1. DNA Sequencing

2. DNA sequencing How we obtain the sequence of nucleotides of a species …ACGTGACTGAGGACCGTG CGACTGAGACTGACTGGGT CTAGCTAGACTACGTTTTA TATATATATACGTCGTCGT ACTGATGACTAGATTACAG ACTGATTTAGATACCTGAC TGATTTTAAAAAAATATT…

3. Which representative of the species? Which human? Answer one: Answer two: it doesn’t matter Polymorphism rate: number of letter changes between two different members of a species Humans: ~1/1,000 Other organisms have much higher polymorphism rates  Population size!

4. Why humans are so similar A small population that interbred reduced the genetic variation Out of Africa ~ 40,000 years ago Out of Africa Heterozygosity: H H = 4Nu/(1 + 4Nu) u ~ 10 -8, N ~ 10 4  H ~ 4  10 -4 N

5. DNA Sequencing Goal: Find the complete sequence of A, C, G, T’s in DNA Challenge: There is no machine that takes long DNA as an input, and gives the complete sequence as output Can only sequence ~900 letters at a time

6. DNA Sequencing – vectors + = DNA Shake DNA fragments Vector Circular genome (bacterium, plasmid) Known location (restriction site)

7. Different types of vectors VECTORSize of insert Plasmid 2,000-10,000 Can control the size Cosmid40,000 BAC (Bacterial Artificial Chromosome) 70,000-300,000 YAC (Yeast Artificial Chromosome) > 300,000 Not used much recently

8. DNA Sequencing – gel electrophoresis 1.Start at primer(restriction site) 2.Grow DNA chain 3.Include dideoxynucleoside (modified a, c, g, t) 4.Stops reaction at all possible points 5.Separate products with length, using gel electrophoresis

9. Current Sanger Sequencing Capacity 3730xl: 690 Kbp/day, 900bp reads … 1550 Kbp/day, 700bp reads … 2100 Kbp/day, 550bp reads

10. Reconstructing the Sequence (Fragment Assembly) Cover region with high redundancy Overlap & extend reads to reconstruct the original genomic region reads

11. Repeats Bacterial genomes:5% Mammals:50% Repeat types: Low-Complexity DNA (e.g. ATATATATACATA…) Microsatellite repeats (a 1 …a k ) N where k ~ 3-6 (e.g. CAGCAGTAGCAGCACCAG) Transposons  SINE (Short Interspersed Nuclear Elements) e.g., ALU: ~300-long, 10 6 copies  LINE (Long Interspersed Nuclear Elements) ~4000-long, 200,000 copies  LTR retroposons (Long Terminal Repeats (~700 bp) at each end) cousins of HIV Gene Families genes duplicate & then diverge (paralogs) Recent duplications ~100,000-long, very similar copies

12. Sequencing and Fragment Assembly AGTAGCACAGA CTACGACGAGA CGATCGTGCGA GCGACGGCGTA GTGTGCTGTAC TGTCGTGTGTG TGTACTCTCCT 3x10 9 nucleotides 50% of human DNA is composed of repeats Error! Glued together two distant regions

13. What can we do about repeats? Two main approaches: Cluster the reads Link the reads

14. What can we do about repeats? Two main approaches: Cluster the reads Link the reads

15. What can we do about repeats? Two main approaches: Cluster the reads Link the reads

16. Pyrosequencing on a chip $10K 400,000 reads/day 200-300 bp/read => ~100Mbp/day $10K 1M reads/day 500 bp/read => ~500Mbp/day

17. Single Molecule Array for Genotyping—Solexa ~$10K ~1.5 Mbp, 36bp reads 3 days

18. Polony Sequencing

19. Nanopore Sequencing http://www.mcb.harvard.edu/branton/index.htm

20. Molecular Inversion Probes

21. Illumina Genotype Arrays

22. Summary – Sequencing in 2008 Mb /day Read Length Paired?Cost Sanger 1.5900-? Pyrosequencing 100 (400) 200 (400) ½ length$10K Solexa/ABI 50036Yes$3K Polony 200025?No$10K Genotyping Array 1M SNP /chip N.A. $300