coding guidelines add to the
complexities of how to assign CPTs
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Thank you
• For more information, contact:
David Mongillo, Vice President for Policy and Medical Affairs
American Clinical Laboratory Association
dmongillo@clinical-labs.org
202-637-9466
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