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Title: An Example Identification Genetics Report
Description: A report detailing the identification of example deceased using genetic material extracted from the bone. (LJMU 2015 UK). I graduated with a 1st class degree in Forensic Anthropology.
Description: A report detailing the identification of example deceased using genetic material extracted from the bone. (LJMU 2015 UK). I graduated with a 1st class degree in Forensic Anthropology.
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Genetic identification of the victims of the 2003
earthquake of Suburbia, Utopia
Case number 008
Ryan Broadley
NATSCI6021 FORENSIC AND ANTHROPOLOGICAL GENETICS
Genetic identification of the victims of the 2003 earthquake of Suburbia, Utopia
Case number: 008
Student number: 608764
1
...
At the time of
this, only 382 of the 575 reported missing individuals were recovered by the authorities
...
In 2013, the Forensic Anthropology team at Liverpool JMU Forensics estimates there
is a minimum number of individuals of 215, from the remains recovered at this site
...
In September 2014, Liverpool JMU Forensics
officially took over the processing of the genetic material from the skeletal material collected
...
There were five skeletal samples selected, and
five reference samples, the DNA of these were extracted and amplified, and then compared with
one another to determine whether or not these samples were related
...
MATERIAL AND METHODS
2
...
Sample selection
Five samples were collected from the materials presented to us
...
Following
these criteria, the bones which were selected for these samples were as follows: a left femur
(80-89
...
9%), a thoracic vertebrae (60 – 69
...
9%), and an upper molar (70 – 79
...
These bones were described to be among those that yield above 50% DNA (Suni, 2007)
...
2
...
DNA extraction
The extraction of the DNA followed different protocols depending on the medium from which the
simple was derived, in this case, the samples were from blood and bone or teeth
...
The DNA
extraction protocols followed that outlined in the lab manual (Fernandez, 2014)
...
2
...
Blood
The extraction of DNA from blood uses an alkaline based protocol, which requires 0
...
This process required frequent centrifugation to form precipitant pellets at
the bottom of the 1
...
The addition of water before each centrifugation allows the pellet
to mix gently, this causes the formation of a pellet and supernatant
...
In the final stage
Sodium Hydroxide is added in the final stages before addition of Tris-Base 0
...
This then
proceeds straight to the PCR reaction
...
2
...
Bone / Teeth
When Bone or Teeth are being extracted from the materials, this procedure uses an organic
method, in that it uses enzymes to break down cell membranes and otherwise until the DNA can
be extracted using Protease solutions
...
2
...
DNA amplification
DNA amplification used a multiplex PCR method which differed for the amplifications of different
types of genetic material
...
2
...
1
...
Due to these being a specific region in the Y chromosome,
therefore this would only produce a reaction in Male individuals
...
3
...
Mitochondrial DNA
For the amplification of bone extracts, firstly the amplification focuses on mitochondrial DNA
(mtDNA), this looks at Hypervariable Region I (HVRI) of the mtDNA
...
The concentrations of each of the PCR components per PCR are included in the appendix
(appendix: table 1)
...
4
...
There is also the
inclusion of the Reference samples to the programme, this is for comparative analysis of
mutations in mutation surveyor
...
5
...
These programs
were: Y Chromosome Haplotype Reference Database (YHRD) (Willuweit and Roewer, 2007) for
Y Chromosomes; STRBase (Gill et al, 2003) for Autosomal Short Tandem Repeats (STRs); for
mtDNA the programs used were EMPOP (Parson and Dür, 2007) and MtDNA Manager (Lee et
al, 2008)
...
STRBase studies STRs
contained in the Applied Biosystems AmpFISTR SGM+ kit, these correspond to the UK core
loci, so can be used to identify any person, regardless of sex, when familial haplotypes are
available to be compared with
...
EMPOP and
MtDNA Manager use the haplotypes from Mutation Surveyor, and assess the frequency of
3
Genetic identification of the victims of the 2003 earthquake of Suburbia, Utopia
Case number: 008
Student number: 608764
every different mtDNA profile in their population, and the geographic distribution of this
...
6
...
This includes establishing the minimum number of individuals in the
bone samples, this uses likelihood ratios (LR) for the determination
...
The
5
equation for autosomal STRs was: “Profile Frequency= ” and the equation for mtDNA and Y
5
2𝑁
chromosomes were: “Profile Frequency= ”
...
After this, individual identification of BS was calculated using uniparental markers (mtDNA and
Y chromosome), this determines whether BS is a member of the family, this is calculated using
𝑃( 𝐷𝐴𝑇𝐴| 𝐻1)
1
the following formula: “LR = (
=
”
...
3
...
The results of the Y chromosome amplification was positive (appendix: figure 6)
...
The estimation of profile frequency results tables are included (appendix: table 2, 3 and 4), this
includes their frequency estimations worldwide and in west Eurasia
...
The estimations of the autosomal STRs showed
the 10 UK core loci and allowed the identification of familial relationship through genotype
analysis
...
4
Genetic identification of the victims of the 2003 earthquake of Suburbia, Utopia
Case number: 008
Student number: 608764
4
...
The frequencies reported for different databases are due to the different sizes of the databases,
EMPOP is more euro-specific and due to the location of Utopia, this is the database used in the
calculation of the likelihood ratio
...
Using worldwide databases is often recommended because Utopians may not be 100%
Eurasian
...
The genetic profiles for autosomal
STRs, Y chromosome STRs, and mitochondrial DNA of bone samples BS and BSa are
identical, this result is 2
...
The combined analysis of autosomal STRs, Y Chromosome STRs and
mitochondrial DNA of bone sample BS008 are 2
...
5
Genetic identification of the victims of the 2003 earthquake of Suburbia, Utopia
Case number: 008
Student number: 608764
CITED BIBLIOGRAPHY
Andrews, R, M, Kubacka, I, Chinnery, P, F,
Lightowlers, R, N, Turnbull, D, M, Howell, N, (1999)
...
Natural
Genetics 23, 147
...
Amplification of the amelogenine
gene and of a repetitive alphoid sequence of the Ychromosome in archaeologic remains in the Basque
Country
...
195200
...
Beyond traditional paternity and identification
cases
...
Forensic Science International
...
Fernandez, E, (2005)
...
University of Barcelona
...
Laboratory Manual,
NATSCI6021, Forensic Anthropological and
Anthropological Genetics
...
Forensic Science
International
...
Lee, H, Y, Song, I, Ha, E, Cho, S, B, Yang, W, I, Shin,
K, J, (2008)
...
BMC Informatics
...
Minton, J, L, Flanagan, S, Ellard, S, (2011)
...
D
...
,Rapley, R
...
), PCR Mutation
Detection Protocols, Methods in Molecular Biology
Humana Press, 143-153
...
EMPOP – A forensic
mtDNA database
...
1, 88–92
...
Identifying Missing U
...
Service
Members from the Korean War
...
10(1)
...
L, (2007)
...
Forensic Science International: Genetics 1(2), 83-7
...
5mM
22mM
1
...
22mM
0
...
25
19
...
85
0
...
099
82
...
65mM
0
...
11units/μl
38μl
62
...
72
1
...
1672
0
...
4
15μM
1μl
0
...
4
15μM
1μl
0
...
747e-5
0
BSa
14
14
30
23
10
14
13
12,
13
10
10
14
18
15
16
25
12
4
...
747e-5
0
RSb
14
14
30
23
10
14
13
12,
13
10
10
14
18
15
16
25
12
4
...
2
BSa
XY
20-21
15-16
19-21
10-16
8-9
15-21
13-14
11-18
11-15
27-31
...
2-30
...
0021e-31
BSc
XY
18-21
16-19
19-27
12-15
9-12
17-20
11-14
21-22
15
...
2
2
...
2
2
...
2
3
...
2
5
...
9716e-20
Table 4 – Results of mtDNA Analysis
Figure 9 – Heat map of the Y haplotype of BS, BSa, RS and RSb
10
Figure 10 - Heat map of the Y haplotype of BSc
Frequency
Europe
1
...
0827e-22
Genetic identification of the victims of the 2003 earthquake of Suburbia, Utopia
Case number: 008
Student number: 608764
Bone Samples with
Same Profile
BS
BSa
Genetic Marker
Profile Frequency
LR
mtDNA
Y chromosome
Autosomal STRs
Combined
mtDNA
Y chromosome
Autosomal STRs
Combined
0
0
0
3
...
135e-4
1
...
8171488e-30
3
...
135e-4
1
...
8171488e-30
0
0
0
Table 5 - Profile Frequencies and Lik elihood Ratios per Profile and Genetic Mark ers
Worldwide
Eurasia
EMPOP
34617
12746
mtDNA
mtDNA Manager
9294
3673
Y chromosome
YHRD
91231
44053
Table 6 - Overall Population sizes of the different analysis databases
mtDNA LR
3
...
135e-4
Autosomal STRs LR
6
...
375733645378e+11
Title: An Example Identification Genetics Report
Description: A report detailing the identification of example deceased using genetic material extracted from the bone. (LJMU 2015 UK). I graduated with a 1st class degree in Forensic Anthropology.
Description: A report detailing the identification of example deceased using genetic material extracted from the bone. (LJMU 2015 UK). I graduated with a 1st class degree in Forensic Anthropology.