The document compares the accuracy and efficacy of commercially available STR typing kits from Applied Biosystems and Promega Corporation using various samples. Studies found that while the kits performed reasonably well on low copy number samples, allelic dropout rates were around 7-14% on average. Optimal DNA sample size for profiling was determined to be around 1-2ng. Motherless paternity testing using one kit produced non-definitive results in over half of cases compared to standard trio testing. Degraded DNA samples showed some loci produced more valid results depending on the kit.
1 of 19
Downloaded 22 times
More Related Content
Comparison Of Commercially Available Str Typing Kits (Nx Power Lite)
1. COMPARISON OF
COMMERCIALLY AVAILABLE
STR TYPING KITS: SAMPLE
CONDITION, ACCURACY,
AND EFFICACY
By Courtney Brennan
Special thanks to my Mentors/Professors:
M. Guido, K. Sweder, and M. Sponsler
2. BACKGROUND
Many labs use commercially available kits to type
DNA samples
These are usually STR (short tandem repeat) typing
kits.
Many labs only use one kit, and most forensic labs
only use one kit per sample.
The two most common producers of these kits are
Applied Biosystems and Promega Corporation.
Many kits include the 13 core loci (CODIS)
A Loci is a specific location on a chromosome where
a sequence or gene is found
Variants of this sequence are known as alleles
3. BACKGROUND (CONT.)
Homozygotes have only
one form of an allele
CC
Heterozygotes have
varying forms of an
allele
These dif ferent
CT variations on the loci
are read and compared
in DNA profiles
Amelogenin, the sex
determination loci, is
TT commonly analyzed in
these kits
http://carcin.oxfordjournals.org/content/25/8/1443/F1.expansion.html
4. UNDERSTANDING ACCURACY
While kits tend to be far within the acceptable
range of accuracy for typing, accuracy has
costs
Increased accuracy may decrease the real-life
application of the kit since contaminants or
mixed profiles would be more difficult to
analyze
Some samples with only a small amount of
DNA can exhibit inaccurate readings if they
have low copy number
5. ANALYSIS OF AMPFISTR速 SGM PLUS
MULTIPLEX SYSTEM FOR EFFECTIVENESS ON
LOW COPY NUMBER SAMPLES
AMPFISTR速 SGM Plus system was tested for
usefulness in analyzing LCN (low copy
number) samples
Low copy number generally refers to samples
in which there is less than 100pg of input
genetic material
This approach can have issues sometimes
one allele is not present in a large enough
amount to be detected properly
6. ALLELIC DROPOUT IN LCN CONDITIONS
Difference #
Allelic dropout (% of
Locus observed in 28 vs. Alleles
expected)
34 cycles
Amelogenin 6 [4H] 4 (14.8)
D3S1358 8 [3L, 2H] 5 (10.6)
HumVWF31 10 [5L, 2H] 7 (10.4)
D16S539 10 [4L, 4H] 8 (17)
D2S1338 13 [4L, 2H] 6 (8.9)
D8S1179 11 [2L, 2H] 6( 8.9)
D21S11 6 [4L, 2H] 4 (14.8)
D18S51 11 [4L, 2H] 6( 8.9)
D19S433 6 [4L, 2H] 6( 8.9)
HUMTHO1 1 [1H] 1 (3.7)
HumFIBRA 13 [2L, 4H] 5 (7.4)
Allelic dropout is when one or more of the alleles present in a sample
are either poorly detected or undetected in a profile
This results in false homozygosity being led to believe a specific loci
is homozygous when in fact the analysis simply failed to pick up the
second allele
7. ANALYSIS OF AMPFISTR速 SGM PLUS MULTIPLEX
SYSTEM FOR EFFECTIVENESS ON LOW COPY
NUMBER SAMPLES (CONT.)
The average allelic dropout rate among the
loci analyzed was, on average, around 7-14%
10% of the heterozygotes analyzed showed
allelic dropout
The author(s) found that while the AMPFISTR速
SGM Plus system was reasonably able to
analyze LCN samples, special consideration
should be taken when reading results from
this type of sample
8. USE OF APPLIED BIOSYSTEMS AMPFLSTR
PROFILER PLUS IN PERSONAL
IDENTIFICATION CASES
This study was examining the effects of
sample size on the ability of the AmpFlSTR
Profiler Plus to clearly detect various alleles
Measurement is in relative fluorescence units
(RFU): units of fluorescence intensity which
signify the strength of DNA detection so to
speak
Different sources were used for the same DNA
profile so that differing amounts of genetic
material were retrieved
10. THE IMPACT OF SAMPLE SIZE ON DETECTION
When the sample size reduced to that of 0.015ng or less
of DNA, only two alleles were even detectable:
X
D21S11
Homozygous alleles were (as expected) easier to detect
Using these numbers, it was determined that the optimal
sample size for DNA was around 1-2 ng of product for the
AmpFlSTR Profiler Plus kit
The authors, Buscemi, et al., concluded that the success
rate in forensic casework samples seeking personal
identification was around 75% before purification
This rate rose to 90% when samples that were not
originally amplifiable used the microcon -30 purification
unit
11. AMPFLSTR速 IDENTIFILER速 AND
MOTHERLESS PATERNITY TESTS
A study was done to determine the effectiveness of
the AmpFLSTR速 Identifiler速 kit in cases where the
mothers sample was not available for comparison in
paternity testing
Paternity testing generally involves three samples;
this method was referred to as the trio of samples:
Potential father
Mother
Child
In some cases, the mothers sample was not available
and testing was only done between potential father
and child. This was referred to as duo testing.
12. VALIDIT Y OF MOTHERLESS PATERNIT Y
TESTING
It was concluded that the results from duo, rather
than trio, testing using the AmpFLSTR速 Identifiler速
kit were not sufficient to prove paternity:
In trio cases, the mean value of probability of paternity was
99.999997%, with a minimum of four excluding loci
In duo cases, over half of the cases were unable to reach the
accepted (99.999%) probability of paternity value.
This is logical due to the fact that in duo
cases, sometimes as few as 1 excluding loci were
found
Consider: Do other kits have similar results when
testing in this manner?
13. T HE USE OF P ROM E G A C ORPORAT I ONS POW E RPLE X 16 A N D
A P P LI E D BI OSYST E MS A M P F LSTR速 SG M P LUS I N T H E
A N ALYSIS OF DE G RA DE D DN A SA M P LE S
The author(s) of this study sought to compare
the Powerplex 16 and AmpFlSTR速 SGM
Plus systems ability to analyze degraded
DNA samples
Even though the kits did not have all loci in
common, the nine loci they did have in
common were used as a basis for comparison
24 samples were analyzed
14. ANALYSIS OF DEGRADED DNA SAMPLES AS
MEASURED BY VALID LOCI RESULTS
Loci Powerplex 16 (%) AmpFlSTR速 SGM Plus (%)
D3S1358 21 (88) 20 (83)
vWA 21 (88) 24 (100)
D16S539 21 (88) 23 (96)
D8S1179 20 (83) 24 (100)
D2S11 20 (83) 20 (83)
D18S51 15 (63) <-compare-> 7 (29)
THO1 23 (96) 20 (83)
FGA 14 (58) 11 (46)
Amelogenin 19 (79) <--compare-> 23 (96)
On average/overall, the two kits were similar (80 versus 81% valid
results)
Differentiation between kits happened more on the level of
individual loci
Assumption that a sample size of 24 is acceptable to draw
general conclusions
15. ADDITIONAL CONSIDERATION: TEMPERATURE
As a side note, this study also compared the loss of
information when samples were stored at different
temperatures other than the (assumed) average storage
value:
Storage Temperature Powerplex 16 AmpFlSTR速 SGM Plus
Room (20-25属C) 18% 7%
4属C 38% 23%
This suggests that storage temperature has a greater
impact on the Powerplex 16 kit than on AmpFlSTR速
SGM Plus
16. GENOT YPING INCONSISTENCIES - AMPFLSTR速
IDENTIFILER速 VS. POWERPLEX速 16
13 STRs were used to compare since they
were shared between both kits
Because different kits use different primers, it
was believed that certain inconsistencies
might exist between them
This issue can be important due to the
common Forensic practice of databasing
Some kits that are produced by the same
company can still have primers that are
designed differently
17. GENOT YPIC DISCORDANCES AND FALSE
HOMOZYGOSITIES BETWEEN STR KITS
STR/alleles AmpFLSTR速 Identifiler速 Powerplex 16 Inconsistencies
D5S818 11-12 12 1
10-12 12 3
10-13 13 1
12 12-13 1
10-11 11 3
9-11 9 1
D8S1179 14 14-16 1
FGA 25-26 26 1
D16S539 9-11 9 2
10-11 10 2
VWA 16 16-18 2
16 16-19 1
16 16-17 1
18 16-18 1
18 17-18 1
Five of the thirteen shared loci showed genetic discrepancies
Of the remaining inconsistencies, most were false homozygosities caused by the
AmpFLSTR速 Identifiler速 at the D5S818 loci
Alternatively, all identified inconsistencies present at the VWA loci were a result
of the Powerplex 16 kit
18. AN OVERVIEW OF FINDINGS
AMPFISTR速 SGM Plus AmpFlSTR Profiler Plus AmpFLSTR速 Identifiler速 Powerplex 16
Effective at Most effective at Not suitable to Roughly 80%
analyzing LCN analyzing 1-2ng of determine paternity accuracy when
samples if DNA without maternal analyzing
approached correctly Gains roughly a 15% sample degraded DNA
Showed better identification rate Falls within acceptable Displays less false
results for valid when coupled with paternity findings when homozygosities in
detection of sex- the microcon-30 analyzing the standard the D5S818 loci
determination loci, purification unit trio samples than the
Amelogenin Unable to detect More relatively AmpFLSTR速
Roughly 80% most loci in amounts accurate at typing the Identifiler速 kit
accuracy when of sample around VWA loci than More relatively
analyzing degraded 0.015 ng or less Powerplex 16 affected by
DNA samples storage
Retention of temperature of
information is less samples than
sensitive to AmpFLSTR速
temperature in Identifiler速 kit
sample storage
19. REFERENCES
1. Butler, John M. Forensic DNA Typing. 2005. Elsevier Academic Press.
2. J. P. Whitaker, E. A. Cotton, P. Gill, A comparison of the characteristics of profiles produced with the
AMPFlSTR(R) SGM Plus(TM) multiplex system for both standard and low copy number (LCN) STR DNA analysis,
Forensic Science International, Volume 123, Issues 2 -3, 1 December 2001, Pages 215 -223, ISSN 0379-0738,
DOI: 10.1016/S0379-0738(01)00557-6.(http://www.sciencedirect.com/science/article/B6T6W -44HSMMP-
N/2/0a3ac8657953802f439cd3ca16687e38 )
3. L. Buscemi, M. Pesaresi, C. Sassaroli, F. Alessandrini, A. Tagliabracci, Further study on suitability of Profiler
Plus in personal identification, International Congress Series, Volume 1239, Progress in Forensic Genetics 9.
Proceedings from the 19th, January 2003, Pages 891 -894, ISSN 0531-5131, DOI: 10.1016/S0531-
5131(02)00575-7. (http://www.sciencedirect.com/science/article/B7581 -47W664D-
1NM/2/f01020ea1b32111cf0a42e42d8445492 )
4. K. Babol-Pokora, R. Jacewicz, Pepinski, S. Szram, Identifiler(TM) system as an inadequate tool for judging
motherless paternity cases, International Congress Series, Volume 1288, Progress in Forensic Genetics 11 -
Proceedings of the 21st International ISFG Congress held in Ponta Delgada, The Azores, Portugal between 13
and 16 September 2005, April 2006, Pages 462 -464, ISSN 0531-5131, DOI: 10.1016/j.ics.2005.09.102.
(http://www.sciencedirect.com/science/article/B7581 -4JSBXBX-
5R/2/7e791e028513dce63232f1a5d4d45460 )
5. B. Glock, R. B. K. Reisacher, S. O. Rennhofer, D. Troscher, E. M. Dauber, W. R. Mayr, Evaluation of
Powerplex(TM) 16 for typing of degraded DNA samples, International Congress Series, Volume 1239, Progress
in Forensic Genetics 9. Proceedings from the 19th, January 2003, Pages 609 -611, ISSN 0531-5131, DOI:
10.1016/S0531-5131(02)00296-0.(http://www.sciencedirect.com/science/article/B7581 -47W664D-
1KB/2/add81b4ca5fbf1a7906672e2318e8a1f )
6. A. Amorim, C. Alves, L. Pereira, L. Gusmao, Genotyping inconsistencies and null alleles using AmpFLSTR(R)
Identifiler(R) and Powerplex(R) 16 kits, International Congress Series, Volume 1261, Progress in Forensic
Genetics 10, April 2004, Pages 176 -178, ISSN 0531-5131, DOI: 10.1016/S0531-5131(03)01496-1.
(http://www.sciencedirect.com/science/article/B7581 -4C4WDDP-
23/2/e458dc9ac25f660bccd6b2cea233202a)