Workshop - Promega/media/files/resources...• Loci with “compound” or “complex” structures...
Transcript of Workshop - Promega/media/files/resources...• Loci with “compound” or “complex” structures...
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Short Tandem Repeat Loci
Workshop Phoenix, AZ
October 4, 2004
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DNA TYPING METHODS
• PCRbased
• Faster results • Less laborintensive • 1 ng DNA • Degraded DNA
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DNA TYPING METHODS
• D1 S80 • single locus • preferential amp.
• DQA1 / PM • interpretational difficulties
Need for new typing method
• PCRbased
• Faster results • Less laborintensive • 1 ng DNA • Degraded DNA
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Repetitive DNA contains sequences Repetitive DNA contains sequences that occur more than once that occur more than once
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REPETITIVE DNA REPETITIVE DNA (20 (20 30% of human genome) 30% of human genome)
è Interspersed:
è Single repeats scattered throughout the genome
è 10% of genome
è Interspersed:
è Single repeats scattered throughout the genome
è 10% of genome
è Tandemly Repeated:
è Headtotail tandem repetition of a common sequence
è 1520% of genome
è Tandemly Repeated:
è Headtotail tandem repetition of a common sequence
è 1520% of genome
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Repeat Polymorphisms
VNTR (RFLP)
980 bp
<500 >23,000 bp
27 bp
100 400 bp 880 bp
100 1,300 bp
AmpFLP
STR
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Short Tandem Repeats
STRs Highly discriminating
Abundant in genome
Amenable to automation
Discrete alleles
Rapid typing
Nonisotopic
Lowquantity DNA PCRbased
Degraded DNA
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SHORT TANDEM REPEATS
• • Arrays of short repeats (2 Arrays of short repeats (2 7 7 bp bp) that are ) that are repeated several times in tandem repeated several times in tandem
• • >30,000 in the human genome >30,000 in the human genome
• • One every 10 kb One every 10 kb
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LENGTH OF REPEAT UNIT
Dinucleotides:
Trinucleotides:
Tetranucleotides:
Pentanucleotides:
2 2 CA CA
3 3 AAT AAT
4 4 AGAT AGAT
5 5 AATGT AATGT
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GENERAL CRITERIA FOR SELECTING STR LOCI
2 2 Dinucleotide repeats:
4 4 Tetranucleotide repeats:
Plentiful, but too much stutter
Demonstrate less stutter
5 5 Pentanucleotide repeats: Less stutter, but greater bp range
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GENERAL CRITERIA FOR SELECTING STR LOCI
4 4 Tetranucleotide repeats:
PD > 0.85
Size 100350 bps
Allele range < 60 bps
Low stutter
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TETRANUCLEOTIDE REPEATS are used in forensics
• Undesired PCR products are greater with di and trinucleotide repeats
• Some trinucleotides are associated with diseases
• Alleles are more readily resolved • 4 bp, not 2 or 3 bp
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SHORT TANDEM REPEATS: Tetramers
AGAT AGAT AGAT AGAT AAAG AAAG AAAG AAAG AATG AATG AATG AATG AAAT AAAT AAAT AAAT
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STRs are POLYMORPHIC
• Usually, variation in the number of tandem repeats that make up the array
• Alleles are designated by the number of repeats that they contain
Sequence variation can affect mobility and thus polymorphic nature native vs denaturing conditions
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5
6
AATG
7
Allele:
AATG AATG AATG AATG
AATG AATG AATG AATG AATG
AATG AATG AATG AATG AATG
AATG
AATG AATG
Flanking region of unique sequence
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....…PCR Primer Binding Sites….…
5
6
7
Allele:
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....…Polymerase Chain Reaction….…
5
6
7
Allele:
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....…Polymerase Chain Reaction….…
5
6
7
Allele:
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TH01, a simple locus è ( AATG ) 511
5 169 bp*
6 173 bp
7 177 bp
8 181 bp
9 185 bp
10 189 bp
11 193 bp
Allele:
*AmpFlSTR
Operational sizing
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STR LOCUS TYPES • SIMPLE
• TH01: (AATG) 511
• COMPOUND • VWA: TCTA (TCTG) 34 (TCTA) n
• COMPLEX • D21S11:(TCTA) 46 (TCTG) 56 (TCTA) 3 TA
(TCTA) 3 TCA(TCTA) 2 TCCATA (TCTA) 816 TC
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13 Core Loci in 2 Amplifications Profiler Plus
FGA VWA D3
D18 D21 D8 D7 D13 D5
D3 CSF TPOX TH01
D5 D16
Overlap
Overlap D7
D3
Cofiler
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13 Core Loci Plus 2 more STR Loci in
1 Amplification
D18S51
Penta D
D21S11
THO1
D3S1358
TPOX
FGA
D8S1179
VWA
Amelogenin
CSF1PO
Penta C
D16S539
D7S820
D13S317
D5S818
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VWA Intron 40 of von Wildebrand factor 12p1212pter
TCTA (TCTG) 34 (TCTA) n
Intron 40 of von Wildebrand factor Anonymous D3S1358 3p
TCTA (TCTG) 13 (TCTA) n
FGA Intron 3 of fibrinogen alpha chain 4q28
(TTTC) 3 TTTT TTCT (CTTT) n CTCC (TTCC) 2
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D18S51 18q21.3
(AGAA) n
Anonymous
D21S11 21
(TCTA) n (TCTG) n [(TCTA) 3 TA (TCTA) 3 TCA
Anonymous
(TCTA) 2 TCCA TA] (TCTA) n
D8S1179 8
(TCTR) n [R = A or G]
Anonymous
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2p232pter Intron 20 of thyroid peroxidase TPOX
(AATG) n
Intron 1 of tyrosine hydroxylase TH01 11p15.5
(AATG) n
5q33.334
(AGAT) n
CSF1PO CSF1 Receptor
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D13S317 13q2231
(GATA) n
Anonymous
D7S820 7q
(GATA) n
Anonymous
D5S818 5q2131
(AGAT) n
Anonymous
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D16S539 16q24qter
(AGAT)
Anonymous
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ALLELIC LADDERS
Used to designate the alleles when genotyping an unknown sample Used to designate the alleles when genotyping an unknown sample
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ALLELIC LADDERS
• Simple Ladder is made with alleles that are 4bp apart and that are within the range of common alleles
• Some variants may be included in the ladder (e.g., TH01 9.3)
• Not all observed variants are included in the ladder
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“OFFLADDER” VARIANTS Offladder (OL) alleles fail to align with the incremental 4bp ladder or reside above or below ladder
To classify the variant allele:
Operationally defined nomenclature
Number of repeats, followed by a decimal point number of nucleotides of partial repeat
Above or below ladder use > or < highest or lowest allele in ladder
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“OFFLADDER” VARIANTS
( AATG ) 9 9 TH01
( AATG ) 10 10 ATG ( AATG ) 6 ( AATG ) 3 9.3
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TH01
( AATG ) 6 ATG ( AATG ) 3 9.3
VWA ( TCTA ) 2 16 ( TCTG ) 4 ( TCTA ) 10 ( TCTA ) 2 ( TCTG ) 4 ( TCTA ) 10 16.2 TA
( AATG ) 9 9
( AATG ) 10 10
“OFFLADDER” VARIANTS
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Designing STR Systems
• Primers • Test primers for compatility:
specificity, balance, primer dimer, full A addition
• Test PCR components MgCl2, KCl, dNTPs, template
• Thermal cycler conditions • PostPCR analytical procedures
fluors, electrophoresis, detection systems, interpretation
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• No size overlap for loci with same fluor • Similar Tm for primers • Avoid hairpin structures • Minimal complementary binding at 3' end • Maximal 3' A addition • Test multiplex at low Tanneal for specificity
STR Primer Design
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Specificity
Chrom. 5 D5S818
Chrom. 13 D13S317
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AmpliTaq Gold
• Hot start • Simplifies PCR set up • Reduces primer design requirements • Decreases primerdimer formation • Facilitates multiplexing • Automation
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Undesired! But inherent.
“Minus A” or “Plus A” Stutter
UNDESIRED PCR PRODUCTS
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The difference between “Minus A” and Stutter
+ A
A
Stutter
4 bases
AL
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NonTemplated Nucleotide Addition (“Plus A”)
• Many DNA polymerases add an extra nucleotide to the blunt end of a DNA product without the use of a template
• Usually A is added • The resulting band/peak is 1bp larger in size than that predicted from the DNA sequence and primer locations
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NonTemplated Nucleotide Addition (“Plus A”)
A
A
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There are two ways to deal with+/A
Either design primers that resist A addition
Or drive the reaction towards addition of A
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If you can’t beat ‘em, join ‘em
One cannot effectively prevent +A. However, one can increase +A
through primer design...
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“Plus A” is the desired product.
Ladder bands / peaks are +A!
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Inefficient adenylation results in 2 bands or peaks
(or oddshaped peaks)
Allele 1, +A Allele 2, +A
A A
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Inefficient adenylation results in 2 bands or peaks
(or oddshaped peaks)
Reduced Peak Height
OL Allele? Or A?
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ADDRESSING “MINUS A”PEAKS
• Repeat final extension step with additional enzyme
• Use knowledge of adenylation efficiency at a given locus
• Use database information to aid in interpretation
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STUTTER
• Characteristic of repetitive DNA amplification • Tetramers have less stutter than dinucleotide repeats
• Usually one repeat unit less in size • Increases with magnesium • 014% of allele
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HOW STUTTER OCCURS
1 2 3 4 5 6
1 2
Template
Amplicon
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5 6
HOW STUTTER OCCURS
1 2 3 4 5
1 2 3 4
Template
Amplicon
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HOW STUTTER OCCURS
1 2 3 4 5
1 2 3 4 5 6
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5 6
TRUE ALLELE PREDOMINATES
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5fold more
product
Minimize stutter by working within the
recommended peak height
range
10%
Actually 10%
Actual % stutter
is the same Threshold of detection is exceeded for main peak …but not for stutter peak
22% 10%
But appears 22%
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5fold more
product
10% 10%
Actual % stutter
is the same Threshold of detection is exceeded for main peak …but not for stutter peak
22% 10%
Percent stutter is falsely
augmented
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STUTTER TRENDS • Different loci exhibit different degrees of stutter • Loci with “compound” or “complex” structures exhibit less stutter than those with “simple” structure (e.g., VWA)
• Also variant alleles at a locus may have less stutter (e.g., VWA)
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Simple:
Compound:
TA
Complex:
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16 ( TCTA ) 2 ( TCTG ) 4 ( TCTA ) 4 ( TCTG) (TCTA ) 5
( TCTA ) 2 16 ( TCTG ) 4 ( TCTA ) 10
Allele 16
Less prone to stutter
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• Different loci exhibit different degrees of stutter • Loci with “compound” or “complex” structures exhibit less stutter than those with “simple” structure
• At any given locus, smaller alleles typically exhibit a lower percent stutter than larger alleles
STUTTER TRENDS
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Alleles at LOCUS A
Alleles at LOCUS B
5
10
15
20
25
30 Percent Stutter Outlying Outlying
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• Different loci exhibit different degrees of stutter • Loci with “compound” or “complex” structures exhibit less stutter than those with “simple” structure
• At any given locus, smaller alleles typically exhibit a lower percent stutter than larger alleles
• General guidelines
STUTTER TRENDS
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The presence of stutter or A is not necessarily a problem
• Stutter is a feature of STR amplification • Lowlevel stutter is manageable, when peaks are within
recommended range • Mixture interpretation • Samples with A can be extended • If +A failure occurs, both alleles at a heterozygous locus tend
to exhibit A • Adenylation failure does not preclude correct enotyping
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Resolution Typing
• SA32 Gel Apparatus, FMBIO • Scan gel after run
• ABI Prism 377, 310, 3100, 3700,… • Detection window
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Detection Methods
•Ethidium Bromide •Silver •Syber Green
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Detection Methods
Fluorescence
Label one of the primers for each locus
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Fluorescence results when a fluorophore or fluorescent dye absorbs incident light and in response emits light at a different wavelength
excitation emission
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Molar Extinction Coefficient is
a measure of a dye’s ability to absorb light
Stokes Shift is
The difference in wavelength between the fluorescence excitation maximum and fluorescence emission maximum
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excitation emission
excitation emission
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The dye’s spectral excitation and spectral emission wavelengths should be compatible with excitation source and filter wavelengths
Spectral Criteria
Spectral Bandwidth
Spectral overlap and the ability of an instrument to distinguish one dye from another
PULLUP
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Comparison of Dichlororhodamine and Rhodamine dye spectra
0
20
40
60
80
100
500 520 540 560 580 600 620 640 660
Rhodamine Emission Spectra
ROX TAMRA R110 R6g
NORMALIZE
D EMISSION IN
TENSITY
WAVELENGTH (nm)
0
20
40
60
80
100
500 520 540 560 580 600 620 640 660
DRhodamines Emission Spectra
DR110 DR6g DROX DTMRA
NORMALIZE
D EMISSION IN
TENSITY
WAVELENGTH (nm)
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Pullup
Due to signal and spectral overlap
Pullup
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Fluorescence Quantum Yield is
The efficiency with which the excited molecule is able to convert absorbed light to emitted light
Dyes also can affect Mobility of DNA molecules
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SUMMARY
• STRs used today in forensics generally are characterized by tandem repeats of 4(or 5)bp units
• STR polymorphism is due to variation in the number of repeated units
• There are different repeat unit sequences (AATG, TCTA, CTTT, etc.)
• STR loci are either simple, compound or complex
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SUMMARY
• Alleles are designated by comparison with an allelic ladder
• Offladder variants of tetramers usually have 1, 2, or 3 extra bases within the repeat array
• Offladder variants also can occur above and below the extremities of the ladder
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SUMMARY
• STR loci “associated with” genes are typically in noncoding regions (i.e., introns or flanking regions)
• Many STR loci are “anonymous,” or not currently known to reside within a known gene
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SUMMARY
• STRs are amplified by the PCR. PCR primers bind to unique sequences that flank the repeat region
• Alleles that align with the allelic ladder have “plus A”
• “Minus A” may occur at some loci but is easily addressed
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SUMMARY
• Stutter is inherent to STR (tetramers) amplification of some loci
• Loci with a simple repeat structure tend to stutter more
• Loci vary in the extent to which they exhibit stutter
• Small alleles show less stutter than larger alleles
• Stutter is generally predictable and general guidelines can be used for profile interpretation
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SUMMARY
• Interpreting electropherograms is faciltated, especially with software
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THE END