Incidence of

Microvariants & Triallelic

Patterns from Caribbean
Population Genetic Data
Name: Joenelle Baptiste
Supervisor: Compton Beecher

INTRODUCTION

INTRODUCTION

INTRODUCTION
This work by Sir Alec Jeffreys, led to
the discovery of STRs:
Which are repeat regions with short
repeat units
7 repeats
8 repeats
9 repeats
10 repeats
11 repeats
12 repeats
13 repeats

Target region
(short tandem repeat)

(Butler 2009)

INTRODUCTION
The characteristics of these STRs
greatly benefit identity testing in
forensic science
13 genetic markers were used to form
the CODIS database in the US
The UK and US alone have more than
5 million profiles in databases that
provide information from these loci or a
subset of the same
Also important in paternity cases

INTRODUCTION
Variation between DNA markers are

extremely important as it is the only

way differentiation between forensic
samples can be achieved
One of the ways variation can be
hindered is the presence of
biological artefacts two of which
are Off-Ladder Alleles (full
insertions/deletions or Microvariants)
and Triallelic patterns

INTRODUCTION
Microvariants are alleles with
incomplete units
Also known as off-ladder alleles
E.g. TH01 9.3 allele: [TCAT]4 -CAT
[TCAT]5

Deletion of T
Clayton et al. (2004) A genetic basis for anomalous band patterns
encountered during DNA STR profiling. J Forensic Sci. 49(6):1207-1214

INTRODUCTION
These artefacts exist for most STR loci
According to (Butler 2009) this encourages the analysis
and discovery of new ones at different STR loci around
the world

Microvariants can be found at the more

polymorphic STR loci
Loci that can express 2 or more forms at the same
locality, which increases due to large and complex
structures (e.g. FGA, D21S11)usually not seen in
more simple loci (e.g. TPOX, CSF1P0)

NIST states that more than 475

Microvariant alleles have been described
for the 13 CODIS core STR loci

INTRODUCTION
Triallelic patterns are artefact
peaks that can occur as a result
of two reasons
Extra chromosomal fragments
present in the sample being
analysed
Duplication of the annealed primer
sequences on one of the existing
chromosomes

INTRODUCTION
The third peak is found at a single locus, negating the presence of a mixture, e.g.

INTRODUCTION
TPOX

D21S11

D18S51

Type 1

Type 2

Sum of heights of
two of the peaks is
equal to the third
Most common in
D18S51 and ..

Balanced peak
heights
Short Tandem Repeats
(STRs). 2008; Available
from:
http://www.forensicdnac
enter.com/

Most common in
TPOX and D21S11

PROBLEM STATEMENT
STR genotyping becomes significantly easier when
there are adequate alleles at each locus in the allelic
ladders to compare to samples being analysed. This
becomes more difficult when artefacts are present in
samples to be analysed as a lot of the allelic ladders
available do not have the artefacts as part of the
ladders.

PURPOSE STATEMENT
It is therefore necessary to identify these artefacts,
so that they can be added to the allelic ladders by kit
manufacturers and therefore aid in forensic and
parentage testing.

HYPOTHESIS
Determination of the sequential
variations in Microvariants and
Triallelic pattern irregularities in STR
loci can be applied directly to
complications of human identity and
parentage testing, in the forensic field.

SIGNIFICANCE OF STUDY
Identifies Microvariants and Triallelic
patterns from Caribbean population
genetic data
Promotes the addition of these
artefacts to the allelic ladders of
prominent kit manufacturers
Increases the efficacy of forensic
and parentage testing in the
Caribbean region

AIM
To ensure that the forensic and
parentage testing fields in this region
can advance with the addition of any of
these artefacts found being added to
established profiling kits.

OBJECTIVES
1. To identify the frequency of
Microvariants and Triallelic patterns
and the markers from which they
are found from previously analysed
Caribbean population DNA samples
2. To add any of these artefacts found
to worldwide DNA databases
3. To encourage the addition of these
Microvariants to established
profiling kits

METHODOLOGY

METHODOLOGY
Sample Collection
All information was obtained from
previously analysed DNA samples of
paternity cases from the year 2014
Which were analysed using the
GeneMapper ID V3.0 software from
applied Biosystems
Only the core CODIS STR loci were
examined for variances

METHODOLOGY
Variant Allele Confirmation
Reamplification was not required as the
samples were already analysed in
duplicate.
The off-ladder variances and threebanded patterns present were confirmed
by the duplicated profiles.
Variances in allele placement and size
were identified by aligning the sequences
for each sample with the particular ladder

METHODOLOGY
Only Microvariants not found within the
manufacturers allelic ladder were
investigated.
The resultant information obtained was
compared to databases in the NIST for
identification.
Those Microvariants not found in the
NIST database were manually assigned
and recommended to the providers of
commercial kits to be added to the allelic
ladders used by analysts

METHODOLOGY

RESULTS
Off-Ladder/Microvariant Alleles
Of all the profiles analysed from within
the 2014 year, 2258 off-ladder alleles
were observed
183 of these were observed within 9
of the Core CODIS STR but were not
found on the manufactuers allelic
ladder:
D3S1358, TH01, D21S11, D18S51, D7S820,
D16S539, CSF1PO, vWA, and FGA.

RESULTS
180 of the 183 were observed in the
NIST STRbase
But the remaining three were not
previously reported
These three loci were identified as
D18S51 (with the genotype 23.3),
vWA (with the genotype 15.2), and
FGA (with the allele size 418.05);
and they were all present once, with
a frequency of 0.0027.

RESULTS
In two instances there were offladder alleles that sized higher and
lower than the allelic ladder range, in
which case the approach for
reporting these alleles as described
by the National Forensic Science
Technology Center was used
Alleles that are less than the lowest allele on the particular
ladder are reported as less than X (as observed with the
D3S1358 locus).
Alleles that are more than the largest allele on the particular
ladder are reported as greater than X (as observed with the
CSF1PO locus).

RESULTS
Triallelic Patterns
Twenty-one three-banded patterns were
observed in the following core CODIS
STR loci: D21S11, D7S820, D16S539, D8S1179,
CSF1PO, TPOX and FGA

Of the 21 triallelic patterns observed, 10

were not found in the NIST database.
The D21S11 locus had the highest rate
of three-banded patterns, with 7 being
observed, the TPOX locus had 6 and the
D7S820 locus had 4

CONCLUSION
It becomes challenging for analysts when,
even though its rare, off-ladder alleles are
observed that have not been previously
reported.
While studies have shown that the allelic
ladder provided by the manufacturers of
the PowerPlex16 commercial STR typing
kit includes all the official allelic variants,
there are times when the rare off-ladder
alleles are observed and have to be
manually assigned.

CONCLUSION
It is important for forensic casework
and other applications that these rare
variants be added to the STRbase as
the publication can aid in its
recommendation to the typing kits of
STR loci.
Doing this helps alleviates the
misinterpretation and incorrect analysis
of results in forensic casework analysis
and other fields. If not, wrong
conclusions can result.

CONCLUSION
Even with all the recent research and
studies being done on the presence
of triallelic patterns within the STR of
varying loci, a compilation of their
frequency across general populations
has yet to be developed.
One study observed a total of 10 triallelic patterns
across the 15 Identifiler loci used to type the individuals
within their database
Another study, which analysed the variances found in 10
000 individuals, identified only 19 three-banded patterns
18 at the TPOX locus and 1 at the CSF1PO locus

CONCLUSION
The development of databases like
the STRbase, provides a much
needed service to analysts when
interpreting and determining results.
However, due to the rarity of the
presence of anomalies like
Microvariants and triallelic patterns,
examination of profiles where they
are observed becomes a challenge
for analysts.

CONCLUSION
Studies like this that identify and document
unreported cases of Microvariants and
triallelic patterns are important, as only
through identification and documentation
can new variances can be found and added
to the allelic ladders of commercial STR
typing kits.

CONCLUSION
When incorrect designations of these
irregularities to the allelic ladder are
made, false exclusions or inclusions
can result, leading to possible medical
or legal upheaval.

RECOMMENDATIONS
Further research that incorporates a
wider range of Caribbean
populations genetic data can be
analysed.
Identifying any correlation between
the presence of variant alleles and
familial relationships
Using any information obtained to
develop an STRbase within the
Caribbean

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