Welcome to

Medical Genetics Web Lab
Web Resources on Medical Genetics Selected and Arranged by Miguel DeArce
Trinity Term 2002-03 Wednesdays 2:00 to 4:00 and Fridays 3:00 to 4:00 in PC room EE1.

(Best viewed in Netscape Navigator 4.7 or Internet Explorer 5.0)

TCD users. This is a web-based course in Medical Genetics, an interactive teaching tool at an experimental stage. It contains no primary information, and it is meant for the use of our Sophister students. If used room EEPC1, the students will find all the software (including Cyrillic) already installed in their machines, accessible from the desktop icon 'My Computer'. EXTERNAL USERS will have to download and install these tools (freeware), as seen in the table below, and buy Cyrillic separately. The present edition (2nd October 2002) is nearly complete. Students are advised to bring a zip disk to record work in progress and results. The course is available as CD rom (full use requires internet connection). Please email the author with any difficulties you may have.

Software needed. Downloads needed for the course can be obtained at the following addresses;

Brief description and contents. This preliminary edition comes in four chapters:

Cytogenetics. The core of ‘Cytogenetics’ is a set of metaphase spreads representing the normal karyotype, and abnormal findings common in the study of acquired, constitutive or prenatal samples. These and the relevant clinical data will be found under the ‘Tools’ page. Also provided is a photo editor with instructions (found under ‘Methods’) to karyotype these metaphases. The exercise on chromosme identification can be done in four different ways, depending on time available. The metaphases may be changed from time to time. Links to several databases should help to put into context these or any other cytogenetic results. Brief references are made to recent advances in fluorescence in situ hybridization (FISH), including comparative genomic hybridization (CGH), spectral karyotyping (SKY), multicolour FISH (m-FISH) and across-species hybridization (Rx-karyotyping), including simple ‘on screen’ experiments.

Pedigrees. This section could be run as a separate unit course of eight two-hour sessions. As a part of the Medical Genetics lab, this chapter should be minimised to just one or two sessions at the discretion of the teacher. The core of the ‘Pedigrees’ section is a collection of about 50 pedigrees showing a disease segregating, with or without additional linked markers. The examples are to be found mostly in recent textbooks and scientific literature. Where required, a calculator made to apply Bayes’ theorem is used to calculate risks for different individuals, bearing in mind previous and outcome information about the genetics of the disease, such as reduced penetrance, late onset etc. Another applet facilitates calculations involving Hardy-Weinberg equilibrium. Trinity College students will have access to a linkage package that will introduce them to the study of linkage.

DNA Sequence Lab. The core of this lab is a ‘Virtual DNA Freezer’ containing DNA samples from virtual Cystic Fibrosis and Fragile X families. Apart from the normal sequence, I have distributed 12 mutations among the CF families, and several numbers of triplet repeats among the FraX families. These are inaccessible to the students, and they are asked to characterise the mutations using original simplified algorithms that simulate different types of DNA electrophoresis, i.e. heteroduplex analysis, denaturing gradient gel electrophoresis (DGGE) and sequencing. The students select samples from the freezer and load them to the electrophoresis gel via a Form, obtaining the results back in the shape of a virtual gel slab much as they would see in the laboratory. Other methods available on the internet, like sequence alignments, DNA translators, Restriction Analysis tools etc. are also used.

Protein Lab. The core of this lab is a download of the Swiss Protein Database Viewer. We are grateful to Nicolas Guex and Manuel Peitsch, from the Glaxo-Wellcome Experimental Research Laboratory, for the use of this tool. Roger Sayle's Rasmol is also used. We illustrate the use of these viewers by asking a number of questions about the normal structure of rhodopsin and the possible structural effects of mutations involved in retinal pathology. Other exercises refer to metabolic pathways, secondary structure prediction, helical wheels, and mouse prion protein.

This website is intended exclusively for academic use. Address any queries to mdearce@tcd.ie. Preliminary launch was 2^nd April 2002. revised version October 2002.