Acute Lymphoblastic

Leukaemia Data (ALL) Package

Presented by:
SAIMA NAWAZ

Introduction of Acute Lymphoblastic

Leukemia
A fast-growing cancer of a type of white blood cells

called lymphocytes.
In ALL, the lymphocytes are cancerous and don't fight
infections very well.
These cancerous cells grow quickly and crowd out the
bone marrow, preventing it from making the normal red
blood cells, white blood cells, and platelets that your body
needs.

Risk Factors for ALL:

Radiation exposure
Exposure to benzene
Smoking and coffee
Genetic conditions
Past chemotherapy
Viruses
Electromagnetic fields
Being overweight
Paint exposure
Weakened immunity

Chemotherapy Treatment of ALL

Remission induction:
Aim is to rapidly kill most tumour cells and get the patient

into remission.

Consolidation:
Uses high doses of intravenous multidrug chemotherapy to

further reduce tumour burden.

Maintenance therapy:
Aim to kill any residual cell that was not killed by remission

induction, and intensification regimens. Although such cells

are few, they will cause relapse if not eradicated.

INTRODUCTION TO ALL
PACKAGE:
It is microarray data from 128 different individuals with

acute lymphoblastic leukaemia (ALL).

Maintained by Ritz Laboratory
The data is presented in the form of an exprSet object.

DATA LIST OF ALL

PACKAGE
ExpressionSet (storageMode: lockedEnvironment)
assayData: 12625 features, 128 samples
element names: exprs
protocolData: none
phenoData
sampleNames: 01005 01010 ... LAL4 (128 total)
varLabels: cod diagnosis ... date last seen (21 total)
varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
pubMedIds: 14684422 16243790
Annotation: hgu95av2

COVARIATES OF PHENODATA
Cod: The patient IDs.
Diagnosis date
Gender
Age
BT: The type and stage of the disease.
remission: A factor with two levels, CR or REF.
CR: A vector with the following values: CR, DEATH IN CR,

DEATH IN INDUCTION, REF.

date.cr: The date on which remission was achieved.
t(4;11), t(9;22)
cyto.normal

COVARIATES OF PHENODATA
citog: A vector indicating the various cytogenetic abnormalities that were

detected.
mol.biol : The assigned molecular biology of the cancer BCR\/ABL,
ALL\/AF4, E2APBX etc.
fusion protein: For those with BCR\/ABL which of the fusion proteins
was detected, p190, p190\/p210, p210.
mdr: The patients response to multidrug resistance, either NEG, or POS.
kinet ploidy: either diploid or hyperd.
ccr: A vector indicating whether the patient had continuous complete
remission nor not.
Relapse: A vector indicating whether the patient had relapse or not.
transplant

COVARIATES OF PHENODATA
f.u Follow-up data. The possible values are
1: AUBMT \/ REL: autologous bone marrow transplant and subsequent relapse;
2: BMT \/ CCR: allogeneic bone marrow transplant andstill in continuous complete

remission;
3: BMT \/ DEATH IN CR: after allogeneic bone marrow transplant patient died without
relapsing;
4: BMT \/ REL: after allogeneic bone marrow transplant patient relapsed;
5: CCR: patient was in continuous complete remission;
6: CCR \/ OFF: patient was in continuous complete remission but off-protocol for some
reasons;
7: DEATH IN CR: died when in complete remission;
8: MUD \/ DEATH IN CR: unrelated allogeneic bone marrow transplant and death
without relapsing;
9: REL: relapse; 10: REL \/ SNC: relapse occurred at central nervous system.

date: last seen Date the patient was last seen.

METHDODOLOGY
Read PhenoData
Euclidean
Canberra
Distance matrix

Manhatten
Minkowski
Single linkage

Hierarchial clustering

Complete linkage
Average linkage

Average silhoutte width

Average Silhouette Width

Distance matrix
methods

Complete linkage

Average linkage

Single linkage

Manhattan

0.68

0.69

0.7

Canberra

0.43

0.46

0.46

Minkowski

0.69

0.7

0.6

Euclidean

0.69

0.7

0.6