Next Generation Sequencing Technologies. Rob Mitra 1/30/17

Transcription

1 Next Generation Sequencing Technologies Rob Mitra 1/30/17

2 Outline Overview of next-generation sequencing How does it work? What technologies are being used? How would one use it in practice? Math basic for Genomics Poisson Distribution

3 Forward Genetics Genotype Phenotype Hypothesis Test Hypothesis By Genetic Manipulation

4 Forward Genetics Two groups: 1. Develop Colorectal cancer At Young Age 2. Do not Phenotype Mutation in APC Gene Genotype Hypothesis APC is a Tumor Supressor Gene Test Hypothesis By Genetic Manipulation Delete APC in Mouse Control: Isogenic APC+

5 The Cycle of Forward Genetics Observation Phenotype?Sequencing? Genotype In 2005 $9 million/genome Not feasible Thinking Hypothesis Test Hypothesis By Genetic Manipulation Gene Deletion/Replacement Recombinant Technology

6 End Runs Linkage Studies (Humans, Model Organisms) Association Studies (GWAS) BUT, these end runs have a cost! 1. Requires a large family (many crosses in model organisms); very difficult to analyze multi-factorial traits 2. Common variants But, these end runs will not be needed in 5-10 years. Why?

7 The Problem with Forward Observation Phenotype Genetics Sequencing Genotype Currently $1,000* /genome Cost is rapidly dropping Thinking Hypothesis Test Hypothesis By Genetic Manipulation Gene Deletion/Replacement Recombinant Technology

8 Bp/US dollar: increases exponentially with time Adapted from Shendure et al 2004

9 Two questions: How was this dramatic acceleration achieved? What has it meant? What is the future?

10 How was this achieved? Integration (Think about sequencing pipeline) Parallelization Miniaturization Same concepts the revolutionarized integrated circuits Plus one additional insight

11 Technology Overview: Solexa/Illumina Sequencing

12 Immobilize DNA to Surface Source:

13 Technology Overview: Solexa Sequencing

14 Sequence Colonies

15 Sequence Colonies

16 Call Sequence

17 What do we do with 100 million, 100 base pair long reads?

18 Paired End Reads are Important! Known Distance Read 1 Read 2 Repetitive DNA Unique DNA Paired read maps uniquely Single read maps to multiple positions

19 Paired Ends are Important Part 2 Deletion Insertion Inversion Shendure et al 2005

20 Credit: -phpapp02/95/ngs-microbiome jpg?cb=

21 How can we generate longer paired end reads?

22 Paried End Library Contruction Credit: -phpapp02/95/ngs-microbiome jpg?cb= From Shendure et al

23 Can we get really long reads?

24 Where does the technology stand? Right now, fully loaded costs are roughly $20/GB at Wash U GTAC.

25 3 rd generation sequencing Pac Bio

26 Pacific Biosciences: A Third Generation Sequencing Technology Eid et al 2008

27 Real Time Sequencing

28 PacBio Mid e6 zero mode waveguides $350,000 instrument Median read length = 8-12kb. Max > 40kb minute runs $700 per run for consumables Throughput ~5-10Gb per flow cell ~95% accuracy Estimate cost at $120 per GB fully loaded

29 Math Aside: Sequencing coverage calculations Let s say you need a base to be sequenced 5x for an accurate base call If you sequence at 10x coverage how much of the genome will be sequenced at least 5 times?

30 Poisson Distribution Deriving the Poisson: (derive from the bionomal for large number of trials but small probability of success) are.com/m odelriskhel p/i ndex.htm #Probability_theory_and_statistics/Stochastic_pr ocesses/d erivi ng_the_poisson_di stributi on_from_the_bi nomial.htm Average coverage = lambda Probability of getting k reads from a base given the average coverage lambda

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32 Example Average coverage = 5x Probability of a given base being sequenced exactly 10 times is: 5 10 e -5 /10! = or about 2% of bases will have 10x coverage.

33 Math Aside: Sequencing coverage calculations If you sequence at 10x coverage how much of the genome will be sequenced at least 5 times? 1 [f(0,10) + f(1,10) + f(2,10) + f(3,10) + f(4,10)] = 0.97

34 A crash course in probability