Transcript Slide 1

Use and Value of Genetic Tests for
Patient Care
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Review of Technologies
Real life examples
Sherri J Bale, PhD, FACMG
Definition of Genetic Testing:
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The analysis of human DNA in any
of its forms or related products
(chromosomes, RNA, proteins)
Uses of Genetic Testing:
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To detect disease-related
genotypes, mutations, phenotypes,
or karyotypes for clinical purposes
Genetic Tests for Constitutional
Mutations
 Cytogenetic
Tests
 Molecular Tests
Cytogenetic Test
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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.
Child with Multiple Congenital
Anomalies and/or Autism
Standard karyotype
CGH array - “molecular
Karyotype”
Patient with Tetralogy of Fallot,
suspected 22q11 deletion
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FISH test, 2 probes,
used in baby, found
deletion, and
confirmed dx.
Provided prognostic
info to family.
Parents tested by
FISH, found to be
negative. Provided
information re: risk in
future children
Child with multiple anomalies and
autism; no specific syndrome
suspected
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Karyotype normal
CGH array followed Karyotype.
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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.
Molecular Test – PCR for wellcharacterized mutations
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KRAS gene test on tumor tissue
from patients with colorectal cancer
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Obtain tumor from patient
Extract DNA; PCR, then treat with
enzyme that allows visualization of the
mutation
Molecular Test – PCR, followed by
sequencing, for identification of mutation
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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.
Molecular diagnosis of Gorlin
Syndrome
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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:
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Teeth were saved; Minimal damage to nose, ears, eyes
Use and Value of Genetic Tests
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Diagnosis
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Prognosis
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Appropriate surveillance leading to early care
and intervention
Risk Information
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Enables physicians to properly care for patient
Is it inherited? What is the recurrence risk in
future pregnancies?
Prenatal/Pre-symptomatic diagnosis
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Allows informed decision making, preventive
care
Human
Genetics
Trends in
Testing
V.M. Pratt, Ph.D., FACMG
Diagnostic Laboratory Testing
Driver of Healthcare Decisions
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Diagnostic testing is foundation of healthcare
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Diagnostic data yields information serving
public and individual
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Information can help identify trends for public health
Data enables physicians to care for individual patients
Data facilitates new test development
Continuum of diagnostic lab testing
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70% of healthcare decisions based on diagnostic data
From diagnosis to predictive and personalized medicine
Diagnostic data increasingly is providing
actionable insights physicians can use to
improve patients’ healthcare outcomes
Genes in the News
The Basics of Genetic Testing
DNA->RNA->Protein
DNA
Cell
membrane
Nucleus
DNA
bases
mRNA
Chain of
amino
acids
Gene
Protein
Ribosome
Gene Tests – Three Common Methods
Mutation Absent
Chromosome
Cytogenetics
DNA
Molecular Genetics
Protein
Biochemical Genetics
Mutation Present
Types of Mutations
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Single nucleotide - traditional
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Deletions/Insertions – copy number variants
(CNVs)
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Missense
Nonsense (creation of stop codon)
Splicing
Regulatory sequences (promoter, 3’ end)
In frame
frameshift
Expansions (triplet repeat disorders)
Epigenetic (methylation)
Translocations and inversions
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
Human Chromosomes
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2
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5
6
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11
12
13
14
15
16
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21
22
X Y
Gene Mutations
Mismatch
Insertion
Deletion
Deletion
General Principles
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Hereditary disorders can affect
multiple organs
Penetrance can be influenced by
modifiers: genes + environment
Complexity of mutational spectrum
varies
Different Genes – Different Functions
Bone Cell
Pancreas Cell
Brain Cell
Disease 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
Why is Genetic Testing ordered?
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For couples who are having difficulty conceiving
For couples who have experienced two or more
miscarriages
To make a diagnosis in an affected individual
To see if pregnancy is at an increased risk for a
genetic disorder
To test people with a family history of a specific
inherited disease; patients may want to know if they
might develop the disease or pass it on to their
children
Continuum of Diagnostic Lab Testing
Diagnostic Predictive
Personalized
► Confirm
diagnosis
► Tailor drug
treatment to
genotype
-Cystic Fibrosis
► Determine higher
chance for disease
before symptoms
appear
-HIV Therapy
-Huntington Disease
Physician
Patient
Pharma
Common genetic disorders
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Inherited (predictive or diagnostic)
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Acquired (predictive or diagnostic)
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Cystic fibrosis
Thrombophilia
Hereditary hemochromatosis
Fragile X syndrome
Chronic myelogenous leukemia (CML)
Pharmacogenetics (personalized)
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Cytochrome P450s
HLA
New Assay/Biomarker Progression
Evidence-based medicine
Retrospective
clinical trials
Clinical
Research
Biomarker
associated
with disease
Prospective
clinical trials
Test
Translation
Clinical
Validity
Clinical
Utility
Lab test
developed Analytical
validation
Test can
predict
clinical
outcomes
Benefits
patients
Emerging Technologies and
Testing
The genome is complex
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High throughput DNA sequencing
microRNAs
Copy Number Variants (CNVs)
Epigenetics
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methylation
Proteomics
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Up and down regulation
Disease-specific patterns
New high throughput DNA sequencing
methods
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454 (Roche)
 20 megabases per 4.5-hour run
 capable of detecting mutations in an amplicon
pool at low sensitivity
 Reads: ~100 base pairs
 Can’t read highly repetitive or long polymers
Solexa (Illumina)
 Can sequence through homopolymers and
repetitive sequences
 10's of millions of short (24-36 bp) reads
 Single-end vs. paired end reads
MicroRNAs (miRNA)
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Single-stranded RNA molecules
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21-23 nt
Transcribed from non-coding DNA
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Regulate gene expression
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Cancer
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May enable classification of cancers
(CUP)
Determine therapy
Copy Number Variants (CNVs)
(Variome)
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Large deletions or duplications of DNA
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Usually cannot be detected by DNA sequencing
Newer technologies
 aCGH
Impacts
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Autism
Alzheimer disease
Parkinson disease
susceptibility to HIV-1
some forms of color blindness
Array CGH
Cross-platform identification and validation of CNVs
Jennifer L. Freeman et al. Genome Res. 2006; 16: 949-961
Epigenetics
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Changes in chromatin structure
(how DNA is packaged) or alters
gene activity without changing the
DNA
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DNA methylation
Modification of histones
Position effects
Cancer and imprinting disorders
Genetic Tests Find Mutations, NOT Disease
Chances of Developing Breast Cancer by Age 65
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10
90
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10
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Altered BRCA1
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Normal BRCA1
Benefits of Gene Testing
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Relief
Fewer Checkups
Informed Decisions
Intervention
Pharmacogenetics
V.M. Pratt, Ph.D., FACMG
Personalized
Medicine/Pharmacogenetics
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Getting the right dose to the right
patient at the right time
Chronic Myelogenous Leukemia (CML) example
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Philadelphia chromosome t(9;22)
 Detectable by standard cytogenetics
(karyotype analysis)
 FISH
Fusion of BCR/ABL genes
 FISH
 Quantitative PCR
Treatable with Gleevac
Some people become resistant to Gleevac
 Mutations in tyrosine kinase domains (DNA
sequencing)
Example: Tamoxifen
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Antiestrogen
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Used to treat estrogen receptor (ER)+
breast cancer
Metabolized by cytochrome P450 2D6
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blocks the activity of estrogen which can stop
the growth of some breast tumors.
Endoxifen (active form of Tamoxifen)
MEDCAC reviewing if should pay for
Medicare population
FDA reviewing whether to revise the drug
label to recommend CYP450 2D6
(CYP2D6) testing
Tamoxifen use
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treat breast cancer that has metastisized.
treat early breast cancer in women who have already
been treated with surgery, radiation, and/or
chemotherapy.
reduce the risk of developing a more serious type of
breast cancer in women who have had ductal
carcinoma in situ (DCIS) and who have been treated
with surgery and radiation.
reduce the risk of breast cancer in women who are at
high risk for the disease due to their age, personal
medical history, and family medical history.
Tamoxifen Metabolism
Various Assays/Platforms for
CYP2D6
Platform
Legal Status
Autogenomics
INFINITI
Luminex xTag
RUO
ParagonDx
IUO
RUO
Roche Amplichip
FDA-cleared
ABI SNaPshot
LDT
Example: Clopidogrel (Plavix)
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inhibit blood clots in coronary artery
disease, peripheral artery disease, and
cerebrovascular disease.
Metabolized by cytochrome P450 2C19 to
active form
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2-{1-[1-(2-chlorophenyl)-2-methoxy-2oxoethyl]-4-sulfanyl-3-piperidinylidene}acetic
acid
FDA-recently announced that clopidogrel
cannot be taken with Prilosec
(omeprazole) and Nexium (esomeprazole)
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Inhibitors of 2C19
Clopidogrel use
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Prevention of vascular ischemic events in
patients with symptomatic
artherosclerosis
Acute coronary syndrome without STsegment elevation (NSTEMI)
ST elevation MI (STEMI)
It is also used, along with aspirin, for the
prevention of thrombosis after placement
of intracoronary stent
Various Assays/Platforms for
CYP2C19
Platform
Legal Status
Autogenomics
INFINITI
Luminex xTag
RUO
Roche Amplichip
FDA-cleared
ABI SNaPshot
LDT
IUO
Laboratory
Procedures and Coding
Presented by
Kaye Jones, MLS(ASCP), CPC
Jan. 13, 2010
Objective
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To improve your understanding of
molecular diagnostic CPT coding
Molecular Codes
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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
Molecular Codes
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Different molecular methods may
be used for the same analyte.
Those methods may vary among
different laboratories.
Therefore, all labs will not
necessarily suggest the same CPT
codes for the same test.
Molecular Codes
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Another concern is that there are no clear
written guidelines for how to assign units of
service.
For example: When a Cystic Fibrosis
procedure for 23 mutations is performed by
two different labs
One lab bills for 23 probes (1 per mutation).
Whereas, 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).
Molecular Codes
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All stakeholders within the industry
recognize the issues surrounding
the assignment and billing of
molecular diagnostic procedures.
These concerns have resulted in a
number of organizations and
entities working together to review
and address the problems.
Cytogenetics
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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.
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88230
88262
88291
picture
Tissue culture
Karyotyping
Interpretation and report with a
of the actual chromosomes
Cytogenetics
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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.
Molecular Diagnostics and
Cytogenetics
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The newer CGH procedure can be
thought of 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.
Molecular Diagnostics and
Cytogenetics
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Array CPTs 88384-88386 are in the
Surgical Pathology section of CPT.
These codes are
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global codes with TC and Professional
components,
only represent the work needed for the
array chip and I&R,
sample preparation is coded with
molecular diagnostic codes, and
only appropriate for when a
physician/pathologist performs the I&R.
Molecular and Cytogenetic
Codes
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In summary:
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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.
Genetics
 Questions?