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Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson
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Fundamental Concepts in Genome Sequencing and Genome Variation/Mutation - Dave Adelson

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  • 1. Fundamental concepts in genome sequencing and genome variation/mutation Dave Adelson University of Adelaide
  • 2. Genome sequencing • Typical mammalian chromosome is between 20-100 x 10^6 bp long. • Maximum length for current sequencing technology <1000bp. • Typical approach is to use massively parallel sequencing to sequence hundreds of millions of genome fragments. 11-Dec-13 1
  • 3. Illumina Sequencing
  • 4. 11-Dec-13 3 http://journal.embnet.org/index.php/embnetjournal/article/download/667/860.
  • 5. The Future: Single Molecule Sequencing 11-Dec-13 4
  • 6. Mutation • Genome sequences are not fixed; they are continually changing as a result of different types of mutations. • Mutations can occur at different scales: – Single/several base(s) – Hundreds/thousands of bases – Chromosomal • Can involve substitution or insertion/deletion (indel) events. 11-Dec-13 5
  • 7. Mutation vs Variation • Many alterations to genome sequences have no apparent phenotype and so are considered variation rather than mutation. Mutation implies an alteration of phenotype or function. • Another way to describe variation is polymorphism. 11-Dec-13 6
  • 8. Replication vs Recombination vs Transposition • Replication errors contribute primarily to nucleotide substitution, Simple Sequence Repeat expansion and small indels. • Recombination based errors contribute to large scale indels/translocations. • Transposition causes indels/ rearrangements. 11-Dec-13 7
  • 9. Single Nucleotide Polymorphism/Variation Homozygotes DNA replication errors can cause SNPs, but environment and fundamental aspects of nucleotide chemistry contribute as well. 11-Dec-13 8
  • 10. SNP (heterozygote) 11-Dec-13 9
  • 11. Nucleotide substitution Keller I, Bensasson D, Nichols RA (2007) Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper 11-Dec-13 Pseudogenes. PLoS Genet 3(2): e22. doi:10.1371/journal.pgen.0030022 10
  • 12. Environmental causes of SNPs Dimers can form between two adjacent pyrimidines. Shown here is (A) thyminethymine cyclobutane-pyrimidine dimer, and (B) thymine-cytosine dimer and their photoreactivation by the enzyme photolyase in the presence of light. http://www.nature.com/scitable/topicpage/dna-damage-repair-mechanisms-for-maintaining-dna-344 11-Dec-13 11
  • 13. DNA Repair If dimer is not recognised in time, it can cause a mutation. Once the mutation has occurred it cannot be detected or repaired. 11-Dec-13 12
  • 14. SNP effects • • • • • • • Silent (neutral substitution) Missense (alters the amino acid) Nonsense (inserts a stop codon) Splice (alters a splice site) Promoter (alters a motif) miRNA 3’UTR (alters a miRNA target) 11-Dec-13 13
  • 15. Some standard examples Sickle-Cell Disease Cystic Fibrosis 11-Dec-13 14
  • 16. Single base mutation rate • It has been estimated that in humans and other mammals, uncorrected errors (= mutations) occur at the rate of about 1 in every 50 million (5 x 107) nucleotides added to the chain. • But with 6 x 109 base pairs in a human somatic cell, that means that each new cell contains some 120 new mutations. 11-Dec-13 15
  • 17. Larger scale changes • Once you get beyond single nucleotide alterations, changes tend to favour indel events rather than substitution events. • You can have indels of different sizes; small ones are consequences of polymerase error. – For example: Simple Sequence Repeats due to “slippage”. 11-Dec-13 16
  • 18. SSR (microsatellite/dinucleotide repeat 11-Dec-13 17
  • 19. Trinucleotide repeat expansion 11-Dec-13 18 biol.lf1.cuni.cz/ucebnice/ images/rep8.jpg
  • 20. Larger scale indels • Unequal crossing over • Translocation event 11-Dec-13 19
  • 21. Recombination • Can lead to formation of arrays of tandemly duplicated genes or deletions via unequal crossing over. • Can lead to inversion. • Can lead to gene conversion. • Recombination mediated mutation is thought to be one of the largest source of mutation in humans. 11-Dec-13 20
  • 22. Non-Allelic Homologous Recombination 11-Dec-13 http://www.sanger.ac.uk/Teams/Team29/ 21
  • 23. Repeated DNA sequences make up much of the genome. • Most DNA repeats are repeated because they can copy themselves. • They are called Transposons or Retrotransposons, depending on how they copy themselves.
  • 24. Retrotransposition Cytoplasm Cell Nucleus 11-Dec-13 23
  • 25. What are Transposons? • Transposons are segments of DNA that can move around to different positions in the genome of a single cell. • These mobile segments of DNA are sometimes called "jumping genes". • ~45% of a typical mammalian genome is made up of transposons, also referred to as repeats or repetitive DNA. • Main type = Retrotransposons
  • 26. Alu repeats and human disease 11-Dec-13&Batzer, Molecular Genetics and Metabolism 67, 183-193 (1999) Article ID mgme.1999.2864, available online at Deininger http://www.idealibrary.com 25
  • 27. Global repeat correlations Cut chromosomes into 1.5 Mbp bins. For each bin, count the number of repeats for each of the repeat groups, the number of genes that started in the bin (gene density), and the percent of known bases that were G or C (G+C content). All bins with at least 1x106 bp excluding Ns were used to calculate Spearman’s rank correlations between each repeat group and the other repeat groups, as well as gene density and G+C content. 11-Dec-13 26
  • 28. Repeat Correlations 11-Dec-13 27
  • 29. Genome comparisons Dog Mouse Rat 11-Dec-13 28
  • 30. Human correlations 11-Dec-13 29
  • 31. Major causes of variation NAHR contributes to one of the most significant types of human variation/mutation: Copy Number Variation (Structural Variation). CNV/SV has been linked to heritable disease phenotypes and to cancer susceptibility. 11-Dec-13 32 http://www.genome.org/cgi/content/full/16/8/949
  • 32. Genome evolution • • • • Genomes are constantly changing. Replication error drives bp level change. Recombination drives gene level change. Retrotransposons, which comprise ~40% of a mammalian genome, drive whole genome change in terms of insertion of new DNA, creation of new genes and regulatory regions. • The latter probably account for much of the differences that arise during speciation. 11-Dec-13 33

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