Introduction

This page is extracted from a Practical Class given to Vertebrate Development students in 1999. The aim was to give students practice with accessing relevant genetic databases.

ANAT2311 Practical 4- WWW Genetic Databases

Developed by M. Hill, 1999.

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This class is an exploration of the available WWW and other database resources that relate to Human genetic diseases. This page contains all the links you will require for this class. The exercise is to explore the Human genome and its retaionship to know human genetic diseases that affect both development and the child and adult.

The WWW links from this page require internet access, and so will not work on some computers in the School of Anatomy.

To start with, think of a specific Human disease and see what you can find out about:

• Known gene?
• What are the major effects of the disorder?
• Does it have an effect/role in development?
• Known mutations?
• Likelyhood of mortality?
• History of the disease?
• Who discovered the cause of the disease?
• Most recent published data relationg to the disease?
• What therapies are being explored?
• Where to next?

There are 4 main sources of DNA information:

1. National Center for Biological Information (NCBI, USA)
2. European Molecular Biology Laboratory (EMBL, Europe)
3. DNA DataBank of Japan (DDBJ, Japan)
4. Australian National Genomic Information Service (Angis, Australia) with access to these databases and other analytical tools.

You should in this class:

1. Start by looking at the current status of the Human Genome Project
2. Read about Genebank sequence Databases.
3. Visit
   1. Australian National Genomic Information Service (Angis, Australia)
   2. European Molecular Biology Laboratory (EMBL/EBI) Nucleotide Sequence Database, Hinxton, UK
      • some of this site is mirrored at WEHI (Melbourne, Aust)
   3. DNA Data Bank of Japan (DDBJ), Mishima, Japan
   4. GenBank National Center for Biotechnology Information (NCBI) Bethesda, MD, USA
4. Then read about the Science98 Genemap with some sample disease genes. Take the opportunity to look at each chromosome.
5. Science98 has recently been updated as Genes and Diseases, with a similar but updated organization to Science 98.
6. If you are interested in cancer look at the Cancer Genome Anatomy Project (CGAP).
7. Then browse OMIM.
8. To explore current published findings you will need to search Medline with a keyword relating to the disease of interest, this can then be restricted to specific years of publication (try 1998 or1999) and specific types of articles (try Review).
9.  Finally have a look at public perception of this field of Genetic Research from a recent TIME article (Jan 11th , 1999) discussing the "Future of Medicine".

A major source of Human Genetic Disease information can be derived from the OMIM Database.

Online Mendelian Inheritence in Man

OMIM Database

Online Mendelian Inheritence in Man. This database is a catalogue of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The total number of entries in OMIM exceeded 10,000 on December 1, 1998. (The entries in the first print edition of 1968 numbered 1487.)

The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE articles and sequence information.

You can search the database from the search window below or directly Search the OMIM Gene Map. There is also a OMIM Morbid Map available to search Search the OMIM Morbid Map.

For those without internet access I have included somelocal copies of sample searches and individual entries from OMIM database.

Browsing OMIM

• Search the OMIM Database
• Search the OMIM Gene Map
• Search the OMIM Morbid Map
• The OMIM numbering system
• How to create WWW links to OMIM
• View the OMIM Update Log
• OMIM Statistics
• Citing OMIM in the literature
• The OMIM Gene List

OMIM Enter one or more search keywords: To Search all fields, leave the following boxes unchecked. To narrow your search to certain specific fields, check the boxes next to those fields' names. See Query Help for other ways to search. Title: OMIM Number: Allelic Variants: Text: References: Clinical Synopsis: Gene Map Disorder: Contributors: See only records which have been changed in the past 7 days 15 days 30 days 60 days 90 days 180 days 365 days No Limit Display at most 50 entries 100 entries 200 entries No Limit

DEVELOPMENTAL ABNORMALITIES ENTRY- from UNSW Embryology Program
PATENT DUCTUS ARTERIOSUS (P.D.A.)	OMIM Database Entry- Patent Ductus Arteriosus
ATRIAL SEPTAL DEFECT (A.S.D.)	OMIM Database Entry- Atrial Septal Defect
TETRALOGY OF FALLOT	OMIM Database Entry- Tetralogy of Fallot
I. TRACHEO-OESOPHAGEAL FISTULA (OESOPHAGEAL ATRESIA)	OMIM Database Entry- Tracheosophageal Fistula
II LOBAR EMPHYSEMA (Overinflated lung)	OMIM Database Entry- Lobar Emphysema

DEVELOPMENTAL ABNORMALITIES LIST- from UNSW Embryology Program
50 entries displayed (out of 71 entries found), searching for "atrial septal defect "	See List
38 entries found, searching for "tetralogy of fallot"	See List

PubMed- Medline database

You can search the Medline database from the search window below or directlyon WWW PubMed- Medline

A local copy of a Medline sample search for "cardiovascular/development/review/2year" is available for computers without internet access.

Search Field: Affiliation All Fields Author Name EC/RN Number Entrez Date Issue Journal Name Language MeSH Major Topic MeSH Terms Page Publication Date Publication Type Subheading Substance Name Text Word Title Word Volume MEDLINE ID PubMed ID Mode: Automatic List Terms PUBMED

• Enter one or more search terms.
• Author names should be entered in the form Smith JB, but initials are optional.
• Journal titles may be entered in full, as valid MEDLINE abbreviations, or as ISSN numbers (see Journal Browser for more information).
• Use pull-down menus to specify fields and search mode.

Boolean search statements can also be entered directly in the search box, using AND, OR, and NOT logic operators. See Boolean Search page for more information.

Additional Information

A Large number of relavant search engine links are also available locally from the Cell Biology Lab and the UNSW Embryology Program.