Gene expressions analysis by massively parallel signature sequencing (MPSS) on microbead arrays

Sydney Brenner et al. Jan 26, 2007

DNA-basic definitionsNucleotide (Base) - consists of a sugar, phosphate and a base

Base-Pair Rule – Hydrogen bonds (A-T, C-G)

Gene - a segment of DNA that codes for a protein, which in turn codes for a trait (skin tone, eye color,…etc), a gene is a stretch of DNA.

DNA Polymerase - Enzymes that catalyze the polymerization of deoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly-polymerized molecule is complementary to the template strand and identical to the template's partner strand.

DNA SequencingSequencing: determining the nucleotide order of a given DNA fragment, called the DNA sequence.

Sanger Method (’75): Chain termination • Prepare single strand DNA (heating)• Add a mixture of deoxy nucleotides (dATP, dGTP, dCTP, dTTP)• Add a mixture of dideoxy nucleotides (ddATP,ddGTP,ddCTP, ddTTP)• Add DNA polymerase I

A lot more deoxynucleotides than dideoxynucleotides

• Sort based on length (gel)

Animation: http://www.dnalc.org/ddnalc/resources/sangerseq.html

Restriction Enzymes• 1978 Nobel Prize in medicine (awarded to Werner Arber, Daniel Nathans, and Hamilton Smith) • Enzymes that cut double stranded DNA• The cleaved chemical bonds can be reformed by ligases• Restriction enzyme cuts only double-helical segments that contain a particular nucleotide sequence (i.e. recognition sequence)• Types of Restriction enzymes: I, II, III:

I,III: recognize specific sequences but the cleavage sites are at variable distancesII: cleavage occurs at specific sites at or close to the

recognition sequence

Fluorescence Activated Cell Sorting (FACS)

First cell sorter: Mack Fulwyler (1965)Expanded by Len Herzenberg

Cells are tagged by antibodies linked to fluorescent dye. The antibody is bound to a protein that is uniquely expressed in the cells that we want sorted.

The nozzle vibrates to form drops which contain single cells

Electrical charge is used to sort the cells

MotivationGoals (upon determination of human genome): 1. To discover and understand the function and variation of genes2. How do these qualities affect health and disease?Available techniques:1. Hybridization of probes into microarrays

Advantages: large scale, capable of detecting a wide range of gene expression levels.

Disadvantages: variability due to probe hybridization, cross reactivity, element to element differences, and microarray to microarray differences

2. Counting of tags or signatures of DNA fragments Advantages: Statistically more robust, don’t require standardization or

repetition, precision and accuracy can be increased by increasing the size of the sample

Disadvantages: Difficult to realize routinely and not cost effective

Massively Parallel Signature Sequencing (MPSS)Cloning on microbeads

# of transcripts: 3-4e4# of oligonucleotides: 1.67e7

# of conjugates: 5-7e11

1% of tags

We want to make sure that # of tags is at least a 100 times the number of templatesthis will ensure that if we take 1% of tags, we have a sample where all DNA’s are represented and they all have unique tags with at least 99% probability.

Massively Parallel Signature Sequencing (MPSS)

PCR is used to amplify the sample. The resulting single stranded DNA’s are hybridized with a population of microbeads. (note: 1% of microbeads are loaded)

Separate loaded microbeads from unloaded ones using FACS. Each microbead has a population of 104-105 identical copies of a

single kind of template molecule

Massively Parallel Signature Sequencing (MPSS)

Decoding…

Ligate 1024 encoders 43 x 16

1

TTCC

TNNN…Fx1

NTNN…Fx2

NNCN…Fx3

NNNC…Fx4

2

Decoders for Fx1…4

3

16x decoding per cycle….repeat

Massively Parallel Signature Sequencing (MPSS)

Massively Parallel Signature Sequencing (MPSS)

Comparison to conventional methods

Compared to PE Biosystems, model 377 DNA Sequencer

Discussion

Method does not require separation of fragments to generate sequence information

Time series of spatially localized microbeads (can pack beads closely in monolayers)

The main advantage: parallel nature of the process-millions of templates can be handled together without need for separation. (Ideal for gene expression)

Conventional sequencing: analyze thousands of templates to give sequences with 100s of bases

MPSS: analyze millions of templates to give sequences of length few 10s of bases

Critique Summary

Strong points: A powerful and innovative technique Lots of work done to prove the functionality

Weak points Not the clearest paper (too much information compacted in a few

sentences) There are more efficient ways of encoding/decoding the adaptors The figures are better shown in a different order It would be good to include some more information about the

cloning of the microbeads I could use more comments on how good the results are (is it just

me!?)

Better encoding (Hansen’s method)

0 1 2 3 4 5 6 7

A A A A 0 0 0 0 0 0 0 0

A A A T 0 0 0 0 0 0 0 1

A A A C 0 0 0 0 0 0 1 0

A A A G 0 0 0 0 0 0 1 1... AAAT------------7

AAAG------------6,7

23 = 8 different encoders required as opposed to 16 used here.