Handouts Metabolomics

7/30/2019 Handouts Metabolomics

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Metabolomics by

NMR

Multivariate AnalysisPrincipalComponent Analysis

PLS

Regression AnalysisApplications toNMR


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Multivariateanalysis

Allowsustoanalysemanyvariablesatthe

sametime

Necessarywhenwehavehundreds(or

thousands)

of

variables Alsoveryusefulforuncoveringhidden

relationships


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PCA(Principal

Component Analysis)

Finds underlying (hidden)datastructures inotherwise

uninterpretable data

Advanced statistical method

Allows grouping ofdataafter combinations ofvariables


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PrincipalComponents

=Axis of

Biggest Spread

Figs from:KimH.Esbensen,Multivariate DataAnalysis inPractice,5th edition,Camo Process ASOslo,2004


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Asimple

example

studenthrlngde[cm]

sko-strrelse

1 50 37

2 10 46

3 2 42

4 30 395 40 39

6 1.5 45

7 0.6 45

8 3 43

9 40 37

10 4 40

11 1.5 43

12 1.8 43

13 3 43

14 2 43

15 25 43

16 30 39

17 25 38

18 45 41

19 3.5 42

20 1 41

21 2 42

22 50 38

23 30 36

24 55 39

25 40 43

26 2 43

27 40 38

28 1.5 43

29 30 37

30 33 39

31 30 38

32 33 35


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First PCisthevector through thedata

with theleast sum

of

square residuals

Shoe size

Hairlength

[cm]


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Rotate tomake Trendline

NewXaxis

Scoreplot


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PC1

PC2

Centerofdata

isused asorigin ofPC

coordinate system

This distance

represents the

scoreofsample

X onto PC1

X

This distance

represents the

scoreofsample

X onto PC2

Thedirection ofthePCaxes isgivenby

theloadings,i.e.relativeweights,of

thevariables


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PCAanalysis yields


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Some math.

X = t1

p1

+ + + E

p2

t2

Your data First principalcomponent

loadings

Second principalcomponent

Residuals

loadings


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Asimple example

Europeandatafrom2006:

Healthylife

expectancy

(by

gender)

Grossdomesticproduct

Percentagesmokers(byage/gender)

Percentageoverweight(byage/gender)

Hospitalbedsper100000

Datafromhttp://ec.europa.eu/eurostat


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Thedata


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3Dplots

reveal nothing

%maleswith overweight


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2Dplotscan reveal some connections

Healthy life yrs.vs.Smoker % Healthy life yrs.vs.overweight%

Some grouping ofcountries can be observed,butthepicture isnotclear

Correlation stronger forsmoker%than foroverweight%


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PCA

brings some order into the

chaos


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Loading plotlets us know the

interdependence ofthe

variables

We findtheexpected anticorrelation between healthy life years andsmoke /overweight.

Again,correlation is

stronger for

smoke%

than for

overweight%.


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Remember

The

data

16

variables!!!


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PCAwith

all

16

variables


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Loading

plot

of

all

16

variables


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Multivariate Modelling (PLSR)

Partial Least SquaresRegression

Model

Predict


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PLSR finding theparametersbest

describing aproperty


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PLSRon females showsunexpected

coincidence


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Modelling based on PLS

R

Healthlife years (realdata)


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What hasitgot todowith NMR???the

hell


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NMR

of

blood serum

Complicated spectrum with thousands oflines

How toget started???


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NMR

data

as

X

matrix


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NMRdataasXmatrix

Thesame

like any other data


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Rapidandnoninvasive diagnosisofthepresenceandseverityofcoronaryheart

diseaseusing

1HNMRbasedmetabonomics

BrindleJ,Antti H,HolmesE,etal.

NatureMedicine,December2002

MunsoorA.

Hanifa


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Study

DesignDiagnosis study

36patientswithprovenCHD

30patients

with

normal

coronary

arteries

Exclusionsincludedpatientswithhighbloodpressure,diabetesorvalve

disease.

OnedimensionalprotonNMR

Principalcomponentanalysis(PCA)

Partial

least

squares

discriminantanalysis(PLSDA)

OrthogonalPLSDA

MunsoorA.

Hanifa


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Study

DesignSeverity study

28

patients

with

single

vessel

disease

20patientswithdoublevesseldisease

28

patients

with

triple

vessel

disease

Similaranalysisasdiagnosis

study

MunsoorA.

Hanifa


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Diagnosis Study

Results

2nd

and

3

rd

principal

componentsofPLSDA

showsomeclustering(PCA

notshown)

OPLS

DA

analysis

gives

a

clearerseparation

triple

vessel

disease

normal

angio

Key:

MunsoorA.

Hanifa


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Diagnosis Study

Results Spectralpeakscorrelated

with

disease: 0.86ppm lipidCH3 1.26,1.30,1.34ppm lipid

CH2

Spectralpeakscorrelatedwithhealth:

1.22ppm lipidCH2 3.22ppm choline

MunsoorA.

Hanifa


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Diagnosis Study

Results PLSDAmodel:

92%sensitivity

93%specificity

triple

vessel

disease

normal

angio

testset

Key:

MunsoorA.

Hanifa


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Severity Study

Results

triplevessel

disease

singlevessel

disease

doublevessel

disease

Key:

Onlypartialseparationofgroupsbasedonseverityofdisease(but

muchbetterthanachievedcurrentlybyusingriskfactors)

MunsoorA.

Hanifa


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Application toFoodAnalysis

Fruit Juices

http://www.brukerbiospin.com/metabolomics_food.html


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Take Nfruit juicesamples

runNMR

spectra on all

of

them

Processing,data

pre

treatment

PCAhttp://www.brukerbiospin.com/fileadmin/be_user/general/public/sgfprofiling0810.pdf


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Authentification of

Origin

http://www.brukerbiospin.com/fileadmin/be_user/general/public/sgf

profiling

0810.pdf

3Dscoresplot


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Cheating with the

Juice?RealJuiceor Concentrate?

http://www.brukerbiospin.com/fileadmin/be_user/nmr/JuiceScreener/BrukerJuiceScreenerEditorial0108.pdf

Extra peak fromhydroxymethyl

furfural

Stemsfromexcessiveheattreatment

Less fruit content than promised?


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And

now for

the

data

on you

Documents

Handouts Metabolomics