1. Gene expression array and SNP array
Microarrays
Introduction to gene expression arrays
Data pre-processing
SNPs
Copy number abberation
Loss of heterozygosity
Association studies

2. Basics of microarrays
An “old” technology - some predict microarrays will be replaced by deep sequencing
Currently – much cheaper/faster than sequencing; widely used
Timeline of DNA Microarray Developments
1991:  Photolithographic printing (Affymetrix)
1994:  First cDNA collections are developed at Stanford
1995:  Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
1996:  Commercialization of arrays (Affymetrix)
1997:  Genome- wide expression monitoring in S. cerevisiae (yeast)
2000:  Portraits/ Signatures of cancer.
2003:  Introduction into clinical practices
2004:  Whole human genome on one microarray
2006: All exons measured on one microarray
2005: first next-generation sequencing machine

3. Basics of microarrays
They utilize the chemical binding between the four nucleotides.
A --- T, and C --- G. The DNA structure is formed through the binding:

4. Basics of microarrays TTAAGTCGTACCCGTGTACGGGCGC
AATTCAGCATGGGCACATGCCCGCG

5. Basics of microarrays Amplified DNA segments  fluorescence labeling
 hybridization on the array
 reading by photo scanner
 digitize into fluorescence values
 quantify amount of each target sequence
Two strategies:
One sample on each array
The amount is calculated from spot intensity.
(2) Two samples, differentially labeled, on each array
The relative amount,
is given by the ratio between the fluorescence.

6. Gene expression arrays
exon
Start codon
Poly A tail
DNA
(2 copies)
intron
The amount of these guys is easy to measure. And it is positively correlated with the protein amount!
mRNA
(multiple copies)
The amount of these guys matter! But they are hard to measure.
Protein
(multiple copies)

7. Gene expression array --- affymetrix
The Affymetrix platform is one of the most widely used.

8. Gene expression arrays -- Affy
Here we use the U133 system for illustration.
Some 20 probes per gene;
Selected from the 3’ end of the gene sequence;
Not necessarily evenly spaced --- sequence property matters;
The probes are located at random locations on the chip;
TTAAGTCGTACCCGTGTACGGGCGC Target sequence
AATTCAGCATGGGCACATGCCCGCG Perfect match (PM) probe
AATTCAGCATGGACACATGCCCGCG Mis-match (MM) probe

9. Gene expression array - affy
The hope was that mismatch probes won’t bind the target sequence.

10. Gene expression arry --- affy

11. ? Microarray data We are going to focus on pre-processing for now.
Downstream analyses are more in the realm of traditional statistics: multiple testing, clustering, classification……
They are common across different high-throughput techniques.

12. Microarray data Issues:
Background level variation caused by variations in overall RNA concentration in the sample, image reader, etc.
Within every probeset, each probe has different sensitivity/specificity, caused by cross-hybridization, different chemical properties etc.
Across chips, the fluorescence intensity-concentration response curve can be different, caused by variations in sample processing, image reader etc.

13. Affy data --- general strategy
Background correction (within chip)
Normalization
(across-chip)
Probe-set level expression value
(within chip)
Presence/absence call
(within chip)
Probeset-level statistical analysis (combining chips)

14. Affy data --- general strategy
There are many processing methods. The most popular include:
MAS 5.0 (Affymetrix)
Flawed. But it comes with the Affymetrix software. Thus widely used by non-experts.
dChip (Cheng Li & Wing Wong)
Good performance and versatile. Stand-alone Windows application. Can handle arrays other than expression array.
RMA (Rafael Irizarry et al.)
Good performance. Easily used in R/Bioconductor.

15. Affy data --- RMA Background correction
For each array, assumes:
lambda=1,miu=1,sigma= lambda=5, miu=1, sigma=1

16. Affy data --- RMA Background correction
For each array, from the PM signal distribution, estimate the parameters,
Find the overall mode by kernel density estimation;
Find the miu and sigma from PM values lower than the overall mode (sample mean and sd)
Find the lambda from PM values higher than the overall mode (1/(sample mean minus the overall mode))
then adjust the PM readings (s is PM signal; lambda is replaced by alpha in this expression):
See the derivation here:

17. Affy data --- normalization
*** This is also relevant to other array platforms !
To reduce chip effect, including non-linear effect.
Difficulty: the sample is different for each chip. We can’t match a gene in chip A to the same gene in chip B hoping they have the same intensity. PM MM
Assumptions on the overall distributions of the signals on each chip are made. For example:
Some house-keeping genes don’t change;
The overall distribution of concentrations don’t change; ……

18. Affy data --- normalization
Quantile normalization --- match the quantiles between two chips.
Assumes that the distribution of gene abundances is the same between samples.
xnorm = F2-1(F1(x)), x: value in the chip to be normalized
F1: distribution function in the chip to be normalized
F2: distribution function in the reference chip
Nature Protocols 2, (2007)

19. Affy data --- RMA summary
Model-fitting: Median Polish (robust against outliers)
alternately removing the row and column medians until convergence
The remainder is the residual;
After subtracting the residual, the row- and column- medians are the estimates of the effects.

20. Affy data ---- rma summary
Remove row median
Remove column median

21. Affy data ---- rma summary
Remove row median
Remove column median

22. Affy data ---- rma summary
Remove row median
Remove column median
Converged. This is the residual.

23. Affy data ---- rma summary
* This reflects the assumption that probe effects have median zero.

24. SNP Variations in DNA sequence.
Single Nucleotide Polymorphism (SNP) --- a single letter change in the DNA.
Occurs every few hundred bases.
Each form is called an “allele”.
Almost all SNPs have only two alleles.
Allele frequencies are often different between ethnic groups.

25. Correlations between SNPs
Why measure the SNP alleles?
DNA change in two ways during evolution:
Point mutation  SNPs
Recombination
This happens in large segments.  Alleles of adjacent SNPs are highly dependent.
Haplotype: A group of alleles linked closely enough to be inherited mostly as a unit.

26. Why SNP? This is on the homepage of the International Hapmap Project
Figure 1: This diagram shows two ancestral chromosomes being scrambled through recombination over many generations to yield different descendant chromosomes. If a genetic variant marked by the A on the ancestral chromosome increases the risk of a particular disease, the two individuals in the current generation who inherit that part of the ancestral chromosome will be at increased risk. Adjacent to the variant marked by the A are many SNPs that can be used to identify the location of the variant.

27. Why SNP? Nature Genetics 26, 151 - 157 (2000) SNPs
Figure 1. Schematic model of trait aetiology. The phenotype under study, Ph, is influenced by diverse genetic, environmental and cultural factors (with interactions indicated in simplified form). Genetic factors may include many loci of small or large effect, GPi, and polygenic background. Marker genotypes, Gx, are near to (and hopefully correlated with) genetic factor, Gp, that affects the phenotype. Genetic epidemiology tries to correlate Gx with Ph to localize Gp. Above the diagram, the horizontal lines represent different copies of a chromosome; vertical hash marks show marker loci in and around the gene, Gp, affecting the trait. The red Pi are the chromosomal locations of aetiologically relevant variants, relative to Ph.
The gene deciding pheonotype

28. SNP array
The SNP array
Affymetrix.com

29. SNP array
The SNP array
40 probes per SNP (20 for forward strand and 20 for reverse strand.)
PM/MM strategy.
Data summary (generating AA/AB/BB calls) omitted here.
Affymetrix.com

30. SNP array Association analysis Linkage analysis Genotype calls
Loss of Heterozygosity
Genotype calls
SNP array
Signal strength
Copy number abberation

31. CNA --- Background Copy Number Aberration (CNA):
A form of chromosomal aberration
Deviation from the regular 2 copies for some segments of the chromosomes
One of the key characteristics of cancer
CNA in cancer:
Reduce the copy number of tumor-suppressor genes
Increase the copy number of oncogenes
Possibly related to metastasis

32. CNA --- the statistician’s task
High density arrays allow us to identify “focused CNA”: copy number change in small DNA segments.
With the high per-probeset noise, how to achieve high sensitivity AND specificity?

33. CNA – maximizing sensitivity/specificity
Two approaches that complement each other:
Reducing noise at the single probeset level:
Based on dose-response (Huang et al., 2006)
Based on sequence properties (Nannya et al., 2005)
Segmentation methods.
Smoothing; Hidden Markov Model-based methods; Circular Binary Segmentation … …

34. HMM data segmentation Amplified Normal Deleted
Fridlyand et al. Journal of Multivariate Analysis, June 2004, V. 90, pp
Amplified
Normal
Deleted

35. Forward-backword fragment assembling

36. Some example: Top: model cell line, 3 copy segment in chromosome 9
Bottom: Cancer sample

37. LOH Loss of Heterozygosity (LOH) Happens in segments of DNA.
Keith W. Brown and Karim T.A. Malik, 2001, Expert Reviews in Molecular Medicine

38. LOH
On SNP array, LOH will yield identical calls (AA or BB, rather than AB) for a number of consecutive SNPs.
Discov Med Jul;12(62):25-32.

39. GWAS http://www.mpg.de/10680/Modern_psychiatry
© Pasieka, Science Photo Library

40. GWAS
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer
Nature Genetics 41, (2009) 

41. GWAS