ABC for the AEA Basic biological concepts for genetic epidemiology Martin Kennedy Department of Pathology Christchurch School of Medicine.

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

DNA, chromosomes & genes

Chromosome structure

Base pairing

Eukaryotic genes are split

•Exons - fused to form mRNA•Introns - spliced out of mRNA(intron = intervening sequence)

Genome statistics

3 billion basepairs

23 pairs of chromosomes

50-60% repeats

5-10% coding

sequences

Transcription & translation

Typical gene structurepromoter

AAAAAAnuclear RNA

transcription

messenger RNA AAAAAA

AUG TAG

5’ UTR 3’ UTR

splicing

Ribonucleic acid (RNA)

From gene to protein

The genetic code

Proteins

Protein folding

Summary

Sex, meiosis, and all that

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

Cell divisions

Mitosis Daughter cells

Meiosis Gametes

Recombination

Meiosis

Gametes

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”

Mendelian inheritanceAutosomal dominant

Mendelian inheritanceAutosomal recessive

Mendelian inheritanceX-linked recessive

Mendelian disorders

Molecular biology methods Nucleic acid collection Nucleic acid hybridization Restriction enzymes Electrophoresis Southern blots Polymerase chain reaction DNA sequencing

Nucleic acid collection

•Buccal swabs

•Blood spot on paper

•Tissue sample

•Blood sample

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

Electrophoresis

Molecular biology methods (demos)

Polymerase chain reaction

Southern blot

DNA sequencing

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

Single nucleotide polymorphisms (SNPs)

Single nucleotide polymorphisms (SNPs)

Equipment

The genome era