2015 MOLECULAR MEDICINE DNA LAB WRITE UP FOR WEEK 2

Name: Garrett Mcfarlane ID# 620088397

Date: October 9, 2015
Course: Molecular Medicine
Group # and Group: Groups 4, MBBS
Title of Lab: Gentics lab, paternity testing
ANSWERS- SECTION A (GENETICS):

Question 1
a. Karyotyping can be described as a technique used to analyse an
individuals chromosomes to ascertain whether or not any chromosomal
anomalies are present which may result in a genetic condition. In
karyotyping, an image of persons chromosomes is displayed in
homologous pairs and compared to a normal set of chromosomes to
determine if there is any genetic anomaly such as monosomy or trisomy.
b. Two chromosomal characteristics that are paid attention to are the length
and the position of the centromeres.
c. Two differences that maybe observed are differences in the position of
centromeres and differences in relative size of chromosomes.

Question 2
a. The steps involved are denaturation, annealing and extension/elongation.
In the denaturation step the reaction is heated to a temperature of 94-98
C. This causes melting/denaturing of the DNA template by disrupting the
hydrogen bonds between complementary bases, which results in singlestranded DNA molecules. In the annealing step the temperature is lowed
to 50-65C for approximately 40 seconds to allow for primers to bind to
their complementary DNA sequences in the DNA sample. In the extension
phase reaction is then heated to 72 C, which is the optimal temperature
for DNA polymerase to act. DNA polymerase then extends the primers,
adding nucleotides onto the primer in a sequential manner, using the
target DNA as a template.
b. Four major reaction components are Denature DNA, primer, a buffer and
DNA polymerase. DNA polymerase is an enzyme that creates a new strand
of DNA through the sequential addition of nucleotides. A Buffer is a salt-

solution that helps to stabilize the DNA and other components of the
reaction.
c. One advantage is that it grants the ability to rapidly identify organisms
that are difficult to culture, another advantage is that PCR tests can be
performed quickly and interpreted the same day as sample submission.
One disadvantage is that, since PCR is extremely sensitive, it is prone to
contaminating DNA which can lead to erroneous results. Another
disadvantage is that PCR amplification is sensitive to certain inhibitors that
may be present in the DNA preparation, an example of this is phenolics.

Question 3
a. Three characteristics that make it suitable are: The smaller size of STR
alleles which make STR markers better for use in forensic s, they are easily
amplified by polymerase chain reaction (PCR) without the issue of
differential amplification and STR alleles tend to have lower mutation
rates, which allows for more accurate data and results.
b. An earlier method to DNA fingerprinting and also a common method for
fingerprinting is restriction fragment length polymorphism in this method,
DNA is extracted from a sample and cut into segments using restriction
enzymes, these segments are then separated using a technique known as
electrophoresis which is used in laboratories in order to separate
macromolecules based on length. The segments are radioactively tagged
to produce a visual pattern known as an autoradiograph, or DNA
fingerprint.

Question 4
a. The gender of the individual would be male as presence of the Y
chromosome indicates the person is of the male gender. To be
considered male genetically, an X and Y chromosome are required,
where as a female would not have a Y chromosome and therefore
cannot be the gender of the person in question.
b. The sex of the individual is female, as the X specific markers
DX56803 and XHPRT recorded two peaks, indicating the presence of
two X chromosomes which is an indication of a female. The marker
DX51187 also detected an X chromosome. There seems to be no
abnormality so this is a normal female (no aneuploidy)( no triple
peaks and no peaks in a 1:2 ratio).

c. XHPRT is a short tandem repeat (STR) marker which is X-specific.

(used for detecting the X chromosome).
TABLE SHOWING GENOTYPES FOR CERTAIN GENETIC
DISORDERS AND TRAITS SHOWN BY THE AFFECTED GENDER
GENOTYP
E

GENDER

GENETIC
DISORDER

XO

Female

Turner
syndrome

Male/Fem
ale

WolfHirschhorn
syndrome

Male/Fem
ale

Downs
Syndrome

Flattened nose, stunted

growth, flat head

Jacobsen
Syndrome

Low-platelets, Wideset eyes, Heart

defects, Displaced
receding chin

trisomy X

Increased risk of delayed

language development,
tall stature

Monosom
y 4p/
deletion
4p
Trisomy
21/ 3rd
copy of
chromoso
me 21
Deletion
of a
terminal
region of
chromoso
me 11
XXX

Male/Fem
ale

Female

TRAITS OF DISEASE
Sex organs don't mature
at adolescence, sterility,
short stature
Facial appearance,
delayed growth and
development, intellectual
disability, and seizures.

RESULTS - SECTION B (PATERNITY TESTING 1)

TABLE SHOWING ALLELES FOR CHILD AND ALLEGED FATHER FOR

SPECIFIC LOCI (Case A)
Loci
D13S317
VWA
D16S539
TPOX
D5S818

Child
8.1,12
13, 15
9, 11
6, 10
10, 13

Alleged Father
9, 12
15, 18
11
8, 9
10, 13

TABLE SHOWING ALLELES FOR CHILD AND ALLEGED FATHER FOR

SPECIFIC LOCI (Case B)
Loci

Child

D13S317
VWA
D16S539
TPOX
D5S818

11, 13
16
12, 13
6, 8
12

Alleged Father
11, 15
16, 20
13, 14
6, 8
12

TABLE DISPLAYING ALLELES OF CHILD AND ALLEDGED FATHER AND

PATERNITY INDEX FOR EACH LOCI (Case B)
Loci

Child

Alleged
Father

Shared
Allele

D13S317
VWA
D16S539
TPOX

11,13
16
12,13
6,8

11,15
16,20
13,14
6,8

11
16
13
6,8

D5S818

12

12

12

Frequenc
y of
Shared
Allele
0.23743
0.26944
0.16507
0.08612,
0.36842
0.35556

Formula

1/4q
1/2q
1/4q
(p+q)/4p
q
1/q

Paternity
Index

1.053
1.856
1.515
3.582
2.812

Calculation for heterozygous:

1/4q= *0.23743= 1.053
Calculation for homozygous
1/q=1/0.35556=2.812
CPI= The product of paternity indexes
CPI=1.053*1.856*1.515*3.582*2.812=29.824
Probability of paternity = (29.824*0.5/(29.824*0.5)+0.5) * 100=96.756%
In case A it is very likely that the alleged father is not the real father of the child
that was tested as the probability of paternity is 0%, however in case B it is very

likely the man in question is the father of the child tested as the
probability is significantly higher at 96.75%.

QUESTIONS- SECTION C (PATERNITY TESTING 2)

Question D

DNA profile- This can be defined as the set of values of a group of

genetic markers identified in an individual's DNA by a process
known as DNA profiling

Heterozygote can be defined as a situation in which an individual has two

different alleles of a particular gene or genes.

Paternity index is a statistical measure of how powerfully a match at a particular

marker indicates
Paternity; it calculates the likelihood that the tested man is the
biological father based on that loci.
Question F

One factor that may increase the likelihood of a mutation occurring is exposure
to large amounts of ultraviolet radiation. Ultraviolet light may cause two
pyrimidine bases adjacent to each other on the same strand to bind to each
other, instead of binding to their rightful partner on the opposite strand; this is
called a pyrimidine dimer. In order to fix this error a process known as the
excision repair takes place but this process may result in a DNA mutation.
Another more natural or biological factor that may result in DNA mutation is
errors by the enzyme DNA polymerase which is involved in replication. During
this process although it is a highly precise one, there can be mispairing of
nucleotides which can result in eventual mutation as a result of errors made by
the enzyme. These two factors may lead to mutations such as deletion, frame
shift, insertion, point, translocation, silent etc.
Question G

The alleged father in this case is not likely the father of the child presented, this is because in
locis D18S5, D13S317 and D3S1358 there are no shared alleles between the father and child. In cases
like this it is highly unlikely that the alleged would be father as there are too many incidences of
mismatching alleles, which cannot be attributed to mutations alone. When calculating the CPI, the
indexes of 0.000 would result in the CPI being 0 and consequently there being a 0.00% probability of
paternity.

SOURCES
Steven Oszust, (August 2004). Summer Research Program for Science
Teachers.
Retrieved (09 Oct. 2015) from
http://www.scienceteacherprogram.org/biology/Oszust04.html

Boundless, (21 Jul. 2015). Amplifying DNA: The Polymerase Chain Reaction.
Retrieved (09 Oct. 2015) from
https://www.boundless.com/microbiology/textbooks/boundless-microbiologytextbook/microbial-genetics-7/bioinformatics-83/amplifying-dna-the-polymerasechain-reaction-458-5372/

"DNA fingerprinting." The Columbia Electronic Encyclopedia. 1994, 2000-2006

on Infoplease.
20002015 Sandbox Networks, Inc., publishing as Infoplease.
Retrieved (09 Oct. 2015) from
http://www.infoplease.com/encyclopedia/science/dna-fingerprintingmethods.html

Susan T. McClure, (Jun 22, 2015). Effects of Ultraviolet Light on DNA.

Retrieved (09 Oct. 2015) from http://www.livestrong.com/article/88549-effectsultraviolet-light-dna/

Polymerase chain reaction.

Retrieved (09 Oct. 2015) from http://www.uvm.edu/~cgep/Education/PCR.html