Today s Topic: Microarrays. but first, student slides from HW

Transcription

1 Today s Topic: Microarrays but first, student slides from HW

2 Back to Microarrays (Reference: Zvelebil and Baum 2008, chap. 15) We refer specifically to DNA microarrays DNA: deoxyribonucleic acid microarray: micro- tiny; 1/1,000,000; μ (Greek mu) (Prefix is from Greek mikros, meaning small.) array grid; lots of things spread out So is a microarray a tiny array, or an array of tiny things?

3 DNA Microarray Structure A glass or silica slide is printed with dots Each dot contains: identical, single-stranded DNA segments we know what segment is in what dot The microarray is dunked in a genetic soup Each dot hybridizes, or not, to stuff in the soup Stuff in the soup has fluorescent labeling We check which dots fluoresce (glow) under UV Now we know what s in the soup

4 DNA Microarrays more details The more stuff in the soup that binds to a dot, the brighter it fluoresces so we have a way to measure amount of this stuff or that stuff The stuff in the soup is what?

5 DNA Microarrays more details The stuff in the soup is what? mrna extracted from tissue that has been tagged with fluorescent dye or Tagged cdna made by reverse transcription or mrna that has been amplified and tagged or Genomic DNA

6 More DNA Microarray Vocabulary Each dot is a probe What is the probeset? What is in the soup?

7 More DNA Microarray Vocabulary Each dot is a probe What is the probeset? All the probes viewed as a group What is in the soup? The sample to be tested Maybe a control Since we often want to do comparisons

8 DNA Microarray Uses Lets list real or possible uses for these microarrays

9 DNA Microarray Uses See what genes are expressed Expressed? Measure expression levels Compare expression levels across experiments See what single-nucleotide polymorphisms (SNPs) are there Could they be used for superfast genome sequencing?

10 Comparing Expression Levels One way is to mix two soups one from control tissue another from experimental tissue (cancerous, water stressed, treated, etc., etc.) label one with Cy5 (fluoresces red) label the other with Cy3 (fluoresces green) What colors can the dots fluoresce?

11 Author: Marc_Mongenet Date: Licensed under the Creative Commons Attribution ShareAlike 2.5

12 Authorized by GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation

13 Original uploader was Paphrag at en.wikipedia. Released to public domain.

14 One-Color Method We ve seen the two-color method One-color method is a little different Instead of mixing the soups and using one chip Use two (unmixed) soups and two chips (What is in the soup again?)

15 Comparing 2-color and 1-color methods Advantages and disadvantages of each?

16 Two- vs. one-color methods Two-color Same chip is used...so inter-chip variation is minimized One-color Chip results can be archived...and reused by many labs when needed

17 Using Results Genes expressed under certain conditions can be determined How? Related genes can be hypothesized What is meant by related? How can they be found? What ways might relatedness show up?

18 Let s Read the Complete Genomics News Article and Discuss What do you think? What s happened since then?

19 Application Bee disease Bees pollinate crops Beekeepers travel around servicing crops (and making honey) Colony collapse disorder (CCD) appeared a few years ago Serious threat to the bee industry Microarrays might help understand the disease!

20 Let s Read the Bees News Article and Discuss What do you think? What s happened since then?

21 High Speed Sequencing Some discussions focus on the gene expression application How do microarrays do that? Other discussions focus on high speed sequencing Why could that render microarrays obsolete? See

22 Genome Sequencing is Improving Exponentially

23 (Found by Drew, Alex) Drew Source: hn- lounsbury/8929- healthcare-costshumangenome.html

24 (Found by Teja, Jie, John) Source:

25 From my summer talk Source:

26 What did you find?

27 Next-Generation Sequencing and Third Generation Sequencing These are so-called non-sanger methods Microarrays can be used (as in the Complete Genomics approach) How many dots would all 70-bp sequences require? How many n-bp sequences does the company s chips handle? So what is n? So how can CG do 70-bp dots??!

28 Genome Sequencing is Improving Exponentially You can do searches for Next-generation sequencing Third generation sequencing Etc....to find out more about them

29 Future Generations of Sequencing first generation sequencing 321,000 (8/26/13) Second generation sequencing 760,000 (8/26/13) Third generation sequencing 331,000 (8/26/13) Fourth generation sequencing 732,000 (8/26/13) Fifth generation sequencing 2 (8/26/13) Sixth generation sequencing 1 (8/26/13 mine!) Google (5/30/12 & 5/21/13): "first generation sequencing" 340,000 & 439,000 hits "second generation sequencing" 267,000 & 1,040,000 hits "third generation sequencing" 115,000 & 398,000 hits "fourth generation sequencing" 47,500 & 461,000 hits "fifth generation sequencing" 1 & 2 hits "sixth generation sequencing" 0 hits