BCH3031 Lecture Notes - Lecture 7: Immunoprecipitation, Medical Genetics, Personal Genomics
25 May 2018
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Lecture 7 – Technologies to Analyse Human Genomes
Compaction of Genome
• Length of human genome: ~2m long (end to end)
• 2.85 billion nucleotides
• 50% is unique sequence
o Rest is repetitive
• 1.5% coding exons
• 3.5% highly conserved
• Divided into 46 chromosomes
• 3D genome
o 46 interphase chromosomes occupy defined territories in nucleus
o Each DNA molecule is packaged to ~10,000 fold shorter molecule
o 2m into 20 um
▪ 1 base = 1 cm
▪ Genome = 3200 km
Chromatin Immunoprecipitation CHIP
• Crosslink protein to DNA
• Isolate DNA with chromatin bound and fragment
o Sheer DNA – precipitate DNA with antibody
• Immunoprecipitate DNA / protein complexes
• Clean up selected fragments – purify
• Analyse
o Gene specific PCR
o High content hybridization approach
o High throughout sequencing
• What do these have in common
o Both depend on base pairing of DNA
▪ Molecular biology techniques harness DNA/RNA modifying
enzymes to select, amplify and analyse sequences of interest
o A unique sequence can find and bind its cognate sequence
o Miss matched bases can be used to identify variant alleles
High Content Data Collection
• Hybridization based enrichment and analysis
(1)
o Advantages
▪ Robust
▪ Cheap analysis is easy and
usually automatic
o Disadvantages
▪ Depth of analysis depends on
what is on the chip and may
not be sensitive to allelic
variation (SNPs)
• Hybridization approaches for personal genomics
o Haplotype map (common variants)
▪ Many diseases we encounter due to common variants
o Ancestry/forensics
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