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ABC for the AEABasic biological concepts for genetic epidemiology
Martin KennedyDepartment of PathologyChristchurch School of Medicine
Topics DNA, chromosomes & genes Transcription and translation Sex, meiosis, and all that Mendelian inheritance Molecular biology methods Types of DNA variation
Eukaryotic genes are split
•Exons - fused to form mRNA•Introns - spliced out of mRNA(intron = intervening sequence)
Typical gene structurepromoter
AAAAAAnuclear RNA
transcription
messenger RNA AAAAAA
AUG TAG
5’ UTR 3’ UTR
splicing
Definitions GeneA functional unit of inheritance GenomeAll of the genetic material in the chromosomes of an organism AlleleAlternative forms of a gene or marker due to changes at the DNA level LocusThe physical location of a gene Genotype The specific alleles present for a given gene or set of genes HaplotypeA particular combination of alleles in a specific region of a chromosome
Mendel’s lawsGood for peas, people and anything else that has sex
Segregation: The reproductive cells of hybrids randomly transmit either one or the other of paired parental alleles to their offspring. The alleles are unchanged during passage through each generation.
Independence: When individuals with different alleles of more than one gene are crossed, alleles of each gene are assorted into the offspring (segregated) independently of the others. This law applies only when there is no linkage between the genes.
Mendelian inheritance
Mendelian conditions generally have a monogenic basis - “causative genes”
Complex disease is polygenic or multifactorial - “susceptibility genes”
Molecular biology methods Nucleic acid collection Nucleic acid hybridization Restriction enzymes Electrophoresis Southern blots Polymerase chain reaction DNA sequencing
Nucleic acid hybridization
The 2 DNA strands can be dissociated by heat or alkali
Complementary strands will reanneal during cooling or under neutral conditions
Reannealing is highly specific: only complementary sequences will anneal
Restriction enzymes
---GATTGAGGATCCTTATAT------CTAACTCCTAGGAATATA------GATTGAGGATCCTTATAT------CTAACTCCTAGGAATATA---
---GATTGAG GATCCTTATAT------CTAACTCCTAG GAATATA---
EcoRI recognition site
DNA variation
Chromosomal loss, gain or rearrangements
Deletions Insertions Inversions Point mutations/polymorphisms Trinucleotide repeats (expansions)
-Polymorphisms occur at more than 1% -Mutations occur at less than 1%
DNA variants can occur anywhere in the genome
AAAAAAnuclear RNA
transcription
messenger RNA AAAAAAAUG TAG
5’ UTR 3’ UTRsplicing
*
*
* * ** *
DNA variants
Polymorphisms and mutations are the basis of genetic diversity
Polymorphisms provide markers with which we can track the inheritance of chromosomal regions and genes
DNA markers
Restriction fragment length polymorphisms (RFLPs)
Variable number tandem repeats (VNTR)
Microsatellites or short tandem repeats (STRs)
Single nucleotide polymorphism (SNPs)
Restriction fragment length polymorphisms (RFLPs)
164bp
527bp
691bp
691bp
Exon 3
AvaII
164bp527bp
•Maximum of two alleles•Of limited use for linkage•Commonly used in association analysis•Detected by blot or PCR
Variable number tandem repeats (VNTRs)
•Tandem repeats of between 14 and 100bp in length•Multiple alleles•Detected by blot or PCR•Of limited application
Microsatellites or short tandem repeats (STRs)
•Detected by PCR•Multiple alleles•Widely used in linkage analysis•Detected by PCR