Note: Descriptions are shown in the official language in which they were submitted.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
SYSTEMS, METHODS AND COMPUTER PROGRAM PRODUCTS FOR
GUIDING SELECTION OF A THERAPEUTIC TREATMENT REGIMEN_
BASED ON THE METHYLATION STATUS OF THE DNA
BACKGROUND OF THE INVENTION
FIELD OF THE INVENTION
This invention concerns systems, methods and computer program products for
guiding the selection of therapeutic treatment regimens for complex disorders
such as
cancer viral and/or bacterial infection, wherein a ranking of available
treatment regimens
is generated based on information about the methylation status at selected
sites of the
DNA of the patient and advisory information clinically useful for treating
patients is
provided.
DESCRIPTION OF RELATED ART
The levels of observation that have been well studied by the methodological
developments of recent years in molecular biology include the gene itself, the
translation
of genes in RNA, and the resulting proteins. When, during the course of the
development
of an individual, a gene is switched on, and how the activation and inhibition
of certain
genes in certain cells and tissues is controlled, can be correlated With a
high degree of
probability with the extent and the character of the methylation of the gene
or the
genome. In this regard, it is reasonable to assume that pathogenic conditions
are
expressed in a modified methylation pattern of individual genes or of the
genome.
The state of the art is a method which allows the study of the methylation
pattern
of individual genes. More recent additional developments of this method also
allow the
analysis of minute quantities ~f starting material, where, however, the total
number of
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
2
measurement points remains at most a two-digit number, in theoretical range of
values of
at least 107 measurement points.
1. State of the art of molecular analysis of cell phenotypes
The study of gene expression can be at the RNA level or at the protein level.
Both
levels in principle reflect important phenotypic parameters. Protein assays
using two-
dimensional gels (McFarrel method) have been known for approximately 1 S
years. Using
these assays, it is possible to elaborate the analysis of the chromatographic
positions of
several thousand proteins. Very early on, such electropherograms were already
processed
or evaluated with data processing means. In principle, the validity of the
method is high,
however, it is inferior to the modern methods of gene expression based on RNA
analysis
in two regards.
In particular, the detection of proteins that are of regulatory importance,
from
small quantities of cells, fails because of the fact that the sensitivity of
the methods used
is much too low. Indeed, in contrast to nucleic acids, proteins cannot be
amplified. In
addition, the method is very complex, not amenable to automation, and very
expensive.
In contrast, RNA analysis presents considerable advantages, and due to of the
use of PGR
it is more sensitive. Above all, each RNA species recognized to be important
can be
identified immediately by its sequence.
Overexpression or underexpression of individual RNAs with a known sequence
can usually be easily detected; however, in connection with the applications
discussed
here, they are only valid in exceptional cases.
The method of "differential displays" at best allows a semiquantitative study
of
expression. Expression products amplified by PCR are separated by gel
electrophoresis.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
3
The validity is limited as a result of the resolution of the gel
electrophoresis. In addition,
the method is insufficiently sensitive and robust fox use in routine diagnosis
(Liang, P,
and Pardee, A. B., Science 257, 967-971).
Genes with high overexpression or underexpression are frequently identified by
subtractive techniques, Here, cDNA clones of a cell or tissue species to be
examined are
plated. Against the clones, cDNA is hybridized as comparison material.
Expression
patterns cannot be reliably prepared using this technique.
One activity of the American "human genome project" is the systematic
sequencing of expressed genes. The data obtained from this can be used to
build
expression chips, which.allow the study of practically all expressed sequences
of a cell or
tissue type in a single experiment.
2. State of the art in the analysis of cancer diseases
Mutations in genes ~'ig~r cancer diseases, that is, cell degeneration. The
causes of these mutations can be exogenous influences, or events in the cell.
Tn a few
exceptional cases, an individual mutation, which frequently affects larger
regions of the
genome -(translocations, deletions), results in the degeneration of the cell;
but in most
cases a chain of mutations on different genes is involved, and it is only
their combined
effect that xesults in the malignant disease. These results on the DNA level
are also
reflected on the RNA and protein levels. In this context, it is highly
probable that a
multiplication occurs, because it is certain that in many cases the quantity
and type of one
RNA influences the extent of the synthesis of several other RNA species. This
leads to a
change in the synthesis rates of the corresponding proteins, which, in turn,
can result in
deregulating metabolism, and thus initiate the mechanism of regulation and
counter
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
4
regulation. The result is a gene expression pattern of the cells in question,
that has been
modified in a very specific (but largely nondeterminable) manner,the
specificity is for a
certain carcinoma, fox the stage of the carcinoma, and the degree of
malignancy of the
carcinoma. So far, such phenomena have been outside the realm of study of
natural
sciences. Indeed, it has been impossible to examine the gene expression or the
metabolism of a cell in its totality. Chip technology for the first time
provided such a
possibility (Schena, M. et al., Science 270, 467-470).
If one wishes to solve the diagnostic problem of early diagnosis of tumors on
the
molecular level, then one is confronted, today, with an insurmountable
difficulty, with
very few exceptions: Because, for most tumors, the knowledge of the molecular
events,
that is, the different mutations, is only fragmentary; researchers do not know
what to look
for in medical examination material. This means it is absolutely impossible to
apply the
remarkable sensitivity and specificity of the polymerase chain reaction.
Examples are
certain intestinal tumors, Ewing's sarcoma, and certain forms of leukemia,
which are in
fact each defined by a single, precisely described mutation. In those cases,
it is possible to
identify the degenerated cell among millions of normal cells. However, even
within these
apparently unambiguously defined tumor groups, there are such differences in
the
behavior that the conclusion must be drawn that additional unknown genetic
parameters
(such as, for example, the genetic background of the individual) play an
important role.
Immunological tumor markers are helpful auxiliary parameters, but they
continue to
make only a modest contribution, in addition to the other conventional
diagnostic
parameters. However, they can be used for the purpose of preselecting suspect
cells.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
Histology plays an important and indispensable role in the identification of
degenerated tissues, but not precisely in early diagnosis.
Thus, because most tumors are not sufficiently characterized for diagnostic
purposes on the molecular level, as a rule, no possibilities exist to proceed
to a
subdivision info stages or even a subdivision by degrees of risk. auch a
subdivision,
however, is an absolute prerequisite for an improved selection of treatments
and, above
all, for the development of effective new drugs and of gene therapy.
3. State of the art in research on the number, type and properties of the
possible stable
states of cells of higher organisms
In recent times, there has been an increase in the number of indications that
complex regulatory systems (an excellent example of which is cell regulation),
when left
alone, can exist in only a limited number of stable states, above a critical
minimum
complexity and below a critical maximum connectivity (of the average number of
the
components, with which any given component is connected) (Kauffman, S. A.,
Origins of
Order, Oxford University Press, 1993). In this context, the word state should
be
understood as the concept of selection for the general phenomenon. In
connection with
cells as biological regulatory systems, one can also talk of differentiation
state or cell
type. Although no such connection has been demonstrated--and even a mere
limitation of
the possible states for biological systems has not been demonstrated--the
practical
implications would be of very great importance: If, regarding the constant
information
content of the cells of an organism (de facto, such constancy essentially
exists within one
species), there were only a limited number of stable states, then it would be
likely that
degenerated cells could also be in only one of these states or in a transition
between the
mnccihlP etatPe At thie time thara io nn mnee;l,ili+v +n ~IP~nP +haoa a+~_~+ne
nn a mnlarnlar
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
6
basis. It is hardly possible to achieve a correlation between the individual
states and the
behavior of the cells according to the state of the art. However, such an
analysis could
make decisive contributions to the diagnosis and prognosis of diseases. It is
even possible
that a correlation could be established between the possible states of
diseased cells and
the best suited therapy. Furthermore, it is probable that such a~method could
also have a
decisive influence in the selection of the time of treatment. For example, if
one were to
discover that the cells of a tumor are in a transition between possible
states, one could
assume that such a population of cells would be more likely to yield to the
selection
pressure resulting from the treatment, and thus could escape more easily. A
cell
population in such a scenario, within such transitional states, would have a
considerably
increased flexibility, and it would be easily forced into a possible stable
state, in which
the selection pressure would be eliminated, and the treatment would thus be
without
effect. A method which could classify cells and cell groups according to
states would
then also contribute to recognizing, understanding and possibly solving such
problems.
However, according to the state of the art, it is not possible to determine
whether only a
limited number of states of cells exists. It follows that it is not possible
to differentiate
groups of cells according to an abstract criterion concerning their states,
and to predict
these states with a certain behavior of the cells.
4. Hereditary diseases
Today, the genetic map of the human genome comprises 2500 so-called
microsatellites. These instruments are used to locate a multitude of genes,
usually genes
whose defect causes a genetic disease, per linkage analysis, and then to
identify them.
Common genetic diseases caused by a single defective gene are thus elucidated,
from the
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
7
point of view of the geneticist's principle, polygenic diseases should also be
understood
in this manner. Many polygenic diseases are very common, so common that they
are
included among the so-called wide-spread diseases. Asthma and diabetes are
examples.
Many carcinoma types are also included. The use of the above-described
strategy of
linkage analysis also produced enormous initial successes. In many instances,
numerous
causal genes of important polygenic diseases such as diabetes, schizophrenia,
atherosclerosis and obesity have been found. Besides the availability of the
molecular
biology laboratory techniques proper, the availability of a relatively large
number of
patients and relatives affected by each disease is a crucial prerequisite for
genetic
elucidation. In the past two years it has become apparent that the number of
several
hundred patients that were originally used for the linkage analysis of
polygenic diseases
very likely is too low by one order of magnitude. This applies, in any case,
to cases where
the entire spectrum of the causal gene is to be elucidated. Because the level
of manual
work required for such a linkage analysis is extraordinarily high, only very
slow progress
can be expected in the analysis of polygenic diseases. Alternative strategies
are sought
because it is precisely these diseases that are of enormous social and
economic
importance.
5. State of the art in methylation analysis
The modification of the genomic base cytosine to 5'-methylcytosine represents
the
epigenetic parameter which to date is the most important one and has been best
examined. Nevertheless, methods exist today to determine comprehensive
genotypes of
cells and individuals, but no comparable methods exist to date to generate and
evaluate
epigenotypic information on a large scale.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
8
In principle, there are three methods that differ in principle for determining
the 5-
methyl state of a cytosine in the sequence context.
The first method is based in principle on the use of restriction endonucleases
(RE), which are methylation-sensitive". REs are characterized in that they
produce a cut
in the DNA at a certain DNA sequence which is usually 4-8 bases long. The
position of
such cuts can be detected by gel electrophoresis, transfer to a membrane and
hybridization. Methylation-sensitive means that certain bases within the
recognition
sequence must be unmethylated for the step to occur. The band pattern after a
restriction
cut and gel electrophoresis thus changes depending on the methylation pattern
of the
DNA. However, most CpG that can be methylated are outside of the recognition
sequences of REs, and thus cannot be examined.
The sensitivity of this method is extremely low (Bird, A. P., Southern, E. M.,
J.
Mol. Biol. 118, 27-47). A variant combines PCR with this method; an
amplification by
two primers located on both sides of the recognition sequence occurs after a
cut only if
the recognition sequence is in the methylated form. In this case, the
sensitivity
theoretically increases to a single molecule of the target sequence; however,
only
individual positions can be examined, at great cost (Shemer, R. et al., PNAS
93, 6371-
6376).
The second variant is based on the partial chemical cleavage of whole DNA,
using the model of a Maxam-Gilbert sequencing reaction, ligation of adaptors
to the ends
thus generated, amplification with generic primers, and separation by gel
electrophoresis.
Using this method, defined regions having a size of less than thousands of
base pairs can
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
9
be examined. However, the method is so complicated and unreliable that it is
practically
no longer used (Ward, C, et al., J. Biol. Chem. 265, 3030-3033).
A new method for the examination of DNA to determine the presence of 5-
methylcytosine is based on the specific xeaction of bisulfate with cytosine.
The latter is
converted under appropriate conditions into uracil, which, as far as base
pairing is
concerned, is equivalent to thymidine, and which also corresponds to another
base. 5-
Methylcytosine is not modified. As a result, the original DNA is converted in
such a
manner that methylcytosine, which originally could not be distinguished from
cytosine by
its hybridization behavior, now can be detected by "normal" molecular
biological
techniques. All of these techniques are based on base pairing, which can now
be
completely exploited. The state of the art, as far as sensitivity is
concerned, is defined by
a method which includes the DNA to be examined in ~an agarose matrix, intended
to
prevent the diffusion and renaturing of the DNA (bisulfate reacts only with
single-
stranded DNA) and to replace all precipitation and purification steps by rapid
dialysis
(Olek, A., et al., Nucl. Acids. Res. 24, 5064-5066). Using this method,
individual cells
can be examined, which illustrates the potential of the method. However, so
far only
individual regions up to approximately 3000 base pairs in length have been
examined,
and an overall examination of cells to identify thousands of possible
rnethylation events
is not possible. However, this method is not capable of reliably analyzing
minute
fragments from small sample quantities. In spite of protection against
diffusion, such
samples are lost through the matrix.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
6. State of the art in the use of the bisulfite technigue
To date, barring few exceptions, (for example, Zeschnigk, M, et al., Eur. J.
Hum.
Gen. 5, 94-98; Kubota, T. et al., Nat. Genet. 16, 16-17), the bisulfate
technique is only
used in research. However, short specific pieces of a known gene after
bisulfate treatment
are routinely amplified and either completely sequenced (Olek, A. and Walter,
J., Nat.
Genet. 17, 275-276) or the presence of individual cytosine positions is
detected by a
"primer extension reaction" (Gonzalgo, M. L. and Jones, P. A., Nucl. Acids.
Res. 25,
2529-2531), or enzyme cut (Xiong, Z. and Laird, P. W., Nucl. Acids. Res. 25,
2532-
2534). Ali these references are from the year 1997. The concept of using
complex
methylation patterns for correlation with phenotypic data pertaining to
complex genetic
diseases, much less via an evaluation algorithm such as, for example, a neural
network,
has, so far, gone unmentioned ~ in the literature; moreover, it cannot be
performed
according to the methodologies of the state of the art.
7. State of the art with respect to Methylation and the diagnosis of human
diseases
In the past, modification of the methylation pattern was analyzed in order to
study
and understand the genetic mechanisms which are involved in the outbreak or
the
progression of a disease. AlI .this research was done in a piece-by-piece
fashion by
studying only one gene/chrornosomal region at a time and no
diagnosis/therapeutic
treatment regimen was based on the methylation pattern modifications. In fact,
the type
of disease associated with the modification of the methylation pattern was
known before
methylation analysis was performed. Therefore, the following publications only
indicate
the widespread connection between modifications of the methylation patterns
and human
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
11
diseases. Modifications can include both hyper- or hypomethylation of selected
sites of
the DNA.
Disease associated with a modification of the methylation patterns axe, for
example:
Leukemia (Aoki E et al. "Methylation status of the pl5INK4B gene in
hematopoietic progenitors and peripheral blood cells in myelodysplastic
syndromes"
Leukemia 2000 Apr;14(4):586-93; Nosaka K et al. "Increasing methylation of the
CDKN2A gene is associated with the progression of adult T-cell leukemia"
Cancer Res
2000 Feb 15;60(4):1043-8; Asirnakopoulos FA et al. "ABL1 methylation is a
distinct
molecular event associated with clonal evolution of chronic myeloid leukemia"
Blood
1999 Oct 1;94(7):2452-60; Fajkusova L. et al. "Detailed Mapping of
Methylcytosine
Positions at the CpG Island Surrounding the Pa Promoter at the bcr-abl Locus
in CML
Patients and in Two Cell Lines, K562 and BV 173" Blood Cells Mol Dis 2000
Jun;26(3):193-204; Litz CE et al. "Methylation status of the major breakpoint
cluster
region in Philadelphia chromosome negative leukemias" Leukemia 1992
Jan;6(1):35-41)
- Head and neck cancer (Sanchez-Cespedes M et al. "Gene promoter
hypermethylation in tumors and serum of head and neck cancer patients" Cancer
Res
2000 Feb 15;60(4):892-5)
- Hodgkin's disease (Garcia JF et al. "Loss of p16 protein expression
associated
with methylation of the pl6INK4A gene is a frequent finding in Hodgkin's
disease" Lab
Invest 1999 Dec;79(12):I453-9)
' - Gastric cancer (Yanagisawa Y et al. "Methylation of the hMLHl promoter in
familial gastric cancer with microsatellite instability" Int J Cancer 2000 Jan
1;85(1):50-3)
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
12
- Prostate cancer (Rennie PS et al. "Epigenetic mechanisms for progression of
prostate cancer" Cancer Metastasis Rev 1998-99;17(4):401-9)
- Renal cancer (Clifford SC et al. "Inactivation of the von Hippel-Lindau
(VHL)
tumor suppresser gene and allelic losses at chromosome arm 3p in primary renal
cell
carcinoma: evidence for a VHL-independent pathway in clear cell renal
tumourigenesis"
Genes Chromosomes Cancer 1998 Ju1;22(3):200-9)
- Bladder cancer (Sardi I et al. "Molecular genetic alterations of c-myc
oncogene
in superficial and locally advanced bladder cancer" Eur LTrol 1998;33(4):424-
30)
- Breast cancer (Mancini DN et al. "CpG methylation within the 5' regulatory
region of the BRCA1 gene is tumor specific and includes a putative CREB
binding site"
Oncogene 1998 Mar 5;16(9):1161-9; Zrihan-Licht S et al. "DNA methylation
status of
the MUC1 gene coding for a breast-cancer-associated protein" Int J Cancer 1995
Jul
28;62(3):245-51; Kass DH et al. "Examination of DNA methylation of chromosomal
hot
spots associated with breast cancer" Anticancer Res 1993 Sep-Oct;l3(5A):1245-
51)
- Burkitt's lymphoma (Tao Q et al. "Epstein-Barr virus (EBV) in endemic
Burkitt's lymphoma: molecular analysis of primary tumor tissue" Blood 1998 Feb
15;91(4):1373-81)
- Wilms tumor (Kleymenova EV et al. "Identification of a tumor-specific
methylation site in the Wilms tumor suppresser gene" Oncogene 1998 Feb
12;16(6):713-
20)
- Prader-WillilAngelman syndrome (Zeschnigh et al. "Imprinted segments in the
human genome: different DNA methylation patterns in the Prader-Willi/Angelman
evnr~rnma raminn ac rlatarm;nr ra 1,V +1t? (T! v1n1Y1tl. C~l~/7111iH1.Y111T
Y1'1P~'~~In~~~ T~nmam 1~/Tn~
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
13
Genetics (1997) (6)3 pp 387-395; Fang P et al. "The spectrum of mutations in
UBE3A
causing Angelman syndrome" Hum Mol Genet 1999 Jan;B(1):129-35)
- ICF syndrome (Tuck-Muller et al. "CMDNA hypomethylation and unusual
chromosome instability in cell lines from ICF syndrome patients" Cytogenet
Cell Genet
2000;89(1-2):121-8)
Dermatofibroma (Chen TC et al. "Dermatofibroma is a clonal proliferative
disease" J Cutan Pathol 2000 Jan;27(I):36-9)
Hypertension (Lee SD et al. "Monoclonal endothelial cell proliferation is
present
in primary but not secondary pulmonary hypertension" J Clin Invest 1998 Mar
1;101 (5):927-34)
- Pediatric Neurobiology (Campos-Castello J et al. "The phenomenon of genomic
"imprinting" and its implications in clinical neuropediatrics" Rev 1'Jeurol
1999 Jan 1-
15;28(1):69-73)
- Autism (Klauck SM et al. "Molecular genetic analysis of the FMR-1 gene in a
large collection of autistic patients" Hum Genet 1997 Aug;100(2):224-9)
- Ulcerative colitis (Gloria L et al. "DNA hypomethylation and proliferative
activity are increased in the rectal mucosa of patients with long-standing
ulcerative
colitis" Cancer 1996 Dec 1;78(11):2300-6)
- Fragile X syndrome (Hornstra III et al. "High resolution methylation
analysis of
the FMRl gene trinucleotide repeat region in fragile X syndrome" Hum Mol Genet
1993
Oct;2(10):1659-65)
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
14
- Huntington's disease (Ferluga J et al. "Possible organ and age-related
epigenetic
factors in Huntington's disease and colorectal carcinoma" Med Hypotheses 1989
May;29(1):51-4)
All the above-cited documents are hereby incorporated by reference.
8. Personalized medicine
A successful therapeutic treatment of a patient in need of such a treatment
depends on several factors.
First, a reliable diagnosis of the disease or the medical condition has to be
achieved. In case of infectious diseases, cancer or other acute life-
threatening diseases,
this diagnosis has to be fast and efficient, since time plays a crucial role
in the survival
rate of patients suffering from those diseases. The ideal diagnosis would
therefore rely on
data of the patient which is easy to assess and does not involve a time-
consuming
diagnosis procedure. In addition, one would prefer the least invasive way in
order to
achieve samples from a patient to be examined. One aspect of the methods to be
patented
here provides new possibilities for the differential diagnosis of, for
example, cancer
diseases.
Second, a therapeutic treatment of an individual patient becomes more
effective if
the diagnosis is precise. Currently, for example cancer is sometimes treated
with a
standard "cocktail" of anti-cancer drugs exhibiting severe side effects for
the patient.
Nevertheless, the survival rate of at least some types of cancer is low. Once
the type of
cancer (or other disease) is precisely determined, an individual treatment
regime for this
type of disease would be exponentially more effective than any other treatment
regimen.
Effectiveness in this case depends directly on the individual application of
the therapeutic
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
treatment to the patient. An even more effective treatment would be possible,
if the
treatment regimen would be cross-checked with regimens already successfully
applied to
other patients.
Further, a precise diagnosis of the disease would lead to reduced costs for
the
individual treatment regimen, since unnecessary and ineffective medication is
avoided.
Further, therapeutic treatment regimens for human diseases, such as AIDS and
cancer are increasingly complex. New data and new therapeutic treatment
regimens
continue to modify the treatments available, and it is difficult for all but
the specialist to
remain current on the latest treatment information.
Further, even those who are current on the latest treatment information
require
time to assimilate that information and understand how it relates to other
treatment
information in order to provide the best available treatment for a patient.
Combination
therapeutic treatment regimens exacerbate this problem by making potential
drug
interactions even more complex.
Finally, an increasingly sophisticated patient population, in the face of a
vast
volume of consumer information on the treatment of disease, makes the mere
statement
of a treatment regime, without explanation, difficult for the patient to
accept.
Another desireable form of treatment would comprise a preventive kind of
treatment regimen which could be applied at the earliest stage of an upcoming
disease. In
order to know when to apply such a treatment regimen, one would need a form of
diagnosis that could determine changes in the health status of the patient
even before an
outbreak of an acute disease could be diagnosed. This outbreak could then be
prevented
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
16
or reduced in severity. by applying a preventive treatment regimen to such non-
acute
patient.
Taken together, the ideal treatment regimen would combine all the above-
mentioned factors in order to apply the most effective medication to the
individual
patient. This individual diagnosis/medication regimen can be summarized using
the term
"personalized medicine".
U.S. Pat. No. 5,672,154 to Sillen describes a method for giving patients
individualized, situation-dependent medication advice. The recommended type of
medicine may include at least two different medicines. No means for ranking
multiple
treatment options is disclosed, and no means for explaining why treatment
options were
rejected is given. Rather, this system is primarily concerned with generating
new rules
from patient information to optimize a particular therapy for diseases such as
Parkinson's
disease, epilepsy and abnormal blood pressure. Sillen does not disclose the
need for a
more precise diagnosis or the use of DNA-methylation for the individualized
medication
advice.
U.S. Pat. No. 5,915,568 to Gjerlov describes a method_ of medicating and
individualizing treatment shampoo for dermatological disturbances of companion
animals. Gjerlov further describes a system for customized provision of
medicated
shampoos which are individualized for treatment of specific dermatological
disturbances
of specific and individual companion animals. The method disclosed involves
diagnosing
the dermatological disturbance and then adding to a pre-mixed base shampoo a
pre-
mixed, medically effective amount of concentrate correlated to the particular
dermatological disturbance, and then the composition is provided to the owner
of the
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
17
animal. Further, a kit apparatus to carry out the method and packaging for
shipment and
display of the apparatus is disclosed.
U.5. Pat. No. 5,694,950 to McMichael describes a method and system for use in
treating a patient with imrnunosuppressants such as cyclosporin. An expert
system is
employed to generate a recommendation on whether the' immunosuppressant dosage
should be changed and, if so, how. Ranking or selection among a plurality of
different
combination therapeutic treatment regimens is not suggested.
U.5. Pat.. No. 5,594,638 to Iliff describes a medical diagnostic system that
provides medical advice to the general public over a telephone network. This
system is
not concerned with generating a recommendation for a combination therapeutic
treatment
regimen for a known disease (see also U.S. Pat. No. 5,660,176 to Iliff).
U.5. Pat. No. 6,081,786 to Barry et al. describes systems, methods and
computer
program products for guiding selection of a therapeutic treatment regimen for
a known
disease such as HTV infection are disclosed. The method comprises (a)
providing patient
information to a computing device (the computer device comprising: a first
knowledge
base comprising a plurality of different therapeutic treatment regimens for
the disease; a
second knowledge base comprising a plurality of expert rules for selecting a
therapeutic
treatment regimen for the disease; and a third knowledge base comprising
advisory
information useful for the treatment of a patient with different constituents
of the
different therapeutic treatment regimens; and (b) generating in the computing
device a
listing (preferably a ranked listing) of therapeutic treatment regimens for
the patient; and
(c) generating in the computing device advisory information for one or more
treatment
regimens in the listing based on the patient information and the expert rules.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
18
SUMMARY OF THE INVENTION
In view of the foregoing, an object of the invention is to provide systems,
methods
and computer program products for treatment regimens for patients in which
available
treatments are listed, and optionally ranked, based on the information of the
methylation
statuses at selected sites of the DNA of the patient.
A further object of the invention is to provide systems, methods and computer
program products for preventive treatment regimens based on the methylation
statuses at
selected sites of the DNA of a patient in order to avoid or delay the acute
outbreak of a
disease.
As a further object of the invention, unavailable or rejected treatment
regimens
(e.g., regimens that would not be effective, or would be dangerous) are not
displayed or
are assigned a low ranle and are indicated to a user as not likely to be
efficacious, or not
preferred due to patient-specific complicating factors such as drug
interaction from
concomitant medications.
A further object of the invention is to provide systems, methods and computer
program products for selecting treatment regimens or preventive treatment
regimens
based on the. methylation statuses at selected sites of the DNA of a patient
in which the
available treatment options can be readily understood.
A further object of the invention is to provide systems, methods and computer
program products for selecting treatment regimens or preventive treatment
regimens
based on the methylation statuses at selected sites of the DNA of a patient in
which the
implications of selecting a particular treatment regimen can be readily
understood.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
19
A further object of the invention is to provide systems, methods and computer
program products for selecting treatment regimens based on the methylation
statuses at
selected sites of the DNA of a patient in which the reasons for rejection of a
particular
regimen can be readily understood.
A still further object of the invention is to provide systems, methods and
computer
program products for obtaining information about the efficacy of previous
treatment
regimens imposed on patients.
A method of the present invention includes providing information about the
methylation status at selected sites of the DNA of the patient to a computing
device that
includes various knowledge bases. For example, a first knowledge base may
include
information about a plurality of different methylation statuses at selected
sites of the
DNA in cells with a known disease or medical condition and/or healthy cells. A
second
knowledge base may include a plurality of expert rules for evaluating and
selecting a type
of disease or medical condition based on the methylation status at selected
sites of the
DNA of a patient.
A listing (preferably a ranked listing) is generated in the computing device
based
on the information about the methylation status at selected sites of the DNA
of the
patient, the first knowledge base and the second knowledge base. Based on this
listing, a
therapeutic treatment regimen can be applied to the patient.
According to one embodiment of the invention, such treatment could be a
preventive treatment in order to prevent the acute outbreak of a disease.
In addition, in a preferred embodiment, the method further comprises a third
knowledge base comprising a plurality of different therapeutic regimens for
diseased
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
cells or medical conditions, a fourth knowledge base comprising a plurality of
expert
rules for evaluating and selecting therapeutic treatment regimens for diseased
cells or
medical conditions, and step of generating in the computing device a ranked
listing of
available therapeutic treatment regimens for the patient based on the
information
generated in step and the third knowledge base and fourth knowledge base.
In a preferred embodiment, the method described above further includes a fifth
knowledge base comprising advisory information useful for the treatment of a
patient
with different constituents of the different therapeutic treatment regimens
and in the
computing device advisory information for one or more treatment regimens in
the ranked
listing based on the information generated according to the method described
above and
the fifth knowledge base is generated.
Tn another embodiment of the method according to the invention, the method
described above further includes the steps of entering a user-defined
therapeutic
treatment regimen for the disease or medical condition that is not included in
the third
knowledge base mentioned above and in the computing device advisory
information for
one or more user-defined combination therapeutic treatment regimen is
generated.
Preferably, the patient information in addition to the information about the
methylation
status at selected sites of the DNA may comprise gender, age, weight,
hemoglobin
information, neuropathy information,. neutrophil information, pancreatitis,
hepatic
function, renal function, drug allergy and intolerance information. The
patient
information may further include prior therapeutic treatment regimen
information. The
patient information may include prior patient information stored in a
computing device.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
21
In another preferred embodiment of the inventive method, the advisory
information may includes warnings to take the patient off a contraindicated
drug before
initiating a corresponding therapeutic treatment regimen; and information
clinically
useful to implement a corresponding therapeutic treatment regimen.
The method according to the present invention may comprise in the computing
device a sixth knowledge base comprising patient therapeutic treatment regimen
history,
the advisory information including previous therapeutic treatment regimen
information
extracted from the sixth knowledge base.
The disease or medical condition treated by the inventive method may be a
cardiovascular disease, a pulmonary disease, a neurologic disease, cancer,
diabetes, a
urinary tract infection, hepatitis or HIV infection.
Further, in another embodiment of the inventive method drug dosage information
is recommended and adjusted if necessary depending upon the patient
information.Yet
another method according to the invention further comprises the step of
accessing, via a
computing device, information for one or more therapeutic treatment regimens
from a
drug reference source.
The invention further provides a method for treatment of a patient with a
disease
or medical condition including the steps of (A) isolating a DNA-containing
sample from
a the patient;(B) analyzing cytosine methylation patterns at selected sites of
the DNA
contained in the sample; (C) providing data about the methylation status at
selected sites
of the DNA of the patient thereby creating a first knowledge base comprising
the data, a
second knowledge base comprising information about a plurality of different
methylation
statuses at selected sites of the DNA in cells with a known disease or medical
condition
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
22
and/or healthy cells, a third knowledge base comprising a plurality of expert
rules for
evaluating and selecting a type of disease or medical condition based on the
methylation
status at selected sites of the DNA of a patient, and the step of (D)
generating a ranked
listing of diseases or medical conditions based on the data of the first
knowledge base, the
second knowledge base and the third knowledge base. In a preffered embodiment
of the
inventive method, the data is provided to a computing device.
Preferably, the inventive method may include a fourth knowledge base
comprising a plurality of different therapeutic regimens for diseased cells or
medical
conditions and a fifth knowledge base comprising a plurality of expert rules
for
evaluating and selecting therapeutic treatment regimens for diseased cells or
medical
conditions. In this case the inventive method includes the step of(E)
generating a ranked
listing of available therapeutic treatment regimens for the patient based on
the
information generated in step (D) described above and the fourth knowledge
base and the
fifth knowledge base.
Another method according to the invention may further include a sixth
knowledge
base comprising advisory information useful for the treatment of a patient
with different
constituents of the different therapeutic treatment regimens; and the step of
(F) generating
advisory information for one or more specific treatment regimens in the ranked
listing
based on the information generated in step (E) described above and the sixth
knowledge
base; and the step of (G) providing the one or more specific treatment
regimens to the
patient with a disease or medical condition based on the advisory information
generated
in step (F).
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
23
Further, in another embodiment of the inventive method, the method may further
include the steps of (H) entering a user-defined therapeutic treatment regimen
for the
disease or medical condition that is not included in the fourth knowledge
base; and (I)
generating advisory information for one or more user-defined combination
therapeutic
treatment regimen.
The above-mentioned patient data in addition to the data about the methylation
status at selected sites of the DNA comprises gender, age, weight, hemoglobin
information, neuropathy information, neutrophil information, pancreatitis,
hepatic
function, renal function, drug allergy and intolerance information. The
patient data may
include prior therapeutic treatment regimen information and may include prior
patient
information stored in the computing device.
In yet a preferred method according to the invention the advisory information
may
include warnings to take the patient off a contraindicated drug before
initiating a
corresponding therapeutic treatment regimen; and information cllinically
useful to
implement a corresponding therapeutic treatment regimen.
Another preferred embodiment of the method according to the invention may
include a seventh knowledge base comprising patient therapeutic treatment
regimen
history, the advisory information including previous therapeutic treatment
regimen
information extracted from the seventh knowledge base. This disease or medical
condition may be a cardiovascular disease, a pulmonary disease, a neurologic
disease,
cancer, diabetes, a urinary tract infection, hepatitis or HIV infection.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
24
In another embodiment of the method according to the invention, the drug
dosage
information is recommended and adjusted if necessary depending upon the
patient
information.
The invention further provides a method which may further inlude the step of
accessing, via a computing device, information for one or more therapeutic
treatment
regimens from a drug reference source.
The invention further provides a system for guiding the selection of a
therapeutic
treatment regimen or a preventive therapeutic treatment regimen for a patient
with a
disease or medical condition. This system includes a computing device which
may
includes a first knowledge base comprising information about a plurality of
different
methylation statuses at selected sites of the DNA in cells with a known
disease or
medical condition and/or healthy cells, a second knowledge base comprising a
plurality
of expert rules for evaluating and selecting a type of disease or medical
condition based
on the methylation status at selected sites of the DNA of a patient, a third
knowledge
base comprising a plurality of different therapeutic regimens for diseased
cells or medical
conditions and a fourth knowledge base comprising a plurality of expert rules
for
evaluating and selecting therapeutic treatment regimens for diseased cells or
medical
conditions.
The system may include means for providing information about the methylation
status at selected sites of the DNA of the patient to computing device; means
for
generating in the computing device a ranked listing of diseases or medical
conditions
based on the information about the methylation status at selected sites of the
DNA of the
patient, the first knowledge base and the second lcnowledge base.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
In a preferred embodiment the system according to the invention further
includes
a fifth knowledge base comprising advisory information useful for the
treatment of a
patient with different constituents of the different therapeutic treatment
regimens; means
for generating in the computing device a ranked listing of available
therapeutic treatment
regimens for the patient; and means for generating in the computing device
advisory
information for one or more treatment regimens in the ranked listing.
Another embodiment of the system according to the invention may further
include means for entering a user-defined therapeutic treatment regimen for
the disease or
medical condition that is not included in the third knowledge base; and means
for
generating in the computing device advisory information for one or more user-
defined
combination therapeutic treatment regimen.
In another system according to the invention, the patient information in
addition
to the information about the methylation status at selected sites of the DNA
may include
gender, age, weight, hemoglobin information, neuropathy information,
neutrophil
information, pancreatitis, hepatic function, renal function, drug allergy and
intolerance
information. The patient information may further include prior therapeutic
treatment
regimen information and the patient information may include prior patient
information
stored in the computing device.
In another system according to the invention, the advisory information may
include warnings to take the patient off a contraindicated drug before
initiating a
corresponding therapeutic treatment regimen; and information clinically useful
to
implement a corresponding therapeutic treatment regimen.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
26
Preferably, the system according to the invention may include a computiyg
device
including a sixth knowledge base comprising patient therapeutic treatment
regimen
history, the advisory information including previous therapeutic treatment
regimen
information extracted from the sixth knowledge base.
In another system according to the invention the disease or medical condition
may
be a cardiovascular disease, a pulmonary disease, a neurologic disease,
cancer, diabetes, a
urinary tract infection, hepatitis or HIV infection.
In another preferred embodiment according to the invention drug dosage
information is recommended and adjusted if necessary depending upon the
patient
information.
Another system according to the invention may further include means for
accessing, via the computing device, information for one or more therapeutic
treatment
regimens from a standard drug reference source.
The invention further provides a computer program product for guiding the
selection of a therapeutic treatment regimen and/or a preventive therapeutic
treatment
regimen for a patient with a disease or medical condition. This computer
program product
includes a computer usable storage medium having computer readable program
code
means embodied in the medium, the computer readable program code means
including
computer readable program code means for generating a first knowledge base
including
information about .a plurality of different methylation statuses at selected
sites of the
DNA in cells with a known disease or medical condition and/or healthy cells, a
second
knowledge base including a plurality of expert rules for evaluating and
selecting a type of
disease or medical condition based on the methylation status at selected sites
of the DNA
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
27
of a patient, a third knowledge base comprising a plurality of different
therapeutic
regimens for diseased cells or medical conditions, a fourth knowledge base
including a
plurality of expert rules for evaluating and selecting therapeutic treatment
regimens for
diseased cells or medical conditions a fifth knowledge base comprising
advisory
information useful for the treatment ~of a patient with different constituents
of the
different therapeutic treatment regimens; and computer readable program code
means for
providing information about the methylation status at selected sites of the
DNA of the
patient; computer readable program code means for generating a ranked listing
of
diseases or medical conditions based on the information about the methylation
status at
selected sites of the DNA of the patient; and computer readable program code
means for
generating in the computing device a ranked listing of available therapeutic
treatment
regimens for the patient.
A preferred embodiment of the computer program product according to the
invention may further include computer readable program code means for
generating in
the computing device advisory information for one or more treatment regimens
in the
v
ranked listing. The computer program product according to the invention may
further
include computer readable program code means entering a user-defined
therapeutic
treatment regimen for the disease or medical condition that is not included in
the third
knowledge base; and computer readable program code means for generating in the
computing device advisory information for one or more user-defined combination
therapeutic treatment regimen.
Preferably, the computer program product according to the invention, the
patient
information in addition to the information about the methylation status at
selected sites of
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
28
the DNA may include gender, age, weight, hemoglobin information, neuropathy
information, neutrophil information, pancreatitis, hepatic function, renal
function, drug
allergy and intolerance information. The patient information may include prior
therapeutic treatment regimen information and the patient information may
further
include prior patient information.
In another preferred embodiment of the computer program product according to
the invention, the advisory information may include warnings to take the
patient off a
contraindicated drug before initiating a corresponding therapeutic treatment
regimen; and
information clinically useful to implement a corresponding therapeutic
treatment
regimen.
In another embodiment of the computer program product according to the
invention the computer readable program code means may include computer
readable
program code means for generating a sixth knowledge base comprising patient
therapeutic treatment regimen history, the advisory information including
previous
therapeutic treatment regimen information extracted from the sixth knowledge
base.
In another preferred embodiment of the computer program product according to
the invention, the disease or medical condition may be a cardiovascular
disease, a
pulmonary disease, a neurologic disease, cancer, diabetes, a urinary tract
infection,
hepatitis or HIV infection.
Further, in another preferred embodiment of a computer program product
according to the invention, drug dosage information is recommended and
adjusted if
necessary depending upon the patient information.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
29
The inventive computer program product according to the invention may further
include computer readable program code means for accessing information for one
or
more therapeutic treatment regimens from a standard drug reference source.
Further objects and aspects of the present invention are explained in detail
in the
drawings herein and the specification set forth below.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
BRIEF DESCRIPTION OF THE DRAWINGS
The accompanying drawings, which are incorporated in and constitute a part of
the specification, illustrate embodiments of the invention and, together with
the
description, serve to explain principles of the invention.
FIG. 1 illustrates a process of the present invention, including routines for
entering data with respect to the methylation status at specific sites of the
patients' DNA,
therapeutic treatment regimen and preventive therapeutic treatment regimen.
FIG. 2 schematically illustrates a system or apparatus of the present
invention.
FIG. 3 illustrates a client-server environment within which the system of FIG.
2
may operate, according to an embodiment of the present invention, and wherein
a central
server is accessible by at Least one local server via a computer network, such
as the
Internet, and wherein each local server is accessible by at least one client.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
31
DETAILED DESCRIPTION OF THE INVENTION
The present invention now will be described more fully hereinafter with
reference
to the accompanying drawings, in which preferred embodiments of the invention
are
shown. This invention may, however, be embodied in many different forms and
should
not be construed as limited to the embodiments set forth herein; rather, these
embodiments are provided so that this disclosure will be thorough and
complete, and will
fully convey the scope of the invention to those skilled in the art. Like
numbers refer to
like elements throughout.
As will be appreciated by one of skill in the art, the present invention may
be
embodied as a method, data processing system, or computer program product.
Accordingly, the present invention may take the form of an entirely hardware
embodiment, an entirely software embodiment, or an embodiment combining
software
and hardware aspects. Furthermore, the present invention may take the form of
a
computer program product on a computer-usable storage medium having computer
readable program code means embodied in the medium. 'Any suitable computer
readable
medium may be utilized including, but not limited to, hard disks, CD-ROMs,
optical
storage devices, and magnetic storage devices.
The present invention is described below with reference to flowchart
illustrations
of methods, apparatus (systems), and computer program products according to an
embodiment of the invention. It will be understood that each block of the
flowchart
illustrations, and combinations of blocks in the flowchart illustrations, can
be
implemented by computer program instructions. These computer program
instructions
may be provided to a processor of a general purpose computer, special purpose
computer,
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
32
or other programmable data processing apparatus to produce a machine, such
that the
instructions, which execute via the processor of the computer or other
programmable data
processing apparatus, create means for implementing the functions specified in
the
flowchart block or blocks.
These computer program instructions may also be stored in a computer-readable
memory that can direct a computer or other programmable data processing
apparatus to
function in a particular manner, such that the instructions stored in the
computer-readable
memory produce an article of manufacture including instruction means which
implement
the function specified in the flowchart block or blocks.
The computer program instructions may also be loaded onto a computer or other
programmable data processing apparatus to cause a series of operational steps
to be
performed on the computer or other programmable apparatus to produce a
computer
implemented process such that the .instructions which execute on the computer
or other
programmable apparatus provide steps for implementing the functions specified
in the
flowchart block or blocks.
A method of the instant invention is illustrated in FIG. 1. In the first step
10, a
sample to be analyzed is taken from the patient and the DNA of the patient is
analyzed in
order to obtain patient data with respect to the methylation status at
selected sites of the
DNA of the patient. This information is then provided to a computing device
11. The
patient may be further examined to obtain further patient information that may
include
one or more of gender, age, weight, CD4+ cell information; viral load
information,
HIV genotype and phenotype information, hemoglobin information, neuropathy
information, neutrophil information, pancreatitis, hepatic function, renal
function, drug
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
33
allergy and intolerance information, and information for drug treatments for
other
conditions. The information may . include historical information on prior
therapeutic
treatment regimens for the disease or medical condition. While the patient is
typically
examined on a first visit to determine the patient information, it will be
appreciated that
patient information may also be stored in the computing device, or transferred
to the
computing device from another computing device, storage device, or hard copy,
when the
information has been previously determined.
The patient information is usually provided to a computing device 11 that
contains a knowledge base about a plurality of different methylation statuses
at selected
sites of the DNA in cells with a known disease or medical condition and/or
healthy cells
12 and a knowledge base that includes a plurality of expert rules for
evaluating and
selecting a type of disease or medical condition based on the methylation
status at
selected sites of the DNA of a patient in light of the provided patient
information 13.
A list (preferably a ranked list) is then generated in the computing device
based
on the information about the methylation status at selected sites of the DNA
of the
patient, the knowledge base about the different methylation statuses at
selected sites of
the DNA in cells with a known disease or medical condition and/or healthy
cells and the
plurality of expert rules for evaluating and selecting a type of disease or
medical
condition based on the methylation status at selected sites of the DNA ~of a
patient.
This ranked list indicates all possible known diseases or medical conditions
of the
patient and can be displayed 14. In one embodiment of the invention, the
displayed
information is then used to manually determine available treatment options for
the patient
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
34
in light of the patient information and to manually generate advisory
information. Based
on the information displayed at 14, a treatment can be applied to the patient
in need 15.
The method illustrated in FIG. 1 further includes a knowledge base 16 that
includes a plurality of different therapeutic regimens for diseased cells or
medical
conditions and a knowledge base 17 that includes a plurality of expert rules
for evaluating
and selecting available treatment options for the patient in light of the
selected type of
disease or medical condition based on the methylation status at selected sites
of the DNA
of the patient.
A list (preferably a ranked list) is then generated in the computing device
based
on the knowledge base 16 that includes a plurality of different therapeutic
regimens for
diseased cells or medical conditions and a knowledge base 17 that includes a
plurality of
expert rules for evaluating and selecting available treatment options for the
patient in
light of the selected type of disease or medical condition based on the
methylation status
at selected sites of the DNA of the patient.
This ranked list indicates all possible known therapeutic regimens for
diseased
cells or medical conditions for the patient and can be displayed 18. In
another
embodiment of the invention, the displayed information is then used to
manually
determine available treatment options for the patient in light of the patient
information
and to manually generate advisory information. Based on the information
displayed at 18,
a treatment can be applied to the patient in need 15.
The method also includes a knowledge base of advisory information 19. A list
of
available advisory information for the available treatments is then generated
on the basis
of the knowledge base of advisory information and the list that indicates all
possible
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
known therapeutic regimens and displayed 111. The advisory information may
include
warnings to take the patient off a contraindicated drug or select a suitable
non
contraindicated drug to treat the condition before initiating a corresponding
treatment
regimen and/or information clinically useful to implement a corresponding
therapeutic
treatment regimen. Based on the information displayed either at 14, 18 or 111,
a
treatment is applied to the patient in need 15. The progress of this treatment
can be
constantly monitored by taking intermediate DNA samples from the patient and
performing an analysis of the changes of the methylation statuses of the
patient similar to
the method described above.
In another embodiment of the invention, the information displayed either at
14, 18
or 111 is used to apply a preventive treatment to the patient in order to
prevent the acute
outbreak of a disease.
Diseases (or medical conditions), the treatment of which may be facilitated or
improved by the present invention, are those for which multiple different
therapy options
are available for selection and treatment. Such diseases and medical
conditions may
include, but are not limited to, cardiovascular disease (including but not
limited to
congestive heart failure, hypertension, hyperlipidemia and angina), pulmonary
disease
(including but not limited to chronic obstructive pulmonary disease, asthma,
pneumonia,
cystic fibrosis, and tuberculosis), neurologic disease (including but not
limited to
Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis,
amyotrophic lateral
sclerosis or ALS, psychoses such as schizophrenia and organic brain syndrome,
neuroses,
including anxiety, depression and bipolar disorder), hepatitis infections
(including
hepatitis B and hepatitis C infection), urinary tract infections, venereal
disease, cancer
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
36
(including but not limited to breast, lung, prostate, and colon cancer), etc.
It should be
appreciated that prevention of development or onset of the above-mentioned
diseases and
medical conditions may be facilitated or improved by the present invention.
The present invention is also useful for cases in which the disease of the
patient is known, for example such as HIV-1 infection (acquired immune
deficiency
syndrome or "AIDS"), or where the known disease is any medical condition for
which a
combination therapeutic treatment regimen can be used. The invention is
particularly
useful when the list of available treatments includes a plurality (e.g., 2, 10
or 15 or more)
of treatment, combination therapeutic treatment regimens (e.g., therapeutic
treatment
regimens incorporating two or more active therapeutic agents), where the
potential for
drug interactions is increased and/or the complexity involved in selecting the
, best
available treatment is multifactorial.
Alternatively, the advisory information can be generated automatically for
non-recommended therapeutic treatment regimens. These various steps can be
repeated in
any sequence in an interactive manner to provide the user with assurance that
all
treatment options have been given adequate and appropriate consideration.
The terms "therapy" and "therapeutic treatment regimen" are interchangeable
herein and, as used herein, mean any pharmaceutical or drug therapy,
regardless of the
route of delivery (e.g., oral, intraveneous, intramuscular, subcutaneous,
intraarterial,
intraperitoneal, intrathecal, etc.), for any disease (including both chronic
and acute
medical conditions, disorders, and the like). ~ In addition, it is understood
that the present
invention is not limited to facilitating or improving the treatment of
diseases. The present
invention may be utilized to facilitate or improve the treatment of patients
having various
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
37
medical conditions, without limitation. The term also includes preventive
therapeutic
treatment regimens, which may be applied in order to prevent an outbreak of an
acute
i
disease.
System Description
The present invention may be embodied as an expert system that provides
decision support to physicians (or other health care providers) treating
patients with a
known or unknown disease, such as an infection. A system according to the
present
invention analyses the methylation statuses at selected sites of the DNA of a
patient,
attaches this information to other knowledge bases and calculates therapy
options and/or
preventive therapy options and attaches all relevant information to those
options.
As known to those of skill in the art, an expert system, also known as
artificial
intelligence (AT), is a computer program that can simulate the judgment and
behavior of a
human or an organization that has expert knowledge and experience in a
particular field.
An expert system typically contains a knowledge base containing accumulated
experience and a set of rules for applying the knowledge base to each
particular situation
that is described to the program. Another expert system is known as neuronal
network
(NN) which is capable to actively accumulate information and knowledge. Other
expert
systems are well known to those of skill in the art and need not be described
further
herein.
As an example, the antibacterial and/or antiretroviral therapy options
(combinations of antiretroviral drugs), are derived using a knowledge base
consisting of a
number of expert system rules and functions which in turn take into account a
given
patient's treatment history, current condition and laboratory values. A system
according
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
38
to the present invention supports the entry, storage, and analysis of patient
data with
respect to the methylation statures at selected sites of the DNA of the
patient in a large
central database. A system according to the present invention has a flexible
data driven
architecture and custom reporting capabilities designed to support patient
therapy
management and clinical drug trial activities such as screening, patient
tracking and
support. It is anticipated that a system according to the present invention
may be used by
health care providers (including physicians), clinical research scientists,
and possibly
healthcare organizations seeking to find the most cost-effective treatment
options for
patients in general as well as the most effective treatment regimen and/or
preventive
treatment regimen for the individual patient while providing the highest
standard of care.
A system 20 for carrying out the present invention is schematically
illustrated
in FIG. 2. The system 20 consists out of two major components 21 and 22. The
first
component 21 is capable of analyzing a sample 30 of the patient for its
methylation
statures of the DNA at selected sites. Such component comprises, for example,
apparatuses for PCR, mass spectrometry, and/or electrophoresis, roboters which
automatically handle the sample to be analyzed during the analysis procedure
together
with components which are capable of converting the generated information into
computer readable signals. . The second component 22 is capable of generating
and
displaying information about the type of disease of the patient and/or
advisory
information with respect to an individual (preventive) treatment regimen for
the patient.
The second component 22 comprises a first knowledge base 23 comprising
information about a plurality of different methylation statures at selected
sites of the
DNA in cells with a known disease or medical condition andlor healthy cells, a
second
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
39
knowledge base 24 comprising a plurality of expert rules for evaluating and
selecting a
type of disease or medical condition based on the methylation status at
selected sites of
the DNA of a patient, a third knowledge base 25 comprising a plurality of
different
therapeutic regimens andlor preventive therapeutic treatment regimens for
diseased cells
or medical conditions, which may be ranked for efficacy (e.g., by a panel of
experts) or
ranked according to system rules, a fourth knowledge base 26 comprising a
plurality of
expert rules for evaluating and selecting therapeutic treatment regimens for
diseased cells
or medical conditions and a fifth knowledge base 27 comprising advisory
information
useful for the treatment of a patient with different constituents of said
different
therapeutic treatment regimens. Optionally, the second component comprises a
knowledge base (not shown) of patient therapy history and additional patient
information.
Patient information is preferably stored within a database and is configured
to
be updated. The knowledge bases and patient information may be updated by an
inputloutput system 28, which can comprise a keyboard (and/or mouse) and video
monitor. Note also that, while the knowledge bases and patient data are shown
as separate
blocks, the knowledge bases and patient data can be combined together (e.g.,
the expert
rules and the advisory information can be combined in a single database).
To carry out the method described above, the information from at least two of
blocks 23-27 is provided to an inference engine 29, which generates the
listing of either
diseases of the patient or of available treatments and the corresponding
advisory
information from the information provided by the blocks.
The inference engine may be implemented as hardware, software, or
combinations thereof. Inference engines are known and any of a variety thereof
may be
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
used to carry out the present invention. Examples include, but are not limited
to, those
described in U.S. Pat. No. 5,263,127 to Barabash et al. (Method for fast rule
execution of
expert systems); U.S. Pat. No. 5,720,009 to Kirk et al. (Method of rule
execution in an
expert system using equivalence classes to group database objects); U.S. Pat.
No.
5,642,471 to Paillet (Production rule filter mechanism and inference engine
for expert
system); U.S. Pat. No. 5,664,062 to Kim (High performance max-min circuit for
a fuzzy
inference engine).
High-speed inference engines are preferred so that the results of data entered
are continually updated as new data is entered. As with the knowledge bases
and patient
information in blocks, the inference engine may be a separate block from the
knowledge
bases and patient information blocks, or may be combined together in a common
program
or routine. Optionally, exterior knowledge bases can be used as well. The
informationrn
that is generated in the inference engine can then be displayed via an
input/output system.
Based on the displayed information, the person in charge of the medical
supervision of
the patient will be able to select and apply a therapeutical treatment regimen
to the
patient. At any time, feedback information on types of diseases, success of
the treatment
regimen and available medicaments can be added via the input/output system.
Optionally,
this data can be supplied from an external source 40, e.g. a remote server.
Note that the advisory information that is generated for any available therapy
may differ from instance to instance based on differences in the patient
information
provided.
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
41
System Architecture
The present invention can be implemented as a system which comprises a first
component 21 able to perform an analysis of the methylation statuses of the
DNA of the
patient. This device is capeable of extracting the DNA from the patienta'
sample provided
to said component and to perform several analytical steps in order to receive
the
methylation statuses at selected sites of the DNA. These analytical steps are
known to the
person skilled in the art and may comprise bisulfate treatments, amplification
cycles of
the DNA employing polymerase chain reaction (PCR) protocols and reactions,
hybridisation reactions, DNA sequencing, mass spectroscopy or measurements of
fluorescence. All parts of the first device are usually combined and arranged
in such a
way that the procedure will be as much automized as possible in order to avoid
human
mistakes and create a high-troughput environment.
The data generated in the first component is provided to a second component
22 which is able to perform calculations using the provided data in order to
generate
information relevant for the following therapeutic treatment of the patient.
The second
component can be implemented as a system running on a stand alone computing
device.
Preferably, the present invention is implemented as a system in a client-
server
environment. As is known to those of skilled in the art, a client application
is the
requesting program in a client-server relationship. A server application is a
program that
awaits and fulfills requests from client programs in the same or other
computers. Client-
server environments may include public networks, such as the Internet, and
private
networks often referred to as "intranets", local area networks (LANs) and wide
area
networks (WANs), neural networks (NN), virtual private networks ('VPNs), frame
relay
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
42
or direct telephone connections. It is understood that a client application or
server
application, including computers hosting client and server applications, or
other apparatus
configured to execute program code embodied within computer usable media,
operates as
means for performing the various functions and carries out the methods of the
various
operations of the present invention. In one preferred embodiment of the
invention, the
results of the calculation of the client can also be reported back to the
server.
Referring now to FIG. 3, a client-server environment 30 according to a
preferred embodiment of the present invention is illustrated. The illustrated
client-server
environment 30 includes a central server 32 that is accessible by at least one
local server
34 via a computer network 36, such as the Internet. A variety of computer
network
transport protocols including, but not limited to TCPJIP, can be utilized for
communicating between the central server 32 and the local servers 34.
Central Server
The central server 32 includes a central database 38, such as the
Microsoft® SQL Server application program, version 6.5 (available from
Microsoft,
Inc., Redmond, Wash.), executing thereon. The central server 32 ensures that
the local
servers 34 are running the most recent version of a knowledge base. The
central server 32
also stores all patient data and data on methylation patterns and possible
treatment
regimens and performs various administrative functions including adding and
deleting
local servers and users to the system (20, FIG. 2). The central server 32 also
provides
authorization before a local server 34~ can be utilized by a user. Patient
data and/or data of
the methylation statuses at selected sites of the DNA of patients, also called
"methylation
patterns" herein, is preferably stored on the central server 32, thereby
providing a central
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
43
repository of patient data and methylation data. However, it is understood
that patient
data can be stored on a local server 34 or on local storage media. Data on
patients and
methylation patterns as well as data with respect to therapeutical treatment
regimens can
be submitted to the central server from the local servers or from a central
device creating
data on methylation patterns, e.g. at a laboratory that analyses samples of
patients on a
large scale and supplies the data of multiple methylation patterns of multiple
patients to
the central server.
Local Server
Each local server 34 typically serves multiple users in a geographical
location.
Each local server 34 includes a server application, an inference engine, one
or more
knowledge bases, and a local database 39. Each local server 34 performs-
artificial
intelligence processing for carrying out operations of the present invention.
When a user
logs on to a local server 34 via a client 35, the user is preferably
authenticated via an
identification and password, as would be understood by those skilled in the
art. Once
authenticated, a user is permitted access to the system (20, FIG. 2) and
certain
administrative privileges are assigned to the user.
Each local server 34 also communicates with the central server 32 to verify
that the most up-to-date version of the knowledge bases) and application are
running on
the requesting local server 34. If not, the requesting local server 34
downloads from the
central server 32 the latest validated knowledge bases) and/or application
before a user
session is established. Once a user has logged onto the system (20, FIG. 2)
and has
established a user session, all data and artificial intelligence processing is
preferably
performed on a local server 34. An advantage of the illustrated client-server
configuration
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
44
is that most of the computationally intensive work occurs on a local server
34, thereby
allowing "thin" clients 35 (i.e., computing devices having minimal hardware)
and
optimizing system speed.
In a preferred embodiment, each local server database 39 is implemented via a
Microsoft® SQL Server application program, Version 6.5. The primary
purpose of
each local database 39 is to store various patient identifiers and to ensure
secure and
authorized access to the system (20, FIG. 2) by a user. It is to be
understood, however,
that both central and local databases 38, 39 may be hosted on the central
server 32.
Local Client
Each local client 35 also includes a client application program that consists
of
a graphical user interface (GUI) and a middle layer program that communicates
with a
local server 34. Program code for the client application program may execute
entirely on
a local client 35, or it may execute partly on a local client 35 and partly on
a local server
34. As will be described below, a user interacts with the system (20, FIG. 2)
by providing
a sample of the patient to the first component (21, FIG. 2) of the system (20,
FIG. 2) and
optionally entering (or accessing) patient data within a GUI displayed within
the client
35. The client 35 then communicates with a local server 34 for analysis of the
.patient
information with respect to the methylation status of the DNA of the patient
at selected
sites of the patients' DNA which is generated in the system (20, FIG. 2)
and/or entered
via the GUI.
Computer program code for carrying out operations of the present invention is
preferably written in an object oriented programming language such as
JAVA®,
Smalltalk, or C++. However, the computer program code for carrying out
operations of
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
the present invention may also be written in conventional procedural
programming
languages, such as the "G" programming language, in an interpreted scripting
language,
such as Perl, or in a functional (or fourth generation) programming language
such as
Lisp, SML, or Forth.
The middle layer program of the client application includes an inference
engine within a local server 34 that provides continuous on-line direction to
users, and
can instantly warn a user when a patient is assigned drugs or a medical
condition that is
contraindicated with, or antagonistic of, the patient's current therapy.
Inference Engine
Inference engines are well known by those of skill in the art and need not be
described further herein. Each knowledge base used by an inference engine
according to
the present invention is a collection of rules and methods authored by a
clinical advisory
panel of disease-treating physicians and scientists. A knowledge base may have
subjective rules, objective rules, and system-generated rules. Objective rules
are based on
undyu~~r established favtS r°vgarv.~x~ilg the w~.°vau a~ri t
~V'f dlsVasVS '~'siiig drug +~.1~'°vrapy and arv°
drawn from the package insert information of ~g m~,~cturers and from
peer reviewed and published journal articles.
For objective rules, the present invention can be configured so as to prevent
a
user from receiving recommendations on new therapy options when certain
crucial data
on the patient has not been entered. JEiowever, it is understood that the
present invention
does not prevent a health care provider, such as a physician, from recording
his/her
therapy decisions, even if the system (20, FIG, 2) has shown reasons why that
therapy
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
46
may be harmful to the patient. The present invention allows a health care
provider to be
the final authority regarding patient therapy.
Subjective rules are based on expert opinions, observations and experience.
Subjective rules are typically developed from "best practices" information
based on
consensus opinion of experts in the field. Such expert opinion may be based on
knowledge of the literature published or presented in the field or their own
experience
from clinical practice, research or clinical trials of approved and
ur~approved medications.
A number of experts are used so that personal bias is reduced.
System generated rules are those derived from the outcomes of patients
tracked in the system who received known and defined therapies and either
improved,
stabilized or worsened during a defined period. Because of the large number of
potential
combinations usable in infections, this system generated database and rules
derived from
them are likely to encompass data beyond that achievable from objective or
subjective
rules databases.
The following non-limiting examples illustrate various aspects of the present
invention. These examples are provided for illustrative purposes only, and are
not
intended to be limiting of the invention.
EXAMPLE 1
Method employing a treatment regimen in order to treat an acute outbreak of a
disease
A tissue sample from a patient suffering from a completely unknown or
insufficiently specified acute disease is taken in the practice of a medical
doctor or from
medical personell in a hospital. In the context of the present invention, the
term
"insufficiently specified acute disease" designates a generally diagnosed
disease like, for
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
47
example, cancer without specifying the exact type of cancer the patient is
affected with.
Further examples would be an acute viral infection or a generally specified
bacterial
infection. The sample of the patient contains DNA from the cells of the
patient to be
examined. Basically all types of samples that contain DNA from the patient can
be
employed in the method of the present invention. The sample can contain either
specific
tissue, like single types of blood cells, single types of liver cells or cells
of a single
tumour, or unspecific tissue, like skin, brain or other organs. The sample is
then shipped
together with additional patient information to a central laboratory m order
to analyse the
methylation statuses at selected sites of the patients' DNA. Optionally, the
sample can be
analysed for its methylation statuses at selected sites of the patients' DNA
in a device
comprising two different components as described above, which is either
located in the
practice of the medical doctor or, for example, in the central laboratory of a
hospital. The
information on the methylation pattern of the individual patient is then
provided to a
computing device again either located in the practice of the medical doctor or
the hospital
or at the central laboratory. Optionally, this information can be provided
either to a
remote server or from the server to the local client for further use and
analyses.
In another method of the invention, tissue samples can be taken from a
selected group of patients in order to, for example, monitor the outbreak of a
plague
caused by a specfic organism or virus, like a neisseria or highly infectious
viral disease.
The information about the methylation patterns) of the patients) is then
processed in the computing device by an inference engine employing the
information
from at least two of blocks 23-27 (FIG. 2), which generates the listing of
either precisely
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
48
defined diseases of the individual patient or of available treatments and the
corresponding
individual advisory information from the 'information provided by the blocks.
The patient is then individually therapeutically treated based on the basis of
the advisory information generated and displayed by the above-mentioned
device. The
treatment employs an individual treatment regimen which is specific for the
type of
disease the patient suffers from, together with additional individual
treatment
modifications which correspond to the individual needs and problems occuring
with the
medication of the patient, like incompatibility with a specific type of drug
or active
compound of a medicament as part of the treatment which is employed.
EXAMPLE 2
Example employing a preventive treatment regimen
A tissue sample from a healthy person or a person suffering from a yet
unidentified or non-acute infection or other disease like cancer in a very
early stage is
taken in the practice of the responsible medical doctor or from other personal
in a
hospital. The sample contains DNA from the patient to be examined. Therefore,
the
sample can contain either specific tissue, like single types of blood cells,
single types of
liver cells or cells of a single tumour, or unspecific tissue, lilce skin,
brain or other organs.
The sample is then shipped together with additional patient information to a
central
laboratory in order to analyse the methylation statuses at selected sites of
the patients'
DNA. Optionally, the sample can be analysed for its methylation statuses at
selected sites
of the patients' DNA in an analytical device as described above, having two
components
as described above, which is either located in the practice of the medical
doctor or in the
laboratory of a hospital. The information on the methylation is then provided
to a
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
49
computing device either located in the practice of the medical doctor or the
hospital or at
the central laboratory. Optionally, this information can be provided either to
a remote
server or from the server to the local client for further use and analyses.
The information about the methylation patterns) of the patient is then
processed in the computing device by an inference engine employing the
information
from at least two of blocks 23-27 (FIG. 2), which generates the listing of
either yet not
identified precisely defined diseases of the individual patient or which
generates a risk-
assessment for the individual.patient, in which the individual statistical
risk for the patient
is calculated, to suffer from the outbreak of an acute disease in the future.
The statistical
risk is calculated based on a comparison of the knowledge bases which contain
the
information about the methylation status of the DNA of healtlhy cells with the
information about the methylation of the patients' DNA. A conclusion is drawn
on the
basis of differences found between these two methylation patterns. Further
factors which
can influence the outcome of such statistical diagnosis include, for example,
patient
information on earlier treatment regimens or acute medication.
The patient is then individually therapeutically treated based. on the
advisory
information generated and displayed by the above-mentioned device. The
preventive
treatment employs an individual treatement regimen which is specific for the
type of
disease the patient will most likely suffer from in order to either prevent an
acute
outbreak of a disease andlor reduce the risk of such an outbreak. One example
of a
preventive treatment could be a special diet in order to limit negative
effects of diabetes,
allergic reactions, cancer or other diseases which can be treated most
efficiently at an
early stage. The preventive treatment is employed together with additional
individual
CA 02427624 2003-05-O1
WO 02/37398 PCT/EPO1/12666
treatment modifications which correspond to the individual needs and problems
occuring
with the medication of the patient, like intolerances or allergies.
The foregoing is illustrative of the present invention and is not to be
construed
as limiting thereof. Although a few exemplary embodiments of this invention
have been
described, those skilled in the art will readily appreciate that many
modifications are
possible in the exemplary embodiments without materially departing from the
novel
teachings and advantages of this invention. Accordingly, all such
modifications are
intended to be included within the scope of this invention as defined in the
claims.
Therefore, it is to be understood that the foregoing is illustrative of the
present invention
and is not to be construed as limited to the specific embodiments disclosed,
and that
modifications to the disclosed embodiments, as well as other embodiments, are
intended
to be included within the scope of the appended claims. The invention is
defined by the
following claims, with equivalents of the claims to be included therein.
