12 Jul GENETICS AND PHENOTYPE
DATA HANDLING LINKED TO MOLECULAR MEDICINE; Mathematical Question in biology
Coursework 1:
Using statistical methods for data analysis
Tasks in the coursework:
A series of experimental results have been collected and should be analysed by statistical methods. Data sets will be provided and the task will be to:
(1) Select adequate statistical methods to analyse the data
(2) Describe briefly the rationale why a method is reasonable and useful for the problems
(3) Perform the analysis
(4) Answer the question(s) associated with the problems and
(5) Draw adequate conclusions on the biological problems given
The final results and any conclusions which can be drawn from the results should be discussed briefly but conclusively. The report should focus on the clear description rationale and presentation of the analysis of the data. This is not an essay (!) but it is useful to introduce the question and the main conclusions from the data. The discussions should be short but clearly define the major conclusions which can be drawn from the data or not.
Calculations
Calculations can be done by hand using the adequate formulas as presented in the lectures/seminars. They will also be found in textbooks on statistics.
Calculations should be limited to adequate decimals.
Statistical analysis packages may be used (like SPSS) or available online calculation programs
Raw data are also posted for easier use on Blackboard (Excel format)
(>BIO-M209 Coursework > Coursework 1 > File: Coursework 1_Supplementary Data_Raw Data)
Tables of critical values for different distributions (t-Test F-Test Chi-square test) are found in most textbooks on statistics and freely available programs
A selected list of some useful programs and potentially needed tables are also found on
Blackboard
(>BIO-M209 Coursework > Coursework 1 > Coursework 1_Supplementary Data_Tables.Formulas)
Presentation in general:
Do not simply present the calculations but explain the rationale of using a statistical method and draw adequate biological conclusions from the results. It should state the result its significance and any other conclusion(s) which may be relevant.
Part 1: Genetics and phenotype of a novel mouse mutant
Introduction: A novel mouse mutant and the corresponding protein mKIAA058 (in the following KIAA) was identified and further analysed. In order to understand the functions of this gene/protein a mouse strain containing a non-functional allele (mKiAA058-; Null-allele) was successfully established. First data indicated an autosomal recessive inheritance as heterozygous (KIAA+/-) as well as homozygous knockout (KIAA-/-) animals were identified. The deficiency of this protein (Knockout KIAA) affects multiple tissues including skeletal defects (delayed/reduced development of bone and cartilage; growth retardation) as well as a progressive form of vascular degeneration. Later a corresponding disease in humans was found in a small number of very young patients. The prospects of the patients are not clear at the time and the analysis of the mouse model may provide some hints for the severity of the disease. The analyses of the molecular mechanisms underlying the disease are still ongoing and some problems and experiments linked to these studies are given in the following. Statistical tests may be used to answer some of the questions.
Experiments 1 and 2: Genetics
In order to define potential effects of the presence/absence of the KIAA protein on the inheritance patterns a number of breedings were performed. The genotypes of the parents were known and the genotypes of the litters (age: 14-16 days) were analysed by allele-specific PCR reactions.
Experiment 1: (Marks: 10)
In three parallel experiments (1.1 1.2 1.3) crossings of 5 wildtype males (KIAA+/+) with 10 heterozygous females (KIAA+/-) were started and all litters (given as total number of mice) were genotyped and the numbers of all possible genotypes are given in the following Table 1. All tested mice appear normal and show no altered phenotype at the tested age (day 14-16).
Breeding: male(KIAA+/+) x female(KIAA+/- )
Table 1: Experiment 1.1 1.2 1.3
Litters Total number 62 90 98
Genotypes KIAA+/+ 34 37 42
KIAA+/- 28 53 56
KIAA-/- 0 0 0
Experiment 2: (Marks: 20)
In three parallel experiments (2.1 2.2 2.3) crossings of 5 heterozygous males (KIAA+/-) with 10 heterozygous females (KIAA+/-) from experiment 1 were started all litters were again genotyped (age: day 14-16) and the numbers of mice with all possible genotypes are given in the following Table 2.
Breeding: male(KIAA+/-) x female(KIAA+/- )
Table 2: Experiment 2.1 2.2 2.3 Sum (2.1-2.3)
Litters Total 71 84 59
Genotypes KIAA+/+ 21 23 18
KIAA+/- 39 46 35
KIAA-/- 11 15 6
Questions to answer:
(A) Discuss briefly which type of genetic inheritance would be most adequate to describe the distribution of genotypes?
(B) Do the distributions of all genotypes (numbers of mice) in experiments 1 and 2 correspond to the expected numbers according to Mendelian laws?
(C) Are there any differences seen in the amount of Wildtype and Heterozygotes? Are the overall numbers of genotypic normal mice (+/+ and +/-) versus Knockout (-/-) significantly different?
(D) Are there any further conclusions possible? If yes what could be possible biological explanations of the observed distribution/s? Which other experiments would be needed?
Experiment 3: Bodyweight of various genotypes (Marks: 30)
The lack of KIAA seems to affect various organ systems (see before) Therefore a series of experiments were performed to define the growth of mice with various genotypes. Wildtype (KIAA+/+) heterozygous carriers (KIAA+/-) and homozygous knockouts (KIAA-/-) were analysed for their body weight (in grams: g) at different ages 10-11 days 20-22 days and 40-42 days. Only female animals were included in this analysis to avoid gender-specific variability.
The following tables contain the collected raw data.
(Raw data are available: >BIO-M209 >Courseworks >Coursework 1 >2014_Coursework 1_Supplementary Data_Raw data)
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