CSF1PO:

APPLICATIONS IN
FORENSIC SCIENCE
ALICAI MORALES, BECKY SMITH, KIMBERLEY MASIH, SUET FAR WONG,
TOBY VICKAR, AND YE JEE ROH

SHORT TANDEM REPEATS IN FORENSIC SCIENCE

What makes a good STR marker?
High heterozygosity among the population (>70%)
Separate chromosomal locations
Reproducibility of results when multiplexed
Low stutter ratio

Low mutation rate

Allele sizes of STR marker should fall within the range of 90-500 base pairs

HISTORY OF CSF1P0
CSF1PO is seen as having moderate to low
discrimination power

CSF1PO is commonly used today due to it

being one of the 13 CODIS core loci
It was one of the first STRs ever discovered

BACKGROUND OF CSF1P0 LOCATION

Located on chromosome 5
(5q33.3-4)
Size range of allelic ladder varies

based on kit/primer used

CSF1P0

BACKGROUND OF CSF1PO
Simple repeat STR: Contains units of identical
length and sequence

CSF1PO in humans (HUMCSF1PO) is a protooncogene for the CSF-1 receptor gene

The common sequence motif in the 5 3
direction is AGAT
It is the number of repeats of "AGAT" at CSF1PO
that varies from one person to another on each
inherited chromosome
http://www.cstl.nist.gov/strbase/str_csf.htm

BACKGROUND OF CSF1P0: PROS AND CONS

PROS
Tetranucleotides are the most commonly used STRs in Forensic Science because of their
low stutter ratio (compared to di- or tri- STRs)
Low mutation rates

High amount of population research done already for this STR

Narrow allele size (which allows: multiplexing, reduces allelic dropout from preferential
amplification of smaller alleles, usage of degraded DNA, reduces stutter product formation
in mixture samples)
CONS
CSF1P0 typically exhibits the least amount of variation between individuals

Not used nowadays in Forensic Laboratories in Europe

STUTTER
Stutter peak: minor allele peak with repeat units shorter or longer than parental
allele peak
Due to slipping of Taq polymerase during PCR
Stutter ratio: height/area of stutter peak over that of allelic peak
For lower stutter level:

Longer repeat units

Complex repeat unit sequence
Shorter allelic length
Ratio should be less than 0.15 to be considered a stutter peak

STUTTER OF CSF1PO
AmpflSTR Profiler DNA Typing System
319 single source DNA samples
Mean stutter rate of CSF1PO was 5.83%
Lower than vWA and FGA, but higher THO1 and TPOX

AmpFlSTR Identifiler PCR Amplification Kit

Minimum of 100 data points from population database samples
Mean stutter percentage of CSF1PO fell within the 8% stutter

GlobalFiler PCR Amplification Kit

Stutter filter percentage calculated for CSF1PO is 8.77%
How % is calculated: Mean stutter for the locus plus three standard
deviations
Peaks in the stutter position below the stutter filter percentage> filtered off

GLOBALFILER PCR AMPLIFICATION KIT

Thermo Fisher Scientific Inc., 2015

STUTTER OF CSF1PO
Stutter percentages from internal validation of different
kits under threshold of 0.15
Shorter length of repeat unit and simple sequence of
CSF1PO contribute to higher stutter ratio compared to
other STR markers
Also influenced by extrinsic factors such as primer designs
used and reaction conditions
Smaller stutter ratio would be more advantageous in
interpretation of sample profile
GlobalFilerTM PCR Amplification Kit User Guide (2015).

PATERNITY TESTING
Has low mutation rate (0.16%): this is good
for paternity testing
Research has been done to improve the
reliability of the use of CSF1PO in paternity
testing

A recent study used CSF1PO and five closely

linked SNPs (SNPSTR) and looked at their
potential uses in paternity testing

Found that paternity probability increased to

99.998%

Balloch et al. (2008)

COMBINED DNA INDEX SYSTEM (CODIS)

Includes 13 STR loci, plus Amelogenin
Why was CSF1PO selected as one of these 13?
CSF1PO and D5S818 are the only two CODIS STRs that share a
chromosome
Recent studies show that CSF1PO does not have a very high
heterozygosity rate
Looking back in the literature to when CODIS was first constructed,
CSF1PO was said to be one of the more discriminating STRs
(Hammond et al, 1994)
More current research shows that CSF1PO has the second lowest
heterozygosity rate of all CODIS STRs (Planz et al., 2012)
In most comparative studies of CODIS vs. Non-CODIS STRs, better
results were found when non-CODIS STRs were used

http://www.cstl.nist.gov/strbase/fbicore.htm

POPULATION DATA

HETEROZYGOSITY RATES
Country
Yugoslavia
South Korea
Mexico
East Malaysia
Brazil
Colombia/Antioquia
Serbia and Montenegro
China (Fujian province)
Russia (Vulga-Ural)
Egypt
Italy

Heterozygosity
0.748
0.716
0.7062
0.714
0.72304
0.687
0.68
0.7208
0.743
0.67
0.67

SUMMARY
Overall, we would NOT add CSF1PO
to our existing kit
Due to a combination of low heterozygosity rates, low
variation among alleles, and comparatively high stutter ratio,
CSF1PO is among the least discriminating STRs we have
today

CSF1PO

REFERENCES

https://www.fbi.gov/about-us/lab/biometric-analysis/codis/codis-and-ndis-fact-sheet

Hammond, H. A., Jin, L., Zhong, Y., Caskey, C. T., & Chakraborty, R. (1994). Evaluation of 13 short tandem repeat loci for use in personal identification applications. American Journal Of Human Genetics, 55(1), 175-189.

Tsai, C. W. , Yang, C. H., Chou, S. L., Cheng, S. G., Pai, C. Y. (2013) Non-CODIS DNA markers could be more effective than CODIS-based STRs in problematic biological relationship cases.Romanian Society of Legal
Medicine, (21), 245-248.

Butler, J. (2005). Forensic DNA Typing: Biology, technology, and genetics of STR markers, Second Edition. Elsevier Academic Press. Pg. (104-108).

D.Y. Wang et al. (2015). Developmental validation of the GlobalFiler Express PCR Amplification Kit: A 6-dye multiplex assay for the direct amplification of reference samples. Forensic Science International: Genetics ,
(19), 148155.

L.K. Boon et al. (2006). Internal validation of the AmpFlSTR Identifiler PCR amplification kit on the ABI PrismR3100 genetic analyzer for use in forensic casework at the Department of Chemistry, Malaysia. International
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L. Blackmore, M.H. Luebke, J.M. Laird & P.J. Newall. (2000). Preferential Amplification and Stutter Observed in Population Database Samples using the AmpflSTR Profiler Multiplex System. Canadian Society of Forensic
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R. Li. (2015). Forensic Biology, 2nd Edition. USA: CRC Press.

GlobalFilerTM PCR Amplification Kit User Guide (2015). Thermo Fisher Scientific Inc.

K.J.D. Balloch, J. Marshall, J. Clugston, J.W. Gow, Reporting paternity testing results when 2 exclusions are encountered, Forensic Science International: Genetics Supplement Series, Volume 1, Issue 1, August 2008,
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Rangel-Villalobos, H. et al. Allele frequency distributions of six Amp-FLPS (D1S80, APO-B, VWA, TH01, CSF1PO and HPRTB) in a Mexican population. Forensic Sci. Int. 105, 125129 (2015).

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Klintschar, M. et al. Genetic variation at the STR loci D12S391 and CSF1PO in four populations from Austria, Italy, Egypt and Yemen. Forensic Sci. Int. 97, 3745 (1998).

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