HRM APPLICATIONS - Gene-Quantification Summary Simple, fast, cost effective method for gene scanning...
Transcript of HRM APPLICATIONS - Gene-Quantification Summary Simple, fast, cost effective method for gene scanning...
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HRM APPLICATIONS
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www.corbettlifescience.com
Andrea A Tesoriero
HRM APPLICATIONS
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High Resolution Melt (HRM)
detailed monitoring of changes in fluorescence as a PCR products are melted
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PCR amplify an amplicon with two primers and an intercalation dye and then melt (dissociate) the product – double stranded to single stranded
Can detect even a single base pair change
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HRM Specifications
Instrument requires:
high-intensity + high sensitivity optics
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high-intensity + high sensitivity optics
high-speed data capture
very precise temperature control and resolution
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The world’s only real-time rotary thermo-optical analyzer
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An ideal platform for HRM
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Cross-section of rotary optics
Reaction Chamber
Detection Filters
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PMT DetectorAssembly
LED Light Source
Assembly
Tubes Spin inRotor (Red)
Lens
Spindle/Motor Assembly
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Thermal Control+0.01
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+0.01
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Centrifugal fan drives air around chamber
Chamber vent seals
Heating mechanism
Heater elements switch on
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Chamber vent seals to contain air
Note: holes in the rotor allow
free airflow
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Centrifugal fan drives air around chamber
Chamber vent opens expelling hot air
Cooling mechanism
Heater elements switch off
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Cool air in
Centrifugal fan Drives air into chamber
expelling hot air
Note: holes in the rotor allow
free airflow
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HRM Profile
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0.02°C
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Data Acquisition
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Melt curves normalized—by selecting linear regions before & after the melt transition
Two regions defined—upper 100% double stranded / lower single stranded baseline
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Normalized Data: Homoduplexes C or T
G A C
C T G
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Homozygotes represented by a single base change are differentiated by a difference in Tm
G A T
C T A
C T G
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Heteroduplex C>T
G A TG A C
G A TG A C
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Heterozygotes form heteroduplexes, which result in lower melt curves and two transition points
C T AC T G
C T GC T A
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Difference Graphs
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Difference graph displays each sample plot subtracted from a given genotype control plotCalculates a percentage confidence relative to a known genotype
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HRM Summary
Simple, fast, cost effective method for gene scanning and detecting a single-base change in your sample
Closed system
NO labeled probes
Has excellent sensitivity and specificity is capable of
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detecting BOTH heterozygous and homozygous changes
Costs less than competing technologies
Sequence directly off the product—sample not consumed
Auto call software
Scanning & genotyping can be done simultaneously in the same reaction
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SNP’s
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Detection of alpha-thalassemia-1 Southeast Asian ty pe using real-time gap-PCR with SYBR Green 1 and high Resolution Melting analysis . Pornprasert S, Phusua A, Suanta S, Saetung R, Sanguansermsri T,Eur J of Haematol. 2008.
Direct Genotyping of Single Nucleotide Polymorphism s in Methyl Metabolism Genes Using Probe-Free High-Resolution Melting Analysis. L S. Kristensen and A.Dobrovic Cancer Epidemiol Biomarkers Prev2008;17(5) May 2008
High-resolution melt analysis for the detection of a mutation associated with permethrin resistance in apopulation of scabies mites C Pasay, L Arlian, M. Morgan, D Vyszenski-Moher, A. Rose, D Holt, S.Waltonand JMcCarthy Medical and Veterinary Entomology (2008) 22, 82–88
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GenotypingClass 4 SNP
SNP Class
Base Change
Typical TmShift
Rarity (in humans)
1 C/T and G/A Large>0.5oC
Very Small >0.2oC
64%
2 C/A and G/T 20%
3 C/G 9%
4 A/T 7%
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Example of a class 4 SNP on the Rotor Gene (MCT A1470T)The rarest and most difficult SNP to discriminate.
SNP classes as described by Venter et al 2002
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Class 4 SNP using Sybr Green 1
SYBR can be used at non-saturating concentrations, for the most demanding HRM applications.
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Extra sensitivity of the Rotor-Gene may be a major reason we do not require saturating dye levels
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Adjacent SNP’s Homozygosis'
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AA GG
GG GG
Homozygotes represented by a 2bp base changes are differentiated by a difference in Tm by about 0.3deg
Data Courtesy of Howard Florey Institute, J.Rubio, C. Jenson
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Adjacent SNP’s Heterozygous
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Heterozygotes form heteroduplexes, which result in lower melt curves and multiple transition points
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AA GG
GG GG
Nomalised Data
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GG CG
GA GGGA CG
Sequences were performed directly from HRM product, variants are 10bp apart
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Maternal Aunt 1
Patient
Paternal Aunt
Maternal Aunt 2
1104Relationship 20 probes
SS sequencing
2 days
X
X
11040401
11430403
1104
2 days
Complex Melts -HLA Compatability
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d e g .8 5 8 5 . 5 8 6 8 6 .5 8 7 8 7 . 5 8 8 8 8 . 5 8 9 8 9 . 5 9 0 9 0 . 5 9 1 9 1 . 5 9 2 9 2 . 5
Nor
m. F
luor
o.
1 1 0
1 0 5
1 0 0
9 5
9 0
8 5
8 0
7 5
7 0
6 5
6 0
5 5
5 0
4 5
4 0
3 5
3 0
2 5
2 0
1 5
1 0 Patient
Maternal Aunt 1
2.5Hrs
2 days
No match
04010403
Red Cross-Melbourne
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Mutation Detection
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Mutation Detection
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Genomic Mutations in LDLR gene- 23 fragments
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Atherosclerosis 194 (2007) 279–286. Development of an affordable, sensitive and rapid s creening method for mutation detection in UK FH subjects C Hubbart, R Whittall, M Scartezini, S Humphries
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White et al. 2006 report
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http://www.ngrl.org.uk/Wessex/downloads.htm
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White et al. 2006 report
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White et al. 2006 report
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White et al. 2006 report
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DNA Quality—late amplificationWhite et al. 2006 report
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DNA quality -Multiplex 100, 200, 300, 400 and 600 bp product
Amplification of 193 bp product
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Sensitivity
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Sensitivity
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“Spiking” Experiments-applicable for acquired mutations and pooling samples
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Royal Melbourne Hospital
Homozygous A
Homozygous B
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“Spiking” Experiments-applicable for acquired mutations and pooling samples
1:1 (50%) spiked mix
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Royal Melbourne Hospital
Homozygous A
Homozygous B
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“Spiking” Experiments-applicable for acquired mutations and pooling samples
1:4 (20%)spiked mix
1:1 (50%) spiked mix
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Royal Melbourne Hospital
Homozygous A
Homozygous B
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“Spiking” Experiments-applicable for acquired mutations and pooling samples
1:4 (20%)spiked mix
1:9 (10%) spiked mix
1:1 (50%) spiked mix
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Courtesy Royal Melbourne Hospital-Hematology
1:9 (10%) spiked mix
1:19 (5%) spiked mix
Homozygous A
Homozygous B
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Acquired Mutation Detection
High resolution melting for mutation scanning of TP53 exons 5-8M Krypuy, A Ahmed, D Etemadmoghadam, S Hyland, Australian Ovarian Cancer Study Group, J Brenton, S Fox, A deFazio, D Bowtell and A Dobrovic BMC Cancer 2007, 7:168
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Bowtell and A Dobrovic BMC Cancer 2007, 7:168
High resolution melting analysis for the rapi d and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutatio ns in non-small cell lung cancer M.Krypuy, G.Newnham, D.Thomas, M.Conron, A.Dobrovic BMC Cancer. 2006 Dec 21;6(1):295
Detection of the transforming AKT1 mutation E17K in non-small cell lung cancer by high resolution melting . H Do, B.Solomon, P.Mitchell, S.Fox ,A.Dobrovic BMC Research Notes 2008, 1:14
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38 G>A Heterozygous
92bp 5% cellular ratio 1:19 dilution
Represents 2.5% allele ratio1 out of 39 alleles
Sensitivity Krypuy et al. 2006 report
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34 G>A Homozygous
35 G>Chypotriploid
possible 2:1 mutant
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Somatic Mutation Discovery KRAS Exon 2 189 bp product 37% GC content-
wt
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?
• Detected small quantities of mutant DNA in a background of wildtype DNA• Confirmed 9/30 positive clinical samples• No homozygous spiking necessary• The heteroduplex shape is not used to determine differences, rather the deviation from wildtype,
as the shape is compromised due to the proportion of normal DNA
Peter MacCallum Cancer Centre Melbourne
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Difference Graph Krypuy et al. 2006 report
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This paper concludes that HRM will allow
“confident screening for mutations in samples that have at least 10% tumor cells”
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that have at least 10% tumor cells”
Krypuy et al. 2006 report
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Species Identification
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Classification of Mycoplasma synoviae strains using s ingle-strand conformation polymorphism and high-resolution melting-curve anal ysis of the vlhA gene single-copy region Nathan Jeffery, Robin B. Gasser, Penelope A. Steer and Amir H. Noormoham Appl Environ Microbiol. 2007; 73: 3431-3436
High-Resolution DNA curve analysis of the clustered regularly interspaced short palindronic-repeat locus of Campylobacter jejuni. Price EP, Smith H, Huygens F, Giffard PM Microbiology (2007), 153, 2679–2688
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Strain Sequence Alignment
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SSCP
400bp PCR Product
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Normalised HRM
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~400 bp fragment, 35 different M. synoviae isolates
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Epigenetics
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Epigenetics
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Methylation-sensitive high resolution melting (MS-HRM): A new approach for sensitive and
high-throughput assessment of methylation.
Tomasz K. Wojdacz, Alexander Dobrovic
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Nucleic Acids Research Feb 2007
“The simplicity and high reproducibility……makes MS-HRM the method of choice”
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What is methylation?
Non methylated GACATCG GATATTG
Addition of a methyl group to cytosine DNA in CpG island
Bisulphate treatment converts non methylated cytosine bases to uracil and methylated remain unaffected
Uracil converted to thymine by PCR
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Non methylated GACATCG GATATTGMethylated GACATmCG GATATCG
Methylation acts to “turn off” transcription
Markers for; Early events in cancerMonitoring progressionMGMT predictive markers treatments
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MGMT MS-HRMEffect of annealing temperature on sensitivity
Wojdacz et al. 2007 report
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60°CDiscrimination at
higher end
62°C 63°C Discrimination at
lower end
increasing temperature
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Low level methylation0.1% MGMT sensitivity MS-HRM
12 CpG’s/ 109bp
Wojdacz et al. 2007 report
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5CpG’s/ 94bp
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Heterogeneous methylation
HeterogeneousMethylationdetected
Wojdacz et al. 2007 report
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MS-HRM is a sensitive, reliable,
fast and cost effective
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fast and cost effective
“…method of choice ”
Wojdacz et al. 2007 report
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Genomic ImprintingRapid detection of methylation change at H19 in huma n imprinting disorders using methylation-sensitive high-resoluti on melting . Wojdacz TK, Dobrovic A, Algar EM. Hum Mutat. 2008 May 12
Methylation-Sensitive High-Resolution Melting-Curve Analysis of the SNRPN Gene as a Diagnostic Screen for Prader-Willi a nd AngelmanSyndromes .H White, V Hall, and N Cross.Clinical chemistry September
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Syndromes .H White, V Hall, and N Cross.Clinical chemistry September 2007
Promoter MethylationBRCA1 promoter methylation in peripheral blood DNA o f mutation negative familial breast cancer patients with a BRC A1 tumour phenotype . C Snell, M Krypuy, E Wong, M Loughrey, A DobrovicBreast Cancer Research 2008
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Applications
Detect small quantities of mutant DNA in background of wildtype DNA species
Important in somatically acquired mutations
Pooling samples—up to 10 samples
Simple for diseases that cause no heterogeneity-like Factor V
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Simple for diseases that cause no heterogeneity-like Factor V Leiden, haemochromotosis, sickle cell anemia, etc
Appropriate for disorders where the mutational spectrum is wide—mismatch repair genes
Newly identified genes—little information
Species identification
Epigenetics
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www.corbettlifescience.com
www.corbettlifescience.com
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Singleplex HRM
A
F1 Hybrid
B
DCF1 Hybrid
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Multiplex HRM
A
Heteroduplex(F1 Hybrid)
B
D