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Last modified by varvio@helsinki_fi on 2024/03/27 10:38
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varvio@helsinki_fi 1.1 1 = (% style="color: rgb(0,51,102);" %)Statistical genetics, fall 2012(%%) =
2
3 === (% style="color: rgb(0,51,102);" %)Lecturer(%%) ===
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5 [[Sirkka-Liisa Varvio>>doc:mathstatHenkilokunta.Varvio, Sirkka-Liisa]]
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7 === (% style="color: rgb(0,51,102);" %)Scope(%%) ===
8
9 2-10 cu + 3cr seminar
10 The course is a set of one week modules. 
11 The program consists of lectures and associated weekly home-exercises, computer work (data-analysis), discussions on scientific papers.
12
13 More information here.pdf
14
15 === (% style="color: rgb(0,51,102);" %)Prerequisites(%%) ===
16
17 Basic probabilistics and interest in bio-applications of statistics.
18 Course is suitable for students with planned orientation to biometry and bioinformatics and also for other students interested in biological applications of statistical inference.
19 Compulsory course in Bioinformatics Master´s program (MBI, degree requirements 2012-2014).
20
21 === (% style="color: rgb(0,51,102);" %)Lectures and computer class sessions(%%) ===
22
23 Weeks 45-50, Tuesdays 14-18, Wednesdays 14-18, C128.
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25 === (% style="color: rgb(0,51,102);" %)[[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=8125||shape="rect"]](%%) ===
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27 === (% style="color: rgb(0,51,102);" %)Content scheme(%%) ===
28
29 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Module I, Intro" borderColor="#ffffff"}}
30 (% style="color: rgb(0,51,102);" %)**Wed 7. 11, 14-18, D123**(%%)
31 (% style="color: rgb(0,0,0);" %)THIS IS EXAM MATERIAL(%%)
32 • Course synopsis
33 • (% class="confluence-link" %)Statistical concepts in a nutshell.pdf(%%)
34 • (% class="confluence-link" %)Basic concepts in genetics and home-exercise 1.pdf(%%)
35 • Review: (% class="confluence-link" %)Linkage disequilibrium.pdf
36 {{/panel}}
37
38 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Module II, Mutations" borderColor="#ffffff"}}
39 (% style="color: rgb(0,51,102);" %)**(Tue 13.11), lecture postponed to Mon 19.11 16-18, C128**(%%)
40 (% style="color: rgb(0,0,0);" %)THIS IS EXAM MATERIAL(%%)
41 • (% class="confluence-link" %)Modelling mutations and home-exercise 2.pdf(%%), (% class="confluence-link" %)For home-exe 2.2.pdf(%%)
42 • (% class="confluence-link" %)Mutation analysis from genome data.pdf(%%)
43 • (% class="confluence-link" %)Universal trend in amino acid gain and loss.pdf
44
45 ----
46
47 (% style="color: rgb(0,51,102);" %)**Wed 14.11, 14-18, C128**(%%)
48 (% style="color: rgb(0,0,0);" %)NOT FOR EXAM(%%) (This is for 1cr in addition to the 4cr from the course, cf this: (% class="confluence-link" %)More information here.pdf(%%))
49 Teacher: (% style="color: rgb(0,51,102);" %)Virginia Brilhante(%%) from Biomedicum (Research Program for Molecular Neurology).
50 Amino acid evolutionary diagnosis of function-altering mutations //in silico// by using the softwares
51 [[SIFT>>url:http://sift.jcvi.org/||shape="rect"]] (Sorting Intolerable From Tolerable) and [[PolyPhen>>url:http://genetics.bwh.harvard.edu/pph2/||shape="rect"]] (prediction of functional effects of human nsSNPs).
52 Work to be done during the computer session:
53 (% class="confluence-link" %)cs1PatientExomeVariantDataSample.xlsx(%%), (% class="confluence-link" %)cs1Guidelines.pdf(%%)
54 (% class="confluence-link" %)cs2PatientExomeVariantDataSample.xlsx(%%), (% class="confluence-link" %)cs2Guidelines.pdf(%%)
55 cs2-data: corrected version added
56 (% class="confluence-link" %)Virginia Brilhante lecture 141112.pdf
57
58 Assignment SIFT_PolyPhen:
59 The work started during the computer session is part A part of the assignment.
60 (% class="confluence-link" %)SIFT_assignment Part B.pdf(%%), (% class="confluence-link" %)cowhaplo1_20.txt(%%), (% class="confluence-link" %)cowSNP_and_reference.txt(%%), (% class="confluence-link" %)cowSNP_and reference_AA.txt(%%)
61 Submission to [[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=8125||shape="rect"]]
62 {{/panel}}
63
64 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Module III, Populations" borderColor="#ffffff"}}
65 (% style="color: rgb(0,51,102);" %)**Tue 20.11, 14-18, C128**(%%)
66 (% style="color: rgb(0,0,0);" %)THIS IS EXAM MATERIAL(%%)
67 • Review: (% class="confluence-link" %)Estimating population genetic structures.pdf(%%)
68 • Review: (% class="confluence-link" %)Data analysis methods.pdf(%%)
69 • (% class="confluence-link" %)Home-exercise 3.pdf(%%),  (% class="confluence-link" %)Appendix to Home-exercise 3.pdf(%%)
70 (% style="color: rgb(0,0,0);" %)Home-exercise 3 was done during the session. During the session Wed 28.11 more background theory.
71
72 Data to be analysed:
73 Tajima D calculator
74 Human population HLA-gene data: (% class="confluence-link" %)Zulu.txt(%%), (% class="confluence-link" %)Toroko.txt(%%), (% class="confluence-link" %)Sioux.txt(%%), (% class="confluence-link" %)South Indian.txt(%%), (% class="confluence-link" %)Mexican.txt(%%), (% class="confluence-link" %)Irish.txt(%%), (% class="confluence-link" %)Filipino.txt(%%), (% class="confluence-link" %)Zulu.txt(%%), (% class="confluence-link" %)Czech.txt(%%), (% class="confluence-link" %)Finn 90.txt(%%), (% class="confluence-link" %)Turk.txt(%%)
75 Bacteria data: (% class="confluence-link" %)USA_before_vacc.txt(%%), (% class="confluence-link" %)USA_after_vacc.txt(%%), (% class="confluence-link" %)Skand_before_vacc.txt(%%), (% class="confluence-link" %)Skand_after_vacc.txt
76
77 Selecton server, (% class="confluence-link" %)Selecton tutorial.pdf(%%)
78 (% class="confluence-link" %)Growth hormone gene.txt(%%), (% class="confluence-link" %)BDNF-gene.txt(%%), (% class="confluence-link" %)HLA gene.txt
79
80 ----
81
82 (% style="color: rgb(0,51,102);" %)**Wed 21.11, 14-18, C128.**(%%)
83 (% style="color: rgb(0,0,0);" %)NOT FOR EXAM (%%) (This is 1cr in addition to the 4cr from the course, cf. this: (% class="confluence-link" %)More information here.pdf(%%))
84 Guidance to practical work in computer class.
85 Data-analysis by the software Arlequin3.5, Manual
86 Example data for training during the session, which is aloso part A for the assignment:
87 (% class="confluence-link" %)HLA_DRB1_freqtable.xlsx(%%), (% class="confluence-link" %)HLA_DRB1_seqs.txt(%%) The script: (% class="confluence-link" %)convertToArlequin.R.txt(%%), (% class="confluence-link" %)Completed data_file to Arlequin.txt(%%), (% class="confluence-link" %)Script comments.txt(%%)
88 This is geographical population data from one very polymorphic human gene (very many alleles, the sequences), collected from here(% style="color: rgb(255,0,0);" %)
89
90 (% style="color: rgb(255,0,0);" %) (% style="color: rgb(0,0,0);" %) (% class="confluence-link" %)Arlequin assignment.pdf(%%), (% class="confluence-link" %)Example 1.pdf(%%), (% class="confluence-link" %)Example 2.pdf
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92 (% style="color: rgb(255,0,0);" %)
93 (%%)Note added 3.12: I have now corrected the datafile which included mistakes in the data-collection step. The inputfile, which you should name again as .arp, instead of .txt, works fine.
94 {{/panel}}
95
96 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Module IV, Coalescence, haplotypes" borderColor="#ffffff"}}
97 (% style="color: rgb(0,51,102);" %)**Wed 28.11,**(%%) (% style="color: rgb(0,51,102);" %)**14-18, C128**(%%)
98 (% style="color: rgb(0,0,0);" %)THIS IS EXAM MATERIAL(%%)
99 Lecture topics: More about previous week theme, statistical tests of neutrality etc. Introduction to the concept and theory coalescence (retrospective population genetics).
100 • (% class="confluence-link" %)Selection tests and coalescence theory.pdf(%%), (% class="confluence-link" %)Kingman´s Coalescence paper.pdf(%%), Human genome Tajima D
101
102 ----
103
104 (% style="color: rgb(0,51,102);" %)**(Wed 28.11, 14-18, C128)**(%%).(% style="color: rgb(0,0,0);" %)See your email for info about this.(%%)
105 (% style="color: rgb(0,0,0);" %)NOT FOR EXAM(%%) (This is 1cr in addition to the 4cr from the course, cf. this: (% class="confluence-link" %)More information here.pdf(%%))
106 Guidance to practical work in computer class.
107 • Haplotype networks by using the software Network, (% class="confluence-link" %)Network_Manual.pdf(%%).
108 The program is installed in C128 computers. Freely available to own computers, too (although under a company´s webpage). Note that installation always expires at the end of a year: install anew at the beginning of a new year.
109 (% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" class="confluence-link" %)Haplotype assignment.pdf(% style="color: rgb(255, 0, 0); color: rgb(0, 0, 0)" %), (% class="confluence-link" %)Article_1.pdf(%%), (% class="confluence-link" %)Article_2.pdf(% style="color: rgb(255,0,0);" %)
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111
112
113 {{/panel}}
114
115 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Module V GWAS-minicourse" borderColor="#ffffff"}}
116 (% style="color: rgb(0,51,102);" %)**Tue 04.12, 14-18, CK112**(%%)
117 (% style="color: rgb(0,51,102);" %)T**eachers: Samuli Ripatti, Matti Pirinen, FIMM**
118
119 Human Genetics and Biostatistics
120 Heritability - Linkage studies - Association studies - Genotyping technologies - Quality control
121 Statistics of association mapping (significance and power vs. priors and evidence)
122 Examples of real studies - Recent topics in GWAS world (e.g. missing heritability, synthetic associations,...)
123 Why do we think that certain phenotype has a genetic component?
124 How does gene mapping work with family data and how does it work with population data?
125 What kind of data modern genotyping technologies produce and how to analyse them?
126 What have we learned during the last five years from genome-wide association studies?
127 And what have we not learned so far?
128
129 (% style="color: rgb(0,0,0);" %)THIS IS EXAM MATERIAL(%%)
130 • Lecture: (% class="confluence-link" %)GWAS_041212.pdf(%%)
131 • Reviews: (% class="confluence-link" %)Anderson_et al_2010.pdf(%%), (% class="confluence-link" %)Risch_2000.pdf
132
133 ----
134
135 (% style="color: rgb(0,51,102);" %)**Wed 05.12, 14-18, C128**(%%)
136 (% style="color: rgb(0,0,0);" %)NOT FOR EXAM(%%) (This is 1cr in  addition to the 4cr from the course, cf. this: (% class="confluence-link" %)More information here.pdf(%%))
137 • Lecture: (% class="confluence-link" %)GWAS_1_051212.pdf(%%), (% class="confluence-link" %)GWAS_2_051212.pdf(%%)
138 • (% class="confluence-link" %)R_matrix_80_Europeans.txt(%%), (% class="confluence-link" %)GWAS_examples.R(%%)
139 • Literature here: www.well.ox.ac.uk/~~mpirinen/GWAS_course
140 • (% class="confluence-link" %)GWAS-assignments.pdf(%%) 
141 {{/panel}}
142
143 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="EXAM" borderColor="#ffffff"}}
144 (% style="color: rgb(0,51,102);" %)**Tue 11.12 or Wed 12.12, 14-18,**(%%) (% style="color: rgb(0,51,102);" %)**C128.**
145
146 Your choice for the exam, inform here: [[exam-DOODLE>>url:http://www.doodle.com/yi4acnpf9kbiu6rt||shape="rect"]]
147 {{/panel}}
148
149 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Journal club" borderColor="#ffffff"}}
150 [[attach:Journal club.pdf]]
151 History of statistics + genetics: , , , , , (% class="confluence-link" %)History_Muller.pdf(%%)
152 • Reserved: Bianca(% class="confluence-link" %)History_Fisher.pdf(%%) and (% class="confluence-link" %)History_Fisher2.pdf(%%), Teemu(% class="confluence-link" %)History_Galton.pdf(%%) and (% class="confluence-link" %)History_Galton2.pdf(%%), Sara(% class="confluence-link" %)History_HW.pdf(%%), Sophie(% class="confluence-link" %)History_Haldane.pdf
153
154 The code origins:
155 • Reserved: Anna K(% class="confluence-link" %)Origins_2.pdf(%%), Filippo(% class="confluence-link" %)Origins_1.pdf(%%) and (% class="confluence-link" %)Origins_3.pdf(%%)
156 Disease mutations with an evolutionary view: , , , (% class="confluence-link" %)Dis_mut_4.pdf(%%), (% class="confluence-link" %)Dis_mut_9.pdf(%%),
157 • Reserved: Jimmy(% class="confluence-link" %)Dis_mut_6.pdf(%%), Anju(% class="confluence-link" %)Dis_mut_3.pdf(%%) and (% class="confluence-link" %)Dis_mut_10.pdf(%%), Johanna(% class="confluence-link" %)Dis_mut_5.pdf(%%), Yujuan(% class="confluence-link" %)Dis_mut_1.pdf(%%) and (% class="confluence-link" %)Dis_mut_2.pdf(%%), Anna K(% class="confluence-link" %)Dis_mut_7.pdf(%%), Sophie(% class="confluence-link" %)Dis_mut_8.pdf(%%),
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159 Statistical genetic studies of populations of various organisms: (% class="confluence-link" %)Pop_1.pdf(%%), (% class="confluence-link" %)Pop_2.pdf(%%), (% class="confluence-link" %)Pop_3.pdf(%%), (% class="confluence-link" %)Pop_4.pdf(%%), (% class="confluence-link" %)Pop_5.pdf(%%), (% class="confluence-link" %)Pop_6.pdf(%%), , (% class="confluence-link" %)Pop_8.pdf(%%), (% class="confluence-link" %)Pop_9.pdf(%%), (% class="confluence-link" %)Pop_10.pdf(%%)
160 • Reserved: Ahmed(% class="confluence-link" %)Pop_7.pdf
161
162 [[MOODLE>>url:https://moodle.helsinki.fi/course/view.php?id=8125||shape="rect"]]
163 {{/panel}}
164
165 {{panel bgColor="#ffffff" titleBGColor="#99ccff" borderStyle="solid" title="Seminar" borderColor="#ffffff"}}
166 Send an email to sirkka-liisa.varvio at helsinki.fi if you want to give a seminar. Presentations during the last course week and written essays in January.
167
168 (% style="color: rgb(0,51,102);" %)**Agreed topics:**
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170
171
172 Your choice for seminar session: [[seminar-DOODLE>>url:http://www.doodle.com/2744syh8apt2wqa5||shape="rect"]] (% style="color: rgb(255,0,0);" %)
173
174 ----
175
176 ----
177 {{/panel}}
178
179 === [[Registration>>url:https://oodi-www.it.helsinki.fi/hy/opintjakstied.jsp?html=1&Tunniste=57734||shape="rect"]] ===
180
181 Did you forget to register? [[What to do>>doc:mathstatOpiskelu.Kysymys4]].[[attach:Roman_b.pdf]]