The Statistics of Forensic DNA Analysis代写BIOL2151
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The Statistics of Forensic DNA Analysis代写BIOL2151
BIOL2151 – Assignment 2 Instructions 1
Assignment 2 - BIOL2151 - 2016
The Statistics of Forensic DNA Analysis
This assignment is worth 25% and is due on Tue Sep 6 at 5 pm.
Overview
Your brief is to prepare a scientific report that addresses the topic:
How many STR loci are required to assist in solving a crime in a series of cities of
increasing population size?
You must base your answers on your statistical analysis of the ANU STR database and appropriate
literature resources. Choose representative cities (and/or countries) of different population size that
are of most interest to you personally (e.g. The ANU, Canberra, NSW, Australia; Yangshou,
Shoaxing, Shanghai, China). Outline the assumptions that you have made in drawing your
conclusions. Where applicable, test whether or not these assumptions hold true for the ANU STR
database. Compare your answers with the common practice in forensic analysis.
Your report must take the form of a research paper written in the format typical of published
scientific papers. The text must be written with full sentences and paragraphs in a precise and
concise scientific writing style (i.e. dot points are not acceptable). Some marks will be allocated to
sentence construction, logical flow, grammar, spelling and formatting. All sources must be cited
within the text using the Harvard format with the full reference provided in the Reference List at the
end of the report. Please see the separate handout on Referencing for more details. Ensure you
comply with the page limits.
About the ANU STR database
The database consists of a list of STR genotypes for 92 DNA samples representing 3 different
human populations: Canberra, Indonesia and PNG.
These samples were typed using the Identifiler kit (Applied Biosystems), which types 15 STR loci
and the sex marker Amelogenin. There are currently 9 standard loci in Australia that are included
on our national database (NCIDD), and all of these 9 loci are included in the Identifiler kit (see the
Practical manual for details). The US database (CODIS) uses 13 loci, and again the Identifiler kit
includes all of those loci.
Check list of the minimum statistical analysis required in your report
• Standard Statistics: Number of alleles Na, observed heterozygosity HO, expected
heterozygosity HE for all loci. Also report the mean of these values over the loci.
• DNA Profile probabilities DPP, across all 15 loci for two different individuals.
• Cumulative PI for increasing combinations of the 15 loci.
• Compute the odds for all probabilities that you calculate (e.g. DPP and PI).
Note that these calculations are not difficult, but require some care. For calculating DPP and PI,
you may wish to use the template provided with your class exercises in the lectures. It is permissible
to share the task of calculations for more complex stats such as DPP or PI with colleagues. In this
case you must acknowledge your collaborators. Alternatively, you may find it easier to complete
you calculations in a spreadsheet program such as Excel. In this case, you are still required to show
a sample of your working out in the appendix.
Other calculations you might consider for testing your assumptions
• Assess whether or not the ANU STR database populations approximate HWE (F=0).
• Compute the degree of differentiation (FST) among the populations in the database.
BIOL2151 – Assignment 2 Instructions 2
Report Instructions
Your report consists of two parts.
Part 1 – The report itself. This must be submitted electronically at the BIOL2151 Wattle site,
which provides submission via Turnitin AND as an identical hard copy with your appendix.
Part 2 – The appendix in which you provide a copy of your representative calculations. This
appendix must be attached to the hard copy version of your report and submitted via the normal
Biology Teaching and Learning submission process. Use a single cover sheet for both parts.
Part 1 (Electronic and hard copy submission)
FORMATTING
Please use a 12 pt Font and at least 1.5 spacing with minimum 2.5 cm margins on all sides. Be sure
to number all pages.
TITLE (Max 25 words)
Provide an informative short title. Also include your name, student number and course details.
WORD COUNT
Include a word count (excluding references, figure and table captions).
ABSTRACT (Max 100 words)
Concisely summarise the purpose, methods and findings of your report.
KEYWORDS (Max 5 words)
Choose up to 5 keywords that broadly represent the content of your report.
INTRODUCTION (Max 500 words)
Use the introduction to provide a brief background to forensic DNA profiling drawing on relevant
supporting references. Conclude the introduction with a clear statement of the question you will
address. Note that your introduction must be concise, focussed and directly relevant to the topic. It
should set the stage and connect to the topic(s) you will explore in the remainder of the report.
MATERIALS AND METHODS (Max 250 words)
Provide a brief overview of the STR database, such as the names of the STR loci used, source of the
DNA samples etc. Identify the statistical calculations performed (and why) and the relevant
formulas used in your analysis of the database. If you choose to report data from other sources or
studies outline the source of such data here (e.g. census data, other STR population databases).
RESULTS (Max 1000 words)
Note that tables, figures and supporting captions are exempt from this word limit and must be
provided after your list of references.
Please do not insert tables and figures in the body of the text.
Summarise the outcomes of your statistical analysis of the database in written form, with reference
to supporting tables and figures. Provide sufficient written detail such that the main message is clear
without the need for the reader to refer to the tables or figures that are presented at the end of the
report. Be sure that your tables and figures include informative captions that allow them to be
interpreted without the need to refer back to the written text. Organise your results section in a way
that works for you. There is more than one way to do this, so your report might be quite different
from other students. However, in general your first paragraph will briefly provide an overview of
the outcomes for the standard statistics (Na, HO, HE).
BIOL2151 – Assignment 2 Instructions 3
DISCUSSION (Max 1000 words)
This is the most important part of your report. It is here that you demonstrate that you understand
what you did, why you did it and, most importantly, what your results mean. Provide a summary of
the key findings and interpret in a forensics context with relevant supporting references.
A High Distinction level report will be both very well written and show evidence of extra library
research well beyond the references provided. You might also compile results across students in
your group or perform extra calculations (e.g. calculate the Fixation Index as an indication of
whether the population sample is in Hardy-Weinberg equilibrium).
ACKNOWLEDGMENTS (30 words max)
Acknowledge any colleagues who provided advice or with whom you shared the calculation tasks.
REFERENCES (Exempt from page limit)
List the full references for all sources you cite in your report following the formatting guidelines
provided in the separate handout entitled: A guide to referencing in BIOL2151/BIOL6006.
TABLES AND FIGURES
Here you provide the table and figures that you have previously described and summarised in
written form in the results section. Be sure that your tables and figures include informative captions
that allow them to be interpreted without the need to refer back to the written text. Note that any
tables or figures that you do not explicitly refer to in Part 1, should be presented in Part 2, rather
than in this section of the report.
Part 2 (Appendix attached to the hard copy of the report)
APPENDIX (Exempt from page limit)
Include a copy of representative calculations e.g. show an example of how your calculated the DNA
Profile Probabilities and Probability of Identity. You do not need to show the calculations for every
sample or locus, but you must demonstrate that you performed the calculation yourself. If you used
Excel to perform calculations include a printout of your spreadsheet showing the formulas used.
Some useful journals (Accessible electronically via the library)
Forensic Science International Elsevier Science Pub. Co.
Journal of Forensic Sciences American Academy of Forensic Sciences
To access go to the ANU library catalogue and search on Title for Electronic Resources Only.
Useful books (On closed reserve)
Butler, JM (2005) Forensic DNA typing: biology, technology, and genetics of STR markers.
Elsevier Academic Press, Amsterdam.
[On closed reserve at HANCOCK RA1057.55.B88 2005; also available as an electronic resource!]
Butler JM. (2010) Fundamentals of forensic DNA typing. Amsterdam: Academic Press/Elsevier.
Buckleton JS, Triggs CM, Walsh SJ (2005) Forensic DNA evidence interpretation
CRC Press, Boca Raton. [On closed reserve at HANCOCK
RA1057.55.F667 2005]
Note that in some cases, there may also be more recent editions of these textbooks.
BIOL2151 – Assignment 2 Instructions 4
About Turnitin
The ANU uses Turnitin to enhance student citation and referencing techniques, and to
assess assignment submissions as a component of the University's approach to managing
Academic Integrity. While the use of Turnitin is not mandatory, the ANU highly
recommends Turnitin is used by both teaching staff and students.
You agree that by submitting your assignment for text matching purposes, that your
assignment will be included as a source document in the Turnitin database. Use of Turnitin
is subject to the Turnitin User Agreement. Should you not agree to these terms, you will
not be able to submit your assignment in to Turnitin.
Your electronic submission of Part 1 via Turnitin is due the same date and time as
the hard copy submission: Tue Sept 6, 5 pm.
If you choose to opt-out of this electronic submission, you must make alternative
submission arrangements with Rod Peakall, not later than Mon Aug 22.
For additional information regarding Turnitin please visit the ANU
Online website.
BIOL2151 – Assignment 2 Instructions 5
HWE?
Because of the large number of alleles at the STR loci, performing a Chi-square test of HWE can be
tricky (but not impossible). If you do choose to test for HWE, be sure to incorporate your
calculations effectively in your report. For example, you could provide the HWE test results when
you critically evaluating the assumptions you have made.
As an alternative for inferring whether on not the populations are close to HWE expectations, you
can also summarise the Fixation index values, F. When values are close to zero, or slightly negative,
such findings are consistent with HWE expectations.
The Statistics of Forensic DNA Analysis代写BIOL2151
