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Molecular Diagnostics
T. Mazzulli, MD, FRCPCDepartment of MicrobiologyUHN/Mount Sinai Hospital
October 19th, 2009
Objectives
Briefly review the concepts of DNA/RNA, bases, etc.
Review the methodologies available for molecular testing and describe some of the advantages and disadvantages
Discuss the currently available commercial assays that are available
The DNA/RNA Backbone
A ribose or a deoxyribose
A negatively charged phosphate group
DNA has an H at C2 so become “deoxy”
RNA has a hydroxyl at C2
C1 linked to a purine or pyrimidine base
Counter-parallel strands bind by H-bonding between nucleotides
http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/basepair.html
Components of DNA/RNA
Base Nucleoside:
Base + Ribose
Nucleotide:
Base + Ribose + Phosphate
Cytosine Cytidine (C) Cytidine monophosphate (CMP)
Uracil Uridine (U) Uridine monophosphate (UMP)
Thymine Thymidine (T) Thymidine monophosphate (TMP)
Adenine Adenosine (A) Adenosine monophosphate (AMP)
Guanine Guanosine (G) Guanosine monophosphate (GMP)
Basepairing is complementary
Chargaff's rule explains the amount of adenine (A) in the DNA of an organism, is the same as the amount of thymine (T) and the amount of guanine (G) is the same as the amount of cytosine (C)The C+G:A+T ratio varies from organism, especially among the prokaryotes
http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/basepair.html
What’s the point of all this? Genetic information is grouped into codons
Codons are triplets of nucleotides
Transcribed into anti-codon mRNA
Translated into amino acids which are the building blocks of proteins
http://www.accessexcellence.org/RC/VL/GG/genetic.html
Hybridization/Annealing
Sequences of DNA that anneal to target DNA or RNA– Must be complimentary– Primers and probes are therefore
specific for the target
No nucleic acid amplification
tatgcattatttaaaggg5’ 3’
3’----atacgtaataaatttccc----5’
Target
Probe
Molecular Methods
Critical to all molecular tests is extraction of RNA/DNAKey steps include extraction, amplification, detectionMay be used for:– Diagnosis– Monitoring– Screening
Three Methods:– Target amplification– Signal amplification– Probe amplification
Target (Nucleic Acid Amplification Tests) Amplification Methods
1. Polymerase Chain Reaction (PCR):– PCR– Reverse transcriptase (RT)-PCR– Real time (RT)-PCR– Nested PCR– Multiplex PCR– Qualitative/Quantitative PCR
2. Transcription-mediated amplification methods (TMA, NASBA)
3. Strand displacement amplification (SDA)
Polymerase Chain Reaction
Four key steps:1. Denature (Melt) DNA
2. Anneal primers (20-25 nucleotides) to DNA target
3. Extension of DNA using target DNA template
4. Detection of amplified product (amplicon)
After n cycles target is amplified by a factor of 2n (e.g. 35 cycles, 235 = 34 billion copies)
Need 30-40 cycles to be efficient
Requires excess of DNA polymerase, equimolar dNTPs, deoxyribonuleotide triphosphates (dNTPs), MgCl2 and buffer
PCR: Benefits
Crude extracts and small amounts of DNA may suffice Detection of the smallest possible quantities of target
DNA in clinical samples Can be automated and utilized in homogenous assay
methods Can utilize in quantitative and high-throughput assays Valuable for identifying cultured and non-cultivatable
organisms Used in epidemiology: repetitive elements PCR spacer
typing, selective amplification of genome restriction fragments, multilocus allelic sequence-based
PCR: Drawbacks
False positives Chance of contamination Need equipment and training May not be validated for all samples
and populations
Reverse Transcriptase (RT)-PCRReverse transcriptase will transcribe both single-stranded RNA and single-stranded DNA templates with equivalent efficiency RNA or DNA primer is required to initiate synthesisGenerates DNA copies of RNAs prior to amplifying that DNA by polymerase chain reaction (PCR)RNase H activity: RNase H is a ribonuclease that degrades the RNA from RNA-DNA hybrids and functions as an endonuclease and exonuclease Problems with nonspecific primer annealing and inefficient primer extension due to secondary structure can be overcome by using Thermus thermophilus reverse transcriptase Kits available for HCV and HIV-1
RNADNA primers
Reverse transcriptase
ssDNA
PCR step
RNA with Secondary structureMelt
Nested PCR
Increases sensitivity due to high # cycles
Increases specificity due to annealing in 2nd amplicon
Contamination risk if tube transfer-can overcome
Often need nucleic acid probe confirmation
Round I
PCR15-30 cycles
Amplicon 1
Primerset 1
Round II Primer set 2
PCR 20-30 cycles
Amplicon 2
Multiplex PCR
Two or more primer sets Different targets in same
reaction tubes produce different amplicons
Primers must have same reaction kinetics and lack complementarity
Complicated to design Less sensitive than single
primer set PCR
ds DNA
Specimen Transport and Storage Affect the Assay
Collection, transport, and assay setup must be compatible with the assay Different viruses are stable in different blood components for different timesFor HIV-1 viral load, HCV RNA & HBV DNA, plasma must be separated from cells within 6 hrs and plasma can be stored at 4oC for several days or -70oC for long-termFor CMV viral load testing virus is stable in blood for 5 days at 4oC or -20oC to -70oC
Detection and Analysis of the Amplicon
Open systems vs closed systems
Gel analysis
Colorimetric Microtiter Plate (CMP) system
Real-time (homogenous/kinetic) PCR
Allele-specific hybridization
Direct sequencing of product
DNA microarrays
How is the amplicon identified?
DNA amplicon
Agarose gelelectrophoresis
Stain with EtBRImage on UV lightbox
Probe or DNA-bindingchemical Automated imaging
system
Denaturelabeled amplicons
Hybridize with captureProbe in 96 well plate
Detect bound producti.e. biotin-streptavidin
Type of sample effects amplification yield…
May need to boil CSF to release nucleic acidsInhibitory substances in urine such as hemoglobin, crystals, beta-human gonadotropin, nitratesHeparin and small volumes of whole blood inhibit Taq polymeraseAcid citrate in vacutainers can inhibit HIV-1 viral load by 15%- volume effect
What are the sources of contamination?
Contamination of specimens in NA extraction step
Contamination with + control material
Carryover contamination of amplified products
Commercially Available PCR-based Assays
Viral:– HCV RNA, HBV DNA, HIV-1 RNA, CMV DNA, HPV
DNA, WNV RNA
Bacterial:– Chlamydia trachomatis/Neisseria gonorrheae,
Mycobacterium tuberculosis
Fungal:– None
Parasites:– None
Transcription Mediated Amplification (TMA)
Reaction occurs isothermally at 41°C 109 increase in target RNA in 2 hrs (produces 100 – 1000
copies per cycle) Since this assay only amplifies RNA it can be used to
detect RNA genome and RNA from viable bacteria Measures replication of DNA viruses by detecting late
mRNA expression Transcription mediated amplification (TMA): RT with own
RNAse and T7 polymerase. Detection by hybridization protection assay-2 fluorophors (Gen-Probe)
NA sequence based amplification (NASBA): RT, RNaseH, T7 bacteriophage RNA polymerase. Detect with hybridization with chemiluinescent probes (bioMeriieux)
Commercially Available TMA-based Assays
Viral:– CMV DNA, HCV RNA, HIV RNA
Bacterial:– Chlamydia trachomatis/Neisseria gonorrheae,
Mycobacterium tuberculosis and others
Fungal:– None
Parasitic:– None
Strand Displacement Amplification (SDA)
Isothermal nucleic acid amplification method that relies on two concurrent polymerization steps and the displacement of 1 nicked strand of genetic materialPrimer containing a restriction site anneals to templateAmplification primers then annealed to 5' adjacent sequences (form a nick) and start amplification at a fixed temperatureNewly synthesized DNA is nicked by restriction enzyme, polymerase starts amplification again, displacing the newly synthesized strands.
109 copies of DNA can be made in one reaction Alleviate non-specific reactions with organic solvents to
increase stringency of reactions If target is low with high background DNA, non-specific
amplification can swamp system and decrease sensitivity
Walker, Linn and Nadeau, Nucleic Acid Research, 1995
Commercially Available SDA-based Assays
Viral:– CMV DNA
Bacterial:– Chlamydia trachomatis/Neisseria
gonorrheae
Fungal:– None
Parasitic:– None
Nucleic Acid Amplification Tests (NAAT) for Detection of RNA/DNA
Lower limit of detection (LLD)– Based on probe-it analysis– Set at amount of target DNA which is detected
>95% of the time– In general, qualitative assays are more sensitive
than quantitative assays
Linearity (Dynamic range) of Quantitative assays– Range of DNA (or RNA) for which the amount can
be accurately extrapolated from a standard curve using quantitative standards
Nucleic Acid Amplification Tests (NAAT) for Detection of RNA/DNA
Quantitation of RNA or DNA may be reported as copies/ml or IU/ml
Conversion factor for copies/ml to IU/ml is not the same for different assays measuring the same target or different targets– HBV DNA: 5.82 copies/IU– HCV RNA: PCR - 2.4 copies/IU; bDNA: 5.2 copies/IU
Coefficient of variation (COV) may range from 15 to 50%
Branched Chain DNA (bDNA) Assay
Multiple target probes capture target nucleic acid on microtiter wellSecond set of target specific probes bind to targetPreamplifier binds to 2nd set of target probes and/or 8 amplifiersThree alkaline phosphatase-labelled probes hybridize to each branch amplifierDetect labelled probes by incubating with dioxetane which emits light in presence of APRemove non-specific hybridization isoC and isoG in preamplifier and label probes which recognize each other but not native C and G
Hybrid Capture Assay
Multiple AP conjugates bind to each hybrid molecule and amply the signalDetect complex with chemiluminescent substrateIntensity of emitted light proportional to amount of DNA in reaction
ds DNAdenature
ss DNAhybridize withRNA probe
Capture hybrids
APAP
Commercially Available Hybridization Assays
Viral:– HBV DNA, HPV DNA
Bacterial:– Chlamydia trachomatis/Neisseria gonorrheae
Probe Amplification Assays
Ligase Chain Reaction (LCR)
Cleavase-Invader Technology
Cycling probe technology
Ligase Chain Reactions (LCR)
Thermostable DNA ligase to ligate together perfectly adjacent oligos. Two sets of oligos anneal to one strand of the gene With a wild-type target sequence, the oligo pairs ligate together and become targets for annealing other oligos in an exponential amplificationAt a point mutation the oligos only completely anneal to the mutant sequences and DNA ligase will not ligate the two oligos of each pair togetherWithdrawn from Chlamydia trachomatis testing
Cleavase Invader Technology
Produced by Third Wave Technologies-bought by PEBIO Invader displaces 5’ of bound probeFEN-1 family of themostable DNA polymerases cleaves 5’ overlapCan heat reaction to allow for primer exchange equilibrium ---new uncleaved probes bind
Detect point mutations because can overlap of invader probe can be only 1 bp—track mutations
Generate distinct fragments of different genotypes
Does not increase amount of target sequence- fewer problems of false + and contamination
Target sequence3’ 5’5’
Invader oligo
5’
3’
Probe oligo
Cleavase
5’ 3’3’ 5’
5’
Cleaved probe
Limitations of Molecular Assays
DNA/RNA extraction is critical
Specimen type: Plasma or serum may be acceptable; tissue, fluids, etc. may not
Plasma/serum must be separated and either frozen or tested within 4 to 6 hours
Expensive equipment is usually required
Genotyping
Used for:– Detection of mutations that confer resistance to
antiviral agents– Genotyping of isolates for epidemiological purposes;
categorizes patient isolates into 8 different HBV genotypes (A to H) and 6 different HCV genotypes (1 to 6 with 24 subtypes)
Methods include:– Sequencing– Hybridization (e.g. Line Probe Assay, Trugene Assay,
Invader assay, etc.)
Genotyping Assays
Pros Cons
Sequencing Discovers Labor-intensive
new mutations Low sensitivity
(15-20% pop.)
Line Probe High throughput Detects known
High sensitivity mutations only
(5-10% pop.)
Marker lineConj.cont.Amp.cont.
L180
M180
M204
V204
I204
V207L207
M207
I207
Amplified Amplified targettarget
StreptavidinStreptavidin
BiotinBiotin
Alkaline Alkaline PhosphatasePhosphatase
Purple Purple precipitateprecipitate
ChromogenChromogen(NBT/BCIP)(NBT/BCIP)
DNA-probeDNA-probeNitrocellulose Nitrocellulose
stripstrip
InnoLiPA Principle
InnoLIPA HBV Drug Resistance
M arke r line
C onj. C on tro lA m p.C ontro lL80 W TV 80 M u tant
80 M u tantV 173 W T G 173 W TL173 M utantL180 W TM 180 M u tantA 181 W TT181 M utan tV 181 M utan tM 204 W TV 204 M utan t
204 M utan tS 204 M utan tN 236 W TT236 M utan t
I
I
1 - 2 - 3 -4 - 5 - 6 - 7 - 8 - 9 -
10 - 11 - 12 - 13 - 14 - 15 - 16 - 17 - 18 - 19 -
Molecular Diagnostics: Summary
NAAT is critical to patient management
Of the many NAAT tests available, PCR, bDNA and TMA remain most popular– Sensitivity and dynamic range varies between assays– Standardization allows (to some degree)
interchangeability of the results with different assays
Resistance/Genotyping requires amplification first– Increasing role in making treatment decisions as more
drugs become available