BIOL

2202 Experimental Design and Analysis in Biology

Semester 2, 2015

Fingerprint analysis: using chi-square testing and regression analysis

Overview: The practical generates a robust data set from which you will address several
questions by developing specific hypotheses and using appropriate statistical tests for each
question. You will then prepare a short report. Report guidelines are a separate document
available on Wattle. This practical has been modified from a Monash University Genetics
Course and is used with the permission of the authors.

Aim of practical: The aim of the experiment is to categorise and analyse fingerprint patterns
in a specific population, and compare this population to another population. The practical
highlights the importance of accurate data collection and interpretation, choosing the
correct statistical analysis test and interpreting the outcomes within the context of specific
questions.

Learning outcomes:
1) Demonstrated ability to collect and present data accurately and effectively, and to
critically evaluate data (including the identification of sources of error).
2) Application and presentation of basic statistical analysis, including chisquare analyses
and t-tests.
3) Demonstrated ability to interpret experimental outcomes and statistical analysis in
relation to the experimental hypothesis.

Skills developed: Basic fingerprinting techniques, data acquisition and analysis, chisquare
analyses, regression analysis, data presentation, interpretation of statistical testing
outcomes, scientific writing skills.


Timeline:
Fingerprint analysis: Part 1
Week 3 Classifying fingerprints, perfecting your fingerprinting technique,
entering your fingerprint data into spreadsheet
If possible, fingerprint both of your biological parents and any
Intervening week
siblings and bring fingerprints to class in Week 4
Fingerprint analysis: Part 2
Analyse familial fingerprint data (either your own or those
Week 4
provided) and enter data into spreadsheet
Discussion of data analysis
Week 7 Short report due Monday Aug 31 by 10:00 pm via Wattle



INTRODUCTION - Background information

Most variation that we observe among individual humans is quantitative or continuous
variation. It can be measured on a continuous scale and does not fall into discrete classes
as might be expected of genetic characteristics which are inherited in a typical single
gene or Mendelian pattern (such as seed coat-colour in peas). However, all evidence now
indicates that such continuous variation is a direct developmental result of the
interactions of many genes. Alternative alleles of many single loci have either a positive
or a negative contribution to a measureable genetically determined character, i.e.
fingerprint pattern. At a population level these continuously varying polygenic
characteristics have predictable patterns of inheritance, although more complex
statistical techniques are necessary for their analysis. Also, and of most importance,
these characteristics may be modified by the environment such that a lot of the variation
within a species is due to the difference between environments in which individuals and
families have developed.

One means of obtaining a measure of the genetic-strength of heritability of a
continuously varying trait is to study the similarity between relatives. The more genes
that such relatives have in common, the more likely they are to have similar values of this
trait.

The examination of fingerprints offers an excellent chance to demonstrate polygenic
inheritance and an objective way of comparing the differences between both sexes and
populations. The measurements taken are considered to be highly objective and are also
of value as they have a high genetic component and are stable after the fourth month of
foetal life.

The most useful and widely employed descriptive measures of fingerprint pattern are
Pattern Type, Pattern Intensity Index and Total Ridge Count. Each of these
measures is defined below:

A: Pattern Type
There are three basic types of fingerprint or pattern types.
v the arch has no triradius (the intersection of three dermal ridges)
v the loop has one triradius
v the whorl has two triradii, one on either side of the pattern

B: Pattern Intensity Index
This is the sum of the number of triradii on all 10 digits of the hands. Values range from a
minimum of 0 (arches on all digits) to a maximum of 20 (whorls on all digits)

C: Total Ridge Count
The ridge count is defined as the number of ridges which are cut, or touched, by a
straight line running from the triradius to the core of the centre of the pattern, with the
exception of the two terminal points. In the case of a whorl you only take into
consideration the larger of the ridge counts. The Total Ridge Count is the sum of the
ridge counts of all 10 digits.

Use larger ridge count only

In this example, ridge on left
Ridge count = 17
EXPERIMENTAL DESIGN AND PROCEDURE:

Part 1 (Week 3): Individual fingerprints

Step 1: Accurate categorisation of fingerprints is important for this study. On your bench is a
sheet of fingerprint examples. Take some time to read the introductory information above
carefully, and then attempt to classify each of these sets of fingerprints. Once your
demonstrator has confirmed that you have correctly determined the Pattern Type, Pattern
Intensity Index and Total Ridge Count for this sample you can move on to the next step.

Step 2: Each student has been provided with an ink pad and a card for recording fingerprints. A
good fingerprinting technique is harder than it sounds, and you should ensure that you practice
several times with each of your digits. While a less than ideal fingerprint is still likely to enable
you to determine the Pattern Type and Pattern Intensity Index, a high quality fingerprint is
required to determine the Total Ridge Count.

Step 3: Having determined the Pattern Type, Pattern Intensity Index and Total Ridge
Count for your fingerprints you should enter these values into the Class Data Table on the
laptop located at the head of your bench. The class data will be available on Wattle about
72 hours after the prac.

Step 4: If possible, gather familial fingerprint data over the next week, for next weeks prac.
Specifically, we need data from BOTH parents and ONE or MORE of their offspring. Many
students live on campus and are unable to do this, but if you can, get data from your
parents and siblings, or from families you know (if they are OK with this). You can take some
fingerprint cards, and borrow an ink pad. Make sure that you identify which set of prints
belong to each family member, and ensure the gender of offspring is recorded.


Part 2 (Week 4): Familial fingerprint sets

Step 1: In addition to the familial fingerprint sets that some students have collected, the
tutors and lecturers have also provided some familial fingerprint data. If neither you nor
your partner were able to collect a familial fingerprint data set please obtain one of the sets
provided by the tutors/lecturers.

Step 2: For each family member determine the Pattern Type, Pattern Intensity Index
and Total Ridge Count. Additionally determine the Mid-parent score, which is the
average of the Total Ridge Count score for the mother and father.

Step 3: Enter these data into the Familial Fingerprint Data Table on the laptop located at the
head of your bench. Whole class data will be available on Wattle about 72 hours after the
prac. You will need these data to write up your short report.


ANALYSING THE DATA:
In this prac we are interested in the answers to several questions:

1. Does the distribution of different Pattern Types vary between males and females?

2. Does the Total Ridge Count differ significantly between males and females?

3. Is the distribution of the different Pattern Types in the BIOL2202 class consistent
with population averages?

4. Is the Total Ridge Count of the parent significantly correlated with the Total Ridge
Count of his/her offspring of the same sex?

5. Is the Mid-parent score significantly correlated with their offspring? (Note: do
male or female offspring).


Heres how we might address these:

Question 1: Does the distribution of different Pattern Types vary between males and
females?

The analysis involves a 2X2 contingency table, and the test is a chisquare homogeneity
test. A contingency table is a matrix format used to analyse and record the relationship
between variables. Homogeneity tests are covered in the lecture handout entitled
Chisquare and twoup.pdf under Daves Lecture Notes. In that example we dealt with
handedness by sex in the same way as we are dealing with fingerprint Pattern Types by
sex here. However, because there are three possible Pattern Types this would not fit into
a 2X2 contingency table. Additionally, because arch pattern types are so uncommon we risk
having an expected value of less than 5, which is problematic for the statistical test, as
explained by Dave in lectures. For these reasons, we will group Arches and Loops together,
thus separating our data into two groups, either Whorls or Not Whorls. Below is the
contingency table you will be testing:

Whorls Not Whorls
male
female

You can follow the steps outlined in the lecture notes, or you can try a shorthand way of
doing exactly the same calculation as given in the lecture notes (instructions below) you
might like to try both to convince yourself, as the two ways look quite different. If you want
to try it using the R software you can do that too; instructions will be given in the R tutorial
(Week 5).

Short hand way to calculate homogeneity test based on contingency table:

Sex Fingerprint Pattern Type Row

Whorls Not whorls Totals

Female (a) = (b) =

Male (c) = (d) =

Column
Totals N =

You apply these additions to the following formula (1):
2 = N (ad bc) 2
(a + b) (c + d) (a + c) (b + d) (1)
(note: while doing it this way is fine, it isnt intuitive and so its harder to remember than the
long-hand method).


Question 2: Does the total ridge count differ significantly between males and females?

This problem can best be answered using a t-test. There are several different types of t-test
and its up to you to decide which is the most appropriate.


Question 3: Is the distribution of the different Pattern Types in BIOL2202 consistent with
population averages?

In this case, we need to get a reference sample to compare with ours. The reference sample
distribution that we will use is from the FBI, which has in excess of 60 million fingerprints on
file and gives the following population averages for the different Pattern Types:

The Arch: 5%
The Loop: 30%
The Whorl: 65%

(www.fbi.gov/about-us/cjis/fingerprints_biometrics)

To do this we will use a chisquare goodness of fit test (refer to lecture notes) to compare
our expected values (based on the reference values from the FBI) with our observed values
based on our class data. On the basis of the limitations of this test discussed in lectures, you
will need to decide whether you can use all three patterns types, or if you will need to pool
two of them.



Questions 4 and 5:

For these questions you should make a scatterplot with the parental (independent variable)
score on the x-axis and the child score (dependent variable, single sex only) on the y-axis.
You should then use a linear regression to determine whether there is a significant
relationship between your variables, as outlined in Daves lectures.

If you want a few bonus points, think of another question you can ask using these data, and
answer it with an appropriate test.

Its amazing how many questions you can ask and how much you can learn from a couple of
rows of numbers!