1.- Continuous Assessment. This course is part of your continuous assessment, and it is worth 20/230 marks, or ~9% of this section of the course. (The other section is your end-of-year exams on the lecture courses). There is no exam at the end but you are requested to do work regularly, and submit your report at the end of term. The course is specific to the Human Genetics moderatorship.

2.- Course Materials. These pages are permanently on the college's server and can be accessed freely from outside the college. These pages contain all the theory, exercises, problems and references you may need. Notes and exercises on the use of Cyrillic 2.1 are found by pressing the button 'Cyrillic Notes' on the left. Jurg Ott's linkage programs for the calculation of lod scores and risk estimation will be supplied to you on a floppy.

3.- Timetable & class schedule. Eight x two-hour sessions in Michaelmas Term. The first session in week 1 takes place in EELT1 at 2;00 pm and at 3;00 pm we move to the adjacent EEPC1 for some computer work. This schedule will be repaeted in week 3. All other weeks we will use EEPC1 from 2 to 4 pm. The contents of the first session can be accessed directly from the web (this course). The second session requires the use of 'cyrillic 2.1', which is installed in the EEPC1 room.

4.- Exercises. These are maked PE1, PE2, etc. and there are a minimum of 20, scattered throughout the course. They may involve the use of taylor-made calculators, public databases, literature references, as well as 'Cyrillic', the pedigree drawing program. Often you are offered a choice of topics for a given exercise. In these cases, you are meant to take only one option. The purpose of the relatively large choice of materials is to provide you with some scope for original work. The exercises require different types of answer. Sometimes you are requested to report on a database search, to do some calculations and prepare a table or a graph with the results, to comment on an unusual pedigree, etc. In all cases, a brief and informed commentary is required.

5.- Problems.These are marked PP1, PP2, and most of them are gathered under the 'Problems' button. There is a minimum of 20 problems, some easier (marked *), some more difficult. Problems have one numerical solution, and I would be looking for the reasoning that led you to the solution.

6.- Computer sessions. Besides 'Exercises' and 'Problems', you have six computer sessions, gathered under the 'Cyrillic Notes' button. Each session requires a separate report, as each contains a number of questions that you should try to answer.

7.- Submitting your work. You are requested to submit your answers to the exercises and problems before 1st January 2003. You could submit the work weekly, as you do it, or all at the same time at the end of term. I will send you an email acknowledging receiving the work. Good quality hard copy and hand-written work are equally acceptable, but presentation does count. You can present your work also on disk, as an illustrated WORD document or a web page (html) that would be viewable in Netscape 4.7 or Explorer 5. Name the file as; 'pedigree_name1_name2_02', where name1_name2 is your name. Please clear your disk of all viruses. Please let me know of you need a zip disk

8.- Work organiser. You are welcome to work at your own pace. However, the following organiser may help you schedule your course work.

9.- Marking scheme. You will be judged by the number and quality of your exercises, problems and computer session reports. The six computer sessions should be reported on by all students taking the course. In addition, good answers to two items per week (one exercises plus one problem i.e. 8 exercises and 8 problems) would bring you to the 2.2 range of marks. Three items per week, of which at least two should be problems would bring you to the 2.1 range, and 4 or more items per week (i.e at least two problems and two exercises) bring you within the 1 range of marks. Notice that the quality and originality of the answers could bring you up or down. Evidence of 'copy and paste' answers could lower your marks significantly. Marks will be posted on the noticeboard before the beginning of Hilary term.

10.- Cooperative work is encouraged for some of the exercises. In these cases, the names of the contributors should be specified. A good form of cooperative work would be to ensure that, in the exercises involving a variety of choices, each member of the group makes a different choice, so that the whole subject is covered. Then the work could be written up and presented collectively. With regard to problems, you are encouraged to attempt your own solutions and to put all your reasoning on paper.

NB.- Course assessment. The mode of teaching this course is an experiment and I would be grateful for your comments and opinions. Please use this form and submit it before the last week of term. You will be provided with a class password to identify you as a student doing this course.

Part 1.- Principles of risk estimation from pedigrees.

1.1 Introduction. Modes of Mendelian inheritance and a priori risks. Bayes theorem. An example of risk modification using Bayes' theorem.

Part 2.- Using the Cyrillic package to estimate risks and linkage.

This is a series of hands-on sessions using the 'cyrillic' and the 'linkage' packages, available only to TCD students using the public computer rooms.

Ian D. Young. Introduction to risk calculation in Genetic Counselling. 2nd ed, OUP 1999, (mostly the first five chapters).

Michael Connor & Malcolm Ferguson-Smith. Essential Medical Genetics. 5th ed. Blackwell Scientific 1997.

Thompson, McInnes & Willard. Genetics in Medicine. 5th ed. WB Saunders & Co., 1991

Harper PS. Practical Genetic Counselling. 3rd ed. Wright, London, 1988

NB. External users.- You could download the demo for Cyrillic 2.1 (or version 3 if you prefer, as it has full functionality).

Technical Note 1 Copying 'cyrillic' pedigrees to word documents or to html pages (as jpegs or gifs).

1. Use 'Cyrillic' to draw the pedigree with annotations etc. (see 'Cyrillic Note #1')

2. Drag the mouse over the pedigree while left clicking. You will see a box around the pedigree.

3. Once the box is drawn,'Control C' or 'Edit > Copy'. You are still in cyrillic.

4. Open a word documents and 'paste' the picture in the clipboard. You can resize from inside the word document.

5. To save pedigree picture as jpeg or gif, select picture in the word document, then open Microsoft Photoeditor (Start > Programs > Microsoft Office Tools).

6. Once in Microsoft photoeditor, File >New, and then Edit > Paste. You have now under 'Image' a range of options to modify (crop, resize) your picture, and a choice of formats to save it, including jpeg and gif.